1
|
Heitzer AM, Rashkin SR, Trpchevska A, Longoria JN, Rampersaud E, Olufadi Y, Wang WC, Raches D, Potter B, Steinberg MH, King AA, Kang G, Takemoto CM, Hankins JS. Catechol-O-methyltransferase gene (COMT) is associated with neurocognitive functioning in patients with sickle cell disease. Curr Res Transl Med 2023; 72:103433. [PMID: 38244277 DOI: 10.1016/j.retram.2023.103433] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/19/2023] [Indexed: 01/22/2024]
Abstract
PURPOSE Neurocognitive impairment is a common and debilitating complication of sickle cell disease (SCD) resulting from a combination of biological and environmental factors. The catechol-O-methyltransferase (COMT) gene modulates levels of dopamine availability in the prefrontal cortex. COMT has repeatedly been implicated in the perception of pain stimuli and frequency of pain crises in patients with SCD and is known to be associated with neurocognitive functioning in the general population. The current study aimed to examine the associations of genetic variants in COMT and neurocognitive functioning in patients with SCD. PATIENTS AND METHODS The Sickle Cell Clinical Research and Intervention Program (SCCRIP) longitudinal cohort was used as a discovery cohort (n = 166). The genotypes for 5 SNPs (rs6269, rs4633, rs4818, rs4680, and rs165599) in COMT were extracted from whole genome sequencing data and analyzed using a dominant model. A polygenic score for COMT (PGSCOMT) integrating these 5 SNPs was analyzed as a continuous variable. The Cooperative Study of Sickle Cell Disease (CSSCD, n = 156) and the Silent Cerebral Infarction Transfusion (SIT, n = 114) Trial were used as 2 independent replication cohorts. Due to previously reported sex differences, all analyses were conducted separately in males and females. The Benjamini and Hochberg approach was used to calculate false discovery rate adjusted p-value (q-value). RESULTS In SCCRIP, 1 out of 5 SNPs (rs165599) was associated with IQ at q<0.05 in males but not females, and 2 other SNPs (rs4633 and rs4680) were marginally associated with sustained attention at p<0.05 in males only but did not maintain at q<0.05. PGSCOMT was negatively associated with IQ and sustained attention at p<0.05 in males only. Using 3 cohorts' data, 4 out of 5 SNPs (rs6269, rs4633, rs4680, rs165599) were associated with IQ (minimum q-value = 0.0036) at q<0.05 among male participants but not female participants. The PGSCOMT was negatively associated with IQ performance among males but not females across all cohorts. CONCLUSION Select COMT SNPs are associated with neurocognitive abilities in males with SCD. By identifying genetic predictors of neurocognitive performance in SCD, it may be possible to risk-stratify patients from a young age to guide implementation of early interventions.
Collapse
Affiliation(s)
- Andrew M Heitzer
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, United States.
| | - Sara R Rashkin
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Ana Trpchevska
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jennifer N Longoria
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Yunusa Olufadi
- Biostatistics Department, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Winfred C Wang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Darcy Raches
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Brian Potter
- Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Martin H Steinberg
- Department of Medicine, Boston University Chobanian & Avidesian School of Medicine, Boston, MA, United States
| | - Allison A King
- Program in Occupational Therapy and Departments of Pediatrics and Medicine, Washington University, St. Louis, MO, United States
| | - Guolian Kang
- Biostatistics Department, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Clifford M Takemoto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jane S Hankins
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States; Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, United States
| |
Collapse
|
2
|
Kirkham JK, Estepp JH, Weiss MJ, Rashkin SR. Genetic Variation and Sickle Cell Disease Severity: A Systematic Review and Meta-Analysis. JAMA Netw Open 2023; 6:e2337484. [PMID: 37851445 PMCID: PMC10585422 DOI: 10.1001/jamanetworkopen.2023.37484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Importance Sickle cell disease (SCD) is a monogenic disorder, yet clinical outcomes are influenced by additional genetic factors. Despite decades of research, the genetics of SCD remain poorly understood. Objective To assess all reported genetic modifiers of SCD, evaluate the design of associated studies, and provide guidelines for future analyses according to modern genetic study recommendations. Data Sources PubMed, Web of Science, and Scopus were searched through May 16, 2023, identifying 5290 publications. Study Selection At least 2 reviewers identified 571 original, peer-reviewed English-language publications reporting genetic modifiers of human SCD phenotypes, wherein the outcome was not treatment response, and the comparison was not between SCD subtypes or including healthy controls. Data Extraction and Synthesis Data relevant to all genetic modifiers of SCD were extracted, evaluated, and presented following STREGA and PRISMA guidelines. Weighted z score meta-analyses and pathway analyses were conducted. Main Outcomes and Measures Outcomes were aggregated into 25 categories, grouped as acute complications, chronic conditions, hematologic parameters or biomarkers, and general or mixed measures of SCD severity. Results The 571 included studies reported on 29 670 unique individuals (50% ≤ 18 years of age) from 43 countries. Of the 17 757 extracted results (4890 significant) in 1552 genes, 3675 results met the study criteria for meta-analysis: reported phenotype and genotype, association size and direction, variability measure, sample size, and statistical test. Only 173 results for 62 associations could be cross-study combined. The remaining associations could not be aggregated because they were only reported once or methods (eg, study design, reporting practice) and genotype or phenotype definitions were insufficiently harmonized. Gene variants regulating fetal hemoglobin and α-thalassemia (important markers for SCD severity) were frequently identified: 19 single-nucleotide variants in BCL11A, HBS1L-MYB, and HBG2 were significantly associated with fetal hemoglobin (absolute value of Z = 4.00 to 20.66; P = 8.63 × 10-95 to 6.19 × 10-5), and α-thalassemia deletions were significantly associated with increased hemoglobin level and reduced risk of albuminuria, abnormal transcranial Doppler velocity, and stroke (absolute value of Z = 3.43 to 5.16; P = 2.42 × 10-7 to 6.00 × 10-4). However, other associations remain unconfirmed. Pathway analyses of significant genes highlighted the importance of cellular adhesion, inflammation, oxidative and toxic stress, and blood vessel regulation in SCD (23 of the top 25 Gene Ontology pathways involve these processes) and suggested future research areas. Conclusions and Relevance The findings of this comprehensive systematic review and meta-analysis of all published genetic modifiers of SCD indicated that implementation of standardized phenotypes, statistical methods, and reporting practices should accelerate discovery and validation of genetic modifiers and development of clinically actionable genetic profiles.
Collapse
Affiliation(s)
- Justin K. Kirkham
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Jeremie H. Estepp
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, Tennessee
- Now with Agios Pharmaceuticals, Cambridge, Massachusetts
| | - Mitch J. Weiss
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Sara R. Rashkin
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
| |
Collapse
|
3
|
Flerlage JE, Myers JR, Maciaszek JL, Oak N, Rashkin SR, Hui Y, Wang YD, Chen W, Wu G, Chang TC, Hamilton K, Tithi SS, Goldin LR, Rotunno M, Caporaso N, Vogt A, Flamish D, Wyatt K, Liu J, Tucker M, Hahn CN, Brown AL, Scott HS, Mullighan C, Nichols KE, Metzger ML, McMaster ML, Yang JJ, Rampersaud E. Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma. Blood 2023; 141:1293-1307. [PMID: 35977101 PMCID: PMC10082357 DOI: 10.1182/blood.2022016056] [Citation(s) in RCA: 1] [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: 03/01/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Familial aggregation of Hodgkin lymphoma (HL) has been demonstrated in large population studies, pointing to genetic predisposition to this hematological malignancy. To understand the genetic variants associated with the development of HL, we performed whole genome sequencing on 234 individuals with and without HL from 36 pedigrees that had 2 or more first-degree relatives with HL. Our pedigree selection criteria also required at least 1 affected individual aged <21 years, with the median age at diagnosis of 21.98 years (3-55 years). Family-based segregation analysis was performed for the identification of coding and noncoding variants using linkage and filtering approaches. Using our tiered variant prioritization algorithm, we identified 44 HL-risk variants in 28 pedigrees, of which 33 are coding and 11 are noncoding. The top 4 recurrent risk variants are a coding variant in KDR (rs56302315), a 5' untranslated region variant in KLHDC8B (rs387906223), a noncoding variant in an intron of PAX5 (rs147081110), and another noncoding variant in an intron of GATA3 (rs3824666). A newly identified splice variant in KDR (c.3849-2A>C) was observed for 1 pedigree, and high-confidence stop-gain variants affecting IRF7 (p.W238∗) and EEF2KMT (p.K116∗) were also observed. Multiple truncating variants in POLR1E were found in 3 independent pedigrees as well. Whereas KDR and KLHDC8B have previously been reported, PAX5, GATA3, IRF7, EEF2KMT, and POLR1E represent novel observations. Although there may be environmental factors influencing lymphomagenesis, we observed segregation of candidate germline variants likely to predispose HL in most of the pedigrees studied.
Collapse
Affiliation(s)
- Jamie E. Flerlage
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Sara R. Rashkin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yawei Hui
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kayla Hamilton
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Saima S. Tithi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Lynn R. Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | - Jia Liu
- Leidos Biomedical, Inc, Frederick, MD
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Christopher N. Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Anna L. Brown
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Monika L. Metzger
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN
| | - Mary L. McMaster
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J. Yang
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| |
Collapse
|
4
|
Gabriel AAG, Atkins JR, Penha RCC, Smith-Byrne K, Gaborieau V, Voegele C, Abedi-Ardekani B, Milojevic M, Olaso R, Meyer V, Boland A, Deleuze JF, Zaridze D, Mukeriya A, Swiatkowska B, Janout V, Schejbalová M, Mates D, Stojšić J, Ognjanovic M, Witte JS, Rashkin SR, Kachuri L, Hung RJ, Kar S, Brennan P, Sertier AS, Ferrari A, Viari A, Johansson M, Amos CI, Foll M, McKay JD. Genetic Analysis of Lung Cancer and the Germline Impact on Somatic Mutation Burden. J Natl Cancer Inst 2022; 114:1159-1166. [PMID: 35511172 PMCID: PMC9360465 DOI: 10.1093/jnci/djac087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 10/13/2021] [Revised: 01/31/2022] [Accepted: 04/13/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Germline genetic variation contributes to lung cancer (LC) susceptibility. Previous genome-wide association studies (GWAS) have implicated susceptibility loci involved in smoking behaviors and DNA repair genes, but further work is required to identify susceptibility variants. METHODS To identify LC susceptibility loci, a family history-based genome-wide association by proxy (GWAx) of LC (48 843 European proxy LC patients, 195 387 controls) was combined with a previous LC GWAS (29 266 patients, 56 450 controls) by meta-analysis. Colocalization was used to explore candidate genes and overlap with existing traits at discovered susceptibility loci. Polygenic risk scores (PRS) were tested within an independent validation cohort (1 666 LC patients vs 6 664 controls) using variants selected from the LC susceptibility loci and a novel selection approach using published GWAS summary statistics. Finally, the effects of the LC PRS on somatic mutational burden were explored in patients whose tumor resections have been profiled by exome (n = 685) and genome sequencing (n = 61). Statistical tests were 2-sided. RESULTS The GWAx-GWAS meta-analysis identified 8 novel LC loci. Colocalization implicated DNA repair genes (CHEK1), metabolic genes (CYP1A1), and smoking propensity genes (CHRNA4 and CHRNB2). PRS analysis demonstrated that these variants, as well as subgenome-wide significant variants related to expression quantitative trait loci and/or smoking propensity, assisted in LC genetic risk prediction (odds ratio = 1.37, 95% confidence interval = 1.29 to 1.45; P < .001). Patients with higher genetic PRS loads of smoking-related variants tended to have higher mutation burdens in their lung tumors. CONCLUSIONS This study has expanded the number of LC susceptibility loci and provided insights into the molecular mechanisms by which these susceptibility variants contribute to LC development.
Collapse
Affiliation(s)
- Aurélie A G Gabriel
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Joshua R Atkins
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Ricardo C C Penha
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Karl Smith-Byrne
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, England
| | - Valerie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Catherine Voegele
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Maja Milojevic
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Robert Olaso
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Anne Boland
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean François Deleuze
- Université Paris-Saclay, The French Alternative Energies and Atomic Energy Commission (CEA), Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Beata Swiatkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Vladimir Janout
- Faculty of Medicine, Palacky University, Olomouc, Czech Republic
| | | | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jelena Stojšić
- Department of Thoracic Pathology, Service of Pathology, University Clinical Centre of Serbia, Belgrade, Serbia
| | - Miodrag Ognjanovic
- International Organisation for Cancer Prevention and Research, Belgrade, Serbia
| | | | - John S Witte
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Anne-Sophie Sertier
- Fondation Synergie Lyon Cancer, Plateforme de bioinformatique Gilles Thomas, Lyon, France
| | - Anthony Ferrari
- Fondation Synergie Lyon Cancer, Plateforme de bioinformatique Gilles Thomas, Lyon, France
| | - Alain Viari
- Fondation Synergie Lyon Cancer, Plateforme de bioinformatique Gilles Thomas, Lyon, France
- Inria Centre de Recherche Grenoble Rhone-Alpes, Grenoble, France
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, USA
| | - Matthieu Foll
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| | - James D McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon, France
| |
Collapse
|
5
|
Rashkin SR, Cleves M, Shaw GM, Nembhard WN, Nestoridi E, Jenkins MM, Romitti PA, Lou XY, Browne ML, Mitchell LE, Olshan AF, Lomangino K, Bhattacharyya S, Witte JS, Hobbs CA. A genome-wide association study of obstructive heart defects among participants in the National Birth Defects Prevention Study. Am J Med Genet A 2022; 188:2303-2314. [PMID: 35451555 PMCID: PMC9283270 DOI: 10.1002/ajmg.a.62759] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 01/19/2023]
Abstract
Obstructive heart defects (OHDs) share common structural lesions in arteries and cardiac valves, accounting for ~25% of all congenital heart defects. OHDs are highly heritable, resulting from interplay among maternal exposures, genetic susceptibilities, and epigenetic phenomena. A genome-wide association study was conducted in National Birth Defects Prevention Study participants (Ndiscovery = 3978; Nreplication = 2507), investigating the genetic architecture of OHDs using transmission/disequilibrium tests (TDT) in complete case-parental trios (Ndiscovery_TDT = 440; Nreplication_TDT = 275) and case-control analyses separately in infants (Ndiscovery_CCI = 1635; Nreplication_CCI = 990) and mothers (case status defined by infant; Ndiscovery_CCM = 1703; Nreplication_CCM = 1078). In the TDT analysis, the SLC44A2 single nucleotide polymorphism (SNP) rs2360743 was significantly associated with OHD (pdiscovery = 4.08 × 10-9 ; preplication = 2.44 × 10-4 ). A CAPN11 SNP (rs55877192) was suggestively associated with OHD (pdiscovery = 1.61 × 10-7 ; preplication = 0.0016). Two other SNPs were suggestively associated (p < 1 × 10-6 ) with OHD in only the discovery sample. In the case-control analyses, no SNPs were genome-wide significant, and, even with relaxed thresholds ( × discovery < 1 × 10-5 and preplication < 0.05), only one SNP (rs188255766) in the infant analysis was associated with OHDs (pdiscovery = 1.42 × 10-6 ; preplication = 0.04). Additional SNPs with pdiscovery < 1 × 10-5 were in loci supporting previous findings but did not replicate. Overall, there was modest evidence of an association between rs2360743 and rs55877192 and OHD and some evidence validating previously published findings.
Collapse
Affiliation(s)
- Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Mario Cleves
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Health Informatics Institute, Tampa, Florida, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Wendy N Nembhard
- Department of Epidemiology and Arkansas Center for Birth Defects and Prevention, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Eirini Nestoridi
- Massachusetts Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul A Romitti
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, USA
| | - Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marilyn L Browne
- Birth Defects Research Section, New York State Department of Health, Albany, New York, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, New York, USA
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, USA
| | - Andrew F Olshan
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sudeepa Bhattacharyya
- Bioinformatics and Data Science at University of Arkansas, Little Rock, Arkansas, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| |
Collapse
|
6
|
Heitzer AM, Longoria J, Rampersaud E, Rashkin SR, Estepp JH, Okhomina VI, Wang WC, Raches D, Potter B, Steinberg MH, King AA, Kang G, Hankins JS. Fetal hemoglobin modulates neurocognitive performance in sickle cell anemia ✰,✰✰. Curr Res Transl Med 2022; 70:103335. [PMID: 35303690 PMCID: PMC9086114 DOI: 10.1016/j.retram.2022.103335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/07/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 12/26/2022]
Abstract
PURPOSE OF THE STUDY Fetal hemoglobin (HbF) is a modifier of the clinical and hematologic phenotype of sickle cell anemia (SCA). Three quantitative trait loci (QTL) modulate HbF expression. The neurocognitive effects of variants in these QTL have yet to be explored. We evaluated the relation between 11 SNPs in the three HbF QTL: BCL11A, MYB, the HBB gene cluster, and full-scale intelligence (IQ) in SCA. PATIENTS AND METHODS The prospective longitudinal cohort study, Sickle Cell Clinical Research and Intervention Program, was used as a discovery cohort (n = 166). The genotypes for 11 SNPs were extracted through whole genome sequencing and were analyzed using an additive model. A polygenic score for HbF (PGSHbF) integrating the numbers of low HbF alleles from 11 SNPs was analyzed as a continuous variable. The Cooperative Study of Sickle Cell Disease (n = 156) and the Silent Cerebral Infarction Transfusion (n = 114) Trial were used as two independent replication cohorts. Benjamini and Hochberg approach was used to calculate false discovery rate adjusted p-value (pFDR). RESULTS HbF was positively associated with IQ (minimum raw p = 0·0018) at pFDR<0·05. HbF mediated the relationship between two BCL11A SNPs, rs1427407 and rs7606173, HBS1L-MYB: rs9494142, and PGSHbF with IQ (minimum raw p = 0·0035) at pFDR<0·05. CONCLUSION As the major modulator of the severity of SCA, HbF also influences neurocognition, which is done through mediation of its QTL. These findings have implications for early identification of neurocognitive risk and targeted intervention.
Collapse
Affiliation(s)
- Andrew M Heitzer
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN.
| | - Jennifer Longoria
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Sara R Rashkin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN; Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | | | | | - Winfred C Wang
- Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Darcy Raches
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Brian Potter
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Allison A King
- Program in Occupational Therapy and Departments of Pediatrics and Medicine, Washington University, St. Louis, MO
| | - Guolian Kang
- Biostatistics, St. Jude Children's Research Hospital, Memphis, TN; Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jane S Hankins
- Hematology, St. Jude Children's Research Hospital, Memphis, TN
| |
Collapse
|
7
|
Rashkin SR, Rampersaud E, Kang G, Ataga KI, Hankins JS, Wang W, Estepp JH, Weiss MJ, Lebensburger J, Zahr RS. Generalization of a genetic risk score for time to first albuminuria in children with sickle cell anaemia: SCCRIP cohort study results. Br J Haematol 2021; 194:469-473. [PMID: 34137022 DOI: 10.1111/bjh.17647] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022]
Abstract
Albuminuria predicts kidney disease progression in individuals with sickle cell anaemia (SCA); however, earlier prediction of kidney disease with introduction of reno-protective therapies prior to the onset of albuminuria may attenuate disease progression. A genetic risk score (GRS) for SCA-related nephropathy may provide an improved one-time test for early identification of high-risk patients. We utilized a GRS from a recent, large, trans-ethnic meta-analysis to identify three single nucleotide polymorphisms that associate individually and in a GRS with time to first albuminuria episode in children with SCA.
Collapse
Affiliation(s)
- Sara R Rashkin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kenneth I Ataga
- Center for Sickle Cell Disease, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jane S Hankins
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Winfred Wang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeremie H Estepp
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey Lebensburger
- Division of Pediatric Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rima S Zahr
- Division of Pediatric Nephrology and Hypertension, University of Tennessee Health Science Center, Memphis, TN, USA
| |
Collapse
|
8
|
Emami NC, Cavazos TB, Rashkin SR, Cario CL, Graff RE, Tai CG, Mefford JA, Kachuri L, Wan E, Wong S, Aaronson D, Presti J, Habel LA, Shan J, Ranatunga DK, Chao CR, Ghai NR, Jorgenson E, Sakoda LC, Kvale MN, Kwok PY, Schaefer C, Risch N, Hoffmann TJ, Van Den Eeden SK, Witte JS. A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility. Cancer Res 2021; 81:1695-1703. [PMID: 33293427 PMCID: PMC8137514 DOI: 10.1158/0008-5472.can-20-2635] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
To identify rare variants associated with prostate cancer susceptibility and better characterize the mechanisms and cumulative disease risk associated with common risk variants, we conducted an integrated study of prostate cancer genetic etiology in two cohorts using custom genotyping microarrays, large imputation reference panels, and functional annotation approaches. Specifically, 11,984 men (6,196 prostate cancer cases and 5,788 controls) of European ancestry from Northern California Kaiser Permanente were genotyped and meta-analyzed with 196,269 men of European ancestry (7,917 prostate cancer cases and 188,352 controls) from the UK Biobank. Three novel loci, including two rare variants (European ancestry minor allele frequency < 0.01, at 3p21.31 and 8p12), were significant genome wide in a meta-analysis. Gene-based rare variant tests implicated a known prostate cancer gene (HOXB13), as well as a novel candidate gene (ILDR1), which encodes a receptor highly expressed in prostate tissue and is related to the B7/CD28 family of T-cell immune checkpoint markers. Haplotypic patterns of long-range linkage disequilibrium were observed for rare genetic variants at HOXB13 and other loci, reflecting their evolutionary history. In addition, a polygenic risk score (PRS) of 188 prostate cancer variants was strongly associated with risk (90th vs. 40th-60th percentile OR = 2.62, P = 2.55 × 10-191). Many of the 188 variants exhibited functional signatures of gene expression regulation or transcription factor binding, including a 6-fold difference in log-probability of androgen receptor binding at the variant rs2680708 (17q22). Rare variant and PRS associations, with concomitant functional interpretation of risk mechanisms, can help clarify the full genetic architecture of prostate cancer and other complex traits. SIGNIFICANCE: This study maps the biological relationships between diverse risk factors for prostate cancer, integrating different functional datasets to interpret and model genome-wide data from over 200,000 men with and without prostate cancer.See related commentary by Lachance, p. 1637.
Collapse
Affiliation(s)
- Nima C Emami
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Clinton L Cario
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Simon Wong
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - David Aaronson
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Joseph Presti
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Jun Shan
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Dilrini K Ranatunga
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Nirupa R Ghai
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Mark N Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Pui-Yan Kwok
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Neil Risch
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - John S Witte
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| |
Collapse
|
9
|
Graff RE, Cavazos TB, Thai KK, Kachuri L, Rashkin SR, Hoffman JD, Alexeeff SE, Blatchins M, Meyers TJ, Leong L, Tai CG, Emami NC, Corley DA, Kushi LH, Ziv E, Van Den Eeden SK, Jorgenson E, Hoffmann TJ, Habel LA, Witte JS, Sakoda LC. Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts. Nat Commun 2021; 12:970. [PMID: 33579919 PMCID: PMC7880989 DOI: 10.1038/s41467-021-21288-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Even distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types. Results are then meta-analyzed across cohorts. Ten positive and one inverse cross-cancer associations are found after multiple testing correction. Two pairs show bidirectional associations; the melanoma PRS is positively associated with oral cavity/pharyngeal cancer and vice versa, whereas the lung cancer PRS is positively associated with oral cavity/pharyngeal cancer, and the oral cavity/pharyngeal cancer PRS is inversely associated with lung cancer. Overall, we validate known, and uncover previously unreported, patterns of pleiotropy that have the potential to inform investigations of risk prediction, shared etiology, and precision cancer prevention strategies.
Collapse
Affiliation(s)
- Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA. .,Department of Health System Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA.
| |
Collapse
|
10
|
Kachuri L, Graff RE, Smith-Byrne K, Meyers TJ, Rashkin SR, Ziv E, Witte JS, Johansson M. Pan-cancer analysis demonstrates that integrating polygenic risk scores with modifiable risk factors improves risk prediction. Nat Commun 2020; 11:6084. [PMID: 33247094 PMCID: PMC7695829 DOI: 10.1038/s41467-020-19600-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [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: 06/11/2020] [Accepted: 10/05/2020] [Indexed: 12/28/2022] Open
Abstract
Cancer risk is determined by a complex interplay of environmental and heritable factors. Polygenic risk scores (PRS) provide a personalized genetic susceptibility profile that may be leveraged for disease prediction. Using data from the UK Biobank (413,753 individuals; 22,755 incident cancer cases), we quantify the added predictive value of integrating cancer-specific PRS with family history and modifiable risk factors for 16 cancers. We show that incorporating PRS measurably improves prediction accuracy for most cancers, but the magnitude of this improvement varies substantially. We also demonstrate that stratifying on levels of PRS identifies significantly divergent 5-year risk trajectories after accounting for family history and modifiable risk factors. At the population level, the top 20% of the PRS distribution accounts for 4.0% to 30.3% of incident cancer cases, exceeding the impact of many lifestyle-related factors. In summary, this study illustrates the potential for improving cancer risk assessment by integrating genetic risk scores.
Collapse
Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Karl Smith-Byrne
- Genetic Epidemiology Group, Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
| | - Mattias Johansson
- Genetic Epidemiology Group, Section of Genetics, International Agency for Research on Cancer, Lyon, France.
| |
Collapse
|
11
|
Kachuri L, Francis SS, Morrison ML, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. Genome Med 2020; 12:93. [PMID: 33109261 PMCID: PMC7590248 DOI: 10.1186/s13073-020-00790-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 05/29/2020] [Accepted: 10/07/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr virus (EBV), Varicella zoster virus (VZV), human herpesvirus 7, (HHV7), and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P < 5.0 × 10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, and CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P = 5.0 × 10-15 (MCV), NTN5: P = 1.1 × 10-9 (BKV), and P2RY13: P = 1.1 × 10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases, from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
Collapse
Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA, USA
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, CA, USA
- Department of Mathematics, The University of Texas, Austin, TX, USA
| | - George A Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Université Laval, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
12
|
Kachuri L, Francis SS, Morrison M, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. medRxiv 2020:2020.05.01.20088054. [PMID: 32511533 PMCID: PMC7273301 DOI: 10.1101/2020.05.01.20088054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr Virus (EBV), Varicella Zoster Virus (VZV), Human Herpes virus 7, (HHV7) and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P<5.×10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, as well as CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P=5.0×10-15 (MCV), NTN5: P=1.1×10-9 (BKV), and P2RY13: P=1.1×10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases; from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
Collapse
Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
| | - Stephen S. Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
| | - Maike Morrison
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, USA
- Department of Mathematics, The University of Texas at Austin, Austin, USA
| | - George A. Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Université Laval, Quebec City, Canada
| | - Taylor B. Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, USA
| | - Sara R. Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Department of Medicine, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California San Francisco, San Francisco, USA
| |
Collapse
|
13
|
Rashkin SR, Graff RE, Kachuri L, Thai KK, Alexeeff SE, Blatchins MA, Cavazos TB, Corley DA, Emami NC, Hoffman JD, Jorgenson E, Kushi LH, Meyers TJ, Van Den Eeden SK, Ziv E, Habel LA, Hoffmann TJ, Sakoda LC, Witte JS. Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts. Nat Commun 2020; 11:4423. [PMID: 32887889 PMCID: PMC7473862 DOI: 10.1038/s41467-020-18246-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [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: 01/02/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Deciphering the shared genetic basis of distinct cancers has the potential to elucidate carcinogenic mechanisms and inform broadly applicable risk assessment efforts. Here, we undertake genome-wide association studies (GWAS) and comprehensive evaluations of heritability and pleiotropy across 18 cancer types in two large, population-based cohorts: the UK Biobank (408,786 European ancestry individuals; 48,961 cancer cases) and the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging cohorts (66,526 European ancestry individuals; 16,001 cancer cases). The GWAS detect 21 genome-wide significant associations independent of previously reported results. Investigations of pleiotropy identify 12 cancer pairs exhibiting either positive or negative genetic correlations; 25 pleiotropic loci; and 100 independent pleiotropic variants, many of which are regulatory elements and/or influence cross-tissue gene expression. Our findings demonstrate widespread pleiotropy and offer further insight into the complex genetic architecture of cross-cancer susceptibility.
Collapse
Affiliation(s)
- Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta A Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Taylor B Cavazos
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California, San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
14
|
Chua KC, Xiong C, Ho C, Mushiroda T, Jiang C, Mulkey F, Lai D, Schneider BP, Rashkin SR, Witte JS, Friedman PN, Ratain MJ, McLeod HL, Rugo HS, Shulman LN, Kubo M, Owzar K, Kroetz DL. Genomewide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy. Clin Pharmacol Ther 2020; 108:625-634. [PMID: 32562552 DOI: 10.1002/cpt.1958] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/04/2020] [Indexed: 12/19/2022]
Abstract
Microtubule targeting agents (MTAs) are anticancer therapies commonly prescribed for breast cancer and other solid tumors. Sensory peripheral neuropathy (PN) is the major dose-limiting toxicity for MTAs and can limit clinical efficacy. The current pharmacogenomic study aimed to identify genetic variations that explain patient susceptibility and drive mechanisms underlying development of MTA-induced PN. A meta-analysis of genomewide association studies (GWAS) from two clinical cohorts treated with MTAs (Cancer and Leukemia Group B (CALGB) 40502 and CALGB 40101) was conducted using a Cox regression model with cumulative dose to first instance of grade 2 or higher PN. Summary statistics from a GWAS of European subjects (n = 469) in CALGB 40502 that estimated cause-specific risk of PN were meta-analyzed with those from a previously published GWAS of European ancestry (n = 855) from CALGB 40101 that estimated the risk of PN. Novel single nucleotide polymorphisms in an enhancer region downstream of sphingosine-1-phosphate receptor 1 (S1PR1 encoding S1PR1 ; e.g., rs74497159, βCALGB 40101 per allele log hazard ratio (95% confidence interval (CI)) = 0.591 (0.254-0.928), βCALGB 40502 per allele log hazard ratio (95% CI) = 0.693 (0.334-1.053); PMETA = 3.62 × 10-7 ) were the most highly ranked associations based on P values with risk of developing grade 2 and higher PN. In silico functional analysis identified multiple regulatory elements and potential enhancer activity for S1PR1 within this genomic region. Inhibition of S1PR1 function in induced pluripotent stem cell-derived human sensory neurons shows partial protection against paclitaxel-induced neurite damage. These pharmacogenetic findings further support ongoing clinical evaluations to target S1PR1 as a therapeutic strategy for prevention and/or treatment of MTA-induced neuropathy.
Collapse
Affiliation(s)
- Katherina C Chua
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Chenling Xiong
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Carol Ho
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Taisei Mushiroda
- Laboratory of Genotyping Development, Riken Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Chen Jiang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA.,Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Flora Mulkey
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA.,Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Dongbing Lai
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Sara R Rashkin
- Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California, USA
| | - John S Witte
- Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California, USA
| | - Paula N Friedman
- Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, Florida, USA
| | - Hope S Rugo
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Lawrence N Shulman
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michiaki Kubo
- Laboratory of Genotyping Development, Riken Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA.,Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
15
|
Kachuri L, Johansson M, Rashkin SR, Graff RE, Bossé Y, Manem V, Caporaso NE, Landi MT, Christiani DC, Vineis P, Liu G, Scelo G, Zaridze D, Shete SS, Albanes D, Aldrich MC, Tardón A, Rennert G, Chen C, Goodman GE, Doherty JA, Bickeböller H, Field JK, Davies MP, Dawn Teare M, Kiemeney LA, Bojesen SE, Haugen A, Zienolddiny S, Lam S, Le Marchand L, Cheng I, Schabath MB, Duell EJ, Andrew AS, Manjer J, Lazarus P, Arnold S, McKay JD, Emami NC, Warkentin MT, Brhane Y, Obeidat M, Martin RM, Relton C, Davey Smith G, Haycock PC, Amos CI, Brennan P, Witte JS, Hung RJ. Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility. Nat Commun 2020; 11:27. [PMID: 31911640 PMCID: PMC6946810 DOI: 10.1038/s41467-019-13855-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/19/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Impaired lung function is often caused by cigarette smoking, making it challenging to disentangle its role in lung cancer susceptibility. Investigation of the shared genetic basis of these phenotypes in the UK Biobank and International Lung Cancer Consortium (29,266 cases, 56,450 controls) shows that lung cancer is genetically correlated with reduced forced expiratory volume in one second (FEV1: rg = 0.098, p = 2.3 × 10-8) and the ratio of FEV1 to forced vital capacity (FEV1/FVC: rg = 0.137, p = 2.0 × 10-12). Mendelian randomization analyses demonstrate that reduced FEV1 increases squamous cell carcinoma risk (odds ratio (OR) = 1.51, 95% confidence intervals: 1.21-1.88), while reduced FEV1/FVC increases the risk of adenocarcinoma (OR = 1.17, 1.01-1.35) and lung cancer in never smokers (OR = 1.56, 1.05-2.30). These findings support a causal role of pulmonary impairment in lung cancer etiology. Integrative analyses reveal that pulmonary function instruments, including 73 novel variants, influence lung tissue gene expression and implicate immune-related pathways in mediating the observed effects on lung carcinogenesis.
Collapse
Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Sara R Rashkin
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca E Graff
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Venkata Manem
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Neil E Caporaso
- Division of Cancer Epidemiology & Genetics, US NCI, Bethesda, MD, USA
| | | | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Geoffrey Liu
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | | | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Sanjay S Shete
- Department of Biostatistics, Division of Basic Sciences, MD Anderson Cancer Center, Houston, TX, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology & Genetics, US NCI, Bethesda, MD, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adonina Tardón
- Faculty of Medicine, University of Oviedo and ISPA and CIBERESP, Campus del Cristo, Oviedo, Spain
| | - Gad Rennert
- Clalit National Cancer Control Center, Technion Faculty of Medicine, Haifa, Israel
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary E Goodman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer A Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-Universität Göttingen, Göttingen, Germany
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, London, UK
| | - Michael P Davies
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, London, UK
| | - M Dawn Teare
- Biostatistics Research Group, Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Aage Haugen
- The National Institute of Occupational Health, Oslo, Norway
| | | | | | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Eric J Duell
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Angeline S Andrew
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Jonas Manjer
- Skåne University Hospital, Lund University, Lund, Sweden
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - James D McKay
- International Agency for Research on Cancer, Lyon, France
| | - Nima C Emami
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Matthew T Warkentin
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Ma'en Obeidat
- University of British Columbia, Centre for Heart Lung Innovation, Vancouver, BC, Canada
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - John S Witte
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA.
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
16
|
Rashkin SR, Chua KC, Ho C, Mulkey F, Jiang C, Mushiroda T, Kubo M, Friedman PN, Rugo HS, McLeod HL, Ratain MJ, Castillos F, Naughton M, Overmoyer B, Toppmeyer D, Witte JS, Owzar K, Kroetz DL. A Pharmacogenetic Prediction Model of Progression-Free Survival in Breast Cancer using Genome-Wide Genotyping Data from CALGB 40502 (Alliance). Clin Pharmacol Ther 2018; 105:738-745. [PMID: 30260474 DOI: 10.1002/cpt.1241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/30/2018] [Indexed: 01/10/2023]
Abstract
Genome-wide genotyping data are increasingly available for pharmacogenetic association studies, but application of these data for development of prediction models is limited. Prediction methods, such as elastic net regularization, have recently been applied to genetic studies but only limitedly to pharmacogenetic outcomes. An elastic net was applied to a pharmacogenetic study of progression-free survival (PFS) of 468 patients with advanced breast cancer in a clinical trial of paclitaxel, nab-paclitaxel, and ixabepilone. A final model included 13 single nucleotide polymorphisms (SNPs) in addition to clinical covariates (prior taxane status, hormone receptor status, disease-free interval, and presence of visceral metastases) with an area under the curve (AUC) integrated over time of 0.81, an increase compared to an AUC of 0.64 for a model with clinical covariates alone. This model may be of value in predicting PFS with microtubule targeting agents and may inform reverse translational studies to understand differential response to these drugs.
Collapse
Affiliation(s)
- Sara R Rashkin
- Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California, USA
| | - Katherina C Chua
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Carol Ho
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Flora Mulkey
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Chen Jiang
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA
| | - Tasei Mushiroda
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Paula N Friedman
- Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hope S Rugo
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, Florida, USA
| | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | | | - Michael Naughton
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Beth Overmoyer
- Dana-Farber/Partners Cancer Care, Boston, Massachusetts, USA
| | - Deborah Toppmeyer
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - John S Witte
- Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California, USA
| | - Kouros Owzar
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|