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Bhatraju PK, Zelnick LR, Stanaway IB, Ikizler TA, Menez S, Chinchilli VM, Coca SG, Kaufman JS, Kimmel PL, Parikh CR, Go AS, Siew ED, Wurfel MM, Himmelfarb J. Acute Kidney Injury, Systemic Inflammation and Long-term Cognitive Function: ASSESS-AKI. Clin J Am Soc Nephrol 2024:01277230-990000000-00386. [PMID: 38728094 DOI: 10.2215/cjn.0000000000000473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Cognitive dysfunction is a well-known complication of chronic kidney disease, but it is less known whether cognitive decline occurs in survivors after acute kidney injury (AKI). We hypothesized that an episode of AKI is associated with poorer cognitive function, mediated, at least in part, by persistent systemic inflammation. METHODS ASSESS-AKI enrolled patients surviving three months after hospitalization with and without AKI matched based on demographics, comorbidities, and baseline kidney function. A subset underwent cognitive testing using the modified mini-mental status examination (3MS) at 3, 12, and 36 months. We examined the association of AKI with 3MS scores using mixed linear models and assessed the proportion of risk mediated by systemic inflammatory biomarkers. RESULTS Among 1538 participants in ASSESS-AKI, 1420 (92%) completed the 3MS assessment at 3 months and had a corresponding matched participant. Participants with AKI had lower 3MS scores at three years (difference -1.1 (95% CI: -2.0, -0.3) P=0.009) compared to participants without AKI. A higher proportion of AKI participants had a clinically meaningful (≥ 5 point) reduction in 3MS scores at three years compared to participants without AKI (14% vs. 10%, P=0.04). In mediation analyses, plasma soluble tumor necrosis factor receptor-1 (sTNFR-1) at three months after AKI mediated 35% (P=0.02) of the AKI related risk for 3MS scores at three years. CONCLUSIONS AKI was associated with lower 3MS scores and sTNFR-1 concentrations appeared to mediate a significant proportion of the risk of long-term cognitive impairment. Further work is needed to determine if AKI is causal or a marker for cognitive impairment.
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Affiliation(s)
- Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington
| | - Leila R Zelnick
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington
| | - T Alp Ikizler
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN
| | - Steven Menez
- Division of Nephrology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Vernon M Chinchilli
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA
| | - Steve G Coca
- Section of Nephrology, Department of Internal Medicine, Mount Sinai School of Medicine, New York, NY
| | - James S Kaufman
- Division of Nephrology, New York University School of Medicine, New York, NY and Division of Nephrology, VA New York Harbor Healthcare System, New York, NY
| | - Paul L Kimmel
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Chirag R Parikh
- Division of Nephrology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Alan S Go
- Division of Nephrology, Department of Medicine, University of California, San Francisco, CA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Edward D Siew
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington
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2
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Hart A, Cesar F, Zelnick LR, O'Connor N, Bailey Z, Lo J, Van Ness K, Stanaway IB, Bammler TK, MacDonald JW, Thau MR, Himmelfarb J, Goss CH, Aitken M, Kelly EJ, Bhatraju PK. Identification of prognostic biomarkers for antibiotic associated nephrotoxicity in cystic fibrosis. J Cyst Fibros 2024; 23:293-299. [PMID: 37949747 PMCID: PMC11076417 DOI: 10.1016/j.jcf.2023.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Our objective was to discover novel urinary biomarkers of antibiotic-associated nephrotoxicity using an ex-vivo human microphysiological system (MPS) and to translate these findings to a prospectively enrolled cystic fibrosis (CF) population receiving aminoglycosides and/or polymyxin E (colistin) for a pulmonary exacerbation. METHODS We populated the MPS with primary human kidney proximal tubule epithelial cells (PTECs) from three donors and modeled nephrotoxin injury through exposure to 50 µg/mL polymyxin E for 72 h. We analyzed gene transcriptional responses by RNAseq and tested MPS effluents. We translated candidate biomarkers to a CF cohort via analysis of urine collected prior to, during and two weeks after antibiotics and patients were followed for a median of 3 years after antibiotic use. RESULTS Polymyxin E treatment resulted in a statistically significant increase in the pro-apoptotic Fas gene relative to control in RNAseq of MPS: fold-change = 1.63, FDR q-value = 7.29 × 10-5. Effluent analysis demonstrated an acute rise of soluble Fas (sFas) concentrations that correlated with cellular injury. In 16 patients with CF, urinary sFas concentrations were significantly elevated during antibiotic treatment, regardless of development of AKI. Over a median of three years of follow up, we identified seven cases of incident chronic kidney disease (CKD). Urinary sFas concentrations during antibiotic treatment were significantly associated with subsequent development of incident CKD (unadjusted relative risk = 2.02 per doubling of urinary sFas, 95 % CI = 1.40, 2.90, p < 0.001). CONCLUSIONS Using an ex-vivo MPS, we identified a novel biomarker of proximal tubule epithelial cell injury, sFas, and translated these findings to a clinical cohort of patients with CF.
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Affiliation(s)
- Andrew Hart
- University of Washington School of Medicine, Seattle, USA
| | - Francine Cesar
- Department of Pharmaceutics, University of Washington, Seattle, USA
| | - Leila R Zelnick
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA
| | - Nick O'Connor
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Zoie Bailey
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Jordan Lo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Kirk Van Ness
- Department of Pharmaceutics, University of Washington, Seattle, USA
| | - Ian B Stanaway
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA
| | - Theo K Bammler
- Division of Pediatric Pulmonary Medicine, University of Washington, Seattle, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Matthew R Thau
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Jonathan Himmelfarb
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA
| | - Christopher H Goss
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA; Division of Pediatric Pulmonary Medicine, University of Washington, Seattle, USA
| | - Moira Aitken
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, USA
| | - Pavan K Bhatraju
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA.
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3
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Kuley R, Duvvuri B, Wallin JJ, Bui N, Adona MV, O’Connor NG, Sahi SK, Stanaway IB, Wurfel MM, Morrell ED, Liles WC, Bhatraju PK, Lood C. Mitochondrial N-formyl methionine peptides contribute to exaggerated neutrophil activation in patients with COVID-19. Virulence 2023; 14:2218077. [PMID: 37248708 PMCID: PMC10231045 DOI: 10.1080/21505594.2023.2218077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/15/2023] [Accepted: 05/20/2023] [Indexed: 05/31/2023] Open
Abstract
Neutrophil dysregulation is well established in COVID-19. However, factors contributing to neutrophil activation in COVID-19 are not clear. We assessed if N-formyl methionine (fMet) contributes to neutrophil activation in COVID-19. Elevated levels of calprotectin, neutrophil extracellular traps (NETs) and fMet were observed in COVID-19 patients (n = 68), particularly in critically ill patients, as compared to HC (n = 19, p < 0.0001). Of note, the levels of NETs were higher in ICU patients with COVID-19 than in ICU patients without COVID-19 (p < 0.05), suggesting a prominent contribution of NETs in COVID-19. Additionally, plasma from COVID-19 patients with mild and moderate/severe symptoms induced in vitro neutrophil activation through fMet/FPR1 (formyl peptide receptor-1) dependent mechanisms (p < 0.0001). fMet levels correlated with calprotectin levels validating fMet-mediated neutrophil activation in COVID-19 patients (r = 0.60, p = 0.0007). Our data indicate that fMet is an important factor contributing to neutrophil activation in COVID-19 disease and may represent a potential target for therapeutic intervention.
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Affiliation(s)
- Runa Kuley
- Department of Medicine, Division of Rheumatology, University of Washington, Seattle, WA, USA
- Center for Life Sciences, Mahindra University, Hyderabad, India
| | - Bhargavi Duvvuri
- Department of Medicine, Division of Rheumatology, University of Washington, Seattle, WA, USA
| | | | - Nam Bui
- Biomarker Sciences, Gilead Sciences Inc, Foster City, CA, USA
| | - Mary Vic Adona
- Biomarker Sciences, Gilead Sciences Inc, Foster City, CA, USA
| | - Nicholas G. O’Connor
- Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Sharon K. Sahi
- Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Ian B. Stanaway
- Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Mark M. Wurfel
- Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Eric D. Morrell
- Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - W. Conrad Liles
- Department of Medicine, University of Washington, Seattle, WA, USA
- Sepsis Center of Research Excellence-UW (SCORE-UW), University of Washington, Seattle, WA, USA
| | - Pavan K. Bhatraju
- Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
- Sepsis Center of Research Excellence-UW (SCORE-UW), University of Washington, Seattle, WA, USA
| | - Christian Lood
- Department of Medicine, Division of Rheumatology, University of Washington, Seattle, WA, USA
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Bhatraju PK, Stanaway IB, Palmer MR, Menon R, Schaub JA, Menez S, Srivastava A, Wilson FP, Kiryluk K, Palevsky PM, Naik AS, Sakr SS, Jarvik GP, Parikh CR, Ware LB, Ikizler TA, Siew ED, Chinchilli VM, Coca SG, Garg AX, Go AS, Kaufman JS, Kimmel PL, Himmelfarb J, Wurfel MM. Genome-wide Association Study for AKI. Kidney360 2023; 4:870-880. [PMID: 37273234 PMCID: PMC10371295 DOI: 10.34067/kid.0000000000000175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/03/2023] [Indexed: 06/06/2023]
Abstract
Key Points Two genetic variants in the DISP1-TLR5 gene locus were associated with risk of AKI. DISP1 and TLR5 were differentially regulated in kidney biopsy tissue from patients with AKI compared with no AKI. Background Although common genetic risks for CKD are well established, genetic factors influencing risk for AKI in hospitalized patients are poorly understood. Methods We conducted a genome-wide association study in 1369 participants in the Assessment, Serial Evaluation, and Subsequent Sequelae of AKI Study; a multiethnic population of hospitalized participants with and without AKI matched on demographics, comorbidities, and kidney function before hospitalization. We then completed functional annotation of top-performing variants for AKI using single-cell RNA sequencing data from kidney biopsies in 12 patients with AKI and 18 healthy living donors from the Kidney Precision Medicine Project. Results No genome-wide significant associations with AKI risk were found in Assessment, Serial Evaluation, and Subsequent Sequelae of AKI (P < 5×10 −8 ). The top two variants with the strongest association with AKI mapped to the dispatched resistance-nodulation-division (RND) transporter family member 1 (DISP1) gene and toll-like receptor 5 (TLR5) gene locus, rs17538288 (odds ratio, 1.55; 95% confidence interval, 1.32 to 182; P = 9.47×10 −8 ) and rs7546189 (odds ratio, 1.53; 95% confidence interval, 1.30 to 1.81; P = 4.60×10 −7 ). In comparison with kidney tissue from healthy living donors, kidney biopsies in patients with AKI showed differential DISP1 expression in proximal tubular epithelial cells (adjusted P = 3.9× 10−2) and thick ascending limb of the loop of Henle (adjusted P = 8.7× 10−3) and differential TLR5 gene expression in thick ascending limb of the loop of Henle (adjusted P = 4.9× 10−30). Conclusions AKI is a heterogeneous clinical syndrome with various underlying risk factors, etiologies, and pathophysiology that may limit the identification of genetic variants. Although no variants reached genome-wide significance, we report two variants in the intergenic region between DISP1 and TLR5 , suggesting this region as a novel risk for AKI susceptibility.
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Affiliation(s)
- Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Melody R Palmer
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Rajasree Menon
- Division of Nephrology, Department of Medicine, Michigan Medicine, Ann Arbor, Michigan
| | - Jennifer A Schaub
- Division of Nephrology, Department of Medicine, Michigan Medicine, Ann Arbor, Michigan
| | - Steven Menez
- Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anand Srivastava
- Department of Medicine, Division of Nephrology and Hypertension, Northwestern University School of Medicine, Chicago, Illinois
| | - F Perry Wilson
- Program of Applied Translational Research, Yale School of Medicine, New Haven, Connecticut
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York City, New York
| | - Paul M Palevsky
- Kidney Medicine Section, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Abhijit S Naik
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan
| | - Sana S Sakr
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lorraine B Ware
- Division of Allergy, Pulmonary and Critical Care, Vanderbilt University Medical Center, Nashville, Tennessee
| | - T Alp Ikizler
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Edward D Siew
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Vernon M Chinchilli
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Steve G Coca
- Section of Nephrology, Department of Internal Medicine, Mount Sinai School of Medicine, New York, New York
| | - Amit X Garg
- Division of Nephrology, Department of Medicine, Western University, London, Ontario, Canada
| | - Alan S Go
- Division of Nephrology, Department of Medicine, University of California, San Francisco, California
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - James S Kaufman
- Division of Nephrology, New York University School of Medicine, New York, New York
- Division of Nephrology, VA New York Harbor Healthcare System, New York, New York
| | - Paul L Kimmel
- Division of Renal Diseases and Hypertension, Department of Medicine, George Washington University Medical Center, Washington, DC
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
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5
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Thau MR, Liu T, Sathe NA, O’Keefe GE, Robinson BRH, Bulger E, Wade CE, Fox EE, Holcomb JB, Liles WC, Stanaway IB, Mikacenic C, Wurfel MM, Bhatraju PK, Morrell ED. Association of Trauma Molecular Endotypes With Differential Response to Transfusion Resuscitation Strategies. JAMA Surg 2023; 158:728-736. [PMID: 37099286 PMCID: PMC10134038 DOI: 10.1001/jamasurg.2023.0819] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/12/2022] [Indexed: 04/27/2023]
Abstract
Importance It is not clear which severely injured patients with hemorrhagic shock may benefit most from a 1:1:1 vs 1:1:2 (plasma:platelets:red blood cells) resuscitation strategy. Identification of trauma molecular endotypes may reveal subgroups of patients with differential treatment response to various resuscitation strategies. Objective To derive trauma endotypes (TEs) from molecular data and determine whether these endotypes are associated with mortality and differential treatment response to 1:1:1 vs 1:1:2 resuscitation strategies. Design, Setting, and Participants This was a secondary analysis of the Pragmatic, Randomized Optimal Platelet and Plasma Ratios (PROPPR) randomized clinical trial. The study cohort included individuals with severe injury from 12 North American trauma centers. The cohort was taken from the participants in the PROPPR trial who had complete plasma biomarker data available. Study data were analyzed on August 2, 2021, to October 25, 2022. Exposures TEs identified by K-means clustering of plasma biomarkers collected at hospital arrival. Main Outcomes and Measures An association between TEs and 30-day mortality was tested using multivariable relative risk (RR) regression adjusting for age, sex, trauma center, mechanism of injury, and injury severity score (ISS). Differential treatment response to transfusion strategy was assessed using an RR regression model for 30-day mortality by incorporating an interaction term for the product of endotype and treatment group adjusting for age, sex, trauma center, mechanism of injury, and ISS. Results A total of 478 participants (median [IQR] age, 34.5 [25-51] years; 384 male [80%]) of the 680 participants in the PROPPR trial were included in this study analysis. A 2-class model that had optimal performance in K-means clustering was found. TE-1 (n = 270) was characterized by higher plasma concentrations of inflammatory biomarkers (eg, interleukin 8 and tumor necrosis factor α) and significantly higher 30-day mortality compared with TE-2 (n = 208). There was a significant interaction between treatment arm and TE for 30-day mortality. Mortality in TE-1 was 28.6% with 1:1:2 treatment vs 32.6% with 1:1:1 treatment, whereas mortality in TE-2 was 24.5% with 1:1:2 treatment vs 7.3% with 1:1:1 treatment (P for interaction = .001). Conclusions and Relevance Results of this secondary analysis suggest that endotypes derived from plasma biomarkers in trauma patients at hospital arrival were associated with a differential response to 1:1:1 vs 1:1:2 resuscitation strategies in trauma patients with severe injury. These findings support the concept of molecular heterogeneity in critically ill trauma populations and have implications for tailoring therapy for patients at high risk for adverse outcomes.
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Affiliation(s)
- Matthew R. Thau
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
| | - Ted Liu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle
| | - Neha A. Sathe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
| | - Grant E. O’Keefe
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
- Department of Surgery, University of Washington, Seattle
| | | | - Eileen Bulger
- Department of Surgery, University of Washington, Seattle
| | - Charles E. Wade
- Center for Translational Injury Research, Division of Acute Care Surgery, Department of Surgery, University of Texas Health Science Center, Houston
| | - Erin E. Fox
- Center for Translational Injury Research, Division of Acute Care Surgery, Department of Surgery, University of Texas Health Science Center, Houston
| | | | - W. Conrad Liles
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Ian B. Stanaway
- Kidney Research Institute, University of Washington, Seattle
- Division of Nephrology, Department of Medicine, University of Washington, Seattle
| | - Carmen Mikacenic
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
- Translational Immunology, Benaroya Research Institute, Seattle, Washington
| | - Mark M. Wurfel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
| | - Pavan K. Bhatraju
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
| | - Eric D. Morrell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle
- Sepsis Center of Research Excellence—University of Washington (SCORE-UW), Seattle
- Hospital and Specialty Medicine, VA Puget Sound Health Care System, Seattle, Washington
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Bitto A, Grillo AS, Ito TK, Stanaway IB, Nguyen BMG, Ying K, Tung H, Smith K, Tran N, Velikanje G, Urfer SR, Snyder JM, Barton J, Sharma A, Kayser EB, Wang L, Smith DL, Thompson JW, DuBois L, DePaolo W, Kaeberlein M. Acarbose suppresses symptoms of mitochondrial disease in a mouse model of Leigh syndrome. Nat Metab 2023; 5:955-967. [PMID: 37365290 DOI: 10.1038/s42255-023-00815-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/04/2023] [Indexed: 06/28/2023]
Abstract
Mitochondrial diseases represent a spectrum of disorders caused by impaired mitochondrial function, ranging in severity from mortality during infancy to progressive adult-onset disease. Mitochondrial dysfunction is also recognized as a molecular hallmark of the biological ageing process. Rapamycin, a drug that increases lifespan and health during normative ageing, also increases survival and reduces neurological symptoms in a mouse model of the severe mitochondrial disease Leigh syndrome. The Ndufs4 knockout (Ndufs4-/-) mouse lacks the complex I subunit NDUFS4 and shows rapid onset and progression of neurodegeneration mimicking patients with Leigh syndrome. Here we show that another drug that extends lifespan and delays normative ageing in mice, acarbose, also suppresses symptoms of disease and improves survival of Ndufs4-/- mice. Unlike rapamycin, acarbose rescues disease phenotypes independently of inhibition of the mechanistic target of rapamycin. Furthermore, rapamycin and acarbose have additive effects in delaying neurological symptoms and increasing maximum lifespan in Ndufs4-/- mice. We find that acarbose remodels the intestinal microbiome and alters the production of short-chain fatty acids. Supplementation with tributyrin, a source of butyric acid, recapitulates some effects of acarbose on lifespan and disease progression, while depletion of the endogenous microbiome in Ndufs4-/- mice appears to fully recapitulate the effects of acarbose on healthspan and lifespan in these animals. To our knowledge, this study provides the first evidence that alteration of the gut microbiome plays a significant role in severe mitochondrial disease and provides further support for the model that biological ageing and severe mitochondrial disorders share underlying common mechanisms.
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Affiliation(s)
- Alessandro Bitto
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Anthony S Grillo
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Takashi K Ito
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Ian B Stanaway
- Division of Nephrology, School of Medicine, University of Washington, Seattle, WA, USA
- Harborview Medical Center, Kidney Research Institute, Seattle, WA, USA
| | - Bao M G Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kejun Ying
- T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | | | - Ngoc Tran
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Gunnar Velikanje
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Silvan R Urfer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica M Snyder
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - Jacob Barton
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Ayush Sharma
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Daniel L Smith
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Laura DuBois
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - William DePaolo
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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7
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Stanaway IB, Wallace JC, Hong S, Wilder CS, Green FH, Tsai J, Knight M, Workman T, Vigoren EM, Smith MN, Griffith WC, Thompson B, Shojaie A, Faustman EM. Alteration of oral microbiome composition in children living with pesticide-exposed farm workers. Int J Hyg Environ Health 2023; 248:114090. [PMID: 36516690 PMCID: PMC9898171 DOI: 10.1016/j.ijheh.2022.114090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/30/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Our prior work shows that azinphos-methyl pesticide exposure is associated with altered oral microbiomes in exposed farmworkers. Here we extend this analysis to show the same association pattern is also evident in their children. Oral buccal swab samples were analyzed at two time points, the apple thinning season in spring-summer 2005 for 78 children and 101 adults and the non-spray season in winter 2006 for 62 children and 82 adults. The pesticide exposure for the children were defined by the farmworker occupation of the cohabitating household adult and the blood azinphos-methyl detection of the cohabitating adult. Oral buccal swab 16S rRNA sequencing determined taxonomic microbiota proportional composition from concurrent samples from both adults and children. Analysis of the identified bacteria showed significant proportional changes for 12 of 23 common oral microbiome genera in association with azinphos-methyl detection and farmworker occupation. The most common significantly altered genera had reductions in the abundance of Streptococcus, suggesting an anti-microbial effect of the pesticide. Principal component analysis of the microbiome identified two primary clusters, with association of principal component 1 to azinphos-methyl blood detection and farmworker occupational status of the household. The children's buccal microbiota composition clustered with their household adult in ∼95% of the households. Household adult farmworker occupation and household pesticide exposure is associated with significant alterations in their children's oral microbiome composition. This suggests that parental occupational exposure and pesticide take-home exposure pathways elicit alteration of their children's microbiomes.
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Affiliation(s)
- Ian B Stanaway
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - James C Wallace
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Sungwoo Hong
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Carly S Wilder
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Foad H Green
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Jesse Tsai
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Misty Knight
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Tomomi Workman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Eric M Vigoren
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Marissa N Smith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - William C Griffith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Beti Thompson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine M Faustman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
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8
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Jasper EA, Hellwege JN, Breeyear JH, Xiao B, Jarvik GP, Stanaway IB, Leppig KA, Chittoor G, Hayes MG, Dikilitas O, Kullo IJ, Holm IA, Verma SS, Edwards TL, Velez Edwards DR. Genetic Predictors of Blood Pressure Traits are Associated with Preeclampsia. medRxiv 2023:2023.02.09.23285734. [PMID: 36824881 PMCID: PMC9949198 DOI: 10.1101/2023.02.09.23285734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background Preeclampsia, a pregnancy complication characterized by hypertension after 20 gestational weeks, is a major cause of maternal and neonatal morbidity and mortality. The mechanisms leading to preeclampsia are unclear; however, there is evidence that preeclampsia is highly heritable. We evaluated the association of polygenic risk scores (PRS) for blood pressure traits and preeclampsia to assess whether there is shared genetic architecture. Methods Participants were obtained from Vanderbilt University's BioVU, the Electronic Medical Records and Genomics network, and the Penn Medicine Biobank. Non-Hispanic Black and White females of reproductive age with indications of pregnancy and genotype information were included. Preeclampsia was defined by ICD codes. Summary statistics for diastolic blood pressure (DBP), systolic blood pressure (SBP), and pulse pressure (PP) PRS were obtained from Giri et al 2019. Associations between preeclampsia and each PRS were evaluated separately by race and study population before evidence was meta-analyzed. Prediction models were developed and evaluated using 10-fold cross validation. Results In the 3,504 Black and 5,009 White individuals included, the rate of preeclampsia was 15.49%. The DBP and SBP PRSs were associated with preeclampsia in Whites but not Blacks. The PP PRS was significantly associated with preeclampsia in Blacks and Whites. In trans-ancestry meta-analysis, all PRSs were associated with preeclampsia (OR DBP =1.10, 95% CI=1.02-1.17, p =7.68×10 -3 ; OR SBP =1.16, 95% CI=1.09-1.23, p =2.23×10 -6 ; OR PP =1.14, 95% CI=1.07-1.27, p =9.86×10 -5 ). However, addition of PRSs to clinical prediction models did not improve predictive performance. Conclusions Genetic factors contributing to blood pressure regulation in the general population also predispose to preeclampsia.
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Liu L, Khan A, Sanchez-Rodriguez E, Zanoni F, Li Y, Steers N, Balderes O, Zhang J, Krithivasan P, LeDesma RA, Fischman C, Hebbring SJ, Harley JB, Moncrieffe H, Kottyan LC, Namjou-Khales B, Walunas TL, Knevel R, Raychaudhuri S, Karlson EW, Denny JC, Stanaway IB, Crosslin D, Rauen T, Floege J, Eitner F, Moldoveanu Z, Reily C, Knoppova B, Hall S, Sheff JT, Julian BA, Wyatt RJ, Suzuki H, Xie J, Chen N, Zhou X, Zhang H, Hammarström L, Viktorin A, Magnusson PKE, Shang N, Hripcsak G, Weng C, Rundek T, Elkind MSV, Oelsner EC, Barr RG, Ionita-Laza I, Novak J, Gharavi AG, Kiryluk K. Author Correction: Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nat Commun 2023; 14:655. [PMID: 36746961 PMCID: PMC9902387 DOI: 10.1038/s41467-023-36340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Lili Liu
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Elena Sanchez-Rodriguez
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yifu Li
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Nicholas Steers
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Olivia Balderes
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Robert A LeDesma
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Clara Fischman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - John B Harley
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Halima Moncrieffe
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bahram Namjou-Khales
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Theresa L Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rachel Knevel
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth W Karlson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas Rauen
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Jürgen Floege
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Frank Eitner
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
- Kidney Diseases Research, Bayer Pharma AG, Wuppertal, Germany
| | - Zina Moldoveanu
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Colin Reily
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Barbora Knoppova
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stacy Hall
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Justin T Sheff
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bruce A Julian
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert J Wyatt
- Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Hitoshi Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jingyuan Xie
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Chen
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xujie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Viktorin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Tatjana Rundek
- Department of Neurology, University of Miami, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami, Miami, FL, USA
| | - Mitchell S V Elkind
- Department of Neurology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Elizabeth C Oelsner
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - R Graham Barr
- Division of General Medicine, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jan Novak
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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10
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Bhatraju PK, Morrell ED, Stanaway IB, Sathe NA, Srivastava A, Postelnicu R, Green R, Andrews A, Gonzalez M, Kratochvil CJ, Kumar VK, Hsiang TY, Gale M, Anesi GL, Wyles D, Broadhurst MJ, Brett-Major D, Mukherjee V, Sevransky JE, Landsittel D, Hung C, Altemeier WA, Gharib SA, Uyeki TM, Cobb JP, Liebler JM, Crosslin DR, Jarvik GP, Segal LN, Evans L, Mikacenic C, Wurfel MM. Angiopoietin-Like4 Is a Novel Marker of COVID-19 Severity. Crit Care Explor 2023; 5:e0827. [PMID: 36600780 PMCID: PMC9803343 DOI: 10.1097/cce.0000000000000827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Vascular dysfunction and capillary leak are common in critically ill COVID-19 patients, but identification of endothelial pathways involved in COVID-19 pathogenesis has been limited. Angiopoietin-like 4 (ANGPTL4) is a protein secreted in response to hypoxic and nutrient-poor conditions that has a variety of biological effects including vascular injury and capillary leak. OBJECTIVES To assess the role of ANGPTL4 in COVID-19-related outcomes. DESIGN SETTING AND PARTICIPANTS Two hundred twenty-five COVID-19 ICU patients were enrolled from April 2020 to May 2021 in a prospective, multicenter cohort study from three different medical centers, University of Washington, University of Southern California and New York University. MAIN OUTCOMES AND MEASURES Plasma ANGPTL4 was measured on days 1, 7, and 14 after ICU admission. We used previously published tissue proteomic data and lung single nucleus RNA (snRNA) sequencing data from specimens collected from COVID-19 patients to determine the tissues and cells that produce ANGPTL4. RESULTS Higher plasma ANGPTL4 concentrations were significantly associated with worse hospital mortality (adjusted odds ratio per log2 increase, 1.53; 95% CI, 1.17-2.00; p = 0.002). Higher ANGPTL4 concentrations were also associated with higher proportions of venous thromboembolism and acute respiratory distress syndrome. Longitudinal ANGPTL4 concentrations were significantly different during the first 2 weeks of hospitalization in patients who subsequently died compared with survivors (p for interaction = 8.1 × 10-5). Proteomics analysis demonstrated abundance of ANGPTL4 in lung tissue compared with other organs in COVID-19. ANGPTL4 single-nuclear RNA gene expression was significantly increased in pulmonary alveolar type 2 epithelial cells and fibroblasts in COVID-19 lung tissue compared with controls. CONCLUSIONS AND RELEVANCE ANGPTL4 is expressed in pulmonary epithelial cells and fibroblasts and is associated with clinical prognosis in critically ill COVID-19 patients.
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Affiliation(s)
- Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
- School of Medicine, University of Washington, Sepsis Center of Research Excellence-University of Washington (SCORE-UW), Seattle, WA
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Eric D Morrell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Neha A Sathe
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Avantika Srivastava
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Radu Postelnicu
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Richard Green
- Departments of Medicine (Division of Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA
| | - Adair Andrews
- Society of Critical Care Medicine, Mount Prospect, IL
| | | | | | | | | | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA
| | - George L Anesi
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David Wyles
- Division of Infectious Diseases, Denver Health Medical Center, Denver, CO
| | - M Jana Broadhurst
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
| | - David Brett-Major
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
| | - Vikramjit Mukherjee
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jonathan E Sevransky
- Division of Pulmonary, Allergy, Critical Care and Sleep, School of Medicine, Emory University, Atlanta, GA
- Emory Critical Care Center, Emory Healthcare, Atlanta, GA
| | - Douglas Landsittel
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN
| | - Chi Hung
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - William A Altemeier
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - J Perren Cobb
- Departments of Surgery and Anesthesiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | - Janice M Liebler
- Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University, School of Medicine, New Orleans, LA
| | - Gail P Jarvik
- Departments of Medicine (Division of Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Laura Evans
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Carmen Mikacenic
- Translational Research, Benaroya Research Institute, Seattle, WA
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
- School of Medicine, University of Washington, Sepsis Center of Research Excellence-University of Washington (SCORE-UW), Seattle, WA
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington Medical Center, Seattle, WA
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Robinson JR, Carroll RJ, Bastarache L, Chen Q, Pirruccello J, Mou Z, Wei WQ, Connolly J, Mentch F, Crane PK, Hebbring SJ, Crosslin DR, Gordon AS, Rosenthal EA, Stanaway IB, Hayes MG, Wei W, Petukhova L, Namjou-Khales B, Zhang G, Safarova MS, Walton NA, Still C, Bottinger EP, Loos RJF, Murphy SN, Jackson GP, Abumrad N, Kullo IJ, Jarvik GP, Larson EB, Weng C, Roden D, Khera AV, Denny JC. Quantifying the phenome-wide disease burden of obesity using electronic health records and genomics. Obesity (Silver Spring) 2022; 30:2477-2488. [PMID: 36372681 PMCID: PMC9691570 DOI: 10.1002/oby.23561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVE High BMI is associated with many comorbidities and mortality. This study aimed to elucidate the overall clinical risk of obesity using a genome- and phenome-wide approach. METHODS This study performed a phenome-wide association study of BMI using a clinical cohort of 736,726 adults. This was followed by genetic association studies using two separate cohorts: one consisting of 65,174 adults in the Electronic Medical Records and Genomics (eMERGE) Network and another with 405,432 participants in the UK Biobank. RESULTS Class 3 obesity was associated with 433 phenotypes, representing 59.3% of all billing codes in individuals with severe obesity. A genome-wide polygenic risk score for BMI, accounting for 7.5% of variance in BMI, was associated with 296 clinical diseases, including strong associations with type 2 diabetes, sleep apnea, hypertension, and chronic liver disease. In all three cohorts, 199 phenotypes were associated with class 3 obesity and polygenic risk for obesity, including novel associations such as increased risk of renal failure, venous insufficiency, and gastroesophageal reflux. CONCLUSIONS This combined genomic and phenomic systematic approach demonstrated that obesity has a strong genetic predisposition and is associated with a considerable burden of disease across all disease classes.
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Affiliation(s)
- Jamie R. Robinson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert J. Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qingxia Chen
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James Pirruccello
- Center for Genomics Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Zongyang Mou
- Department of Surgery, University of California, San Diego, CA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Connolly
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frank Mentch
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul K. Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Scott J. Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Adam S. Gordon
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elisabeth A. Rosenthal
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
| | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - M. Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Wei Wei
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lynn Petukhova
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Bahram Namjou-Khales
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Ge Zhang
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Mayya S. Safarova
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Nephi A. Walton
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Christopher Still
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, The Mindich Child Health and Development Institute, New York, NY, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, The Mindich Child Health and Development Institute, New York, NY, USA
| | - Shawn N. Murphy
- Department of Neurology, Partners Healthcare, Boston, MA, USA
| | - Gretchen P. Jackson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Naji Abumrad
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iftikhar J. Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Gail P. Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Dan Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amit V. Khera
- Center for Genomics Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua C. Denny
- All of Us Research Program, National Institutes of Health, Bethesda, MD
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12
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Liu L, Khan A, Sanchez-Rodriguez E, Zanoni F, Li Y, Steers N, Balderes O, Zhang J, Krithivasan P, LeDesma RA, Fischman C, Hebbring SJ, Harley JB, Moncrieffe H, Kottyan LC, Namjou-Khales B, Walunas TL, Knevel R, Raychaudhuri S, Karlson EW, Denny JC, Stanaway IB, Crosslin D, Rauen T, Floege J, Eitner F, Moldoveanu Z, Reily C, Knoppova B, Hall S, Sheff JT, Julian BA, Wyatt RJ, Suzuki H, Xie J, Chen N, Zhou X, Zhang H, Hammarström L, Viktorin A, Magnusson PKE, Shang N, Hripcsak G, Weng C, Rundek T, Elkind MSV, Oelsner EC, Barr RG, Ionita-Laza I, Novak J, Gharavi AG, Kiryluk K. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nat Commun 2022; 13:6859. [PMID: 36369178 PMCID: PMC9651905 DOI: 10.1038/s41467-022-34456-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and is involved in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed a genome-wide association study of serum IgA levels in 41,263 individuals of diverse ancestries and identified 20 genome-wide significant loci, including 9 known and 11 novel loci. Co-localization analyses with expression QTLs prioritized candidate genes for 14 of 20 significant loci. Most loci encoded genes that produced immune defects and IgA abnormalities when genetically manipulated in mice. We also observed positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes, and body mass index, and negative correlations with celiac disease, inflammatory bowel disease, and several infections. Mendelian randomization supported elevated serum IgA as a causal factor in IgA nephropathy. African ancestry was consistently associated with higher serum IgA levels and greater frequency of IgA-increasing alleles compared to other ancestries. Our findings provide novel insights into the genetic regulation of IgA levels and its potential role in human disease.
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Affiliation(s)
- Lili Liu
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Atlas Khan
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Elena Sanchez-Rodriguez
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Francesca Zanoni
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Yifu Li
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Nicholas Steers
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Olivia Balderes
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Junying Zhang
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Priya Krithivasan
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Robert A. LeDesma
- grid.16750.350000 0001 2097 5006Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ USA
| | - Clara Fischman
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Scott J. Hebbring
- grid.280718.40000 0000 9274 7048Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI USA
| | - John B. Harley
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA ,grid.413848.20000 0004 0420 2128US Department of Veterans Affairs Medical Center, Cincinnati, OH USA
| | - Halima Moncrieffe
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Leah C. Kottyan
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Bahram Namjou-Khales
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Theresa L. Walunas
- grid.16753.360000 0001 2299 3507Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Rachel Knevel
- grid.62560.370000 0004 0378 8294Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Soumya Raychaudhuri
- grid.62560.370000 0004 0378 8294Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Elizabeth W. Karlson
- grid.62560.370000 0004 0378 8294Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Joshua C. Denny
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Ian B. Stanaway
- grid.34477.330000000122986657Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA USA
| | - David Crosslin
- grid.34477.330000000122986657Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA USA
| | - Thomas Rauen
- grid.1957.a0000 0001 0728 696XDepartment of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Jürgen Floege
- grid.1957.a0000 0001 0728 696XDepartment of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Frank Eitner
- grid.1957.a0000 0001 0728 696XDepartment of Nephrology, RWTH University of Aachen, Aachen, Germany ,grid.420044.60000 0004 0374 4101Kidney Diseases Research, Bayer Pharma AG, Wuppertal, Germany
| | - Zina Moldoveanu
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Colin Reily
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Barbora Knoppova
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Stacy Hall
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Justin T. Sheff
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Bruce A. Julian
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Robert J. Wyatt
- grid.267301.10000 0004 0386 9246Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN USA
| | - Hitoshi Suzuki
- grid.258269.20000 0004 1762 2738Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jingyuan Xie
- grid.16821.3c0000 0004 0368 8293Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Chen
- grid.16821.3c0000 0004 0368 8293Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xujie Zhou
- grid.11135.370000 0001 2256 9319Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Hong Zhang
- grid.11135.370000 0001 2256 9319Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Lennart Hammarström
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Viktorin
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K. E. Magnusson
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ning Shang
- grid.21729.3f0000000419368729Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - George Hripcsak
- grid.21729.3f0000000419368729Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Chunhua Weng
- grid.21729.3f0000000419368729Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Tatjana Rundek
- grid.26790.3a0000 0004 1936 8606Department of Neurology, University of Miami, Miami, FL USA ,grid.26790.3a0000 0004 1936 8606Evelyn F. McKnight Brain Institute, University of Miami, Miami, FL USA
| | - Mitchell S. V. Elkind
- grid.21729.3f0000000419368729Department of Neurology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Elizabeth C. Oelsner
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - R. Graham Barr
- grid.21729.3f0000000419368729Division of General Medicine, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA ,grid.21729.3f0000000419368729Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY USA
| | - Iuliana Ionita-Laza
- grid.21729.3f0000000419368729Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY USA
| | - Jan Novak
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Ali G. Gharavi
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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13
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Tcheandjieu C, Zhu X, Hilliard AT, Clarke SL, Napolioni V, Ma S, Lee KM, Fang H, Chen F, Lu Y, Tsao NL, Raghavan S, Koyama S, Gorman BR, Vujkovic M, Klarin D, Levin MG, Sinnott-Armstrong N, Wojcik GL, Plomondon ME, Maddox TM, Waldo SW, Bick AG, Pyarajan S, Huang J, Song R, Ho YL, Buyske S, Kooperberg C, Haessler J, Loos RJF, Do R, Verbanck M, Chaudhary K, North KE, Avery CL, Graff M, Haiman CA, Le Marchand L, Wilkens LR, Bis JC, Leonard H, Shen B, Lange LA, Giri A, Dikilitas O, Kullo IJ, Stanaway IB, Jarvik GP, Gordon AS, Hebbring S, Namjou B, Kaufman KM, Ito K, Ishigaki K, Kamatani Y, Verma SS, Ritchie MD, Kember RL, Baras A, Lotta LA, Kathiresan S, Hauser ER, Miller DR, Lee JS, Saleheen D, Reaven PD, Cho K, Gaziano JM, Natarajan P, Huffman JE, Voight BF, Rader DJ, Chang KM, Lynch JA, Damrauer SM, Wilson PWF, Tang H, Sun YV, Tsao PS, O'Donnell CJ, Assimes TL. Large-scale genome-wide association study of coronary artery disease in genetically diverse populations. Nat Med 2022; 28:1679-1692. [PMID: 35915156 PMCID: PMC9419655 DOI: 10.1038/s41591-022-01891-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/08/2022] [Indexed: 02/03/2023]
Abstract
We report a genome-wide association study (GWAS) of coronary artery disease (CAD) incorporating nearly a quarter of a million cases, in which existing studies are integrated with data from cohorts of white, Black and Hispanic individuals from the Million Veteran Program. We document near equivalent heritability of CAD across multiple ancestral groups, identify 95 novel loci, including nine on the X chromosome, detect eight loci of genome-wide significance in Black and Hispanic individuals, and demonstrate that two common haplotypes at the 9p21 locus are responsible for risk stratification in all populations except those of African origin, in which these haplotypes are virtually absent. Moreover, in the largest GWAS for angiographically derived coronary atherosclerosis performed to date, we find 15 loci of genome-wide significance that robustly overlap with established loci for clinical CAD. Phenome-wide association analyses of novel loci and polygenic risk scores (PRSs) augment signals related to insulin resistance, extend pleiotropic associations of these loci to include smoking and family history, and precisely document the markedly reduced transferability of existing PRSs to Black individuals. Downstream integrative analyses reinforce the critical roles of vascular endothelial, fibroblast, and smooth muscle cells in CAD susceptibility, but also point to a shared biology between atherosclerosis and oncogenesis. This study highlights the value of diverse populations in further characterizing the genetic architecture of CAD.
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Affiliation(s)
- Catherine Tcheandjieu
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
| | - Xiang Zhu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | - Shoa L Clarke
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Valerio Napolioni
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Huaying Fang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Fei Chen
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Yingchang Lu
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Noah L Tsao
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sridharan Raghavan
- Medicine Service, VA Eastern Colorado Health Care System, Aurora, CO, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Bryan R Gorman
- VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Derek Klarin
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Vascular Surgery and Endovascular Therapy, University of Florida School of Medicine, Gainesville, FL, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | - Michael G Levin
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nasa Sinnott-Armstrong
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mary E Plomondon
- Department of Medicine, Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- CART Program, VHA Office of Quality and Patient Safety, Washington, DC, USA
| | - Thomas M Maddox
- Healthcare Innovation Lab, JC HealthCare/Washington University School of Medicine, St Louis, MO, USA
- Division of Cardiology, Washington University School of Medicine, St Louis, MO, USA
| | - Stephen W Waldo
- Department of Medicine, Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- CART Program, VHA Office of Quality and Patient Safety, Washington, DC, USA
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Alexander G Bick
- Department of Biomedical Informatics, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jie Huang
- VA Boston Healthcare System, Boston, MA, USA
- Department of Global Health, Peking University School of Public Health, Beijing, China
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, China
| | | | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marie Verbanck
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- EA 7537 BioSTM, Université de Paris, Paris, France
| | - Kumardeep Chaudhary
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Loïc Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Hampton Leonard
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Data Tecnica Int'l, LLC, Glen Echo, MD, USA
| | - Botong Shen
- Health Disparities Research Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Leslie A Lange
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ayush Giri
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Obstetrics and Gynecology, Division of Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ian B Stanaway
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Gail P Jarvik
- Department of Medicine, Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Adam S Gordon
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Scott Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences - The University of Tokyo, Tokyo, Japan
| | - Shefali S Verma
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rachel L Kember
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - Elizabeth R Hauser
- Cooperative Studies Program Epidemiology Center-Durham, Durham VA Health Care System, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Donald R Miller
- Center for Healthcare Organization and Implementation Research, Bedford VA Healthcare System, Bedford, MA, USA
- Center for Population Health, Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - Jennifer S Lee
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Danish Saleheen
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, Division of Cardiology, Columbia University, New York, NY, USA
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Benjamin F Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julie A Lynch
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- College of Nursing and Health Sciences, University of Massachusetts, Boston, MA, USA
| | - Scott M Damrauer
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter W F Wilson
- Atlanta VA Medical Center, Atlanta, GA, USA
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yan V Sun
- Atlanta VA Health Care System, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Feng YCA, Stanaway IB, Connolly JJ, Denny JC, Luo Y, Weng C, Wei WQ, Weiss ST, Karlson EW, Smoller JW. Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach. BMC Genomics 2022; 23:385. [PMID: 35590255 PMCID: PMC9121574 DOI: 10.1186/s12864-022-08600-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As genomic sequencing moves closer to clinical implementation, there has been an increasing acceptance of returning incidental findings to research participants and patients for mutations in highly penetrant, medically actionable genes. A curated list of genes has been recommended by the American College of Medical Genetics and Genomics (ACMG) for return of incidental findings. However, the pleiotropic effects of these genes are not fully known. Such effects could complicate genetic counseling when returning incidental findings. In particular, there has been no systematic evaluation of psychiatric manifestations associated with rare variation in these genes. RESULTS Here, we leveraged a targeted sequence panel and real-world electronic health records from the eMERGE network to assess the burden of rare variation in the ACMG-56 genes and two psychiatric-associated genes (CACNA1C and TCF4) across common mental health conditions in 15,181 individuals of European descent. As a positive control, we showed that this approach replicated the established association between rare mutations in LDLR and hypercholesterolemia with no visible inflation from population stratification. However, we did not identify any genes significantly enriched with rare deleterious variants that confer risk for common psychiatric disorders after correction for multiple testing. Suggestive associations were observed between depression and rare coding variation in PTEN (P = 1.5 × 10-4), LDLR (P = 3.6 × 10-4), and CACNA1S (P = 5.8 × 10-4). We also observed nominal associations between rare variants in KCNQ1 and substance use disorders (P = 2.4 × 10-4), and APOB and tobacco use disorder (P = 1.1 × 10-3). CONCLUSIONS Our results do not support an association between psychiatric disorders and incidental findings in medically actionable gene mutations, but power was limited with the available sample sizes. Given the phenotypic and genetic complexity of psychiatric phenotypes, future work will require a much larger sequencing dataset to determine whether incidental findings in these genes have implications for risk of psychopathology.
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Affiliation(s)
- Yen-Chen A Feng
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, USA. .,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. .,Master of Public Health Program, National Taiwan University, Taipei, Taiwan.
| | - Ian B Stanaway
- Division of Nephrology, School of Medicine, Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,All of Us Research Program, National Institutes of Health, Besthesda, MD, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott T Weiss
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth W Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Jordan W Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, USA. .,Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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15
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Mansour SG, Bhatraju PK, Coca SG, Obeid W, Wilson FP, Stanaway IB, Jia Y, Thiessen-Philbrook H, Go AS, Ikizler TA, Siew ED, Chinchilli VM, Hsu CY, Garg AX, Reeves WB, Liu KD, Kimmel PL, Kaufman JS, Wurfel MM, Himmelfarb J, Parikh SM, Parikh CR. Angiopoietins as Prognostic Markers for Future Kidney Disease and Heart Failure Events after Acute Kidney Injury. J Am Soc Nephrol 2022; 33:613-627. [PMID: 35017169 PMCID: PMC8975075 DOI: 10.1681/asn.2021060757] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/15/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The mechanisms underlying long-term sequelae after AKI remain unclear. Vessel instability, an early response to endothelial injury, may reflect a shared mechanism and early trigger for CKD and heart failure. METHODS To investigate whether plasma angiopoietins, markers of vessel homeostasis, are associated with CKD progression and heart failure admissions after hospitalization in patients with and without AKI, we conducted a prospective cohort study to analyze the balance between angiopoietin-1 (Angpt-1), which maintains vessel stability, and angiopoietin-2 (Angpt-2), which increases vessel destabilization. Three months after discharge, we evaluated the associations between angiopoietins and development of the primary outcomes of CKD progression and heart failure and the secondary outcome of all-cause mortality 3 months after discharge or later. RESULTS Median age for the 1503 participants was 65.8 years; 746 (50%) had AKI. Compared with the lowest quartile, the highest quartile of the Angpt-1:Angpt-2 ratio was associated with 72% lower risk of CKD progression (adjusted hazard ratio [aHR], 0.28; 95% confidence interval [CI], 0.15 to 0.51), 94% lower risk of heart failure (aHR, 0.06; 95% CI, 0.02 to 0.15), and 82% lower risk of mortality (aHR, 0.18; 95% CI, 0.09 to 0.35) for those with AKI. Among those without AKI, the highest quartile of Angpt-1:Angpt-2 ratio was associated with 71% lower risk of heart failure (aHR, 0.29; 95% CI, 0.12 to 0.69) and 68% less mortality (aHR, 0.32; 95% CI, 0.15 to 0.68). There were no associations with CKD progression. CONCLUSIONS A higher Angpt-1:Angpt-2 ratio was strongly associated with less CKD progression, heart failure, and mortality in the setting of AKI.
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Affiliation(s)
- Sherry G Mansour
- Clinical Translational Research Accelerator, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut.,Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington.,Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Steven G Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Wassim Obeid
- Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Francis P Wilson
- Clinical Translational Research Accelerator, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut.,Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Yaqi Jia
- Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Alan S Go
- Division of Nephrology, Department of Medicine, University of California, San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California.,Division of Nephrology, Department of Medicine, Stanford University, Palo Alto, California.,Department of Health Research and Policy, Stanford University, Palo Alto, California.,Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - T Alp Ikizler
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Edward D Siew
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Vernon M Chinchilli
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Chi-Yuan Hsu
- Division of Nephrology, Department of Medicine, University of California, San Francisco, San Francisco, California.,Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Amit X Garg
- Division of Nephrology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,ICES, Ontario, Canada
| | - W Brian Reeves
- Division of Nephrology, Department of Medicine, University of Texas Joe and Teresa Long School of Medicine, San Antonio, Texas
| | - Kathleen D Liu
- Division of Nephrology, Department of Medicine, University of California, San Francisco, San Francisco, California.,Department of Anesthesia, Division of Critical Care Medicine, University of California, San Francisco, San Francisco, California
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - James S Kaufman
- Division of Nephrology, Veterans Affairs New York Harbor Healthcare System and New York University School of Medicine, New York, New York
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington.,Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Samir M Parikh
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Chirag R Parikh
- Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
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16
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Helms L, Marchiano S, Stanaway IB, Hsiang TY, Juliar BA, Saini S, Zhao YT, Khanna A, Menon R, Alakwaa F, Mikacenic C, Morrell ED, Wurfel MM, Kretzler M, Harder JL, Murry CE, Himmelfarb J, Ruohola-Baker H, Bhatraju PK, Gale M, Freedman BS. Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations. JCI Insight 2021; 6:e154882. [PMID: 34767537 PMCID: PMC8783682 DOI: 10.1172/jci.insight.154882] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Kidneys are critical target organs of COVID-19, but susceptibility and responses to infection remain poorly understood. Here, we combine SARS-CoV-2 variants with genome-edited kidney organoids and clinical data to investigate tropism, mechanism, and therapeutics. SARS-CoV-2 specifically infects organoid proximal tubules among diverse cell types. Infections produce replicating virus, apoptosis, and disrupted cell morphology, features of which are revealed in the context of polycystic kidney disease. Cross-validation of gene expression patterns in organoids reflects proteomic signatures of COVID-19 in the urine of critically ill patients indicating interferon pathway upregulation. SARS-CoV-2 viral variants alpha, beta, gamma, kappa, and delta exhibit comparable levels of infection in organoids. Infection is ameliorated in ACE2-/- organoids and blocked via treatment with de novo-designed spike binder peptides. Collectively, these studies clarify the impact of kidney infection in COVID-19 as reflected in organoids and clinical populations, enabling assessment of viral fitness and emerging therapies.
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Affiliation(s)
- Louisa Helms
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
| | - Silvia Marchiano
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
| | - Ian B. Stanaway
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
| | - Tien-Ying Hsiang
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin A. Juliar
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
| | - Shally Saini
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
| | - Yan Ting Zhao
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
| | - Akshita Khanna
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Center for Cardiovascular Biology
| | - Rajasree Menon
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fadhl Alakwaa
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Mikacenic
- Department of Medicine
- Translational Research, Benaroya Research Institute, Seattle, Washington, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eric D. Morrell
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark M. Wurfel
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer L. Harder
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles E. Murry
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
- Sana Biotechnology, Seattle, Washington, USA
| | | | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Pavan K. Bhatraju
- Department of Medicine
- Kidney Research Institute
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin S. Freedman
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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17
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Mehrotra R, Stanaway IB, Jarvik GP, Lambie M, Morelle J, Perl J, Himmelfarb J, Heimburger O, Johnson DW, Imam TH, Robinson B, Stenvinkel P, Devuyst O, Davies SJ. A genome-wide association study suggests correlations of common genetic variants with peritoneal solute transfer rates in patients with kidney failure receiving peritoneal dialysis. Kidney Int 2021; 100:1101-1111. [PMID: 34197840 PMCID: PMC8545920 DOI: 10.1016/j.kint.2021.05.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/19/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022]
Abstract
Movement of solutes across the peritoneum allows for the use of peritoneal dialysis to treat kidney failure. However, there is a large inter-individual variability in the peritoneal solute transfer rate (PSTR). Here, we tested the hypothesis that common genetic variants are associated with variability in PSTR. Of the 3561 participants from 69 centers in six countries, 2850 with complete data were included in a genome-wide association study. PSTR was defined as the four-hour dialysate/plasma creatinine ratio from the first peritoneal equilibration test after starting PD. Heritability of PSTR was estimated using genomic-restricted maximum-likelihood analysis, and the association of PSTR with a genome-wide polygenic risk score was also tested. The mean four-hour dialysate/plasma creatinine ratio in participants was 0.70. In 2212 participants of European ancestry, no signal reached genome-wide significance but 23 single nucleotide variants at four loci demonstrated suggestive associations with PSTR. Meta-analysis of ancestry-stratified regressions in 2850 participants revealed five single-nucleotide variants at four loci with suggestive correlations with PSTR. Association across ancestry strata was consistent for rs28644184 at the KDM2B locus. The estimated heritability of PSTR was 19%, and a permuted model polygenic risk score was significantly associated with PSTR. Thus, this genome-wide association study of patients receiving peritoneal dialysis bolsters evidence for a genetic contribution to inter-individual variability in PSTR.
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Affiliation(s)
- Rajnish Mehrotra
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA.
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mark Lambie
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Keele, UK
| | - Johann Morelle
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Experimentale et Clinique, UClouvain, Brussels, Belgium
| | - Jeffrey Perl
- Division of Nephrology, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Olof Heimburger
- Division of Renal Medicine, Department of Clinical Science, Intervention, and Technology, Karolinska Institute, Stockholm, Sweden
| | - David W Johnson
- Australasian Trials Network, University of Queensland, Brisbane, Australia
| | - Talha H Imam
- Department of Nephrology, Kaiser Permanente, Fontana, California, USA
| | - Bruce Robinson
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, USA
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention, and Technology, Karolinska Institute, Stockholm, Sweden
| | - Olivier Devuyst
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Experimentale et Clinique, UClouvain, Brussels, Belgium
| | - Simon J Davies
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Keele, UK
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18
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Williams AT, Shrine N, Naghra-van Gijzel H, Betts JC, Hessel EM, John C, Packer R, Reeve NF, Yeo AJ, Abner E, Åsvold BO, Auvinen J, Bartz TM, Bradford Y, Brumpton B, Campbell A, Cho MH, Chu S, Crosslin DR, Feng Q, Esko T, Gharib SA, Hayward C, Hebbring S, Hveem K, Jarvelin MR, Jarvik GP, Landis SH, Larson EB, Liu J, Loos RJ, Luo Y, Moscati A, Mullerova H, Namjou B, Porteous DJ, Quint JK, Ritchie MD, Sliz E, Stanaway IB, Thomas L, Wilson JF, Hall IP, Wain LV, Michalovich D, Tobin MD. Genome-wide association study of susceptibility to hospitalised respiratory infections. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17230.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Globally, respiratory infections contribute to significant morbidity and mortality. However, genetic determinants of respiratory infections are understudied and remain poorly understood. Methods: We conducted a genome-wide association study in 19,459 hospitalised respiratory infection cases and 101,438 controls from UK Biobank. We followed-up well-imputed top signals from the UK Biobank discovery analysis in 50,912 respiratory infection cases and 150,442 controls from 11 cohorts. We aggregated effect estimates across studies using inverse variance-weighted meta-analyses. Additionally, we investigated the function of the top signals in order to gain understanding of the underlying biological mechanisms. Results: In the discovery analysis, we report 56 signals at P<5×10-6, one of which was genome-wide significant (P<5×10-8). The genome-wide significant signal was in an intron of PBX3, a gene that encodes pre-B-cell leukaemia transcription factor 3, a homeodomain-containing transcription factor. Further, the genome-wide significant signal was found to colocalise with gene-specific expression quantitative trait loci (eQTLs) affecting expression of PBX3 in lung tissue, where the respiratory infection risk alleles were associated with decreased PBX3 expression in lung tissue, highlighting a possible biological mechanism. Of the 56 signals, 40 were well-imputed in UK Biobank and were investigated in the 11 follow-up cohorts. None of the 40 signals replicated, with effect estimates attenuated. Conclusions: Our discovery analysis implicated PBX3 as a candidate causal gene and suggests a possible role of transcription factor binding activity in respiratory infection susceptibility. However, the PBX3 signal, and the other well-imputed signals, did not replicate when aggregating effect estimates across 11 independent cohorts. Significant phenotypic heterogeneity and differences in study ascertainment may have contributed to this lack of statistical replication. Overall, our study highlighted putative associations and possible biological mechanisms that may provide insight into respiratory infection susceptibility.
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19
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Kordahi MC, Stanaway IB, Avril M, Chac D, Blanc MP, Ross B, Diener C, Jain S, McCleary P, Parker A, Friedman V, Huang J, Burke W, Gibbons SM, Willis AD, Darveau RP, Grady WM, Ko CW, DePaolo RW. Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer. Cell Host Microbe 2021; 29:1589-1598.e6. [PMID: 34536346 DOI: 10.1016/j.chom.2021.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/13/2021] [Accepted: 08/24/2021] [Indexed: 01/06/2023]
Abstract
Colorectal cancer is a major health concern worldwide. Growing evidence for the role of the gut microbiota in the initiation of CRC has sparked interest in approaches that target these microorganisms. However, little is known about the composition and role of the microbiota associated with precancerous polyps. Here, we found distinct microbial signatures between patients with and without polyps and between polyp subtypes using sequencing and culturing techniques. We found a correlation between Bacteroides fragilis recovered and the level of inflammatory cytokines in the mucosa adjacent to the polyp. Additional analysis revealed that B. fragilis from patients with polyps are bft-negative, activate NF-κB through Toll-like receptor 4, induce a pro-inflammatory response, and are enriched in genes associated with LPS biosynthesis. This study provides fundamental insight into the microbial microenvironment of the pre-neoplastic polyp by highlighting strain-specific genomic and proteomic differences, as well as more broad compositional differences in the microbiome.
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Affiliation(s)
- Melissa C Kordahi
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA
| | - Ian B Stanaway
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA
| | - Marion Avril
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Denise Chac
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA
| | - Marie-Pierre Blanc
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Benjamin Ross
- Department of Microbiology and Immunology at Dartmouth College, Hanover, NH 03755, USA
| | - Christian Diener
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Institute for Systems Biology, Seattle, WA 98105
| | - Sumita Jain
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA 98195, USA
| | - Paul McCleary
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA
| | - Ana Parker
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA
| | - Vincent Friedman
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA
| | - Jennifer Huang
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Wynn Burke
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sean M Gibbons
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Institute for Systems Biology, Seattle, WA 98105
| | - Amy D Willis
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Biostatistics University of Washington, Seattle, WA 98195, USA
| | - Richard P Darveau
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA 98195, USA
| | - William M Grady
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Cynthia W Ko
- Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - R William DePaolo
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Center for Microbiome Science & Therapeutics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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20
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Fan X, Wynn J, Shang N, Liu C, Fedotov A, Hallquist MLG, Buchanan AH, Williams MS, Smith ME, Hoell C, Rasmussen-Torvik LJ, Peterson JF, Wiesner GL, Murad AM, Jarvik GP, Gordon AS, Rosenthal EA, Stanaway IB, Crosslin DR, Larson EB, Leppig KA, Henrikson NB, Williams JL, Li R, Hebbring S, Weng C, Shen Y, Crew KD, Chung WK. Penetrance of Breast Cancer Susceptibility Genes From the eMERGE III Network. JNCI Cancer Spectr 2021; 5:pkab044. [PMID: 34377931 PMCID: PMC8346699 DOI: 10.1093/jncics/pkab044] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/08/2021] [Accepted: 04/22/2021] [Indexed: 01/03/2023] Open
Abstract
Background Unbiased estimates of penetrance are challenging but critically important to make informed choices about strategies for risk management through increased surveillance and risk-reducing interventions. Methods We studied the penetrance and clinical outcomes of 7 breast cancer susceptibility genes (BRCA1, BRCA2, TP53, CHEK2, ATM, PALB2, and PTEN) in almost 13 458 participants unselected for personal or family history of breast cancer. We identified 242 female participants with pathogenic or likely pathogenic variants in 1 of the 7 genes for penetrance analyses, and 147 women did not previously know their genetic results. Results Out of the 147 women, 32 women were diagnosed with breast cancer at an average age of 52.8 years. Estimated penetrance by age 60 years ranged from 17.8% to 43.8%, depending on the gene. In clinical-impact analysis, 42.3% (95% confidence interval = 31.3% to 53.3%) of women had taken actions related to their genetic results, and 2 new breast cancer cases were identified within the first 12 months after genetic results disclosure. Conclusions Our study provides population-based penetrance estimates for the understudied genes CHEK2, ATM, and PALB2 and highlights the importance of using unselected populations for penetrance studies. It also demonstrates the potential clinical impact of genetic testing to improve health care through early diagnosis and preventative screening.
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Affiliation(s)
- Xiao Fan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Ning Shang
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | - Maureen E Smith
- Department of Medicine, Northwestern University, Chicago Feinberg School of Medicine, Chicago, IL, USA
| | - Christin Hoell
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Georgia L Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrea M Murad
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Adam S Gordon
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Kathleen A Leppig
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Nora B Henrikson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Scott Hebbring
- Center for Precision Medicine Research, Marshfield Clinic, Marshfield, WI, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Katherine D Crew
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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21
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Suri P, Stanaway IB, Zhang Y, Freidin MB, Tsepilov YA, Carrell DS, Williams FM, Aulchenko YS, Hakonarson H, Namjou B, Crosslin DR, Jarvik GP, Lee MT. Genome-wide association studies of low back pain and lumbar spinal disorders using electronic health record data identify a locus associated with lumbar spinal stenosis. Pain 2021; 162:2263-2272. [PMID: 33729212 PMCID: PMC8277660 DOI: 10.1097/j.pain.0000000000002221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/15/2021] [Indexed: 12/30/2022]
Abstract
ABSTRACT Identifying genetic risk factors for lumbar spine disorders may lead to knowledge regarding underlying mechanisms and the development of new treatments. We conducted a genome-wide association study involving 100,811 participants with genotypes and longitudinal electronic health record data from the Electronic Medical Records and Genomics Network and Geisinger Health. Cases and controls were defined using validated algorithms and clinical diagnostic codes. Electronic health record-defined phenotypes included low back pain requiring healthcare utilization (LBP-HC), lumbosacral radicular syndrome (LSRS), and lumbar spinal stenosis (LSS). Genome-wide association study used logistic regression with additive genetic effects adjusting for age, sex, site-specific factors, and ancestry (principal components). A fixed-effect inverse-variance weighted meta-analysis was conducted. Genetic variants of genome-wide significance (P < 5 × 10-8) were carried forward for replication in an independent sample from UK Biobank. Phenotype prevalence was 48.8% for LBP-HC, 19.8% for LSRS, and 7.9% for LSS. No variants were significantly associated with LBP-HC. One locus was associated with LSRS (lead variant rs146153280:C>G, odds ratio [OR] = 1.17 for G, P = 2.1 × 10-9), but was not replicated. Another locus on chromosome 2 spanning GFPT1, NFU1, and AAK1 was associated with LSS (lead variant rs13427243:G>A, OR = 1.10 for A, P = 4.3 × 10-8) and replicated in UK Biobank (OR = 1.11, P = 5.4 × 10-5). This was the first genome-wide association study meta-analysis of lumbar spinal disorders using electronic health record data. We identified 2 novel associations with LSRS and LSS; the latter was replicated in an independent sample.
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Affiliation(s)
- Pradeep Suri
- Seattle Epidemiologic Research and Information Center, VA Puget Sound Health Care System, 1660 S. Columbian Way, Seattle, WA 98108, USA
- Division of Rehabilitation Care Services, 1660 S. Columbian Way, Seattle, WA 98108, USA
- Clinical Learning, Evidence, and Research Center, University of Washington, 325 Ninth Avenue, Box 359612 Seattle, WA 98104, USA
- Department of Rehabilitation Medicine, University of Washington, 325 Ninth Avenue, Box 359612 Seattle, WA 98104, USA
| | - Ian B. Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, 3720 15th Ave NE, Seattle, WA 98105, USA
| | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger, 100 N. Academy Avenue, Danville, PA 17822, USA
| | - Maxim B. Freidin
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London, SE1 7EH, UK
| | - Yakov A. Tsepilov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University, 1 Pirogova Street, Novosibirsk, 630090, Russia
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
- PolyOmica, s’-Hetogenbosch,5237 PA, The Netherlands
| | - David S. Carrell
- Kaiser Permante Washington Health Research Institute, 1700 Minor Ave, Suite 1600, Seattle, WA 98101, USA
| | - Frances M.K. Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London, SE1 7EH, UK
| | - Yurii S. Aulchenko
- PolyOmica, s’-Hetogenbosch,5237 PA, The Netherlands
- Kurchatov Genomics Center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Hakon Hakonarson
- Department of Pediatrics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd.Philadelphia, PA 19104, USA
| | - Bahram Namjou
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - David R. Crosslin
- Department of Biomedical Informatics and Education, University of Washington, 3720 15th Ave NE, Seattle, WA 98105, USA
| | - Gail P. Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, 3720 15th Ave NE, Seattle, WA 98105, USA
| | - Ming Ta Lee
- Genomic Medicine Institute, Geisinger, 100 N. Academy Avenue, Danville, PA 17822, USA
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22
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Khan A, Shang N, Petukhova L, Zhang J, Shen Y, Hebbring SJ, Moncrieffe H, Kottyan LC, Namjou-Khales B, Knevel R, Raychaudhuri S, Karlson EW, Harley JB, Stanaway IB, Crosslin D, Denny JC, Elkind MS, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical Records-Based Genetic Studies of the Complement System. J Am Soc Nephrol 2021; 32:2031-2047. [PMID: 33941608 PMCID: PMC8455263 DOI: 10.1681/asn.2020091371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/09/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Genetic variants in complement genes have been associated with a wide range of human disease states, but well-powered genetic association studies of complement activation have not been performed in large multiethnic cohorts. METHODS We performed medical records-based genome-wide and phenome-wide association studies for plasma C3 and C4 levels among participants of the Electronic Medical Records and Genomics (eMERGE) network. RESULTS In a GWAS for C3 levels in 3949 individuals, we detected two genome-wide significant loci: chr.1q31.3 (CFH locus; rs3753396-A; β=0.20; 95% CI, 0.14 to 0.25; P=1.52x10-11) and chr.19p13.3 (C3 locus; rs11569470-G; β=0.19; 95% CI, 0.13 to 0.24; P=1.29x10-8). These two loci explained approximately 2% of variance in C3 levels. GWAS for C4 levels involved 3998 individuals and revealed a genome-wide significant locus at chr.6p21.32 (C4 locus; rs3135353-C; β=0.40; 95% CI, 0.34 to 0.45; P=4.58x10-35). This locus explained approximately 13% of variance in C4 levels. The multiallelic copy number variant analysis defined two structural genomic C4 variants with large effect on blood C4 levels: C4-BS (β=-0.36; 95% CI, -0.42 to -0.30; P=2.98x10-22) and C4-AL-BS (β=0.25; 95% CI, 0.21 to 0.29; P=8.11x10-23). Overall, C4 levels were strongly correlated with copy numbers of C4A and C4B genes. In comprehensive phenome-wide association studies involving 102,138 eMERGE participants, we cataloged a full spectrum of autoimmune, cardiometabolic, and kidney diseases genetically related to systemic complement activation. CONCLUSIONS We discovered genetic determinants of plasma C3 and C4 levels using eMERGE genomic data linked to electronic medical records. Genetic variants regulating C3 and C4 levels have large effects and multiple clinical correlations across the spectrum of complement-related diseases in humans.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Lynn Petukhova
- Department of Dermatology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Jun Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, New York
| | - Scott J. Hebbring
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | - Halima Moncrieffe
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Leah C. Kottyan
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Bahram Namjou-Khales
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Rachel Knevel
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Elizabeth W. Karlson
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - John B. Harley
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Ian B. Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - David Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee
| | - Mitchell S.V. Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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23
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Shang N, Khan A, Polubriaginof F, Zanoni F, Mehl K, Fasel D, Drawz PE, Carrol RJ, Denny JC, Hathcock MA, Arruda-Olson AM, Peissig PL, Dart RA, Brilliant MH, Larson EB, Carrell DS, Pendergrass S, Verma SS, Ritchie MD, Benoit B, Gainer VS, Karlson EW, Gordon AS, Jarvik GP, Stanaway IB, Crosslin DR, Mohan S, Ionita-Laza I, Tatonetti NP, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. NPJ Digit Med 2021; 4:70. [PMID: 33850243 PMCID: PMC8044136 DOI: 10.1038/s41746-021-00428-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Chronic Kidney Disease (CKD) represents a slowly progressive disorder that is typically silent until late stages, but early intervention can significantly delay its progression. We designed a portable and scalable electronic CKD phenotype to facilitate early disease recognition and empower large-scale observational and genetic studies of kidney traits. The algorithm uses a combination of rule-based and machine-learning methods to automatically place patients on the staging grid of albuminuria by glomerular filtration rate ("A-by-G" grid). We manually validated the algorithm by 451 chart reviews across three medical systems, demonstrating overall positive predictive value of 95% for CKD cases and 97% for healthy controls. Independent case-control validation using 2350 patient records demonstrated diagnostic specificity of 97% and sensitivity of 87%. Application of the phenotype to 1.3 million patients demonstrated that over 80% of CKD cases are undetected using ICD codes alone. We also demonstrated several large-scale applications of the phenotype, including identifying stage-specific kidney disease comorbidities, in silico estimation of kidney trait heritability in thousands of pedigrees reconstructed from medical records, and biobank-based multicenter genome-wide and phenome-wide association studies.
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Affiliation(s)
- Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Fernanda Polubriaginof
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Karla Mehl
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - David Fasel
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Paul E Drawz
- Department of Medicine, University of Minnesota, Minnesota, MN, USA
| | - Robert J Carrol
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Departments of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | | | | | - Richard A Dart
- Marshfield Clinic Research Institute, Marshfield, WI, USA
| | | | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | | | | | | | | | - Adam S Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian B Stanaway
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David R Crosslin
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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24
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Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L. Response to Li and Hopper. Am J Hum Genet 2021; 108:527-529. [PMID: 33667396 PMCID: PMC8008475 DOI: 10.1016/j.ajhg.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jeffrey K Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Franzel J B van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen 176700, the Netherlands
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA 90089, USA
| | - Christopher H Dampier
- Department of Surgery, University of Virginia Health System, Charlottesville, VA 22903, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna 1090, Austria
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå 90187, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 90187, Sweden
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock 18051, Germany
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel D Buchanan
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David C Muller
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ 85003, USA
| | - David R Crosslin
- Department of Bioinformatics and Medical Education, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02108, USA
| | - Eric Larson
- Kaiser Permanente Washington Research Institute, Seattle, WA 98101, USA
| | - Flora Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica Minnier
- School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg 20246, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden 01062, Germany
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, NY 10065, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | | | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL A1B 3R7, Canada
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ 85260, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 85054, USA
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G1X5, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona 08908, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08907, Spain; ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Biomedicine Institute (IBIOMED), University of León, León 24071, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy Chung
- Office of Research & Development, Department of Veterans Affairs, Washington, DC 20420, USA; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA; Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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Rosenthal EA, Crosslin DR, Gordon AS, Carrell DS, Stanaway IB, Larson EB, Grafton J, Wei WQ, Denny JC, Feng QP, Shah AS, Sturm AC, Ritchie MD, Pacheco JA, Hakonarson H, Rasmussen-Torvik LJ, Connolly JJ, Fan X, Safarova M, Kullo IJ, Jarvik GP. Association between triglycerides, known risk SNVs and conserved rare variation in SLC25A40 in a multi-ancestry cohort. BMC Med Genomics 2021; 14:11. [PMID: 33407432 PMCID: PMC7789246 DOI: 10.1186/s12920-020-00854-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
Background Elevated triglycerides (TG) are associated with, and may be causal for, cardiovascular disease (CVD), and co-morbidities such as type II diabetes and metabolic syndrome. Pathogenic variants in APOA5 and APOC3 as well as risk SNVs in other genes [APOE (rs429358, rs7412), APOA1/C3/A4/A5 gene cluster (rs964184), INSR (rs7248104), CETP (rs7205804), GCKR (rs1260326)] have been shown to affect TG levels. Knowledge of genetic causes for elevated TG may lead to early intervention and targeted treatment for CVD. We previously identified linkage and association of a rare, highly conserved missense variant in SLC25A40, rs762174003, with hypertriglyceridemia (HTG) in a single large family, and replicated this association with rare, highly conserved missense variants in a European American and African American sample. Methods Here, we analyzed a longitudinal mixed-ancestry cohort (European, African and Asian ancestry, N = 8966) from the Electronic Medical Record and Genomics (eMERGE) Network. We tested associations between median TG and the genes of interest, using linear regression, adjusting for sex, median age, median BMI, and the first two principal components of ancestry. Results We replicated the association between TG and APOC3, APOA5, and risk variation at APOE, APOA1/C3/A4/A5 gene cluster, and GCKR. We failed to replicate the association between rare, highly conserved variation at SLC25A40 and TG, as well as for risk variation at INSR and CETP. Conclusions Analysis using data from electronic health records presents challenges that need to be overcome. Although large amounts of genotype data is becoming increasingly accessible, usable phenotype data can be challenging to obtain. We were able to replicate known, strong associations, but were unable to replicate moderate associations due to the limited sample size and missing drug information.
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Affiliation(s)
- Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, 1705 NE Pacific St, Box 357720, Seattle, WA, 98195, USA.
| | - David R Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adam S Gordon
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jane Grafton
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi-Ping Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy S Shah
- Division of Endocrinology, Department of Pediatrics, Cincinnati Children's Hospital and the University of Cincinnati, Cincinnati, OH, USA
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Fan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Maya Safarova
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.,Gonda Vascular Center, Mayo Clinic, Rochester, MN, USA
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, 1705 NE Pacific St, Box 357720, Seattle, WA, 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Jarvik GP, Wang X, Fontanillas P, Kim E, Chanprasert S, Gordon AS, Bastarache L, Kowdley KV, Harrison T, Rosenthal EA, Stanaway IB, Bézieau S, Weinstein SJ, Newcomb PA, Casey G, Platz EA, Visvanathan K, Le Marchand L, Ulrich CM, Hardikar S, Li CI, van Duijnhoven FJ, Gsur A, Campbell PT, Moreno V, Vodička P, Brenner H, Chang-Claude J, Hoffmeister M, Slattery ML, Gunter MJ, Aglago EK, Castellví-Bel S, Kweon SS, Chan AT, Li L, Zheng W, Bishop DT, Giles GG, Rennert G, Offit K, Keku TO, Woods MO, Hampe J, Van Guelpen B, Gallinger SJ, de la Chapelle A, Hampel H, Berndt SI, Tangen CM, Lindblom A, Wolk A, Burnett-Hartman A, Wu AH, White E, Gruber SB, Jenkins MA, Mountain J, Peters U, Crosslin DR. Hemochromatosis risk genotype is not associated with colorectal cancer or age at its diagnosis. HGG Adv 2020; 1:100010. [PMID: 35047832 PMCID: PMC8756515 DOI: 10.1016/j.xhgg.2020.100010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/12/2020] [Indexed: 11/28/2022] Open
Abstract
Homozygotes for the higher penetrance hemochromatosis risk allele, HFE c.845G>A (p.Cys282Tyr, or C282Y), have been reported to be at a 2- to 3-fold increased risk for colorectal cancer (CRC). These results have been reported for small sample size studies with no information about age at diagnosis for CRC. An association with age at diagnosis might alter CRC screening recommendations. We analyzed two large European ancestry datasets to assess the association of HFE genotype with CRC risk and age at CRC diagnosis. The first dataset included 59,733 CRC or advanced adenoma cases and 72,351 controls from a CRC epidemiological study consortium. The second dataset included 13,564 self-reported CRC cases and 2,880,218 controls from the personal genetics company, 23andMe. No association of the common hereditary hemochromatosis (HH) risk genotype and CRC was found in either dataset. The odds ratios (ORs) for the association of CRC and HFE C282Y homozygosity were 1.08 (95% confidence interval [CI], 0.91-1.29; p = 0.4) and 1.01 (95% CI, 0.78-1.31, p = 0.9) in the two cohorts, respectively. Age at CRC diagnosis also did not differ by HFE C282Y/C282Y genotype in either dataset. These results indicate no increased CRC risk in individuals with HH genotypes and suggest that persons with HH risk genotypes can follow population screening recommendations for CRC.
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Affiliation(s)
- Gail P. Jarvik
- University of Washington Medical Center, Seattle, WA, USA
| | - Xiaoliang Wang
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Polly A. Newcomb
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA
| | - Graham Casey
- University of Virginia, Charlottesville, VA, USA
| | | | - Kala Visvanathan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | | | | | | | | | | | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) and Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), L’Hospitalet, 08908, Barcelona, Spain
| | - Pavel Vodička
- Institute of Experimental Medicine, Czech Academy of Sciences, Biomedical Center, Medical Faculty Pilsen and 1st Medical Faculty, Charles University, Prague, Czech Republic
| | | | | | | | | | - Marc J. Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Elom K. Aglago
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Sun-Seog Kweon
- Chonnam National University Medical School, Gwangju, Korea
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Li Li
- University of Virginia, Charlottesville, VA, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Graham G. Giles
- Cancer Council Victoria, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Monash University, Melbourne, VIC, Australia
| | - Gad Rennert
- Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Jochen Hampe
- Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Bethan Van Guelpen
- Department of Radiation Sciences, Oncology, Umeå University and Wallenberg Centre for Molecular Medicine, Umeå University, Sweden
| | | | | | | | - Sonja I. Berndt
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alicja Wolk
- Karolinska Institutet, Stockholm, Sweden
- Uppsala University, Uppsala, Sweden
| | | | - Anna H. Wu
- University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, VIC, Australia
| | | | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Medicine, Seattle, WA, USA
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28
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Palmer MR, Kim DS, Crosslin DR, Stanaway IB, Rosenthal EA, Carrell DS, Cronkite DJ, Gordon A, Du X, Li YK, Williams MS, Weng C, Feng Q, Li R, Pendergrass SA, Hakonarson H, Fasel D, Sohn S, Sleiman P, Handelman SK, Speliotes E, Kullo IJ, Larson EB, Jarvik GP. Loci identified by a genome-wide association study of carotid artery stenosis in the eMERGE network. Genet Epidemiol 2020; 45:4-15. [PMID: 32964493 PMCID: PMC7891640 DOI: 10.1002/gepi.22360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
Carotid artery atherosclerotic disease (CAAD) is a risk factor for stroke. We used a genome-wide association (GWAS) approach to discover genetic variants associated with CAAD in participants in the electronic Medical Records and Genomics (eMERGE) Network. We identified adult CAAD cases with unilateral or bilateral carotid artery stenosis and controls without evidence of stenosis from electronic health records at eight eMERGE sites. We performed GWAS with a model adjusting for age, sex, study site, and genetic principal components of ancestry. In eMERGE we found 1793 CAAD cases and 17,958 controls. Two loci reached genome-wide significance, on chr6 in LPA (rs10455872, odds ratio [OR] (95% confidence interval [CI]) = 1.50 (1.30-1.73), p = 2.1 × 10-8 ) and on chr7, an intergenic single nucleotide variant (SNV; rs6952610, OR (95% CI) = 1.25 (1.16-1.36), p = 4.3 × 10-8 ). The chr7 association remained significant in the presence of the LPA SNV as a covariate. The LPA SNV was also associated with coronary heart disease (CHD; 4199 cases and 11,679 controls) in this study (OR (95% CI) = 1.27 (1.13-1.43), p = 5 × 10-5 ) but the chr7 SNV was not (OR (95% CI) = 1.03 (0.97-1.09), p = .37). Both variants replicated in UK Biobank. Elevated lipoprotein(a) concentrations ([Lp(a)]) and LPA variants associated with elevated [Lp(a)] have previously been associated with CAAD and CHD, including rs10455872. With electronic health record phenotypes in eMERGE and UKB, we replicated a previously known association and identified a novel locus associated with CAAD.
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Affiliation(s)
- Melody R Palmer
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel S Kim
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - David J Cronkite
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Adam Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | - Xiaomeng Du
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yatong K Li
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Qiping Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | - Hakon Hakonarson
- Department of Pediatrics, The Center for Applied Genomics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Fasel
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | | | - Patrick Sleiman
- Department of Pediatrics, The Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samuel K Handelman
- Division of Gastroenterology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth Speliotes
- Division of Gastroenterology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
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- The electronic Medical Records and GEnomics Network, NHGRI, NIH, Bethesda, Maryland, USA
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, USA
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29
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Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L. Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk. Am J Hum Genet 2020; 107:432-444. [PMID: 32758450 PMCID: PMC7477007 DOI: 10.1016/j.ajhg.2020.07.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/13/2020] [Indexed: 02/08/2023] Open
Abstract
Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
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Affiliation(s)
- Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jeffrey K Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Franzel J B van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen 176700, the Netherlands
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA 90089, USA
| | - Christopher H Dampier
- Department of Surgery, University of Virginia Health System, Charlottesville, VA 22903, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna 1090, Austria
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå 90187, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 90187, Sweden
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock 18051, Germany
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel D Buchanan
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David C Muller
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ 85003, USA
| | - David R Crosslin
- Department of Bioinformatics and Medical Education, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02108, USA
| | - Eric Larson
- Kaiser Permanente Washington Research Institute, Seattle, WA 98101, USA
| | - Flora Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica Minnier
- School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg 20246, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden 01062, Germany
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, NY 10065, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | | | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL A1B 3R7, Canada
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ 85260, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 85054, USA
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G1X5, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona 08908, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08907, Spain; ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Biomedicine Institute (IBIOMED), University of León, León 24071, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy Chung
- Office of Research & Development, Department of Veterans Affairs, Washington, DC 20420, USA; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA; Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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Joo YY, Actkins K, Pacheco JA, Basile AO, Carroll R, Crosslin DR, Day F, Denny JC, Velez Edwards DR, Hakonarson H, Harley JB, Hebbring SJ, Ho K, Jarvik GP, Jones M, Karaderi T, Mentch FD, Meun C, Namjou B, Pendergrass S, Ritchie MD, Stanaway IB, Urbanek M, Walunas TL, Smith M, Chisholm RL, Kho AN, Davis L, Hayes MG. A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies. J Clin Endocrinol Metab 2020; 105:dgz326. [PMID: 31917831 PMCID: PMC7453038 DOI: 10.1210/clinem/dgz326] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/07/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT As many as 75% of patients with polycystic ovary syndrome (PCOS) are estimated to be unidentified in clinical practice. OBJECTIVE Utilizing polygenic risk prediction, we aim to identify the phenome-wide comorbidity patterns characteristic of PCOS to improve accurate diagnosis and preventive treatment. DESIGN, PATIENTS, AND METHODS Leveraging the electronic health records (EHRs) of 124 852 individuals, we developed a PCOS risk prediction algorithm by combining polygenic risk scores (PRS) with PCOS component phenotypes into a polygenic and phenotypic risk score (PPRS). We evaluated its predictive capability across different ancestries and perform a PRS-based phenome-wide association study (PheWAS) to assess the phenomic expression of the heightened risk of PCOS. RESULTS The integrated polygenic prediction improved the average performance (pseudo-R2) for PCOS detection by 0.228 (61.5-fold), 0.224 (58.8-fold), 0.211 (57.0-fold) over the null model across European, African, and multi-ancestry participants respectively. The subsequent PRS-powered PheWAS identified a high level of shared biology between PCOS and a range of metabolic and endocrine outcomes, especially with obesity and diabetes: "morbid obesity", "type 2 diabetes", "hypercholesterolemia", "disorders of lipid metabolism", "hypertension", and "sleep apnea" reaching phenome-wide significance. CONCLUSIONS Our study has expanded the methodological utility of PRS in patient stratification and risk prediction, especially in a multifactorial condition like PCOS, across different genetic origins. By utilizing the individual genome-phenome data available from the EHR, our approach also demonstrates that polygenic prediction by PRS can provide valuable opportunities to discover the pleiotropic phenomic network associated with PCOS pathogenesis.
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Affiliation(s)
- Yoonjung Yoonie Joo
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ky'Era Actkins
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Anna O Basile
- Department of Biomedical Informatics, Columbia University New York, New York
| | - Robert Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Wahington
| | - Felix Day
- MRC Epidemiology Unit, Cambridge Biomedical Campus, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Joshua C Denny
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Digna R Velez Edwards
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine; US Department of Veterans Affairs, Cincinnati, Ohio
| | - Scott J Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Kevin Ho
- Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical School, Seattle, Wahington
| | - Michelle Jones
- Center for Bioinformatics & Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Tugce Karaderi
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy Meun
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sarah Pendergrass
- Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Wahington
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Theresa L Walunas
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maureen Smith
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Abel N Kho
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lea Davis
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Anthropology, Northwestern University, Evanston, Illinois
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31
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Robinson JR, Carroll RJ, Bastarache L, Chen Q, Mou Z, Wei WQ, Connolly JJ, Mentch F, Sleiman P, Crane PK, Hebbring SJ, Stanaway IB, Crosslin DR, Gordon AS, Rosenthal EA, Carrell D, Hayes MG, Wei W, Petukhova L, Namjou B, Zhang G, Safarova MS, Walton NA, Still C, Bottinger EP, Loos RJF, Murphy SN, Jackson GP, Kullo IJ, Hakonarson H, Jarvik GP, Larson EB, Weng C, Roden DM, Denny JC. Association of Genetic Risk of Obesity with Postoperative Complications Using Mendelian Randomization. World J Surg 2020; 44:84-94. [PMID: 31605180 PMCID: PMC6925615 DOI: 10.1007/s00268-019-05202-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The extent to which obesity and genetics determine postoperative complications is incompletely understood. METHODS We performed a retrospective study using two population cohorts with electronic health record (EHR) data. The first included 736,726 adults with body mass index (BMI) recorded between 1990 and 2017 at Vanderbilt University Medical Center. The second cohort consisted of 65,174 individuals from 12 institutions contributing EHR and genome-wide genotyping data to the Electronic Medical Records and Genomics (eMERGE) Network. Pairwise logistic regression analyses were used to measure the association of BMI categories with postoperative complications derived from International Classification of Disease-9 codes, including postoperative infection, incisional hernia, and intestinal obstruction. A genetic risk score was constructed from 97 obesity-risk single-nucleotide polymorphisms for a Mendelian randomization study to determine the association of genetic risk of obesity on postoperative complications. Logistic regression analyses were adjusted for sex, age, site, and race/principal components. RESULTS Individuals with overweight or obese BMI (≥25 kg/m2) had increased risk of incisional hernia (odds ratio [OR] 1.7-5.5, p < 3.1 × 10-20), and people with obesity (BMI ≥ 30 kg/m2) had increased risk of postoperative infection (OR 1.2-2.3, p < 2.5 × 10-5). In the eMERGE cohort, genetically predicted BMI was associated with incisional hernia (OR 2.1 [95% CI 1.8-2.5], p = 1.4 × 10-6) and postoperative infection (OR 1.6 [95% CI 1.4-1.9], p = 3.1 × 10-6). Association findings were similar after limitation of the cohorts to those who underwent abdominal procedures. CONCLUSIONS Clinical and Mendelian randomization studies suggest that obesity, as measured by BMI, is associated with the development of postoperative incisional hernia and infection.
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Affiliation(s)
- Jamie R Robinson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA.
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
| | - Qingxia Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zongyang Mou
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
| | - John J Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frank Mentch
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Adam S Gordon
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Wei Wei
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lynn Petukhova
- Departments of Dermatology and Epidemiology, Columbia University, New York, NY, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Maya S Safarova
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Nephi A Walton
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Christopher Still
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, The Mindich Child Health and Development Institute, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, The Mindich Child Health and Development Institute, New York, NY, USA
| | - Shawn N Murphy
- Department of Neurology, Partners Healthcare, Boston, MA, USA
| | - Gretchen P Jackson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
- Department of Pediatric Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, 1161 21st Ave S, CCC-4312 MCN, Nashville, TN, 37232-2730, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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32
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Wegner SH, Park JJ, Workman T, Hermsen SAB, Wallace J, Stanaway IB, Kim HY, Griffith WC, Hong S, Faustman EM. Anchoring a dynamic in vitro model of human neuronal differentiation to key processes of early brain development in vivo. Reprod Toxicol 2020; 91:116-130. [PMID: 31740287 PMCID: PMC6980388 DOI: 10.1016/j.reprotox.2019.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 01/04/2023]
Abstract
We characterize temporal pathway dynamics of differentiation in an in vitro neurotoxicity model with the aim of informing design and interpretation of toxicological assays. Human neural progenitor cells (hNPCs) were cultured in differentiation conditions up to 21 days. Genes significantly changed through time were identified and grouped according to temporal dynamics. Quantitative pathway analysis identified gene ontology (GO) terms enriched among significantly changed genes and provided a temporal roadmap of pathway trends in vitro. Gene expression in hNPCs was compared with publicly available gene expression data from developing human brain tissue in vivo. Quantitative pathway analysis of significantly changed genes and targeted analysis of specific pathways of interest identified concordance between in vivo and in vitro expression associated with proliferation, migration, differentiation, synapse formation, and neurotransmission. Our analysis anchors gene expression patterns in vitro to sensitive windows of in vivo development, helping to define appropriate applications of the model.
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Affiliation(s)
- Susanna H Wegner
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Julie Juyoung Park
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Tomomi Workman
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Sanne A B Hermsen
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Jim Wallace
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Ian B Stanaway
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Hee Yeon Kim
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - William C Griffith
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Sungwoo Hong
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Elaine M Faustman
- Institute for Risk Analysis and Risk Communication, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States.
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33
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Zouk H, Venner E, Lennon NJ, Muzny DM, Abrams D, Adunyah S, Albertson-Junkans L, Ames DC, Appelbaum P, Aronson S, Aufox S, Babb LJ, Balasubramanian A, Bangash H, Basford M, Bastarache L, Baxter S, Behr M, Benoit B, Bhoj E, Bielinski SJ, Bland HT, Blout C, Borthwick K, Bottinger EP, Bowser M, Brand H, Brilliant M, Brodeur W, Caraballo P, Carrell D, Carroll A, Almoguera B, Castillo L, Castro V, Chandanavelli G, Chiang T, Chisholm RL, Christensen KD, Chung W, Chute CG, City B, Cobb BL, Connolly JJ, Crane P, Crew K, Crosslin D, De Andrade M, De la Cruz J, Denson S, Denny J, DeSmet T, Dikilitas O, Friedrich C, Fullerton SM, Funke B, Gabriel S, Gainer V, Gharavi A, Glazer AM, Glessner JT, Goehringer J, Gordon AS, Graham C, Green RC, Gundelach JH, Dayal J, Hain HS, Hakonarson H, Harden MV, Harley J, Harr M, Hartzler A, Hayes MG, Hebbring S, Henrikson N, Hershey A, Hoell C, Holm I, Howell KM, Hripcsak G, Hu J, Jarvik GP, Jayaseelan JC, Jiang Y, Joo YY, Jose S, Josyula NS, Justice AE, Kalla SE, Kalra D, Karlson E, Kelly MA, Keating BJ, Kenny EE, Key D, Kiryluk K, Kitchner T, Klanderman B, Klee E, Kochan DC, Korchina V, Kottyan L, Kovar C, Kudalkar E, Kullo IJ, Lammers P, Larson EB, Lebo MS, Leduc M, Lee MT(M, Leppig KA, Leslie ND, Li R, Liang WH, Lin CF, Linder J, Lindor NM, Lingren T, Linneman JG, Liu C, Liu W, Liu X, Lynch J, Lyon H, Macbeth A, Mahadeshwar H, Mahanta L, Malin B, Manolio T, Marasa M, Marsolo K, Dinsmore MJ, Dodge S, Hynes ED, Dunlea P, Edwards TL, Eng CM, Fasel D, Fedotov A, Feng Q, Fleharty M, Foster A, Freimuth R, McGowan ML, McNally E, Meldrim J, Mentch F, Mosley J, Mukherjee S, Mullen TE, Muniz J, Murdock DR, Murphy S, Murugan M, Myers MF, Namjou B, Ni Y, Obeng AO, Onofrio RC, Taylor CO, Person TN, Peterson JF, Petukhova L, Pisieczko CJ, Pratap S, Prows CA, Puckelwartz MJ, Rahm AK, Raj R, Ralston JD, Ramaprasan A, Ramirez A, Rasmussen L, Rasmussen-Torvik L, Rasouly HM, Raychaudhuri S, Ritchie MD, Rives C, Riza B, Roden D, Rosenthal EA, Santani A, Schaid D, Scherer S, Scott S, Scrol A, Sengupta S, Shang N, Sharma H, Sharp RR, Singh R, Sleiman PM, Slowik K, Smith JC, Smith ME, Smoller JW, Sohn S, Stanaway IB, Starren J, Stroud M, Su J, Tolwinski K, Van Driest SL, Vargas SM, Varugheese M, Veenstra D, Verbitsky M, Vicente G, Wagner M, Walker K, Walunas T, Wang L, Wang Q, Wei WQ, Weiss ST, Wiesner GL, Wells Q, Weng C, White PS, Wiley KL, Williams JL, Williams MS, Wilson MW, Witkowski L, Woods LA, Woolf B, Wu TJ, Wynn J, Yang Y, Yi V, Zhang G, Zhang L, Rehm HL, Gibbs RA. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network. Am J Hum Genet 2019; 105:588-605. [PMID: 31447099 PMCID: PMC6731372 DOI: 10.1016/j.ajhg.2019.07.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.
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34
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Namjou B, Lingren T, Huang Y, Parameswaran S, Cobb BL, Stanaway IB, Connolly JJ, Mentch FD, Benoit B, Niu X, Wei WQ, Carroll RJ, Pacheco JA, Harley ITW, Divanovic S, Carrell DS, Larson EB, Carey DJ, Verma S, Ritchie MD, Gharavi AG, Murphy S, Williams MS, Crosslin DR, Jarvik GP, Kullo IJ, Hakonarson H, Li R, Xanthakos SA, Harley JB. GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network. BMC Med 2019; 17:135. [PMID: 31311600 PMCID: PMC6636057 DOI: 10.1186/s12916-019-1364-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver illness with a genetically heterogeneous background that can be accompanied by considerable morbidity and attendant health care costs. The pathogenesis and progression of NAFLD is complex with many unanswered questions. We conducted genome-wide association studies (GWASs) using both adult and pediatric participants from the Electronic Medical Records and Genomics (eMERGE) Network to identify novel genetic contributors to this condition. METHODS First, a natural language processing (NLP) algorithm was developed, tested, and deployed at each site to identify 1106 NAFLD cases and 8571 controls and histological data from liver tissue in 235 available participants. These include 1242 pediatric participants (396 cases, 846 controls). The algorithm included billing codes, text queries, laboratory values, and medication records. Next, GWASs were performed on NAFLD cases and controls and case-only analyses using histologic scores and liver function tests adjusting for age, sex, site, ancestry, PC, and body mass index (BMI). RESULTS Consistent with previous results, a robust association was detected for the PNPLA3 gene cluster in participants with European ancestry. At the PNPLA3-SAMM50 region, three SNPs, rs738409, rs738408, and rs3747207, showed strongest association (best SNP rs738409 p = 1.70 × 10- 20). This effect was consistent in both pediatric (p = 9.92 × 10- 6) and adult (p = 9.73 × 10- 15) cohorts. Additionally, this variant was also associated with disease severity and NAFLD Activity Score (NAS) (p = 3.94 × 10- 8, beta = 0.85). PheWAS analysis link this locus to a spectrum of liver diseases beyond NAFLD with a novel negative correlation with gout (p = 1.09 × 10- 4). We also identified novel loci for NAFLD disease severity, including one novel locus for NAS score near IL17RA (rs5748926, p = 3.80 × 10- 8), and another near ZFP90-CDH1 for fibrosis (rs698718, p = 2.74 × 10- 11). Post-GWAS and gene-based analyses identified more than 300 genes that were used for functional and pathway enrichment analyses. CONCLUSIONS In summary, this study demonstrates clear confirmation of a previously described NAFLD risk locus and several novel associations. Further collaborative studies including an ethnically diverse population with well-characterized liver histologic features of NAFLD are needed to further validate the novel findings.
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Affiliation(s)
- Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.
- College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
| | - Todd Lingren
- College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yongbo Huang
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Beth L Cobb
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA
| | - Barbara Benoit
- Research IS and Computing, Partners HealthCare, Harvard University, Somerville, MA, USA
| | - Xinnan Niu
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Wei-Qi Wei
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Robert J Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Isaac T W Harley
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Senad Divanovic
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, USA
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Shefali Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ali G Gharavi
- Department of Medicine, Columbia University, New York City, NY, USA
| | - Shawn Murphy
- Research Information Science and Computing, Partners HealthCare, Boston, MA, USA
| | - Marc S Williams
- Genomic Medicine Institute (M.S.W.), Geisinger, Danville, PA, USA
| | - David R Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stavra A Xanthakos
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
- College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
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35
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Zhang X, Veturi Y, Verma S, Bone W, Verma A, Lucas A, Hebbring S, Denny JC, Stanaway IB, Jarvik GP, Crosslin D, Larson EB, Rasmussen-Torvik L, Pendergrass SA, Smoller JW, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput 2019; 24:272-283. [PMID: 30864329 PMCID: PMC6457436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The link between cardiovascular diseases and neurological disorders has been widely observed in the aging population. Disease prevention and treatment rely on understanding the potential genetic nexus of multiple diseases in these categories. In this study, we were interested in detecting pleiotropy, or the phenomenon in which a genetic variant influences more than one phenotype. Marker-phenotype association approaches can be grouped into univariate, bivariate, and multivariate categories based on the number of phenotypes considered at one time. Here we applied one statistical method per category followed by an eQTL colocalization analysis to identify potential pleiotropic variants that contribute to the link between cardiovascular and neurological diseases. We performed our analyses on ~530,000 common SNPs coupled with 65 electronic health record (EHR)-based phenotypes in 43,870 unrelated European adults from the Electronic Medical Records and Genomics (eMERGE) network. There were 31 variants identified by all three methods that showed significant associations across late onset cardiac- and neurologic- diseases. We further investigated functional implications of gene expression on the detected "lead SNPs" via colocalization analysis, providing a deeper understanding of the discovered associations. In summary, we present the framework and landscape for detecting potential pleiotropy using univariate, bivariate, multivariate, and colocalization methods. Further exploration of these potentially pleiotropic genetic variants will work toward understanding disease causing mechanisms across cardiovascular and neurological diseases and may assist in considering disease prevention as well as drug repositioning in future research.
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Affiliation(s)
- Xinyuan Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA*Authors contributed equally to this work
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36
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Stanaway IB, Hall TO, Rosenthal EA, Palmer M, Naranbhai V, Knevel R, Namjou-Khales B, Carroll RJ, Kiryluk K, Gordon AS, Linder J, Howell KM, Mapes BM, Lin FTJ, Joo YY, Hayes MG, Gharavi AG, Pendergrass SA, Ritchie MD, de Andrade M, Croteau-Chonka DC, Raychaudhuri S, Weiss ST, Lebo M, Amr SS, Carrell D, Larson EB, Chute CG, Rasmussen-Torvik LJ, Roy-Puckelwartz MJ, Sleiman P, Hakonarson H, Li R, Karlson EW, Peterson JF, Kullo IJ, Chisholm R, Denny JC, Jarvik GP, Crosslin DR. The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype. Genet Epidemiol 2018; 43:63-81. [PMID: 30298529 PMCID: PMC6375696 DOI: 10.1002/gepi.22167] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/10/2018] [Accepted: 08/28/2018] [Indexed: 12/30/2022]
Abstract
The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome‐wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single‐nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA‐B herpes zoster (shingles) association and discovered a novel zoster‐associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).
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Affiliation(s)
- Ian B Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Taryn O Hall
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | - Melody Palmer
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | - Vivek Naranbhai
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.,Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Rachel Knevel
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Bahram Namjou-Khales
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Robert J Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University, New York City, New York
| | - Adam S Gordon
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | - Jodell Linder
- Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Kayla Marie Howell
- Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Brandy M Mapes
- Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Frederick T J Lin
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | - M Geoffrey Hayes
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ali G Gharavi
- Department of Medicine, Columbia University, New York City, New York
| | | | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Soumya Raychaudhuri
- Harvard Medical School, Harvard University, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Technical Institute and Harvard University, Cambridge, Massachusetts
| | - Scott T Weiss
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Matt Lebo
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Sami S Amr
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - David Carrell
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Patrick Sleiman
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth W Karlson
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Josh F Peterson
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee
| | | | - Rex Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Joshua Charles Denny
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
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- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David R Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
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Rosenthal EA, Shirts BH, Amendola LM, Horike-Pyne M, Robertson PD, Hisama FM, Bennett RL, Dorschner MO, Nickerson DA, Stanaway IB, Nassir R, Vickers KT, Li C, Grady WM, Peters U, Jarvik GP. Rare loss of function variants in candidate genes and risk of colorectal cancer. Hum Genet 2018; 137:795-806. [PMID: 30267214 PMCID: PMC6283057 DOI: 10.1007/s00439-018-1938-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023]
Abstract
Although ~ 25% of colorectal cancer or polyp (CRC/P) cases show familial aggregation, current germline genetic testing identifies a causal genotype in the 16 major genes associated with high penetrance CRC/P in only 20% of these cases. As there are likely other genes underlying heritable CRC/P, we evaluated the association of variation at novel loci with CRC/P. We evaluated 158 a priori selected candidate genes by comparing the number of rare potentially disruptive variants (PDVs) found in 84 CRC/P cases without an identified CRC/P risk-associated variant and 2440 controls. We repeated this analysis using an additional 73 CRC/P cases. We also compared the frequency of PDVs in select genes among CRC/P cases with two publicly available data sets. We found a significant enrichment of PDVs in cases vs. controls: 20% of cases vs. 11.5% of controls with ≥ 1 PDV (OR = 1.9, p = 0.01) in the original set of cases. Among the second cohort of CRC/P cases, 18% had a PDV, significantly different from 11.5% (p = 0.02). Logistic regression, adjusting for ancestry and multiple testing, indicated association between CRC/P and PDVs in NTHL1 (p = 0.0001), BRCA2 (p = 0.01) and BRIP1 (p = 0.04). However, there was no significant difference in the frequency of PDVs at each of these genes between all 157 CRC/P cases and two publicly available data sets. These results suggest an increased presence of PDVs in CRC/P cases and support further investigation of the association of NTHL1, BRCA2 and BRIP1 variation with CRC/P.
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Affiliation(s)
- Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA.
| | - Brian H Shirts
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Laura M Amendola
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Martha Horike-Pyne
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fuki M Hisama
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Robin L Bennett
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Michael O Dorschner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of Washington, Seattle, WA, USA
| | | | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rami Nassir
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Kathy T Vickers
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
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38
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Wang L, Pittman KJ, Barker JR, Salinas RE, Stanaway IB, Williams GD, Carroll RJ, Balmat T, Ingham A, Gopalakrishnan AM, Gibbs KD, Antonia AL, Heitman J, Lee SC, Jarvik GP, Denny JC, Horner SM, DeLong MR, Valdivia RH, Crosslin DR, Ko DC. An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 2018; 24:308-323.e6. [PMID: 30092202 PMCID: PMC6093297 DOI: 10.1016/j.chom.2018.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/28/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
Abstract
Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HOST Phenome Project (H2P2): a catalog of cellular genome-wide association studies (GWAS) comprising 79 infection-related phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance for infection-associated phenotypes ranging from pathogen replication to cytokine production. We combined H2P2 with clinical association data from patients to identify a SNP near CXCL10 as a risk factor for inflammatory bowel disease. A SNP in the transcriptional repressor ZBTB20 demonstrated pleiotropy, likely through suppression of multiple target genes, and was associated with viral hepatitis. These data are available on a web portal to facilitate interpreting human genome variation through the lens of cell biology and should serve as a rich resource for the research community.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey R Barker
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raul E Salinas
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Graham D Williams
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Tom Balmat
- Social Science Research Institute, Duke University, Durham, NC 27710, USA
| | - Andy Ingham
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Anusha M Gopalakrishnan
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Soo Chan Lee
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, College of Sciences, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Mark R DeLong
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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Rubinstein M, Patowary A, Stanaway IB, McCord E, Nesbitt RR, Archer M, Scheuer T, Nickerson D, Raskind WH, Wijsman EM, Bernier R, Catterall WA, Brkanac Z. Association of rare missense variants in the second intracellular loop of Na V1.7 sodium channels with familial autism. Mol Psychiatry 2018; 23:231-239. [PMID: 27956748 PMCID: PMC5468514 DOI: 10.1038/mp.2016.222] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 01/21/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder often accompanied by intellectual disability, language impairment and medical co-morbidities. The heritability of autism is high and multiple genes have been implicated as causal. However, most of these genes have been identified in de novo cases. To further the understanding of familial autism, we performed whole-exome sequencing on five families in which second- and third-degree relatives were affected. By focusing on novel and protein-altering variants, we identified a small set of candidate genes. Among these, a novel private missense C1143F variant in the second intracellular loop of the voltage-gated sodium channel NaV1.7, encoded by the SCN9A gene, was identified in one family. Through electrophysiological analysis, we show that NaV1.7C1143F exhibits partial loss-of-function effects, resulting in slower recovery from inactivation and decreased excitability in cultured cortical neurons. Furthermore, for the same intracellular loop of NaV1.7, we found an excess of rare variants in a case-control variant-burden study. Functional analysis of one of these variants, M932L/V991L, also demonstrated reduced firing in cortical neurons. However, although this variant is rare in Caucasians, it is frequent in Latino population, suggesting that genetic background can alter its effects on phenotype. Although the involvement of the SCN1A and SCN2A genes encoding NaV1.1 and NaV1.2 channels in de novo ASD has previously been demonstrated, our study indicates the involvement of inherited SCN9A variants and partial loss-of-function of NaV1.7 channels in the etiology of rare familial ASD.
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Affiliation(s)
- M Rubinstein
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - A Patowary
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - I B Stanaway
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - E McCord
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - R R Nesbitt
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - M Archer
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - T Scheuer
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - D Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - W H Raskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - E M Wijsman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - R Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - W A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA, USA,Department of Pharmacology, University of Washington, Seattle, WA 98195, USA E-mail:
| | - Z Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA,Department of Psychiatry and Behavioral Science, University of Washington, 1959N.E. Pacific Street, Room BB1526, Seattle, WA 98195-6560, USA. E-mail:
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40
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Kim DS, Kim JH, Burt AA, Crosslin DR, Burnham N, Kim CE, McDonald-McGinn DM, Zackai EH, Nicolson SC, Spray TL, Stanaway IB, Nickerson DA, Heagerty PJ, Hakonarson H, Gaynor JW, Jarvik GP. Burden of potentially pathologic copy number variants is higher in children with isolated congenital heart disease and significantly impairs covariate-adjusted transplant-free survival. J Thorac Cardiovasc Surg 2015; 151:1147-51.e4. [PMID: 26704054 DOI: 10.1016/j.jtcvs.2015.09.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/14/2015] [Accepted: 09/14/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Copy number variants (CNVs) are duplications or deletions of genomic regions. Large CNVs are potentially pathogenic and are overrepresented in children with congenital heart disease (CHD). We sought to determine the frequency of large CNVs in children with isolated CHD, and to evaluate the relationship of these potentially pathogenic CNVs with transplant-free survival. METHODS These cases are derived from a prospective cohort of patients with nonsyndromic CHD (n = 422) identified before first surgery. Healthy pediatric controls (n = 500) were obtained from the electronic Medical Records and Genetic Epidemiology Network, and CNV frequency was contrasted for CHD cases and controls. CNVs were determined algorithmically; subsequently screened for >95% overlap between 2 methods, size (>300 kb), quality score, overlap with a gene, and novelty (absent from databases of known, benign CNVs); and separately validated by quantitative polymerase chain reaction. Survival likelihoods for cases were calculated using Cox proportional hazards modeling to evaluate the joint effect of CNV burden and known confounders on transplant-free survival. RESULTS Children with nonsyndromic CHD had a higher burden of potentially pathogenic CNVs compared with pediatric controls (12.1% vs 5.0%; P = .00016). Presence of a CNV was associated with significantly decreased transplant-free survival after surgery (hazard ratio, 3.42; 95% confidence interval, 1.66-7.09; P = .00090) with confounder adjustment. CONCLUSIONS We confirm that children with isolated CHD have a greater burden of rare/large CNVs. We report a novel finding that these CNVs are associated with an adjusted 2.55-fold increased risk of death or transplant. These data suggest that CNV burden is an important modifier of survival after surgery for CHD.
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Affiliation(s)
- Daniel Seung Kim
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash; Department of Genome Sciences, University of Washington, Seattle, Wash; Department of Biostatistics, University of Washington, Seattle, Wash
| | - Jerry H Kim
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Wash
| | - Amber A Burt
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash
| | - David R Crosslin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash; Department of Genome Sciences, University of Washington, Seattle, Wash
| | - Nancy Burnham
- Division of Cardiothoracic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Cecilia E Kim
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | | | - Elaine H Zackai
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Susan C Nicolson
- Division of Cardiothoracic Anesthesiology, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Thomas L Spray
- Division of Cardiothoracic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Ian B Stanaway
- Department of Genome Sciences, University of Washington, Seattle, Wash
| | | | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - J William Gaynor
- Division of Cardiothoracic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash; Department of Genome Sciences, University of Washington, Seattle, Wash.
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Kim DS, Kim JH, Burt AA, Crosslin DR, Burnham N, McDonald-McGinn DM, Zackai EH, Nicolson SC, Spray TL, Stanaway IB, Nickerson DA, Russell MW, Hakonarson H, Gaynor JW, Jarvik GP. Patient genotypes impact survival after surgery for isolated congenital heart disease. Ann Thorac Surg 2014; 98:104-10; discussion 110-1. [PMID: 24811984 DOI: 10.1016/j.athoracsur.2014.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/21/2014] [Accepted: 03/05/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Survival after cardiac surgery in infancy requires adaptive responses from oxidative stress management and vascular regulation pathways. We tested the hypothesis that genetic variation in these pathways influences postoperative survival in nonsyndromic congenital heart disease children. METHODS This is an analysis of a cohort of nonsyndromic congenital heart disease patients who underwent cardiac surgery with cardiopulmonary bypass before 6 months of age (n=422). Six single nucleotide polymorphisms (SNPs) in six genes involved in oxidative stress and vascular response pathways, identified through a priori literature search, were tested for effects on transplant-free survival. Survival curves, adjusting for confounding covariates, were calculated using the Cox proportional hazard models. RESULTS Long-term survival was strongly associated with vascular endothelial growth factor A gene SNP rs833069 (p=7.03×10(-4)) and superoxide dismutase 2 gene SNP rs2758331 (p=0.019). To test for joint effects of the two SNPs on transplant-free survival, the genotypes were grouped to form a risk score reflecting the cumulative number of risk alleles (0 to 4 alleles per patient). A higher risk score based on the VEGFA and SOD2 SNP genotypes was associated with worse transplant-free survival (p=3.02×10(-4)) after confounder adjustment. The total burden of risk alleles was additive; subjects with the highest risk score of 4 (n=59 subjects, 14.2% of the cohort) had a total covariate-adjusted hazard ratio of 15.64 for worse transplant-free survival. CONCLUSIONS After cardiac surgery, infants who are homozygous for the high-risk alleles for both the VEGFA and SOD2 SNPs have an approximately 16-fold increased risk of death or heart transplant, suggesting that genetic variants are important modifiers of survival after surgery for congenital heart disease.
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Affiliation(s)
- Daniel Seung Kim
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Jerry H Kim
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Amber A Burt
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington
| | - David R Crosslin
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Nancy Burnham
- Division of Cardiothoracic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Elaine H Zackai
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Susan C Nicolson
- Division of Cardiothoracic Anesthesiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Thomas L Spray
- Division of Cardiothoracic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ian B Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Mark W Russell
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - J William Gaynor
- Division of Cardiothoracic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.
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Marchani EE, Chapman NH, Cheung CYK, Ankenman K, Stanaway IB, Coon HH, Nickerson D, Bernier R, Brkanac Z, Wijsman EM. Identification of rare variants from exome sequence in a large pedigree with autism. Hum Hered 2013; 74:153-64. [PMID: 23594493 DOI: 10.1159/000346560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We carried out analyses with the goal of identifying rare variants in exome sequence data that contribute to disease risk for a complex trait. We analyzed a large, 47-member, multigenerational pedigree with 11 cases of autism spectrum disorder, using genotypes from 3 technologies representing increasing resolution: a multiallelic linkage marker panel, a dense diallelic marker panel, and variants from exome sequencing. Genome-scan marker genotypes were available on most subjects, and exome sequence data was available on 5 subjects. We used genome-scan linkage analysis to identify and prioritize the chromosome 22 region of interest, and to select subjects for exome sequencing. Inheritance vectors (IVs) generated by Markov chain Monte Carlo analysis of multilocus marker data were the foundation of most analyses. Genotype imputation used IVs to determine which sequence variants reside on the haplotype that co-segregates with the autism diagnosis. Together with a rare-allele frequency filter, we identified only one rare variant on the risk haplotype, illustrating the potential of this approach to prioritize variants. The associated gene, MYH9, is biologically unlikely, and we speculate that for this complex trait, the key variants may lie outside the exome.
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Affiliation(s)
- E E Marchani
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
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O’Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O’Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012; 338:1619-22. [PMID: 23160955 PMCID: PMC3528801 DOI: 10.1126/science.1227764] [Citation(s) in RCA: 922] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or disrupt splicing. We estimate that recurrent disruptive mutations in six genes-CHD8, DYRK1A, GRIN2B, TBR1, PTEN, and TBL1XR1-may contribute to 1% of sporadic ASDs. Our data support associations between specific genes and reciprocal subphenotypes (CHD8-macrocephaly and DYRK1A-microcephaly) and replicate the importance of a β-catenin-chromatin-remodeling network to ASD etiology.
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Affiliation(s)
- Brian J. O’Roak
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jarrett D. Egertson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian B. Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian G. Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Gemma Carvill
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Akash Kumar
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katy Ankenman
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph B. Hiatt
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily H. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Roie Levy
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Diana R. O’Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Heather C. Mefford
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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Kim DS, Stanaway IB, Rajagopalan R, Bernbaum JC, Solot CB, Burnham N, Zackai EH, Clancy RR, Nicolson SC, Gerdes M, Nickerson DA, Hakonarson H, Gaynor JW, Jarvik GP. Results of genome-wide analyses on neurodevelopmental phenotypes at four-year follow-up following cardiac surgery in infancy. PLoS One 2012; 7:e45936. [PMID: 23049896 PMCID: PMC3457986 DOI: 10.1371/journal.pone.0045936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/23/2012] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Adverse neurodevelopmental sequelae are reported among children who undergo early cardiac surgery to repair congenital heart defects (CHD). APOE genotype has previously been determined to contribute to the prediction of these outcomes. Understanding further genetic causes for the development of poor neurobehavioral outcomes should enhance patient risk stratification and improve both prevention and treatment strategies. METHODS We performed a prospective observational study of children who underwent cardiac surgery before six months of age; this included a neurodevelopmental evaluation between their fourth and fifth birthdays. Attention and behavioral skills were assessed through parental report utilizing the Attention Deficit-Hyperactivity Disorder-IV scale preschool edition (ADHD-IV), and Child Behavior Checklist (CBCL/1.5-5), respectively. Of the seven investigated, three neurodevelopmental phenotypes met genomic quality control criteria. Linear regression was performed to determine the effect of genome-wide genetic variation on these three neurodevelopmental measures in 316 subjects. RESULTS This genome-wide association study identified single nucleotide polymorphisms (SNPs) associated with three neurobehavioral phenotypes in the postoperative children ADHD-IV Impulsivity/Hyperactivity, CBCL/1.5-5 PDPs, and CBCL/1.5-5 Total Problems. The most predictive SNPs for each phenotype were: a LGALS8 intronic SNP, rs4659682, associated with ADHD-IV Impulsivity (P=1.03 × 10(-6)); a PCSK5 intronic SNP, rs2261722, associated with CBCL/1.5-5 PDPs (P=1.11 × 10(-6)); and an intergenic SNP, rs11617488, 50 kb from FGF9, associated with CBCL/1.5-5 Total Problems (P=3.47 × 10(-7)). 10 SNPs (3 for ADHD-IV Impulsivity, 5 for CBCL/1.5-5 PDPs, and 2 for CBCL/1.5-5 Total Problems) had p<10(-5). CONCLUSIONS No SNPs met genome-wide significance for our three neurobehavioral phenotypes; however, 10 SNPs reached a threshold for suggestive significance (p<10(-5)). Given the unique nature of this cohort, larger studies and/or replication are not possible. Studies to further investigate the mechanisms through which these newly identified genes may influence neurodevelopment dysfunction are warranted.
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Affiliation(s)
- Daniel S. Kim
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ian B. Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ramakrishnan Rajagopalan
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Judy C. Bernbaum
- Division of General Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Cynthia B. Solot
- Center for Childhood Communication, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Nancy Burnham
- Division of Cardiothoracic Surgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Elaine H. Zackai
- Division of Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Robert R. Clancy
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Susan C. Nicolson
- Division of Cardiothoracic Anesthesiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Marsha Gerdes
- Division of Psychology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - J. William Gaynor
- Division of Cardiothoracic Surgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Gail P. Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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45
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O’Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 2012; 485:246-50. [PMID: 22495309 PMCID: PMC3350576 DOI: 10.1038/nature10989] [Citation(s) in RCA: 1563] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 02/23/2012] [Indexed: 02/08/2023]
Abstract
It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.
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Affiliation(s)
- Brian J. O’Roak
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Santhosh Girirajan
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Emre Karakoc
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nik Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Roie Levy
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arthur Ko
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Emily H. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian B. Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Beau Reilly
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | - Mark J. Rieder
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML. IGF1R variants associated with isolated single suture craniosynostosis. Am J Med Genet A 2011; 155A:91-7. [PMID: 21204214 DOI: 10.1002/ajmg.a.33781] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The genetic contribution to the pathogenesis of isolated single suture craniosynostosis is poorly understood. The role of mutations in genes known to be associated with syndromic synostosis appears to be limited. We present our findings of a candidate gene resequencing approach to identify rare variants associated with the most common forms of isolated craniosynostosis. Resequencing of the coding regions, splice junction sites, and 5' and 3' untranslated regions of 27 candidate genes in 186 cases of isolated non-syndromic single suture synostosis revealed three novel and two rare sequence variants (R406H, R595H, N857S, P190S, M446V) in insulin-like growth factor I receptor (IGF1R) that are enriched relative to control samples. Mapping the resultant amino acid changes to the modeled homodimer protein structure suggests a structural basis for segregation between these and other disease-associated mutations found in IGF1R. These data suggest that IGF1R mutations may contribute to the risk and in some cases cause single suture craniosynostosis.
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Affiliation(s)
- Michael L Cunningham
- Seattle Children's Hospital Craniofacial Center, University of Washington, 98195, USA.
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Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, Ramirez J, Liu W, Lin YS, Moloney C, Aldred SF, Trinklein ND, Schuetz E, Nickerson DA, Thummel KE, Rieder MJ, Rettie AE, Ratain MJ, Cox NJ, Brown CD. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 2011; 7:e1002078. [PMID: 21637794 PMCID: PMC3102751 DOI: 10.1371/journal.pgen.1002078] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/28/2011] [Indexed: 01/10/2023] Open
Abstract
The discovery of expression quantitative trait loci ("eQTLs") can help to unravel genetic contributions to complex traits. We identified genetic determinants of human liver gene expression variation using two independent collections of primary tissue profiled with Agilent (n = 206) and Illumina (n = 60) expression arrays and Illumina SNP genotyping (550K), and we also incorporated data from a published study (n = 266). We found that ∼30% of SNP-expression correlations in one study failed to replicate in either of the others, even at thresholds yielding high reproducibility in simulations, and we quantified numerous factors affecting reproducibility. Our data suggest that drug exposure, clinical descriptors, and unknown factors associated with tissue ascertainment and analysis have substantial effects on gene expression and that controlling for hidden confounding variables significantly increases replication rate. Furthermore, we found that reproducible eQTL SNPs were heavily enriched near gene starts and ends, and subsequently resequenced the promoters and 3'UTRs for 14 genes and tested the identified haplotypes using luciferase assays. For three genes, significant haplotype-specific in vitro functional differences correlated directly with expression levels, suggesting that many bona fide eQTLs result from functional variants that can be mechanistically isolated in a high-throughput fashion. Finally, given our study design, we were able to discover and validate hundreds of liver eQTLs. Many of these relate directly to complex traits for which liver-specific analyses are likely to be relevant, and we identified dozens of potential connections with disease-associated loci. These included previously characterized eQTL contributors to diabetes, drug response, and lipid levels, and they suggest novel candidates such as a role for NOD2 expression in leprosy risk and C2orf43 in prostate cancer. In general, the work presented here will be valuable for future efforts to precisely identify and functionally characterize genetic contributions to a variety of complex traits.
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Affiliation(s)
- Federico Innocenti
- Cancer Research Center, Committee on Clinical
Pharmacology and Pharmacogenomics, Department of Medicine, The University of
Chicago, Chicago, Illinois, United States of America
| | - Gregory M. Cooper
- Department of Genome Sciences, University of
Washington, Seattle, Washington, United States of America
| | - Ian B. Stanaway
- Department of Genome Sciences, University of
Washington, Seattle, Washington, United States of America
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of
Medicine, The University of Chicago, Chicago, Illinois, United States of
America
| | - Joshua D. Smith
- Department of Genome Sciences, University of
Washington, Seattle, Washington, United States of America
| | - Snezana Mirkov
- Section of Hematology/Oncology, Department of
Medicine, The University of Chicago, Chicago, Illinois, United States of
America
| | - Jacqueline Ramirez
- Section of Hematology/Oncology, Department of
Medicine, The University of Chicago, Chicago, Illinois, United States of
America
| | - Wanqing Liu
- Section of Hematology/Oncology, Department of
Medicine, The University of Chicago, Chicago, Illinois, United States of
America
| | - Yvonne S. Lin
- Department of Medicinal Chemistry, School of
Pharmacy, University of Washington, Seattle, Washington, United States of
America
- Department of Pharmaceutics, University of
Washington, Seattle, Washington, United States of America
| | - Cliona Moloney
- Merck Research Laboratories, Boston,
Massachusetts, United States of America
| | | | | | - Erin Schuetz
- Department of Pharmaceutical Sciences, St.
Jude Children's Research Hospital, Memphis, Tennessee, United States of
America
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of
Washington, Seattle, Washington, United States of America
| | - Ken E. Thummel
- Department of Medicinal Chemistry, School of
Pharmacy, University of Washington, Seattle, Washington, United States of
America
- Department of Pharmaceutics, University of
Washington, Seattle, Washington, United States of America
| | - Mark J. Rieder
- Department of Genome Sciences, University of
Washington, Seattle, Washington, United States of America
| | - Allan E. Rettie
- Department of Medicinal Chemistry, School of
Pharmacy, University of Washington, Seattle, Washington, United States of
America
| | - Mark J. Ratain
- Cancer Research Center, Committee on Clinical
Pharmacology and Pharmacogenomics, Department of Medicine, The University of
Chicago, Chicago, Illinois, United States of America
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of
Medicine, The University of Chicago, Chicago, Illinois, United States of
America
| | - Christopher D. Brown
- Institute for Genomics and Systems Biology,
The University of Chicago and Argonne National Laboratory, Chicago, Illinois,
United States of America
- Departments of Human Genetics and Ecology
and Evolution, The University of Chicago, Chicago, Illinois, United States of
America
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48
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Heike CL, Starr JR, Rieder MJ, Cunningham ML, Edwards KL, Stanaway IB, Crawford DC. Single nucleotide polymorphism discovery in TBX1 in individuals with and without 22q11.2 deletion syndrome. ACTA ACUST UNITED AC 2010; 88:54-63. [PMID: 19645056 DOI: 10.1002/bdra.20604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Children with 22q11.2 deletion syndrome (22q11.2DS) have a wide range of clinical features. TBX1 has been proposed as a candidate gene for some of the features in this condition. Polymorphisms in the nondeleted TBX1, which may affect the function of the sole TBX1 gene in individuals with the 22q11.2DS, may be a key to understanding the phenotypic variability among individuals with a shared deletion. Comprehensive single nucleotide polymorphism (SNP) discovery by resequencing candidate genes can identify genetic variants that influence a given phenotype. The purpose of this study was to further characterize the sequence variability in TBX1 by identifying all common SNPs in this gene. METHODS We resequenced TBX1 in 29 children with a documented 22q11.2 deletion and 95 nondeleted, healthy individuals. We estimated allele frequencies, performed tagSNP selection, and inferred haplotypes. We also compared SNP frequencies between 22q11.2DS and control samples. RESULTS We identified 355 biallelic markers among the 190 chromosomes resequenced in the control panel. The vast majority of the markers identified were SNPs (n = 331), and the remainder indels (n = 24). We did not identify SNPs or indels in the cis- regulatory element (FOX-binding site) upstream of TBX1. In children with 22q11.2DS we detected 187 biallelic markers, six of which were indels. Four of the seven coding SNPs identified in the controls were identified in children with 22q11.2DS. CONCLUSIONS This comprehensive SNP discovery data can be used to select SNPs to genotype for future association studies assessing the role of TBX1 and phenotypic variability in individuals with 22q11.2DS.
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Affiliation(s)
- Carrie L Heike
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington and Seattle Children's Hospital, Seattle, Washington 98105-5371, USA.
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Rieder MJ, Livingston RJ, Stanaway IB, Nickerson DA. The environmental genome project: reference polymorphisms for drug metabolism genes and genome-wide association studies. Drug Metab Rev 2008; 40:241-61. [PMID: 18464045 DOI: 10.1080/03602530801952880] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Environmental Genome Project (EGP) has generated a comprehensive resource of commonly occurring single nucleotide polymorphisms (SNPs) in more than six hundred environmental response genes, including a number of drug metabolism genes. The gene-oriented sequence variation discovery carried out by the EGP is complementary to the HapMap and enables genome-wide association studies (GWAS) that survey a large portion of the known common variation. For GWAS focused on drug metabolism genes and phenotypes, it is important to know the proportion of common SNPs covered by the commercially available high-throughput genotyping chips. Herein, we review a subset of Phase I cytochrome P450 genes studied by the EGP, approaches to GWAS, and the sensitivity of available genotyping platforms to capture common sequence variation in this subset of drug metabolism genes.
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Affiliation(s)
- Mark J Rieder
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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Abstract
Pinpointing genetic associations in the human genome relies heavily on the accuracy of the underlying genotype data. Null alleles can generate significant inaccuracies in genotype data and can negatively affect the statistical power of a study. Existing quality control (QC) tests, including tests of Hardy-Weinberg equilibrium, are not sensitive enough to detect the presence of even moderately frequent null alleles in the data. We show that direct analysis of raw data from a quantitative genotyping platform can detect up to 75% of null alleles, even at frequencies below the sensitivity of more traditional methods. Detecting unexpected null alleles not only has benefits in QC of genotype data but may also be valuable in detecting rare, functional null alleles that would otherwise be missed.
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Affiliation(s)
- Christopher S Carlson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-7730, USA
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