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Diao JA, Shi I, Murthy VL, Buckley TA, Patel CJ, Pierson E, Yeh RW, Kazi DS, Wadhera RK, Manrai AK. Projected Changes in Statin and Antihypertensive Therapy Eligibility With the AHA PREVENT Cardiovascular Risk Equations. JAMA 2024:2821624. [PMID: 39073797 PMCID: PMC11287447 DOI: 10.1001/jama.2024.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/07/2024] [Indexed: 07/30/2024]
Abstract
Importance Since 2013, the American College of Cardiology (ACC) and American Heart Association (AHA) have recommended the pooled cohort equations (PCEs) for estimating the 10-year risk of atherosclerotic cardiovascular disease (ASCVD). An AHA scientific advisory group recently developed the Predicting Risk of cardiovascular disease EVENTs (PREVENT) equations, which incorporated kidney measures, removed race as an input, and improved calibration in contemporary populations. PREVENT is known to produce ASCVD risk predictions that are lower than those produced by the PCEs, but the potential clinical implications have not been quantified. Objective To estimate the number of US adults who would experience changes in risk categorization, treatment eligibility, or clinical outcomes when applying PREVENT equations to existing ACC and AHA guidelines. Design, Setting, and Participants Nationally representative cross-sectional sample of 7765 US adults aged 30 to 79 years who participated in the National Health and Nutrition Examination Surveys of 2011 to March 2020, which had response rates ranging from 47% to 70%. Main Outcomes and Measures Differences in predicted 10-year ASCVD risk, ACC and AHA risk categorization, eligibility for statin or antihypertensive therapy, and projected occurrences of myocardial infarction or stroke. Results In a nationally representative sample of 7765 US adults aged 30 to 79 years (median age, 53 years; 51.3% women), it was estimated that using PREVENT equations would reclassify approximately half of US adults to lower ACC and AHA risk categories (53.0% [95% CI, 51.2%-54.8%]) and very few US adults to higher risk categories (0.41% [95% CI, 0.25%-0.62%]). The number of US adults receiving or recommended for preventive treatment would decrease by an estimated 14.3 million (95% CI, 12.6 million-15.9 million) for statin therapy and 2.62 million (95% CI, 2.02 million-3.21 million) for antihypertensive therapy. The study estimated that, over 10 years, these decreases in treatment eligibility could result in 107 000 additional occurrences of myocardial infarction or stroke. Eligibility changes would affect twice as many men as women and a greater proportion of Black adults than White adults. Conclusion and Relevance By assigning lower ASCVD risk predictions, application of the PREVENT equations to existing treatment thresholds could reduce eligibility for statin and antihypertensive therapy among 15.8 million US adults.
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Affiliation(s)
- James A. Diao
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Ivy Shi
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Thomas A. Buckley
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Emma Pierson
- Department of Computer Science, Cornell University, New York, New York
- Department of Population Health Sciences, Weill Cornell Medical College, New York, New York
| | - Robert W. Yeh
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Richard A. and Susan F. Smith Center for Outcomes Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Dhruv S. Kazi
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Richard A. and Susan F. Smith Center for Outcomes Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Rishi K. Wadhera
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Richard A. and Susan F. Smith Center for Outcomes Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Arjun K. Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
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2
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Terradas M, Schubert SA, Viana-Errasti J, Ruano D, Aiza G, Nielsen M, Marciel P, Tops CM, Parra G, Morreau H, Torrents D, van Leerdam ME, Capellá G, de Miranda NFCC, Valle L, van Wezel T. Germline NPAT inactivating variants as cause of hereditary colorectal cancer. Eur J Hum Genet 2024; 32:871-875. [PMID: 38778081 PMCID: PMC11219789 DOI: 10.1038/s41431-024-01625-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Two independent exome sequencing initiatives aimed to identify new genes involved in the predisposition to nonpolyposis colorectal cancer led to the identification of heterozygous loss-of-function variants in NPAT, a gene that encodes a cyclin E/CDK2 effector required for S phase entry and a coactivator of histone transcription, in two families with multiple members affected with colorectal cancer. Enrichment of loss-of-function and predicted deleterious NPAT variants was identified in familial/early-onset colorectal cancer patients compared to non-cancer gnomAD individuals, further supporting the association with the disease. Previous studies in Drosophila models showed that NPAT abrogation results in chromosomal instability, increase of double strand breaks, and induction of tumour formation. In line with these results, colorectal cancers with NPAT somatic variants and no DNA repair defects have significantly higher aneuploidy levels than NPAT-wildtype colorectal cancers. In conclusion, our findings suggest that constitutional inactivating NPAT variants predispose to mismatch repair-proficient nonpolyposis colorectal cancer.
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Affiliation(s)
- Mariona Terradas
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Stephanie A Schubert
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julen Viana-Errasti
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gemma Aiza
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Paula Marciel
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Genís Parra
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gabriel Capellá
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Laura Valle
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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3
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Nolan JJ, Forrest J, Ormondroyd E. Additional findings from the 100,000 Genomes Project: A qualitative study of recipient perspectives. Genet Med 2024; 26:101103. [PMID: 38411041 DOI: 10.1016/j.gim.2024.101103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
PURPOSE Participants in the 100,000 Genomes Project, a clinical/research initiative delivered through the UK National Health Service, were offered screening for "additional findings" (AFs): pathogenic/likely pathogenic secondary findings in genes associated with familial hypercholesterolemia or a cancer predisposition syndrome. Understanding the psychological and behavioral responses to secondary findings can inform the clinical utility of a search and disclose policy. METHODS Thirty-two adult AF recipients took part in semi-structured interviews analyzed using deductive and inductive thematic analysis. RESULTS Five themes were constructed: cognitive responses to an AF, emotional and psychological responses, personal control, perceived risk of AF-associated disease, and family implications. Many participants had misunderstood or incompletely remembered consent for AFs, and most were surprised or shocked to receive an AF. Although many ultimately appreciated knowing about the risk conferred, some struggled to make sense of their disease risk, which complicated decision making about risk management, particularly for women with a BRCA AF. Recipients sought control through seeking clinical evaluation and information, and informing relatives. Difficulties with conceptualizing risk and lack of AF-associated disease family history meant that some hesitated to inform relatives. CONCLUSION Genome sequencing programs offering secondary findings require attention to consent processes. Post-disclosure care should aim to promote recipients' perceived personal control.
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Affiliation(s)
- Joshua J Nolan
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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4
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Li B, Chen Z, Wang G, Liu Y, Ning S. Synchronous Multiple Primary Malignant Adenocarcinoma of the Descending Colon and Fungating Bleeding Adenocarcinoma of the Terminal Ileum Presenting Massive Rectal Bleeding: A Trap for the Unwary. Onco Targets Ther 2024; 17:363-368. [PMID: 38711919 PMCID: PMC11073142 DOI: 10.2147/ott.s453682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Primary cancer of the ileum is rare, and when it occurs in conjunction with primary colon cancer, it becomes even more infrequent and challenging to diagnose prior to surgical intervention. Primary small bowel cancers can be overlooked and may be misidentified as small bowel mesenchymal tumours or advanced metastases from colon cancer. We present an exceedingly uncommon case of ruptured primary ileal cancer combined with primary descending colon cancer presenting with gastrointestinal bleeding. Based on our understanding, instances of dual tumours concurrently occurring are exceedingly infrequent. In this patient, there was a preoperative suspicion of bleeding from colon cancer in the descending region. However, intraoperative exploration revealed that the location of the bleeding was a terminal ileal mass. Following the surgical intervention, the patient recovered satisfactorily. Intraoperative exploration of the entire gastrointestinal tract is therefore necessary in patients with gastrointestinal haemorrhage, especially in those who require urgent surgery without adequate preoperative investigations. If a mass is detected at the end of the ileum, intraoperative pathology should be performed if feasible. Subsequently, if the diagnosis reveals an adenocarcinoma, terminal ileocolic resection and right hemicolectomy are necessary for appropriate resection.
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Affiliation(s)
- Baicheng Li
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, 116023, People’s Republic of China
| | - Zhao Chen
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, 116023, People’s Republic of China
| | - Guangzhi Wang
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, 116023, People’s Republic of China
| | - Yaqing Liu
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, 116023, People’s Republic of China
| | - Shili Ning
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, 116023, People’s Republic of China
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5
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McRonald FE, Pethick J, Santaniello F, Shand B, Tyson A, Tulloch O, Goel S, Lüchtenborg M, Borthwick GM, Turnbull C, Shaw AC, Monahan KJ, Frayling IM, Hardy S, Burn J. Identification of people with Lynch syndrome from those presenting with colorectal cancer in England: baseline analysis of the diagnostic pathway. Eur J Hum Genet 2024; 32:529-538. [PMID: 38355963 PMCID: PMC11061113 DOI: 10.1038/s41431-024-01550-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
It is believed that >95% of people with Lynch syndrome (LS) remain undiagnosed. Within the National Health Service (NHS) in England, formal guidelines issued in 2017 state that all colorectal cancers (CRC) should be tested for DNA Mismatch Repair deficiency (dMMR). We used a comprehensive population-level national dataset to analyse implementation of the agreed diagnostic pathway at a baseline point 2 years post-publication of official guidelines. Using real-world data collected and curated by the National Cancer Registration and Analysis Service (NCRAS), we retrospectively followed up all people diagnosed with CRC in England in 2019. Nationwide laboratory diagnostic data incorporated somatic (tumour) testing for dMMR (via immunohistochemistry or microsatellite instability), somatic testing for MLH1 promoter methylation and BRAF status, and constitutional (germline) testing of MMR genes. Only 44% of CRCs were screened for dMMR; these figures varied over four-fold with respect to geography. Of those CRCs identified as dMMR, only 51% underwent subsequent diagnostic testing. Overall, only 1.3% of patients with colorectal cancer had a germline MMR genetic test performed; up to 37% of these tests occurred outside of NICE guidelines. The low rates of molecular diagnostic testing in CRC support the premise that Lynch syndrome is underdiagnosed, with significant attrition at all stages of the testing pathway. Applying our methodology to subsequent years' data will allow ongoing monitoring and analysis of the impact of recent investment. If the diagnostic guidelines were fully implemented, we estimate that up to 700 additional people with LS could be identified each year.
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Affiliation(s)
| | - Joanna Pethick
- National Disease Registration Service, NHS England, London, UK
| | - Francesco Santaniello
- National Disease Registration Service, NHS England, London, UK
- Health Data Insight, Cambridge, UK
| | - Brian Shand
- National Disease Registration Service, NHS England, London, UK
- Health Data Insight, Cambridge, UK
| | - Adele Tyson
- National Disease Registration Service, NHS England, London, UK
- Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Oliver Tulloch
- National Disease Registration Service, NHS England, London, UK
- Health Data Insight, Cambridge, UK
| | - Shilpi Goel
- National Disease Registration Service, NHS England, London, UK
- Health Data Insight, Cambridge, UK
| | - Margreet Lüchtenborg
- National Disease Registration Service, NHS England, London, UK
- Cancer Epidemiology and Cancer Services Research, King's College London, London, UK
| | - Gillian M Borthwick
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Adam C Shaw
- Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Kevin J Monahan
- St Mark's Hospital Centre for Familial Intestinal Cancer, Imperial College, London, UK
| | - Ian M Frayling
- St Mark's Hospital Centre for Familial Intestinal Cancer, Imperial College, London, UK
- St Vincent's University Hospital, Dublin, Ireland
| | - Steven Hardy
- National Disease Registration Service, NHS England, London, UK
| | - John Burn
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
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6
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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Huerta-Chagoya A, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Zaitlen N, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry polygenic mechanisms of type 2 diabetes. Nat Med 2024; 30:1065-1074. [PMID: 38443691 PMCID: PMC11175990 DOI: 10.1038/s41591-024-02865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
Type 2 diabetes (T2D) is a multifactorial disease with substantial genetic risk, for which the underlying biological mechanisms are not fully understood. In this study, we identified multi-ancestry T2D genetic clusters by analyzing genetic data from diverse populations in 37 published T2D genome-wide association studies representing more than 1.4 million individuals. We implemented soft clustering with 650 T2D-associated genetic variants and 110 T2D-related traits, capturing known and novel T2D clusters with distinct cardiometabolic trait associations across two independent biobanks representing diverse genetic ancestral populations (African, n = 21,906; Admixed American, n = 14,410; East Asian, n =2,422; European, n = 90,093; and South Asian, n = 1,262). The 12 genetic clusters were enriched for specific single-cell regulatory regions. Several of the polygenic scores derived from the clusters differed in distribution among ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a body mass index (BMI) of 30 kg m-2 in the European subpopulation and 24.2 (22.9-25.5) kg m-2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg m-2 in the East Asian group. Thus, these multi-ancestry T2D genetic clusters encompass a broader range of biological mechanisms and provide preliminary insights to explain ancestry-associated differences in T2D risk profiles.
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Affiliation(s)
- Kirk Smith
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron J Deutsch
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carolyn McGrail
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Hyunkyung Kim
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah Hsu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Alicia Huerta-Chagoya
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ravi Mandla
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip H Schroeder
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth E Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lukasz Szczerbinski
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Timothy D Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Williamson
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melina Claussnitzer
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C Florez
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M Mercader
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Miriam S Udler
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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7
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Huntley C, Loong L, Mallinson C, Bethell R, Rahman T, Alhaddad N, Tulloch O, Zhou X, Lee J, Eves P, McRonald F, Torr B, Burn J, Shaw A, Morris EJ, Monahan K, Hardy S, Turnbull C. The comprehensive English National Lynch Syndrome Registry: development and description of a new genomics data resource. EClinicalMedicine 2024; 69:102465. [PMID: 38356732 PMCID: PMC10864212 DOI: 10.1016/j.eclinm.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
Background Lynch Syndrome (LS) is a cancer predisposition syndrome caused by constitutional pathogenic variants in the mismatch repair (MMR) genes. To date, fragmentation of clinical and genomic data has restricted understanding of national LS ascertainment and outcomes, and precluded evaluation of NICE guidance on testing and management. To address this, via collaboration between researchers, the National Disease Registration Service (NDRS), NHS Genomic Medicine Service Alliances (GMSAs), and NHS Regional Clinical Genetics Services, a comprehensive registry of LS carriers in England has been established. Methods For comprehensive ascertainment of retrospectively identified MMR pathogenic variant (PV) carriers (diagnosed prior to January 1, 2023), information was retrieved from all clinical genetics services across England, then restructured, amalgamated, and validated via a team of trained experts in NDRS. An online submission portal was established for prospective ascertainment from January 1, 2023. The resulting data, stored in a secure database in NDRS, were used to investigate the demographic and genetic characteristics of the cohort, censored at July 25, 2023. Cancer outcomes were investigated via linkage to the National Cancer Registration Dataset (NCRD). Findings A total of 11,722 retrospective and 570 prospective data submissions were received, resulting in a comprehensive English National Lynch Syndrome Registry (ENLSR) comprising 9030 unique individuals. The most frequently identified pathogenic MMR genes were MSH2 and MLH1 at 37.2% (n = 3362) and 29.1% (n = 2624), respectively. 35.9% (n = 3239) of the ENLSR cohort received their LS diagnosis before their first cancer diagnosis (presumptive predictive germline test). Of these, 6.3% (n = 204) developed colorectal cancer, at a median age of initial diagnosis of 51 (IQR 40-62), compared to 73 years (IQR 64-80) in the general population (p < 0.0001). Interpretation The ENLSR represents the first comprehensive national registry of PV carriers in England and one of the largest cohorts of MMR PV carriers worldwide. The establishment of a secure, centralised infrastructure and mechanism for routine registration of newly identified carriers ensures sustainability of the data resource. Funding This work was funded by the Wellcome Trust, Cancer Research UK and Bowel Cancer UK. The funder of this study had no role in study design, data collection, data analysis, data interpretation, or writing of the report.
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Affiliation(s)
- Catherine Huntley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- National Disease Registration Service, NHS England, London, UK
| | - Lucy Loong
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- National Disease Registration Service, NHS England, London, UK
| | | | - Rachel Bethell
- National Disease Registration Service, NHS England, London, UK
| | - Tameera Rahman
- National Disease Registration Service, NHS England, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Neelam Alhaddad
- National Disease Registration Service, NHS England, London, UK
| | - Oliver Tulloch
- National Disease Registration Service, NHS England, London, UK
| | - Xue Zhou
- National Disease Registration Service, NHS England, London, UK
| | - Jason Lee
- National Disease Registration Service, NHS England, London, UK
| | - Paul Eves
- National Disease Registration Service, NHS England, London, UK
| | - Fiona McRonald
- National Disease Registration Service, NHS England, London, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - John Burn
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Adam Shaw
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Eva J.A. Morris
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kevin Monahan
- The Lynch Syndrome and Family Cancer Clinic, St Mark's Hospital and Academic Institute, Harrow, London, UK
- Imperial College London, London, UK
| | - Steven Hardy
- National Disease Registration Service, NHS England, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- National Disease Registration Service, NHS England, London, UK
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8
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Zhang Y, Dron JS, Bellows BK, Khera AV, Liu J, Balte PP, Oelsner EC, Amr SS, Lebo MS, Nagy A, Peloso GM, Natarajan P, Rotter JI, Willer C, Boerwinkle E, Ballantyne CM, Lutsey PL, Fornage M, Lloyd-Jones DM, Hou L, Psaty BM, Bis JC, Floyd JS, Vasan RS, Heard-Costa NL, Carson AP, Hall ME, Rich SS, Guo X, Kazi DS, de Ferranti SD, Moran AE. Familial Hypercholesterolemia Variant and Cardiovascular Risk in Individuals With Elevated Cholesterol. JAMA Cardiol 2024; 9:263-271. [PMID: 38294787 PMCID: PMC10831623 DOI: 10.1001/jamacardio.2023.5366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/22/2023] [Indexed: 02/01/2024]
Abstract
Importance Familial hypercholesterolemia (FH) is a genetic disorder that often results in severely high low-density lipoprotein cholesterol (LDL-C) and high risk of premature coronary heart disease (CHD). However, the impact of FH variants on CHD risk among individuals with moderately elevated LDL-C is not well quantified. Objective To assess CHD risk associated with FH variants among individuals with moderately (130-189 mg/dL) and severely (≥190 mg/dL) elevated LDL-C and to quantify excess CHD deaths attributable to FH variants in US adults. Design, Setting, and Participants A total of 21 426 individuals without preexisting CHD from 6 US cohort studies (Atherosclerosis Risk in Communities study, Coronary Artery Risk Development in Young Adults study, Cardiovascular Health Study, Framingham Heart Study Offspring cohort, Jackson Heart Study, and Multi-Ethnic Study of Atherosclerosis) were included, 63 of whom had an FH variant. Data were collected from 1971 to 2018, and the median (IQR) follow-up was 18 (13-28) years. Data were analyzed from March to May 2023. Exposures LDL-C, cumulative past LDL-C, FH variant status. Main Outcomes and Measures Cox proportional hazards models estimated associations between FH variants and incident CHD. The Cardiovascular Disease Policy Model projected excess CHD deaths associated with FH variants in US adults. Results Of the 21 426 individuals without preexisting CHD (mean [SD] age 52.1 [15.5] years; 12 041 [56.2%] female), an FH variant was found in 22 individuals with moderately elevated LDL-C (0.3%) and in 33 individuals with severely elevated LDL-C (2.5%). The adjusted hazard ratios for incident CHD comparing those with and without FH variants were 2.9 (95% CI, 1.4-6.0) and 2.6 (95% CI, 1.4-4.9) among individuals with moderately and severely elevated LDL-C, respectively. The association between FH variants and CHD was slightly attenuated when further adjusting for baseline LDL-C level, whereas the association was no longer statistically significant after adjusting for cumulative past LDL-C exposure. Among US adults 20 years and older with no history of CHD and LDL-C 130 mg/dL or higher, more than 417 000 carry an FH variant and were projected to experience more than 12 000 excess CHD deaths in those with moderately elevated LDL-C and 15 000 in those with severely elevated LDL-C compared with individuals without an FH variant. Conclusions and Relevance In this pooled cohort study, the presence of FH variants was associated with a 2-fold higher CHD risk, even when LDL-C was only moderately elevated. The increased CHD risk appeared to be largely explained by the higher cumulative LDL-C exposure in individuals with an FH variant compared to those without. Further research is needed to assess the value of adding genetic testing to traditional phenotypic FH screening.
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Affiliation(s)
- Yiyi Zhang
- Division of General Medicine, Columbia University, New York, New York
| | - Jacqueline S. Dron
- Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
| | | | - Amit V. Khera
- Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Division of Cardiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Junxiu Liu
- Department of Population Health Science and Policy, Icahn School of Medicine, Mount Sinai, New York, New York
| | - Pallavi P. Balte
- Division of General Medicine, Columbia University, New York, New York
| | | | - Sami Samir Amr
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Laboratory for Molecular Medicine, Personalized Medicine, Mass General Brigham, Cambridge, Massachusetts
| | - Matthew S. Lebo
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Laboratory for Molecular Medicine, Personalized Medicine, Mass General Brigham, Cambridge, Massachusetts
| | - Anna Nagy
- Laboratory for Molecular Medicine, Personalized Medicine, Mass General Brigham, Cambridge, Massachusetts
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Pradeep Natarajan
- Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Cristen Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor
- Department of Human Genetics, University of Michigan, Ann Arbor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston
| | | | - Pamela L. Lutsey
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis
| | - Myriam Fornage
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston
| | | | - Lifang Hou
- Northwestern University, Chicago, Illinois
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
- Department of Epidemiology, University of Washington, Seattle
- Department of Health Systems and Population Health, University of Washington, Seattle
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
| | - James S. Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
- Department of Epidemiology, University of Washington, Seattle
| | - Ramachandran S. Vasan
- The Framingham Heart Study, Framingham, Massachusetts
- Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Nancy L. Heard-Costa
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson
| | - Michael E. Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Dhruv S. Kazi
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Richard A. and Susan F. Smith Center for Outcomes Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Sarah D. de Ferranti
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Andrew E. Moran
- Division of General Medicine, Columbia University, New York, New York
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9
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Nolan J, Buchanan J, Taylor J, Almeida J, Bedenham T, Blair E, Broadgate S, Butler S, Cazeaux A, Craft J, Cranston T, Crawford G, Forrest J, Gabriel J, George E, Gillen D, Haeger A, Hastings Ward J, Hawkes L, Hodgkiss C, Hoffman J, Jones A, Karpe F, Kasperaviciute D, Kovacs E, Leigh S, Limb E, Lloyd-Jani A, Lopez J, Lucassen A, McFarlane C, O'Rourke AW, Pond E, Sherman C, Stewart H, Thomas E, Thomas S, Thomas T, Thomson K, Wakelin H, Walker S, Watson M, Williams E, Ormondroyd E. Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure. Genet Med 2024; 26:101051. [PMID: 38131308 DOI: 10.1016/j.gim.2023.101051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs. METHODS An observational study in an area representing one-fifth of England. RESULTS Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF. CONCLUSION Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.
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Affiliation(s)
- Joshua Nolan
- Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, United Kingdom
| | - John Taylor
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joao Almeida
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Tina Bedenham
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Suzanne Broadgate
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Samantha Butler
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Angela Cazeaux
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Judith Craft
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Treena Cranston
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Gillian Crawford
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Jessica Gabriel
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elaine George
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Donna Gillen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Ash Haeger
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Claire Hodgkiss
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jonathan Hoffman
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Alan Jones
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Fredrik Karpe
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Dalia Kasperaviciute
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Erika Kovacs
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Sarah Leigh
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Limb
- Population Health Research Institute, St George's University of London, London, United Kingdom
| | - Anjali Lloyd-Jani
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Javier Lopez
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Anneke Lucassen
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Centre for Personalised Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Carlos McFarlane
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Anthony W O'Rourke
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Emily Pond
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Sherman
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ellen Thomas
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Simon Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tessy Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Thomson
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Wakelin
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Susan Walker
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Melanie Watson
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Eleanor Williams
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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10
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Valle L, Monahan KJ. Genetic predisposition to gastrointestinal polyposis: syndromes, tumour features, genetic testing, and clinical management. Lancet Gastroenterol Hepatol 2024; 9:68-82. [PMID: 37931640 DOI: 10.1016/s2468-1253(23)00240-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 11/08/2023]
Abstract
Gastrointestinal tract polyposis is characterised by the presence of multiple polyps, particularly in the colorectum, and encompasses both cancer predisposition genetic syndromes and non-syndromic clinical manifestations. The sources of the heterogeneity observed in polyposis syndromes relate to genetic cause, mode of inheritance, polyp burden and histological type, and spectrum and frequency of extracolonic manifestations. These features determine the clinical management of carriers, including strategies for cancer prevention and early detection, and oncological treatments. Despite substantial progress in identifying the genetic causes of polyposis, a large proportion of cases remain genetically unexplained. Although some of these cases might be due to lifestyle, environmental factors, or cancer treatments, it is likely that additional polyposis predisposition genes will be identified. This Review provides an overview of the known syndromes and genes, genetic testing, and clinical management of patients with polyposis, and recent advances and challenges in the field of gastrointestinal polyposis.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Programme, Catalan Institute of Oncology, Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Kevin J Monahan
- The St Mark's Centre for Familial Intestinal Cancer Lynch Syndrome & Family Cancer Clinic & Polyposis Registry, St Mark's Hospital, London, UK; Imperial College, London, UK.
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11
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Fahed AC, Natarajan P. Clinical applications of polygenic risk score for coronary artery disease through the life course. Atherosclerosis 2023; 386:117356. [PMID: 37931336 PMCID: PMC10842813 DOI: 10.1016/j.atherosclerosis.2023.117356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Coronary artery disease (CAD) remains a leading cause of morbidity and mortality worldwide, highlighting the limitations of current primary and secondary prevention frameworks. In this review, we detail how the polygenic risk score for CAD can improve our current preventive and treatment frameworks across three clinical applications that span the life course: (i) identification and treatment of people at increased risk early in the life course prior to the onset of clinical risk factors, (ii) improving the precision around risk estimation in middle age, and (ii) guiding treatment decisions and enabling more efficient clinical trials even after the onset of CAD. We end by summarizing the efforts needed as we head towards more widespread use of polygenic risk score for CAD in clinical practice.
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Affiliation(s)
- Akl C Fahed
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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12
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Benusiglio PR, Dardenne A, Fallet V, Cadranel J. Emerging cancer risks in BRCA2 pathogenic germline variant carriers. Eur J Hum Genet 2023; 31:1355-1356. [PMID: 37758835 PMCID: PMC10689811 DOI: 10.1038/s41431-023-01465-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Patrick R Benusiglio
- Sorbonne Université, UF d'Oncogénétique Clinique, Département de Génétique Médicale, Hôpital Pitié-Salpêtrière, AP-HP, 47-83 Boulevard de l'Hôpital, F-75013, Paris, France.
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de Recherche Saint-Antoine (CRSA), Equipe Instabilité des Microsatellites et Cancer, F-75012, Paris, France.
| | - Antoine Dardenne
- Sorbonne Université, Service de Chirurgie Digestive, Hôpital Saint-Antoine, APHP, F-75012, Paris, France
| | - Vincent Fallet
- Sorbonne Université, GRC-04 Theranoscan et Service de Pneumologie et Oncologie Thoracique, Hôpital Tenon, APHP, F-75020, Paris, France
| | - Jacques Cadranel
- Sorbonne Université, GRC-04 Theranoscan et Service de Pneumologie et Oncologie Thoracique, Hôpital Tenon, APHP, F-75020, Paris, France
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13
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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity. RESEARCH SQUARE 2023:rs.3.rs-3399145. [PMID: 37886436 PMCID: PMC10602111 DOI: 10.21203/rs.3.rs-3399145/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
We identified genetic subtypes of type 2 diabetes (T2D) by analyzing genetic data from diverse groups, including non-European populations. We implemented soft clustering with 650 T2D-associated genetic variants, capturing known and novel T2D subtypes with distinct cardiometabolic trait associations. The twelve genetic clusters were distinctively enriched for single-cell regulatory regions. Polygenic scores derived from the clusters differed in distribution between ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a BMI of 30 kg/m2 in the European subpopulation and 24.2 (22.9-25.5) kg/m2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg/m2 in the East Asian group, explaining about 75% of the difference in BMI thresholds. Thus, these multi-ancestry T2D genetic subtypes encompass a broader range of biological mechanisms and help explain ancestry-associated differences in T2D risk profiles.
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Affiliation(s)
- Kirk Smith
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron J. Deutsch
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carolyn McGrail
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hyunkyung Kim
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah Hsu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ravi Mandla
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip H. Schroeder
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth E. Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lukasz Szczerbinski
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Williamson
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Melina Claussnitzer
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C. Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K. Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M. Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Miriam S. Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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14
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Albuquerque J, Medeiros AM, Alves AC, Jannes CE, Mancina RM, Pavanello C, Chora JR, Mombelli G, Calabresi L, Pereira ADC, Krieger JE, Romeo S, Bourbon M, Antunes M. Generation and validation of a classification model to diagnose familial hypercholesterolaemia in adults. Atherosclerosis 2023; 383:117314. [PMID: 37813054 DOI: 10.1016/j.atherosclerosis.2023.117314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND AND AIMS The early diagnosis of familial hypercholesterolaemia is associated with a significant reduction in cardiovascular disease (CVD) risk. While the recent use of statistical and machine learning algorithms has shown promising results in comparison with traditional clinical criteria, when applied to screening of potential FH cases in large cohorts, most studies in this field are developed using a single cohort of patients, which may hamper the application of such algorithms to other populations. In the current study, a logistic regression (LR) based algorithm was developed combining observations from three different national FH cohorts, from Portugal, Brazil and Sweden. Independent samples from these cohorts were then used to test the model, as well as an external dataset from Italy. METHODS The area under the receiver operating characteristics (AUROC) and precision-recall (AUPRC) curves was used to assess the discriminatory ability among the different samples. Comparisons between the LR model and Dutch Lipid Clinic Network (DLCN) clinical criteria were performed by means of McNemar tests, and by the calculation of several operating characteristics. RESULTS AUROC and AUPRC values were generally higher for all testing sets when compared to the training set. Compared with DLCN criteria, a significantly higher number of correctly classified observations were identified for the Brazilian (p < 0.01), Swedish (p < 0.01), and Italian testing sets (p < 0.01). Higher accuracy (Acc), G mean and F1 score values were also observed for all testing sets. CONCLUSIONS Compared to DLCN criteria, the LR model revealed improved ability to correctly classify observations, and was able to retain a similar number of FH cases, with less false positive retention. Generalization of the LR model was very good across all testing samples, suggesting it can be an effective screening tool if applied to different populations.
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Affiliation(s)
- João Albuquerque
- Departamento de Biomedicina, Unidade de Bioquímica, Faculdade de Medicina, Universidade do Porto, 4200-319, Porto, Portugal; Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal; Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal.
| | - Ana Margarida Medeiros
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal; Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Ana Catarina Alves
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal; Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Cinthia Elim Jannes
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, São Paulo, Brazil
| | - Rosellina M Mancina
- Sahlgrenska Academy, Institute of Medicine, Department of Molecular and Clinical Medicine, Wallenberg Laboratory, University of Gothenburg, Sweden
| | - Chiara Pavanello
- Centro Grossi Paoletti, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133, Milano, Italy
| | - Joana Rita Chora
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal; Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Giuliana Mombelli
- Centro Dislipidemie, ASST Grande Ospedale Metropolitano Niguarda, 20162, Milano, Italy
| | - Laura Calabresi
- Centro Grossi Paoletti, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133, Milano, Italy
| | | | - José Eduardo Krieger
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, São Paulo, Brazil
| | - Stefano Romeo
- Sahlgrenska Academy, Institute of Medicine, Department of Molecular and Clinical Medicine, Wallenberg Laboratory, University of Gothenburg, Sweden; Cardiology Department, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Clinical and Surgical Sciences, Nutrition Unit, University Magna Graecia, Catanzaro, Italy
| | - Mafalda Bourbon
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal; Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Marília Antunes
- Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal; Departamento de Estatística e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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15
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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.28.23296294. [PMID: 37808749 PMCID: PMC10557820 DOI: 10.1101/2023.09.28.23296294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
We identified genetic subtypes of type 2 diabetes (T2D) by analyzing genetic data from diverse groups, including non-European populations. We implemented soft clustering with 650 T2D-associated genetic variants, capturing known and novel T2D subtypes with distinct cardiometabolic trait associations. The twelve genetic clusters were distinctively enriched for single-cell regulatory regions. Polygenic scores derived from the clusters differed in distribution between ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a BMI of 30 kg/m2 in the European subpopulation and 24.2 (22.9-25.5) kg/m2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg/m2 in the East Asian group, explaining about 75% of the difference in BMI thresholds. Thus, these multi-ancestry T2D genetic subtypes encompass a broader range of biological mechanisms and help explain ancestry-associated differences in T2D risk profiles.
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Affiliation(s)
- Kirk Smith
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron J. Deutsch
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carolyn McGrail
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hyunkyung Kim
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah Hsu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ravi Mandla
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip H. Schroeder
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth E. Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lukasz Szczerbinski
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Williamson
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Melina Claussnitzer
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C. Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K. Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M. Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Miriam S. Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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16
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Deflaux N, Selvaraj MS, Condon HR, Mayo K, Haidermota S, Basford MA, Lunt C, Philippakis AA, Roden DM, Denny JC, Musick A, Collins R, Allen N, Effingham M, Glazer D, Natarajan P, Bick AG. Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis. Nat Commun 2023; 14:5419. [PMID: 37669985 PMCID: PMC10480504 DOI: 10.1038/s41467-023-41185-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Recently, large scale genomic projects such as All of Us and the UK Biobank have introduced a new research paradigm where data are stored centrally in cloud-based Trusted Research Environments (TREs). To characterize the advantages and drawbacks of different TRE attributes in facilitating cross-cohort analysis, we conduct a Genome-Wide Association Study of standard lipid measures using two approaches: meta-analysis and pooled analysis. Comparison of full summary data from both approaches with an external study shows strong correlation of known loci with lipid levels (R2 ~ 83-97%). Importantly, 90 variants meet the significance threshold only in the meta-analysis and 64 variants are significant only in pooled analysis, with approximately 20% of variants in each of those groups being most prevalent in non-European, non-Asian ancestry individuals. These findings have important implications, as technical and policy choices lead to cross-cohort analyses generating similar, but not identical results, particularly for non-European ancestral populations.
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Affiliation(s)
| | - Margaret Sunitha Selvaraj
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Henry Robert Condon
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelsey Mayo
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara Haidermota
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
| | - Melissa A Basford
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chris Lunt
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Anjene Musick
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford, Oxfordshire, UK
- UK Biobank, Cheadle, Stockport, UK
| | - Naomi Allen
- Nuffield Department of Population Health, University of Oxford, Oxford, Oxfordshire, UK
- UK Biobank, Cheadle, Stockport, UK
| | | | | | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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17
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Saadatagah S, Naderian M, Dikilitas O, Hamed ME, Bangash H, Kullo IJ. Polygenic Risk, Rare Variants, and Family History: Independent and Additive Effects on Coronary Heart Disease. JACC. ADVANCES 2023; 2:100567. [PMID: 38939477 PMCID: PMC11198423 DOI: 10.1016/j.jacadv.2023.100567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2024]
Abstract
Background Genetic factors are not included in prediction models for coronary heart disease (CHD). Objectives The authors assessed the predictive utility of a polygenic risk score (PRS) for CHD (defined as myocardial infarction, coronary revascularization, or cardiovascular death) and whether the risks due to monogenic familial hypercholesterolemia (FH) and family history (FamHx) are independent of and additive to the PRS. Methods In UK-biobank participants, PRSCHD was calculated using metaGRS, and 10-year risk for incident CHD was estimated using the pooled cohort equations (PCE). The area under the curve (AUC) of the receiver operator curve and net reclassification improvement (NRI) were assessed. FH was defined as the presence of a pathogenic or likely pathogenic variant in LDLR, APOB, or PCSK9. FamHx was defined as a diagnosis of CHD in first-degree relatives. Independent and additive effects of PRSCHD, FH, and FamHx were evaluated in stratified analyses. Results In 323,373 participants with genotype data, the addition of PRSCHD to PCE increased the AUC from 0.759 (95% CI: 0.755-0.763) to 0.773 (95% CI: 0.769-0.777). The AUC and NRIEvent for PRSCHD were higher before the age of 55 years. Of 199,997 participants with exome sequence data, 10,000 had a PRSCHD ≥95th percentile (PRSP95), 673 had FH, and 46,163 had FamHx. The CHD risk associated with PRSP95 was independent of FH and FamHx. The risks associated with combinations of PRSCHD, FH, and FamHx were additive and comprehensive estimates could be obtained by multiplying the risk from each genetic factor. Conclusions Incorporating PRSCHD into the PCE improves risk prediction for CHD, especially at younger ages. The associations of PRSCHD, FH, and FamHx with CHD were independent and additive.
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Affiliation(s)
| | | | - Ozan Dikilitas
- Departments of Internal Medicine and Cardiovascular Medicine, and Mayo Clinician-Investigator Training Program, Mayo Clinic, Rochester, Minnesota, USA
| | - Marwan E. Hamed
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Gonda Vascular Center, Mayo Clinic, Rochester, Minnesota, USA
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18
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Monahan KJ, Swinyard O, Latchford A. Biology of Precancers and Opportunities for Cancer Interception: Lesson from Colorectal Cancer Susceptibility Syndromes. Cancer Prev Res (Phila) 2023; 16:421-427. [PMID: 37001883 DOI: 10.1158/1940-6207.capr-22-0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/28/2023] [Accepted: 03/28/2023] [Indexed: 04/04/2023]
Abstract
Hereditary gastrointestinal cancer is associated with molecular and neoplastic precursors which have revealed much about sporadic carcinogenesis. Therefore, an appreciation of constitutional and somatic events linked to these syndromes have provided a useful model for the development of risk models and preventative strategies. In this review, we focus of two of the best characterized syndromes, Lynch syndrome (LS) and familial adenomatous polyposis (FAP). Our understanding of the neoplasia-immune interaction in LS has contributed to the development of immune mediated therapies including cancer preventing vaccines and immunotherapy for cancer precursors. Chemoprevention in LS with aspirin and nonsteroidal anti-inflammatory drugs has also translated into clinical cancer, however the efficacy of such agents in FAP remains elusive when cancer is applied as an endpoint in trials rather than the use of 'indirect' endpoints such as polyp burden, and requires further elucidation of biological mechanisms in FAP. Finally, we review controversies in gastrointestinal surveillance for LS and FAP, including limitations and opportunities of upper and lower gastrointestinal endoscopy in the prevention and early detection of cancer.
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Affiliation(s)
- Kevin J Monahan
- Centre for Familial Intestinal Cancer, St. Marks Hospital & Imperial College, London, United Kingdom
| | - Ottilie Swinyard
- Evolution and Cancer Lab, Centre of Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Genomics and Evolutionary Dynamics Lab, Division of Molecular Pathology, Institute of Cancer Research, Sutton, London, United Kingdom
| | - Andrew Latchford
- Centre for Familial Intestinal Cancer, St. Marks Hospital & Imperial College, London, United Kingdom
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19
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Valle L. Lynch Syndrome: A Single Hereditary Cancer Syndrome or Multiple Syndromes Defined by Different Mismatch Repair Genes? Gastroenterology 2023; 165:20-23. [PMID: 37142200 DOI: 10.1053/j.gastro.2023.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology and, Oncobell Program, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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20
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Cerrato C, Pandolfo SD, Autorino R, Panunzio A, Tafuri A, Porcaro AB, Veccia A, De Marco V, Cerruto MA, Antonelli A, Derweesh IH, Maresma MCM. Gender-specific counselling of patients with upper tract urothelial carcinoma and Lynch syndrome. World J Urol 2023; 41:1741-1749. [PMID: 36964236 DOI: 10.1007/s00345-023-04344-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
PURPOSE Lynch syndrome (LS) is an autosomal dominant genetic syndrome resulting in a wide spectrum of malignancies caused by germline mutations in mismatch repair genes (MMR). Gene mutations have different effects and penetrance between the two genders. The aim of this review is to offer a gender-specific evidence-based clinical guide on diagnosis, screening, surveillance, and counselling of UTUC patients with LS. METHODS Using MEDLINE, a non-systematic review was performed including articles between 2004 and 2022. English language original articles, reviews, and editorials were selected based on their clinical relevance. RESULTS Upper tract urothelial carcinoma (UTUC) is the third most common malignancy in Lynch syndrome. Up to 21% of new UTUC cases may have unrecognized LS as the underlying cause. LS-UTUC does not have a clear gender prevalence, even if it seems to slightly prefer the male gender. The MSH6 variant is significantly associated with female gender (p < 0.001) and with gynecological malignancies. Female MSH2 and MLH1 carriers have higher rates for endometrial and ovarian cancer with respect to the general population, while male MSH2 and MLH1 carriers have, respectively, higher rate of prostate cancer and upper GI tract, or biliary or pancreatic cancers. Conflicting evidence remains on the association of testicular cancer with LS. CONCLUSION LS is a polyhedric disease, having a great impact on patients and their families that requires a multidisciplinary approach. UTUC patients should be systematically screened for LS, and urologists have to be aware that the same MMR mutation may lead to different malignancies according to the patient's gender.
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Affiliation(s)
- Clara Cerrato
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Riccardo Autorino
- Department of Urology, Rush University Medical Center, Chicago, IL, USA
| | - Andrea Panunzio
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Antonio Benito Porcaro
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Alessandro Veccia
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Vincenzo De Marco
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Maria Angela Cerruto
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Alessandro Antonelli
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Ithaar H Derweesh
- Department of Urology, UC San Diego School of Medicine, La Jolla, USA
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21
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Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV. A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease. Nat Med 2023; 29:1793-1803. [PMID: 37414900 PMCID: PMC10353935 DOI: 10.1038/s41591-023-02429-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPSMult, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPSMult strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P < 0.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPSMult was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P < 0.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPSMult demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPSMult for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.
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Affiliation(s)
- Aniruddh P Patel
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Minxian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Yunfeng Ruan
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Satoshi Koyama
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Veteran Affairs Boston Healthcare System, Boston, MA, USA
| | - Shoa L Clarke
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Xiong Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | | | - Saaket Agrawal
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Akl C Fahed
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Philip S Tsao
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Yan V Sun
- Veteran Affairs Atlanta Healthcare System, Decatur, GA, USA
| | - Kelly Cho
- Veteran Affairs Boston Healthcare System, Boston, MA, USA
| | | | - Themistocles L Assimes
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, and Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Krishna G Aragam
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Amit V Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Verve Therapeutics, Boston, MA, USA.
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22
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Li C, Pan Y, Zhang R, Huang Z, Li D, Han Y, Larkin C, Rao V, Sun X, Kelly TN. Genomic Innovation in Early Life Cardiovascular Disease Prevention and Treatment. Circ Res 2023; 132:1628-1647. [PMID: 37289909 PMCID: PMC10328558 DOI: 10.1161/circresaha.123.321999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality globally. Although CVD events do not typically manifest until older adulthood, CVD develops gradually across the life-course, beginning with the elevation of risk factors observed as early as childhood or adolescence and the emergence of subclinical disease that can occur in young adulthood or midlife. Genomic background, which is determined at zygote formation, is among the earliest risk factors for CVD. With major advances in molecular technology, including the emergence of gene-editing techniques, along with deep whole-genome sequencing and high-throughput array-based genotyping, scientists now have the opportunity to not only discover genomic mechanisms underlying CVD but use this knowledge for the life-course prevention and treatment of these conditions. The current review focuses on innovations in the field of genomics and their applications to monogenic and polygenic CVD prevention and treatment. With respect to monogenic CVD, we discuss how the emergence of whole-genome sequencing technology has accelerated the discovery of disease-causing variants, allowing comprehensive screening and early, aggressive CVD mitigation strategies in patients and their families. We further describe advances in gene editing technology, which might soon make possible cures for CVD conditions once thought untreatable. In relation to polygenic CVD, we focus on recent innovations that leverage findings of genome-wide association studies to identify druggable gene targets and develop predictive genomic models of disease, which are already facilitating breakthroughs in the life-course treatment and prevention of CVD. Gaps in current research and future directions of genomics studies are also discussed. In aggregate, we hope to underline the value of leveraging genomics and broader multiomics information for characterizing CVD conditions, work which promises to expand precision approaches for the life-course prevention and treatment of CVD.
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Affiliation(s)
- Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Yang Pan
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Ruiyuan Zhang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Zhijie Huang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Davey Li
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Yunan Han
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Claire Larkin
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Varun Rao
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
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23
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Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. Am J Hum Genet 2023; 110:940-949. [PMID: 37236177 PMCID: PMC10257006 DOI: 10.1016/j.ajhg.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
While pathogenic variants can significantly increase disease risk, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2, large cohort studies find no significant association between breast cancer and rare missense variants collectively. Here, we introduce REGatta, a method to estimate clinical risk from variants in smaller segments of individual genes. We first define these regions by using the density of pathogenic diagnostic reports and then calculate the relative risk in each region by using over 200,000 exome sequences in the UK Biobank. We apply this method in 13 genes with established roles across several monogenic disorders. In genes with no significant difference at the gene level, this approach significantly separates disease risk for individuals with rare missense variants at higher or lower risk (BRCA2 regional model OR = 1.46 [1.12, 1.79], p = 0.0036 vs. BRCA2 gene model OR = 0.96 [0.85, 1.07] p = 0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare our method with existing methods and the use of protein domains (Pfam) as regions and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors and are potentially useful for improving risk assessment for genes associated with monogenic diseases.
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Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
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24
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Hamilton MC, Fife JD, Akinci E, Yu T, Khowpinitchai B, Cha M, Barkal S, Thi TT, Yeo GH, Ramos Barroso JP, Francoeur MJ, Velimirovic M, Gifford DK, Lettre G, Yu H, Cassa CA, Sherwood RI. Systematic elucidation of genetic mechanisms underlying cholesterol uptake. CELL GENOMICS 2023; 3:100304. [PMID: 37228746 PMCID: PMC10203276 DOI: 10.1016/j.xgen.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/02/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we substantially improve the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of the genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.
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Affiliation(s)
- Marisa C. Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James D. Fife
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sammy Barkal
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Thi Tun Thi
- Precision Medicine Research Programme, Cardiovascular Disease Research Programme, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Grace H.T. Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juan Pablo Ramos Barroso
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Jake Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minja Velimirovic
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K. Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Haojie Yu
- Precision Medicine Research Programme, Cardiovascular Disease Research Programme, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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25
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Clarke SL. Does low-density lipoprotein fully explain atherosclerotic risk in familial hypercholesterolemia? Curr Opin Lipidol 2023; 34:52-58. [PMID: 36853849 PMCID: PMC9994798 DOI: 10.1097/mol.0000000000000868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
PURPOSE OF REVIEW Familial hypercholesterolemia (FH) is a monogenic disorder of elevated low-density lipoprotein cholesterol (LDL-C) from birth leading to increased risk for atherosclerotic cardiovascular disease. However, not all carriers of FH variants display an FH phenotype. Despite this fact, FH variants confer increased risk for atherosclerotic disease in population cohorts. An important question to consider is whether measurements of LDL-C can fully account for this risk. RECENT FINDINGS The atherosclerotic risk associated with FH variants is independent of observed adult LDL-C levels. Modeling adult longitudinal LDL-C accounts for more of this risk compared to using a single measurement. Still, even when adjusting for observed longitudinal LDL-C in adult cohorts, FH variant carriers are at increased risk for coronary artery disease. Genetic analyses, observational studies, and clinical trials all suggest that cumulative LDL-C is a critical driver of cardiovascular risk that may not be fully appreciated by routine LDL-C measurements in adulthood. As such, FH variants confer risk independent of adult LDL-C because these variants increase cumulative LDL-C exposure starting from birth. SUMMARY Both research and clinical practice focus on LDL-C measurements in adults, but measurements during adulthood do not reflect lifelong cumulative exposure to LDL-C. Genetic assessments may compliment clinical assessments by better identifying patients who have experienced greater longitudinal LDL-C exposure.
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Affiliation(s)
- Shoa L. Clarke
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford, California, USA
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26
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Dron JS, Patel AP, Zhang Y, Jurgens SJ, Maamari DJ, Wang M, Boerwinkle E, Morrison AC, de Vries PS, Fornage M, Hou L, Lloyd-Jones DM, Psaty BM, Tracy RP, Bis JC, Vasan RS, Levy D, Heard-Costa N, Rich SS, Guo X, Taylor KD, Gibbs RA, Rotter JI, Willer CJ, Oelsner EC, Moran AE, Peloso GM, Natarajan P, Khera AV. Association of Rare Protein-Truncating DNA Variants in APOB or PCSK9 With Low-density Lipoprotein Cholesterol Level and Risk of Coronary Heart Disease. JAMA Cardiol 2023; 8:258-267. [PMID: 36723951 PMCID: PMC9996405 DOI: 10.1001/jamacardio.2022.5271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/29/2022] [Indexed: 02/02/2023]
Abstract
Importance Protein-truncating variants (PTVs) in apolipoprotein B (APOB) and proprotein convertase subtilisin/kexin type 9 (PCSK9) are associated with significantly lower low-density lipoprotein (LDL) cholesterol concentrations. The association of these PTVs with coronary heart disease (CHD) warrants further characterization in large, multiracial prospective cohort studies. Objective To evaluate the association of PTVs in APOB and PCSK9 with LDL cholesterol concentrations and CHD risk. Design, Setting, and Participants This studied included participants from 5 National Heart, Lung, and Blood Institute (NHLBI) studies and the UK Biobank. NHLBI study participants aged 5 to 84 years were recruited between 1971 and 2002 across the US and underwent whole-genome sequencing. UK Biobank participants aged 40 to 69 years were recruited between 2006 and 2010 in the UK and underwent whole-exome sequencing. Data were analyzed from June 2021 to October 2022. Exposures PTVs in APOB and PCSK9. Main Outcomes and Measures Estimated untreated LDL cholesterol levels and CHD. Results Among 19 073 NHLBI participants (10 598 [55.6%] female; mean [SD] age, 52 [17] years), 139 (0.7%) carried an APOB or PCSK9 PTV, which was associated with 49 mg/dL (95% CI, 43-56) lower estimated untreated LDL cholesterol level. Over a median (IQR) follow-up of 21.5 (13.9-29.4) years, incident CHD was observed in 12 of 139 carriers (8.6%) vs 3029 of 18 934 noncarriers (16.0%), corresponding to an adjusted hazard ratio of 0.51 (95% CI, 0.28-0.89; P = .02). Among 190 464 UK Biobank participants (104 831 [55.0%] female; mean [SD] age, 57 [8] years), 662 (0.4%) carried a PTV, which was associated with 45 mg/dL (95% CI, 42-47) lower estimated untreated LDL cholesterol level. Estimated CHD risk by age 75 years was 3.7% (95% CI, 2.0-5.3) in carriers vs 7.0% (95% CI, 6.9-7.2) in noncarriers, corresponding to an adjusted hazard ratio of 0.51 (95% CI, 0.32-0.81; P = .004). Conclusions and Relevance Among 209 537 individuals in this study, 0.4% carried an APOB or PCSK9 PTV that was associated with less exposure to LDL cholesterol and a 49% lower risk of CHD.
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Affiliation(s)
- Jacqueline S. Dron
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aniruddh P. Patel
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston
| | - Yiyi Zhang
- Division of General Medicine, Columbia University, New York, New York
| | - Sean J. Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Experimental Cardiology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Dimitri J. Maamari
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Minxian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Donald M. Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
- Department of Epidemiology, University of Washington, Seattle
- Department of Health Systems and Population Health, University of Washington, Seattle
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine at the University of Vermont, Colchester, Vermont
- Department of Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, Vermont
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
| | - Ramachandran S. Vasan
- Sections of Preventive Medicine and Epidemiology, Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Nancy Heard-Costa
- Framingham Heart Study, Framingham, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | | | | | - Andrew E. Moran
- Division of General Medicine, Columbia University, New York, New York
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Pradeep Natarajan
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston
| | - Amit V. Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Verve Therapeutics, Boston, Massachusetts
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27
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Yao Q, Gorevic P, Shen B, Gibson G. Genetically transitional disease: a new concept in genomic medicine. Trends Genet 2023; 39:98-108. [PMID: 36564319 DOI: 10.1016/j.tig.2022.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/02/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Traditional classification of genetic diseases as monogenic and polygenic has lagged far behind scientific progress. In this opinion article, we propose and define a new terminology, genetically transitional disease (GTD), referring to cases where a large-effect mutation is necessary, but not sufficient, to cause disease. This leads to a working disease nosology based on gradients of four types of genetic architecture: monogenic, polygenic, GTD, and mixed. We present four scenarios under which GTD may occur; namely, subsets of traditionally Mendelian disease, modifiable Tier 1 monogenic conditions, variable penetrance, and situations where a genetic mutational spectrum produces qualitatively divergent pathologies. The implications of the new nosology in precision medicine are discussed, in which therapeutic options may target the molecular cause or the disease phenotype.
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Affiliation(s)
- Qingping Yao
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA.
| | - Peter Gorevic
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA
| | - Bo Shen
- Center for Inflammatory Bowel Diseases, New York-Presbyterian/Columbia University Irving Medical Center, New York, NY, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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28
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Abstract
Polygenic scores quantify inherited risk by integrating information from many common sites of DNA variation into a single number. Rapid increases in the scale of genetic association studies and new statistical algorithms have enabled development of polygenic scores that meaningfully measure-as early as birth-risk of coronary artery disease. These newer-generation polygenic scores identify up to 8% of the population with triple the normal risk based on genetic variation alone, and these individuals cannot be identified on the basis of family history or clinical risk factors alone. For those identified with increased genetic risk, evidence supports risk reduction with at least two interventions, adherence to a healthy lifestyle and cholesterol-lowering therapies, that can substantially reduce risk. Alongside considerable enthusiasm for the potential of polygenic risk estimation to enable a new era of preventive clinical medicine is recognition of a need for ongoing research into how best to ensure equitable performance across diverse ancestries, how and in whom to assess the scores in clinical practice, as well as randomized trials to confirm clinical utility.
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Affiliation(s)
- Aniruddh P Patel
- Division of Cardiology and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA; , .,Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Amit V Khera
- Division of Cardiology and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA; , .,Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Verve Therapeutics, Cambridge, Massachusetts, USA
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29
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Georgiou D, Monje-Garcia L, Miles T, Monahan K, Ryan NAJ. A Focused Clinical Review of Lynch Syndrome. Cancer Manag Res 2023; 15:67-85. [PMID: 36699114 PMCID: PMC9868283 DOI: 10.2147/cmar.s283668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Lynch syndrome (LS) is an autosomal dominant condition that increases an individual's risk of a constellation of cancers. LS is defined when an individual has inherited pathogenic variants in the mismatch repair genes. Currently, most people with LS are undiagnosed. Early detection of LS is vital as those with LS can be enrolled in cancer reduction strategies through chemoprophylaxis, risk reducing surgery and cancer surveillance. However, these interventions are often invasive and require refinement. Furthermore, not all LS associated cancers are currently amenable to surveillance. Historically only those with a strong family history suggestive of LS were offered testing; this has proved far too restrictive. New criteria for testing have recently been introduced including the universal screening for LS in associated cancers. This has increased the number of people being diagnosed with LS but has also brought about unique challenges such as when to consent for germline testing and questions over how and who should carry out the consent. The results of germline testing for LS can be complicated and the diagnostic pathway is not always clear. Furthermore, by testing only those with cancer for LS we fail to identify these individuals before they develop potentially fatal pathology. This review will outline these challenges and explore solutions. Furthermore, we consider the potential future of LS care and the related treatments and interventions which are the current focus of research.
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Affiliation(s)
- Demetra Georgiou
- Genomics and Personalised Medicine Service, Charing Cross Hospital, London, UK
| | - Laura Monje-Garcia
- The St Mark's Centre for Familial Intestinal Cancer Polyposis, St Mark's Hospital, London, UK.,School of Public Health, Imperial College, London, UK
| | - Tracie Miles
- South West Genomics Medicine Service Alliance, Bristol, UK
| | - Kevin Monahan
- The St Mark's Centre for Familial Intestinal Cancer Polyposis, St Mark's Hospital, London, UK.,Department of Gastroenterology, Imperial College, London, UK
| | - Neil A J Ryan
- Department of Gynaecological Oncology, Royal Infirmary of Edinburgh, Edinburgh, UK.,The College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
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30
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Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.06.23284281. [PMID: 36711752 PMCID: PMC9882564 DOI: 10.1101/2023.01.06.23284281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
While pathogenic variants significantly increase disease risk in many genes, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2 , large cohort studies find no significant association between breast cancer and rare germline missense variants collectively. Here we introduce REGatta, a method to improve the estimation of clinical risk in gene segments. We define gene regions using the density of pathogenic diagnostic reports, and then calculate the relative risk in each of these regions using 109,581 exome sequences from women in the UK Biobank. We apply this method in seven established breast cancer genes, and identify regions in each gene with statistically significant differences in breast cancer incidence for rare missense carriers. Even in genes with no significant difference at the gene level, this approach significantly separates rare missense variant carriers at higher or lower risk ( BRCA2 regional model OR=1.46 [1.12, 1.79], p=0.0036 vs. BRCA2 gene model OR=0.96 [0.85,1.07] p=0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare with existing methods and the use of protein domains (Pfam) as regions, and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors which can potentially be used to improve risk assessment and clinical management.
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Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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31
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Yu T, Fife JD, Adzhubey I, Sherwood R, Cassa CA. Joint estimation and imputation of variant functional effects using high throughput assay data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.06.23284280. [PMID: 36711907 PMCID: PMC9882428 DOI: 10.1101/2023.01.06.23284280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Deep mutational scanning assays enable the functional assessment of variants in high throughput. Phenotypic measurements from these assays are broadly concordant with clinical outcomes but are prone to noise at the individual variant level. We develop a framework to exploit related measurements within and across experimental assays to jointly estimate variant impact. Drawing from a large corpus of deep mutational scanning data, we collectively estimate the mean functional effect per AA residue position within each gene, normalize observed functional effects by substitution type, and make estimates for individual allelic variants with a pipeline called FUSE (Functional Substitution Estimation). FUSE improves the correlation of functional screening datasets covering the same variants, better separates estimated functional impacts for known pathogenic and benign variants (ClinVar BRCA1, p=2.24×10-51), and increases the number of variants for which predictions can be made (2,741 to 10,347) by inferring additional variant effects for substitutions not experimentally screened. For UK Biobank patients who carry a rare variant in TP53, FUSE significantly improves the separation of patients who develop cancer syndromes from those without cancer (p=1.77×10-6). These approaches promise to improve estimates of variant impact and broaden the utility of screening data generated from functional assays.
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Affiliation(s)
- Tian Yu
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - James D. Fife
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ivan Adzhubey
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Richard Sherwood
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher A. Cassa
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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Williams MH, Hadjinicolaou AV, Norton B, Kader R, Lovat LB. Lynch syndrome: from detection to treatment. Front Oncol 2023; 13:1166238. [PMID: 37197422 PMCID: PMC10183578 DOI: 10.3389/fonc.2023.1166238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023] Open
Abstract
Lynch syndrome (LS) is an inherited cancer predisposition syndrome associated with high lifetime risk of developing tumours, most notably colorectal and endometrial. It arises in the context of pathogenic germline variants in one of the mismatch repair genes, that are necessary to maintain genomic stability. LS remains underdiagnosed in the population despite national recommendations for empirical testing in all new colorectal and endometrial cancer cases. There are now well-established colorectal cancer surveillance programmes, but the high rate of interval cancers identified, coupled with a paucity of high-quality evidence for extra-colonic cancer surveillance, means there is still much that can be achieved in diagnosis, risk-stratification and management. The widespread adoption of preventative pharmacological measures is on the horizon and there are exciting advances in the role of immunotherapy and anti-cancer vaccines for treatment of these highly immunogenic LS-associated tumours. In this review, we explore the current landscape and future perspectives for the identification, risk stratification and optimised management of LS with a focus on the gastrointestinal system. We highlight the current guidelines on diagnosis, surveillance, prevention and treatment and link molecular disease mechanisms to clinical practice recommendations.
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Affiliation(s)
- Madeleine H. Williams
- Department of Gastroenterology, Guy’s and St. Thomas NHS Foundation Trust, London, United Kingdom
| | - Andreas V. Hadjinicolaou
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Andreas V. Hadjinicolaou,
| | - Benjamin C. Norton
- Department of Gastroenterology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Rawen Kader
- Wellcome-EPSRC Centre for Interventional and Surgical Sciences, University College London, London, United Kingdom
| | - Laurence B. Lovat
- Wellcome-EPSRC Centre for Interventional and Surgical Sciences, University College London, London, United Kingdom
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Khera AV, Wang M, Chaffin M, Emdin CA, Samani NJ, Schunkert H, Watkins H, McPherson R, Elosua R, Boerwinkle E, Ardissino D, Butterworth AS, Di Angelantonio E, Naheed A, Danesh J, Chowdhury R, Krumholz HM, Sheu WHH, Rich SS, Rotter JI, Chen YDI, Gabriel S, Lander ES, Saleheen D, Kathiresan S. Gene Sequencing Identifies Perturbation in Nitric Oxide Signaling as a Nonlipid Molecular Subtype of Coronary Artery Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003598. [PMID: 36215124 PMCID: PMC9771961 DOI: 10.1161/circgen.121.003598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/24/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND A key goal of precision medicine is to disaggregate common, complex diseases into discrete molecular subtypes. Rare coding variants in the low-density lipoprotein receptor gene (LDLR) are identified in 1% to 2% of coronary artery disease (CAD) patients, defining a molecular subtype with risk driven by hypercholesterolemia. METHODS To search for additional subtypes, we compared the frequency of rare, predicted loss-of-function and damaging missense variants aggregated within a given gene in 41 081 CAD cases versus 217 115 controls. RESULTS Rare variants in LDLR were most strongly associated with CAD, present in 1% of cases and associated with 4.4-fold increased CAD risk. A second subtype was characterized by variants in endothelial nitric oxide synthase gene (NOS3), a key enzyme regulating vascular tone, endothelial function, and platelet aggregation. A rare predicted loss-of-function or damaging missense variants in NOS3 was present in 0.6% of cases and associated with 2.42-fold increased risk of CAD (95% CI, 1.80-3.26; P=5.50×10-9). These variants were associated with higher systolic blood pressure (+3.25 mm Hg; [95% CI, 1.86-4.65]; P=5.00×10-6) and increased risk of hypertension (adjusted odds ratio 1.31; [95% CI, 1.14-1.51]; P=2.00×10-4) but not circulating cholesterol concentrations, suggesting that, beyond lipid pathways, nitric oxide synthesis is a key nonlipid driver of CAD risk. CONCLUSIONS Beyond LDLR, we identified an additional nonlipid molecular subtype of CAD characterized by rare variants in the NOS3 gene.
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Affiliation(s)
- Amit V. Khera
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
- Cardiology Division, Dept of Medicine, Massachusetts General Hospital, Boston, MA
| | - Minxian Wang
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
- CAS Key Laboratory of Genome Sciences & Information, Beijing Inst of Genomics, Chinese Academy of Sciences & China National Ctr for Bioinformation, Beijing, China
| | - Mark Chaffin
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
| | - Connor A. Emdin
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
| | - Nilesh J. Samani
- Dept of Cardiovascular Sciences, Univ of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Ctr, Glenfield Hospital, Leicester, UK
| | - Heribert Schunkert
- Dept of Cardiology, German Heart Ctr Munich, Technical Univ of Munich, Munich, Germany
- DZHK (German Ctr for Cardiovascular Research), Partner site Munich, Munich Heart Alliance, Munich, Germany
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Dept of Medicine, Univ of Oxford, Headington, UK
- Wellcome Trust Ctr for Human Genetics, Univ of Oxford, Oxford, UK
| | - Ruth McPherson
- Inst for Cardiogenetics, Univ of Lübeck, Lübeck, Schleswig-Holstein, Germany
- German Research Ctr for Cardiovascular Research, Partner Site Hamburg/Lübeck/Kiel & Univ Heart Center Lübeck (J.E.), Berlin, Brandenburg, Germany
- Depts of Medicine & Biochemistry, Univ of Ottawa Heart Inst, Ottawa, ON, Canada
| | - Roberto Elosua
- Cardiovascular Epidemiology & Genetics, Hospital del Mar Research Inst, Barcelona, Spain
- CIBER Enfermedades Cardiovasculares, Barcelona, Spain
- Facultat de Medicina, Universitat de Vic-Central de Cataluña, Barcelona, Spain
| | - Eric Boerwinkle
- Ctr for Human Genetics & Dept. of Epidemiology, Univ of Texas Health Science Ctr School of Public Health, Houston, TX
| | - Diego Ardissino
- Cardiology, Azienda Ospedaliero-Universitaria di Parma, Univ of Parma, Parma, Italy
- Associazione per lo Studio Della Trombosi in Cardiologia, Pavia, Italy
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- National Inst for Health Research Blood & Transplant Research Unit in Donor Health & Genomics, Univ of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus & Univ of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus & Univ of Cambridge, Cambridge, UK
- NIHR Blood & Transplant Research Unit in Donor Health & Genomics, Univ of Cambridge, Cambridge, UK
- BHF Ctr of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, Univ of Cambridge, Cambridge, UK
- Health Data Science Research Ctr, Human Technopole, Milan, Italy
| | - Aliya Naheed
- Initiative for Noncommunicable Bangladesh, Diseases, Health Systems & Population Studies Division, International Ctr for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- National Inst for Health Research Blood & Transplant Research Unit in Donor Health & Genomics, Univ of Cambridge, Cambridge, UK
- British Heart Foundation Ctr of Research Excellence, Univ of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus & Univ of Cambridge, Cambridge, UK
- Dept of Human Genetics, Wellcome Sanger Inst, Hinxton, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Dept of Public Health & Primary Care, Univ of Cambridge, Cambridge, UK
- Centre for Non-Communicable Disease Research, Dhaka, Bangladesh
| | - Harlan M. Krumholz
- Section of Cardiovascular Medicine, Dept of Medicine, Yale Univ, New Haven, CT
- Ctr for Outcomes Research & Evaluation, Yale-New Haven Hospital, New Haven, CT
| | - Wayne H-H Sheu
- Cardiovascular Research Ctr, Dept of Medicine, National Yang Ming Univ School of Medicine, Taipei, Taiwan
| | - Stephen S. Rich
- Ctr for Public Health Genomics, Univ of Virginia, Charlottesville, VA
| | - Jerome I. Rotter
- The Inst for Translational Genomics & Population Sciences, Dept of Pediatrics, The Lundquist Inst for Biomedical Innovation at Harbor-UCLA Medical Ctr, Torrance, CA
| | - Yii-der Ida Chen
- The Inst for Translational Genomics & Population Sciences, Dept of Pediatrics, The Lundquist Inst for Biomedical Innovation at Harbor-UCLA Medical Ctr, Torrance, CA
| | - Stacey Gabriel
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
| | - Eric S. Lander
- Program in Medical & Population Genetics, Broad Inst of MIT & Harvard, Cambridge, MA
- Dept of Biology, MIT, Cambridge, MA
- Dept of Systems Biology, Harvard Medical School, Boston, MA
| | - Danish Saleheen
- Dept of Medicine, Columbia Univ, New York, NY
- Ctr for Non-Communicable Diseases, Karachi, Sindh, Pakistan
| | - Sekar Kathiresan
- Ctr for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
- Cardiology Division, Dept of Medicine, Massachusetts General Hospital, Boston, MA
- Verve Therapeutics, Cambridge, MA
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Briggs SEW, Law P, East JE, Wordsworth S, Dunlop M, Houlston R, Hippisley-Cox J, Tomlinson I. Integrating genome-wide polygenic risk scores and non-genetic risk to predict colorectal cancer diagnosis using UK Biobank data: population based cohort study. BMJ 2022; 379:e071707. [PMID: 36351667 PMCID: PMC9644277 DOI: 10.1136/bmj-2022-071707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To evaluate the benefit of combining polygenic risk scores with the QCancer-10 (colorectal cancer) prediction model for non-genetic risk to identify people at highest risk of colorectal cancer. DESIGN Population based cohort study. SETTING Data from the UK Biobank study, collected between March 2006 and July 2010. PARTICIPANTS 434 587 individuals with complete data for genetics and QCancer-10 predictions were included in the QCancer-10 plus polygenic risk score modelling and validation cohorts. MAIN OUTCOME MEASURES Prediction of colorectal cancer diagnosis by genetic, non-genetic, and combined risk models. Using data from UK Biobank, six different polygenic risk scores for colorectal cancer were developed using LDpred2 polygenic risk score software, clumping, and thresholding approaches, and a model based on genome-wide significant polymorphisms. The top performing genome-wide polygenic risk score and the score containing genome-wide significant polymorphisms were combined with QCancer-10 and performance was compared with QCancer-10 alone. Case-control (logistic regression) and time-to-event (Cox proportional hazards) analyses were used to evaluate risk model performance in men and women. RESULTS Polygenic risk scores derived using the LDpred2 program performed best, with an odds ratio per standard deviation of 1.584 (95% confidence interval 1.536 to 1.633), and top age and sex adjusted C statistic of 0.733 (95% confidence interval 0.710 to 0.753) in logistic regression models in the validation cohort. Integrated QCancer-10 plus polygenic risk score models out-performed QCancer-10 alone. In men, the integrated LDpred2 model produced a C statistic of 0.730 (0.720 to 0.741) and explained variation of 28.2% (26.3 to 30.1), compared with 0.693 (0.682 to 0.704) and 21.0% (18.9 to 23.1) for QCancer-10 alone. In women, the C statistic for the integrated LDpred2 model was 0.687 (0.673 to 0.702) and explained variation was 21.0% (18.7 to 23.7), compared with 0.645 (0.631 to 0.659) and 12.4% (10.3 to 14.6) for QCancer-10 alone. In the top 20% of individuals at highest absolute risk, the sensitivity and specificity of the integrated LDpred2 models for predicting colorectal cancer diagnosis was 47.8% and 80.3% respectively in men, and 42.7% and 80.1% respectively in women, with increases in absolute risk in the top 5% of risk in men of 3.47-fold and in women of 2.77-fold compared with the median. Illustrative decision curve analysis indicated a small incremental improvement in net benefit with QCancer-10 plus polygenic risk score models compared with QCancer-10 alone. CONCLUSIONS Integrating polygenic risk scores with QCancer-10 modestly improves risk prediction over use of QCancer-10 alone. Given that QCancer-10 data can be obtained relatively easily from health records, use of polygenic risk score in risk stratified population screening for colorectal cancer currently has no clear justification. The added benefit, cost effectiveness, and acceptability of polygenic risk scores should be carefully evaluated in a real life screening setting before implementation in the general population.
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Affiliation(s)
- Sarah E W Briggs
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James E East
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sarah Wordsworth
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Julia Hippisley-Cox
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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Dardenne A, Sirmai L, Metras J, Enea D, Svrcek M, Benusiglio PR. Prédispositions génétiques au cancer gastrique et leur association au type histologique. Bull Cancer 2022; 110:512-520. [PMID: 35963792 DOI: 10.1016/j.bulcan.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 11/27/2022]
Abstract
About 5% of gastric cancers are associated with hereditary cancer syndromes. Histology is paramount in this context, as major susceptibility genes are associated with specific subtypes. Germline pathogenic variants in CDH1 and CTNNA1 cause Hereditary Diffuse Gastric Cancer (HDGC). Major advances have been made in the past ten years regarding HDGC. Penetrance estimates for diffuse cancer are now lower than previously thought, at 30-40%. Surveillance upper gastrointestinal endoscopy is now an acceptable alternative to prophylactic total gastrectomy. Indeed, its sensitivity in detecting advanced disease is satisfactory assuming it is performed by an expert and according to a specific protocol. The risk of intestinal-type gastric cancer is increased in patients with Lynch syndrome, although it is much lower than the risk of colorectal and endometrial cancer. Intestinal-type gastric cancers are also observed in excess in patients with hereditary polyposis, the main one being APC-associated familial adenomatous polyposis. The main and most clinically relevant manifestations in patients with polyposes remain colorectal and duodenal polyps and carcinomas, well ahead of gastric cancer. Finally, recent data point towards increased gastric cancer risk in hereditary breast and ovarian cancer.
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Maamari DJ, Brockman DG, Aragam K, Pelletier RC, Folkerts E, Neben CL, Okumura S, Hull LE, Philippakis AA, Natarajan P, Ellinor PT, Ng K, Zhou AY, Khera AV, Fahed AC. Clinical Implementation of Combined Monogenic and Polygenic Risk Disclosure for Coronary Artery Disease. JACC. ADVANCES 2022; 1:100068. [PMID: 36147540 PMCID: PMC9491373 DOI: 10.1016/j.jacadv.2022.100068] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND State-of-the-art genetic risk interpretation for a common complex disease such as coronary artery disease (CAD) requires assessment for both monogenic variants-such as those related to familial hypercholesterolemia-as well as the cumulative impact of many common variants, as quantified by a polygenic score. OBJECTIVES The objective of the study was to describe a combined monogenic and polygenic CAD risk assessment program and examine its impact on patient understanding and changes to clinical management. METHODS Study participants attended an initial visit in a preventive genomics clinic and a disclosure visit to discuss results and recommendations, primarily via telemedicine. Digital postdisclosure surveys and chart review evaluated the impact of disclosure. RESULTS There were 60 participants (mean age 51 years, 37% women, 72% with no known CAD), including 30 (50%) referred by their cardiologists and 30 (50%) self-referred. Two (3%) participants had a monogenic variant pathogenic for familial hypercholesterolemia, and 19 (32%) had a high polygenic score in the top quintile of the population distribution. In a postdisclosure survey, both the genetic test report (in 80% of participants) and the discussion with the clinician (in 89% of participants) were ranked as very or extremely helpful in understanding the result. Of the 42 participants without CAD, 17 or 40% had a change in management, including statin initiation, statin intensification, or coronary imaging. CONCLUSIONS Combined monogenic and polygenic assessments for CAD risk provided by preventive genomics clinics are beneficial for patients and result in changes in management in a significant portion of patients.
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Affiliation(s)
- Dimitri J. Maamari
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Deanna G. Brockman
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Krishna Aragam
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Renée C. Pelletier
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Emma Folkerts
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Leland E. Hull
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anthony A. Philippakis
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, Massachusetts, USA
| | | | - Amit V. Khera
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Verve Therapeutics, Cambridge, Massachusetts, USA
| | - Akl C. Fahed
- Center for Genomic Medicine, Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Patel AP, Dron JS, Wang M, Pirruccello JP, Ng K, Natarajan P, Lebo M, Ellinor PT, Aragam KG, Khera AV. Association of Pathogenic DNA Variants Predisposing to Cardiomyopathy With Cardiovascular Disease Outcomes and All-Cause Mortality. JAMA Cardiol 2022; 7:723-732. [PMID: 35544052 PMCID: PMC9096692 DOI: 10.1001/jamacardio.2022.0901] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Importance Pathogenic variants associated with inherited cardiomyopathy are recognized as important and clinically actionable when identified, leading some clinicians to recommend population-wide genomic screening. Objective To determine the prevalence and clinical importance of pathogenic variants associated with inherited cardiomyopathy within the context of contemporary clinical care. Design, Setting, and Participants This was a genetic association study of participants in Atherosclerosis in Risk Communities (ARIC), recruited from 1987 to 1989, with median follow-up of 27 years, and the UK Biobank, recruited from 2006 to 2010, with median follow-up of 10 years. ARIC participants were recruited from 4 sites across the US. UK Biobank participants were recruited from 22 sites across the UK. Participants in the US were of African and European ancestry; those in the UK were of African, East Asian, South Asian, and European ancestry. Statistical analyses were performed between August 1, 2021, and February 9, 2022. Exposures Rare genetic variants predisposing to inherited cardiomyopathy. Main Outcomes and Measures Pathogenicity of observed DNA sequence variants in sequenced exomes of 13 genes (ACTC1, FLNC, GLA, LMNA, MYBPC3, MYH7, MYL2, MYL3, PRKAG2, TNNI3, TNNT2, TPM1, and TTN) associated with inherited cardiomyopathies were classified by a blinded clinical geneticist per American College of Medical Genetics recommendations. Incidence of all-cause mortality, heart failure, and atrial fibrillation were determined. Cardiac magnetic resonance imaging, echocardiography, and electrocardiogram measures were assessed in a subset of participants. Results A total of 9667 ARIC participants (mean [SD] age, 54.0 [5.7] years; 4232 women [43.8%]; 2658 African [27.5%] and 7009 European [72.5%] ancestry) and 49 744 UK Biobank participants (mean [SD] age, 57.1 [8.0] years; 27 142 women [54.5%]; 1006 African [2.0%], 173 East Asian [0.3%], 939 South Asian [1.9%], and 46 449 European [93.4%] European ancestry) were included in the study. Of those, 59 participants (0.61%) in ARIC and 364 participants (0.73%) in UK Biobank harbored an actionable pathogenic or likely pathogenic variant associated with dilated or hypertrophic cardiomyopathy. Carriers of these variants were not reliably identifiable by imaging. However, the presence of these variants was associated with increased risk of heart failure (hazard ratio [HR], 1.7; 95% CI, 1.1-2.8), atrial fibrillation (HR, 2.9; 95% CI, 1.9-4.5), and all-cause mortality (HR, 1.5; 95% CI, 1.1-2.2) in ARIC. Similar risk patterns were observed in the UK Biobank. Conclusions and Relevance Results of this genetic association study suggest that approximately 0.7% of study participants harbored a pathogenic variant associated with inherited cardiomyopathy. These variant carriers would be challenging to identify within clinical practice without genetic testing but are at increased risk for cardiovascular disease and all-cause mortality.
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Affiliation(s)
- Aniruddh P Patel
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston.,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Jacqueline S Dron
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts
| | - Minxian Wang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - James P Pirruccello
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston.,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, Massachusetts
| | - Pradeep Natarajan
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston.,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Matthew Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Patrick T Ellinor
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston.,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Krishna G Aragam
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston.,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Amit V Khera
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston.,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston.,Cardiovascular Disease Initiative, Broad Institute of MIT, Harvard, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Verve Therapeutics, Cambridge, Massachusetts
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Albuquerque J, Medeiros AM, Alves AC, Bourbon M, Antunes M. Comparative study on the performance of different classification algorithms, combined with pre- and post-processing techniques to handle imbalanced data, in the diagnosis of adult patients with familial hypercholesterolemia. PLoS One 2022; 17:e0269713. [PMID: 35749402 PMCID: PMC9231719 DOI: 10.1371/journal.pone.0269713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 05/26/2022] [Indexed: 11/27/2022] Open
Abstract
Familial Hypercholesterolemia (FH) is an inherited disorder of cholesterol metabolism. Current criteria for FH diagnosis, like Simon Broome (SB) criteria, lead to high false positive rates. The aim of this work was to explore alternative classification procedures for FH diagnosis, based on different biological and biochemical indicators. For this purpose, logistic regression (LR), naive Bayes classifier (NB), random forest (RF) and extreme gradient boosting (XGB) algorithms were combined with Synthetic Minority Oversampling Technique (SMOTE), or threshold adjustment by maximizing Youden index (YI), and compared. Data was tested through a 10 × 10 repeated k-fold cross validation design. The LR model presented an overall better performance, as assessed by the areas under the receiver operating characteristics (AUROC) and precision-recall (AUPRC) curves, and several operating characteristics (OC), regardless of the strategy to cope with class imbalance. When adopting either data processing technique, significantly higher accuracy (Acc), G-mean and F1 score values were found for all classification algorithms, compared to SB criteria (p < 0.01), revealing a more balanced predictive ability for both classes, and higher effectiveness in classifying FH patients. Adjustment of the cut-off values through pre or post-processing methods revealed a considerable gain in sensitivity (Sens) values (p < 0.01). Although the performance of pre and post-processing strategies was similar, SMOTE does not cause model’s parameters to loose interpretability. These results suggest a LR model combined with SMOTE can be an optimal approach to be used as a widespread screening tool.
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Affiliation(s)
- João Albuquerque
- Departamento de Biomedicina, Unidade de Bioquímica, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
- Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
- * E-mail:
| | - Ana Margarida Medeiros
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
- Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Catarina Alves
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
- Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mafalda Bourbon
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
- Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Marília Antunes
- Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Estatística e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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39
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Bellows BK, Khera AV, Zhang Y, Ruiz-Negrón N, Stoddard HM, Wong JB, Kazi DS, de Ferranti SD, Moran AE. Estimated Yield of Screening for Heterozygous Familial Hypercholesterolemia With and Without Genetic Testing in US Adults. J Am Heart Assoc 2022; 11:e025192. [PMID: 35583136 PMCID: PMC9238728 DOI: 10.1161/jaha.121.025192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Heterozygous familial hypercholesterolemia (FH) is a common genetic disorder causing premature cardiovascular disease. Despite this, there is no national screening program in the United States to identify individuals with FH or likely pathogenic FH genetic variants. Methods and Results The clinical characteristics and FH variant status of 49 738 UK Biobank participants were used to develop a regression model to predict the probability of having any FH variants. The regression model and modified Dutch Lipid Clinic Network criteria were applied to 39 790 adult participants (aged ≥20 years) in the National Health and Nutrition Examination Survey to estimate the yield of FH screening programs using Dutch Lipid Clinic Network clinical criteria alone (excluding genetic variant status), genetic testing alone, or combining clinical criteria with genetic testing. The regression model accurately predicted FH variant status in UK Biobank participants (observed prevalence, 0.27%; predicted, 0.26%; area under the receiver-operator characteristic curve, 0.88). In the National Health and Nutrition Examination Survey, the estimated yield per 1000 individuals screened (95% CI) was 3.7 (3.0-4.6) FH cases with the Dutch Lipid Clinic Network clinical criteria alone, 3.8 (2.7-5.1) cases with genetic testing alone, and 6.6 (5.3-8.0) cases by combining clinical criteria with genetic testing. In young adults aged 20 to 39 years, using clinical criteria alone was estimated to yield 1.3 (95% CI, 0.6-2.5) FH cases per 1000 individuals screened, which was estimated to increase to 4.2 (95% CI, 2.6-6.4) FH cases when combining clinical criteria with genetic testing. Conclusions Screening for FH using a combination of clinical criteria with genetic testing may increase identification and the opportunity for early treatment of individuals with FH.
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Affiliation(s)
| | - Amit V Khera
- Center for Genomic Medicine Massachusetts General Hospital Boston MA.,Cardiovascular Disease Initiative Broad Institute of MIT and Harvard Cambridge MA.,Department of Medicine Harvard Medical School Boston MA
| | - Yiyi Zhang
- Department of Medicine Columbia University New York NY
| | | | | | - John B Wong
- Department of Medicine Tufts Medical Center Boston MA
| | - Dhruv S Kazi
- Department of Medicine Harvard Medical School Boston MA.,Richard A. and Susan F. Smith Center for Outcomes Research in Cardiology Beth Israel Deaconess Medical Center Boston MA
| | - Sarah D de Ferranti
- Department of Pediatrics Harvard Medical School Boston MA.,Department of Cardiology Boston Children's Hospital Boston MA
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40
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Smail C, Ferraro NM, Hui Q, Durrant MG, Aguirre M, Tanigawa Y, Keever-Keigher MR, Rao AS, Justesen JM, Li X, Gloudemans MJ, Assimes TL, Kooperberg C, Reiner AP, Huang J, O'Donnell CJ, Sun YV, Rivas MA, Montgomery SB. Integration of rare expression outlier-associated variants improves polygenic risk prediction. Am J Hum Genet 2022; 109:1055-1064. [PMID: 35588732 PMCID: PMC9247823 DOI: 10.1016/j.ajhg.2022.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/25/2022] [Indexed: 11/28/2022] Open
Abstract
Polygenic risk scores (PRSs) quantify the contribution of multiple genetic loci to an individual's likelihood of a complex trait or disease. However, existing PRSs estimate this likelihood with common genetic variants, excluding the impact of rare variants. Here, we report on a method to identify rare variants associated with outlier gene expression and integrate their impact into PRS predictions for body mass index (BMI), obesity, and bariatric surgery. Between the top and bottom 10%, we observed a 20.8% increase in risk for obesity (p = 3 × 10-14), 62.3% increase in risk for severe obesity (p = 1 × 10-6), and median 5.29 years earlier onset for bariatric surgery (p = 0.008), as a function of expression outlier-associated rare variant burden when controlling for common variant PRS. We show that these predictions were more significant than integrating the effects of rare protein-truncating variants (PTVs), observing a mean 19% increase in phenotypic variance explained with expression outlier-associated rare variants when compared with PTVs (p = 2 × 10-15). We replicated these findings by using data from the Million Veteran Program and demonstrated that PRSs across multiple traits and diseases can benefit from the inclusion of expression outlier-associated rare variants identified through population-scale transcriptome sequencing.
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Affiliation(s)
- Craig Smail
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA; Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA.
| | - Nicole M Ferraro
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Qin Hui
- Atlanta VA Health Care System, Decatur, GA, USA; Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Matthew G Durrant
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Aguirre
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Marissa R Keever-Keigher
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - Abhiram S Rao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Johanne M Justesen
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Xin Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Michael J Gloudemans
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Themistocles L Assimes
- Palo Alto VA Health Care System, Palo Alto, CA, USA; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Jie Huang
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Christopher J O'Donnell
- Boston VA Health Care System, Boston, MA, USA; Division of Cardiology, Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Cardiology, Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Yan V Sun
- Atlanta VA Health Care System, Decatur, GA, USA; Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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Edwards P, Monahan KJ. Diagnosis and management of Lynch syndrome. Frontline Gastroenterol 2022; 13:e80-e87. [PMID: 35812033 PMCID: PMC9234730 DOI: 10.1136/flgastro-2022-102123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
Lynch syndrome (LS) is a dominantly inherited cancer susceptibility syndrome defined by presence of pathogenic variants in DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2, or in deletions of the EPCAM gene. Although LS is present in about 1 in 400 people in the UK, it estimated that only 5% of people with this condition are aware of the diagnosis. Therefore, testing for LS in all new diagnoses of colorectal or endometrial cancers is now recommended in the UK, and gastroenterologists can offer 'mainstreamed' genetic testing for LS to patients with cancer. Because LS results in a high lifetime risk of colorectal, endometrial, gastric, ovarian, hepatobiliary, brain and other cancers, the lifelong care of affected individuals and their families requires a coordinated multidisciplinary approach. Interventions such as high-quality 2-yearly colonoscopy, prophylactic gynaecological surgery, and aspirin are proven to prevent and facilitate early diagnosis and prevention of cancers in this population, and improve patient outcomes. Recently, an appreciation of the mechanism of carcinogenesis in LS-associated cancers has contributed to the development of novel therapeutic and diagnostic approaches, with a gene-specific approach to disease management, with potential cancer-preventing vaccines in development. An adaptive approach to surgical or oncological management of LS-related cancers may be considered, including an important role for novel checkpoint inhibitor immunotherapy in locally advanced or metastatic disease. Therefore, a personalised approach to lifelong gene-specific management for people with LS provides many opportunities for cancer prevention and treatment which we outline in this review.
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Affiliation(s)
- Penelope Edwards
- Gastrointestinal and Lymphoma Units, Royal Marsden NHS Foundation Trust, London, UK
| | - Kevin J Monahan
- Lynch Syndrome Clinic, The Centre for Familial Intestinal Cancer, St Marks Hospital, London, UK,Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
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42
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Elhanan G, Kiser D, Neveux I, Dabe S, Bolze A, Metcalf WJ, Lu JT, Grzymski JJ. Incomplete Penetrance of Population-Based Genetic Screening Results in Electronic Health Record. Front Genet 2022; 13:866169. [PMID: 35571025 PMCID: PMC9091193 DOI: 10.3389/fgene.2022.866169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/31/2022] [Indexed: 11/23/2022] Open
Abstract
The clinical value of population-based genetic screening projects depends on the actions taken on the findings. The Healthy Nevada Project (HNP) is an all-comer genetic screening and research project based in northern Nevada. HNP participants with CDC Tier 1 findings of hereditary breast and ovarian cancer syndrome (HBOC), Lynch syndrome (LS), or familial hypercholesterolemia (FH) are notified and provided with genetic counseling. However, the HNP subsequently takes a “hands-off” approach: it is the responsibility of notified participants to share their findings with their healthcare providers, and providers are expected to implement the recommended action plans. Thus, the HNP presents an opportunity to evaluate the efficiency of participant and provider responses to notification of important genetic findings, using electronic health records (EHRs) at Renown Health (a large regional hospital in northern Nevada). Out of 520 HNP participants with findings, we identified 250 participants who were notified of their findings and who had an EHR. 107 of these participants responded to a survey, with 76 (71%) indicating that they had shared their findings with their healthcare providers. However, a sufficiently specific genetic diagnosis appeared in the EHRs and problem lists of only 22 and 10%, respectively, of participants without prior knowledge. Furthermore, review of participant EHRs provided evidence of possible relevant changes in clinical care for only a handful of participants. Up to 19% of participants would have benefited from earlier screening due to prior presentation of their condition. These results suggest that continuous support for both participants and their providers is necessary to maximize the benefit of population-based genetic screening. We recommend that genetic screening projects require participants’ consent to directly document their genetic findings in their EHRs. Additionally, we recommend that they provide healthcare providers with ongoing training regarding documentation of findings and with clinical decision support regarding subsequent care.
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Affiliation(s)
- Gai Elhanan
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | - Daniel Kiser
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | | | | | - William J. Metcalf
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | | | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
- Renown Health, Reno, NV, United States
- *Correspondence: Joseph J. Grzymski,
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43
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Clarke SL, Tcheandjieu C, Hilliard AT, Lee KM, Lynch J, Chang KM, Miller D, Knowles JW, O’Donnell C, Tsao P, Rader DJ, Wilson PW, Sun YV, Gaziano M, Assimes TL. Coronary Artery Disease Risk of Familial Hypercholesterolemia Genetic Variants Independent of Clinically Observed Longitudinal Cholesterol Exposure. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003501. [PMID: 35143253 PMCID: PMC10593360 DOI: 10.1161/circgen.121.003501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/17/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) genetic variants confer risk for coronary artery disease independent of LDL-C (low-density lipoprotein cholesterol) when considering a single measurement. In real clinical settings, longitudinal LDL-C data are often available through the electronic health record. It is unknown whether genetic testing for FH variants provides additional risk-stratifying information once longitudinal LDL-C is considered. METHODS We used the extensive electronic health record data available through the Million Veteran Program to conduct a nested case-control study. The primary outcome was coronary artery disease, derived from electronic health record codes for acute myocardial infarction and coronary revascularization. Incidence density sampling was used to match case/control exposure windows, defined by the date of the first LDL-C measurement to the date of the first coronary artery disease code of the index case. Adjustments for the first, maximum, or mean LDL-C were analyzed. FH variants in LDLR, APOB, and PCSK9 (Proprotein convertase subtilisin/kexin type 9) were assessed by custom genotype array. RESULTS In a cohort of 23 091 predominantly prevalent cases at enrollment and 230 910 matched controls, FH variant carriers had an increased risk for coronary artery disease (odds ratio [OR], 1.53 [95% CI, 1.24-1.89]). Adjusting for mean LDL-C led to the greatest attenuation of the risk estimate, but significant risk remained (odds ratio, 1.33 [95% CI, 1.08-1.64]). The degree of attenuation was not affected by the number and the spread of LDL-C measures available. CONCLUSIONS The risk associated with carrying an FH variant cannot be fully captured by the LDL-C data available in the electronic health record, even when considering multiple LDL-C measurements spanning more than a decade.
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Affiliation(s)
- Shoa L. Clarke
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
| | - Austin T. Hilliard
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
| | - Kyung Min Lee
- VA Informatics & Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT
| | - Julie Lynch
- VA Informatics & Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT
- College of Nursing & Health Sciences, Univ of Massachusetts, Boston, MA
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
- Dept of Medicine, Univ of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Donald Miller
- Edith Nourse Rogers Memorial VA Hospital, Bedford, MA
- Center for Population Health, Univ of Massachusetts, Lowell, MA
| | - Joshua W. Knowles
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
- Diabetes Research Center, Stanford Univ School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford Univ School of Medicine, Stanford, CA
| | - Christopher O’Donnell
- VA Boston Healthcare System, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
| | - Phil Tsao
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford Univ School of Medicine, Stanford, CA
| | - Daniel J. Rader
- Dept of Medicine, Univ of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Peter W. Wilson
- Atlanta VA Medical Center, Decatur, GA
- Dept of Medicine, Emory Univ School of Medicine, Atlanta, GA
- Dept of Epidemiology, Emory Univ Rollins School of Public Health, Atlanta, GA
| | - Yan V. Sun
- Atlanta VA Medical Center, Decatur, GA
- Dept of Epidemiology, Emory Univ Rollins School of Public Health, Atlanta, GA
| | | | - Themistocles L. Assimes
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford Univ School of Medicine, Stanford, CA
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44
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Fahed AC, Wang M, Patel AP, Ajufo E, Maamari DJ, Aragam KG, Brockman DG, Vosburg T, Ellinor PT, Ng K, Khera AV. Association of the Interaction Between Familial Hypercholesterolemia Variants and Adherence to a Healthy Lifestyle With Risk of Coronary Artery Disease. JAMA Netw Open 2022; 5:e222687. [PMID: 35294538 PMCID: PMC8928007 DOI: 10.1001/jamanetworkopen.2022.2687] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
IMPORTANCE Familial hypercholesterolemia variants impair clearance of cholesterol from the circulation and increase risk of coronary artery disease (CAD). The extent to which adherence to a healthy lifestyle is associated with a lower risk of CAD in carriers and noncarriers of variants warrants further study. OBJECTIVE To assess the association of the interaction between familial hypercholesterolemia variants and adherence to a healthy lifestyle with risk of CAD. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study used 2 independent data sets with gene sequencing and lifestyle data from the UK Biobank: a case-control study of 4896 cases and 5279 controls and a cohort study of 39 920 participants. Participants were recruited from 22 sites across the UK between March 21, 2006, and October 1, 2010. The case-control study included participants with CAD and controls at enrollment. The cohort study used a convenience sample of individuals with available gene sequencing data. Statistical analysis was performed from April 2, 2019, to January 20, 2022. EXPOSURES Pathogenic or likely pathogenic DNA variants classified by a clinical laboratory geneticist and adherence to a healthy lifestyle based on a 4-point scoring system (1 point for each of the following: healthy diet, regular exercise, not smoking, and absence of obesity). MAIN OUTCOMES AND MEASURES Coronary artery disease, defined as myocardial infarction in the case-control study, and myocardial infarction, ischemic heart disease, or coronary revascularization procedure in the cohort study. RESULTS The case-control study included 10 175 participants (6828 men [67.1%]; mean [SD] age, 58.6 [7.2] years), and the cohort study included 39 920 participants (18 802 men [47.1%]; mean [SD] age at the end of follow-up, 66.4 [8.0] years). A variant was identified in 35 of 4896 cases (0.7%) and 12 of 5279 controls (0.2%), corresponding to an odds ratio of 3.0 (95% CI, 1.6-5.9), and a variant was identified in 108 individuals (0.3%) in the cohort study, in which the hazard ratio for CAD was 3.8 (95% CI, 2.5-5.8). However, this risk appeared to vary according to lifestyle categories in both carriers and noncarriers of familial hypercholesterolemia variants, without a significant interaction between carrier status and lifestyle (odds ratio, 1.2 [95% CI, 0.6-2.5]; P = .62). Among carriers, a favorable lifestyle conferred 86% lower risk of CAD compared with an unfavorable lifestyle (hazard ratio, 0.14 [95% CI, 0.04-0.41]). The estimated risk of CAD by the age of 75 years varied according to lifestyle, ranging from 10.2% among noncarriers with a favorable lifestyle to 24.0% among noncarriers with an unfavorable lifestyle and ranging from 34.5% among carriers with a favorable lifestyle to 66.2% among carriers with an unfavorable lifestyle. CONCLUSIONS AND RELEVANCE This study suggests that, among carriers and noncarriers of a familial hypercholesterolemia variant, significant gradients in risk of CAD are noted according to adherence to a healthy lifestyle pattern. Similar to the general population, individuals who carry familial hypercholesterolemia variants are likely to benefit from lifestyle interventions to reduce their risk of CAD.
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Affiliation(s)
- Akl C. Fahed
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Minxian Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aniruddh P. Patel
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ezimamaka Ajufo
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, UT Southwestern Medical Center, Dallas, Houston, Texas
| | - Dimitri J. Maamari
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Krishna G. Aragam
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Deanna G. Brockman
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Trish Vosburg
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Patrick T. Ellinor
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, Massachusetts
| | - Amit V. Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, UT Southwestern Medical Center, Dallas, Houston, Texas
- Verve Therapeutics, Cambridge, Massachusetts
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Shah SM, Demidova EV, Lesh RW, Hall MJ, Daly MB, Meyer JE, Edelman MJ, Arora S. Therapeutic implications of germline vulnerabilities in DNA repair for precision oncology. Cancer Treat Rev 2022; 104:102337. [PMID: 35051883 PMCID: PMC9016579 DOI: 10.1016/j.ctrv.2021.102337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022]
Abstract
DNA repair vulnerabilities are present in a significant proportion of cancers. Specifically, germline alterations in DNA repair not only increase cancer risk but are associated with treatment response and clinical outcomes. The therapeutic landscape of cancer has rapidly evolved with the FDA approval of therapies that specifically target DNA repair vulnerabilities. The clinical success of synthetic lethality between BRCA deficiency and poly(ADP-ribose) polymerase (PARP) inhibition has been truly revolutionary. Defective mismatch repair has been validated as a predictor of response to immune checkpoint blockade associated with durable responses and long-term benefit in many cancer patients. Advances in next generation sequencing technologies and their decreasing cost have supported increased genetic profiling of tumors coupled with germline testing of cancer risk genes in patients. The clinical adoption of panel testing for germline assessment in high-risk individuals has generated a plethora of genetic data, particularly on DNA repair genes. Here, we highlight the therapeutic relevance of germline aberrations in DNA repair to identify patients eligible for precision treatments such as PARP inhibitors (PARPis), immune checkpoint blockade, chemotherapy, radiation therapy and combined treatment. We also discuss emerging mechanisms that regulate DNA repair.
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Affiliation(s)
- Shreya M. Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States,Science Scholars Program, Temple University, Philadelphia, PA, United States
| | - Elena V. Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States,Kazan Federal University, Kazan, Russian Federation
| | - Randy W. Lesh
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States,Geisinger Commonwealth School of Medicine, Scranton, PA, United States
| | - Michael J. Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States,Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Mary B. Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States,Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Joshua E. Meyer
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Martin J. Edelman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States,Correspondence: Sanjeevani Arora, PhD, Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497, OR Martin J Edelman, MD, Department of Hematology/Oncology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497,
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
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46
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Rosman N, Nawawi HM, Al-Khateeb A, Chua YA, Chua AL. Development of an Optimized Tetra-Amplification Refractory Mutation System PCR for Detection of 12 Pathogenic Familial Hypercholesterolemia Variants in the Asian Population. J Mol Diagn 2022; 24:120-130. [PMID: 35074074 DOI: 10.1016/j.jmoldx.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/03/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Early detection of genetic diseases such as familial hypercholesterolemia (FH), and the confirmation of related pathogenic variants, are crucial in reducing the risk for premature coronary artery disease. Currently, next-generation sequencing is used for detecting FH-related candidate genes but is expensive and time-consuming. There is a lack of kits suitable for the detection of the common FH-related variants in the Asia-Pacific region. Thus, this study addressed that need with the development of an optimized tetra-amplification mutation system (T-ARMS) PCR-based assay for the detection of 12 pathogenic variants of FH in the Asian population. The two important parameters for T-ARMS PCR assay performance-annealing temperature and the ratio of outer/inner primer concentrations-were optimized in this study. The optimal annealing temperature of all 12 T-ARMS PCR reactions was 64.6°C. The ideal ratios of outer/inner primer concentrations with each pathogenic variant were: A1, 1:2; A2, 1:4; L1, 1:10; L2, 1:1; L3, 1:2; L4, 1:8; L5, 1:1; L6, 1:2; L7, 1:8; L8, 1:8; L9, 1:2; and L10, 1:8. The lowest limit of detection using DNA extracted from patients was 0.1 ng. The present article highlights the beneficial findings on T-ARMS PCR as part of the development of a PCR-based detection kit for use in detecting FH in economically developing countries in Asia with a greater prevalence of FH.
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Affiliation(s)
- Norhidayah Rosman
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Hapizah M Nawawi
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Alyaa Al-Khateeb
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Yung-An Chua
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Ang-Lim Chua
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
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47
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Albuquerque J, Medeiros AM, Alves AC, Bourbon M, Antunes M. Performance comparison of different classification algorithms applied to the diagnosis of familial hypercholesterolemia in paediatric subjects. Sci Rep 2022; 12:1164. [PMID: 35064162 PMCID: PMC8782861 DOI: 10.1038/s41598-022-05063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/28/2021] [Indexed: 12/03/2022] Open
Abstract
Familial Hypercholesterolemia (FH) is an inherited disorder of lipid metabolism, characterized by increased low density lipoprotein cholesterol (LDLc) levels. The main purpose of the current work was to explore alternative classification methods to traditional clinical criteria for FH diagnosis, based on several biochemical and biological indicators. Logistic regression (LR), decision tree (DT), random forest (RF) and naive Bayes (NB) algorithms were developed for this purpose, and thresholds were optimized by maximization of Youden index (YI). All models presented similar accuracy (Acc), specificity (Spec) and positive predictive values (PPV). Sensitivity (Sens) and G-mean values were significantly higher in LR and RF models, compared to the DT. When compared to Simon Broome (SB) biochemical criteria for FH diagnosis, all models presented significantly higher Acc, Spec and G-mean values (p < 0.01), and lower negative predictive value (NPV, p < 0.05). Moreover, LR and RF models presented comparable Sens values. Adjustment of the cut-off point by maximizing YI significantly increased Sens values, with no significant loss in Acc. The obtained results suggest such classification algorithms can be a viable alternative to be used as a widespread screening method. An online application has been developed to assess the performance of the LR model in a wider population.
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Affiliation(s)
- João Albuquerque
- Departamento de Biomedicina, Unidade de Bioquímica, Faculdade de Medicina, Universidade do Porto, 4200-319, Porto, Portugal.
- Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
| | - Ana Margarida Medeiros
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal
- Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Ana Catarina Alves
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal
- Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Mafalda Bourbon
- Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisboa, Portugal
- Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Marília Antunes
- Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
- Departamento de Estatística e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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48
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Haas ME, Pirruccello JP, Friedman SN, Wang M, Emdin CA, Ajmera VH, Simon TG, Homburger JR, Guo X, Budoff M, Corey KE, Zhou AY, Philippakis A, Ellinor PT, Loomba R, Batra P, Khera AV. Machine learning enables new insights into genetic contributions to liver fat accumulation. CELL GENOMICS 2021; 1:100066. [PMID: 34957434 PMCID: PMC8699145 DOI: 10.1016/j.xgen.2021.100066] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Excess liver fat, called hepatic steatosis, is a leading risk factor for end-stage liver disease and cardiometabolic diseases but often remains undiagnosed in clinical practice because of the need for direct imaging assessments. We developed an abdominal MRI-based machine-learning algorithm to accurately estimate liver fat (correlation coefficients, 0.97-0.99) from a truth dataset of 4,511 middle-aged UK Biobank participants, enabling quantification in 32,192 additional individuals. 17% of participants had predicted liver fat levels indicative of steatosis, and liver fat could not have been reliably estimated based on clinical factors such as BMI. A genome-wide association study of common genetic variants and liver fat replicated three known associations and identified five newly associated variants in or near the MTARC1, ADH1B, TRIB1, GPAM, and MAST3 genes (p < 3 × 10-8). A polygenic score integrating these eight genetic variants was strongly associated with future risk of chronic liver disease (hazard ratio > 1.32 per SD score, p < 9 × 10-17). Rare inactivating variants in the APOB or MTTP genes were identified in 0.8% of individuals with steatosis and conferred more than 6-fold risk (p < 2 × 10-5), highlighting a molecular subtype of hepatic steatosis characterized by defective secretion of apolipoprotein B-containing lipoproteins. We demonstrate that our imaging-based machine-learning model accurately estimates liver fat and may be useful in epidemiological and genetic studies of hepatic steatosis.
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Affiliation(s)
- Mary E. Haas
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Molecular Biology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James P. Pirruccello
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Medicine, Harvard Medical School, Boston, MA 02114, USA,Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Machine Learning for Health, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samuel N. Friedman
- Machine Learning for Health, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Minxian Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Connor A. Emdin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Veeral H. Ajmera
- NAFLD Research Center, Department of Medicine, University of California San Diego, La Jolla, CA 92103, USA
| | - Tracey G. Simon
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA,Liver Center, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Xiuqing Guo
- The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Matthew Budoff
- The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kathleen E. Corey
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA,Liver Center, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Anthony Philippakis
- Machine Learning for Health, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Medicine, Harvard Medical School, Boston, MA 02114, USA,Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Machine Learning for Health, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rohit Loomba
- NAFLD Research Center, Department of Medicine, University of California San Diego, La Jolla, CA 92103, USA
| | - Puneet Batra
- Machine Learning for Health, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit V. Khera
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston, MA 02114, USA,Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Machine Learning for Health, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Corresponding author
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49
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Marquina C, Lacaze P, Tiller J, Riaz M, Sturm AC, Nelson MR, Ference BA, Pang J, Watts GF, Nicholls SJ, Zoungas S, Liew D, McNeil J, Ademi Z. Population genomic screening of young adults for familial hypercholesterolaemia: a cost-effectiveness analysis. Eur Heart J 2021; 43:3243-3254. [PMID: 34788414 DOI: 10.1093/eurheartj/ehab770] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/29/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022] Open
Abstract
AIMS The aim of this study was to assess the impact and cost-effectiveness of offering population genomic screening to all young adults in Australia to detect heterozygous familial hypercholesterolaemia (FH). METHODS AND RESULTS We designed a decision analytic Markov model to compare the current standard of care for heterozygous FH diagnosis in Australia (opportunistic cholesterol screening and genetic cascade testing) with the alternate strategy of population genomic screening of adults aged 18-40 years to detect pathogenic variants in the LDLR/APOB/PCSK9 genes. We used a validated cost-adaptation method to adapt findings to eight high-income countries. The model captured coronary heart disease (CHD) morbidity/mortality over a lifetime horizon, from healthcare and societal perspectives. Risk of CHD, treatment effects, prevalence, and healthcare costs were estimated from published studies. Outcomes included quality-adjusted life years (QALYs), costs and incremental cost-effectiveness ratio (ICER), discounted 5% annually. Sensitivity analyses were undertaken to explore the impact of key input parameters on the robustness of the model. Over the lifetime of the population (4 167 768 men; 4 129 961 women), the model estimated a gain of 33 488years of life lived and 51 790 QALYs due to CHD prevention. Population genomic screening for FH would be cost-effective from a healthcare perspective if the per-test cost was ≤AU$250, yielding an ICER of <AU$28 000 per QALY gained. From a societal perspective, population genomic screening would be cost-saving. ICERs from societal perspective remained cost-saving after adaptation to other countries. CONCLUSION Based on our model, offering population genomic screening to all young adults for FH could be cost-effective, at testing costs that are feasible.
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Affiliation(s)
- Clara Marquina
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Paul Lacaze
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Jane Tiller
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Moeen Riaz
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Amy C Sturm
- Genomic Medicine Institute, 100 North Academy Avenue, Geisinger, PA 17822, USA
| | - Mark R Nelson
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia.,Menzies Institute for Medical Research, 17 Liverpool St, Hobart, TAS 7000, Australia
| | - Brian A Ference
- University of Cambridge, Centre for Naturally Randomised Trials, The Old Schools, Trinity Ln, Cambridge CB2 1TN, UK
| | - Jing Pang
- School of Medicine, Faculty of Health and Medical Sciences, University of Western Australia, 35 Stirling Hwy, Perth, WA 6009, Australia
| | - Gerald F Watts
- School of Medicine, Faculty of Health and Medical Sciences, University of Western Australia, 35 Stirling Hwy, Perth, WA 6009, Australia.,Lipid Disorders Clinic, Cardiometabolic Service, Department of Cardiology, Royal Perth Hospital, Victoria Square, Perth, WA 6000, Australia.,Lipid Disorders Clinic, Cardiometabolic Service, Department of Internal Medicine, Royal Perth Hospital, Victoria Square, Perth, WA 6000, Australia
| | - Stephen J Nicholls
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Sophia Zoungas
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Danny Liew
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - John McNeil
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
| | - Zanfina Ademi
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia
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50
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Sun TH, Shao YHJ, Mao CL, Hung MN, Lo YY, Ko TM, Hsiao TH. A Novel Quality-Control Procedure to Improve the Accuracy of Rare Variant Calling in SNP Arrays. Front Genet 2021; 12:736390. [PMID: 34764980 PMCID: PMC8577504 DOI: 10.3389/fgene.2021.736390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Single-nucleotide polymorphism (SNP) arrays are an ideal technology for genotyping genetic variants in mass screening. However, using SNP arrays to detect rare variants [with a minor allele frequency (MAF) of <1%] is still a challenge because of noise signals and batch effects. An approach that improves the genotyping quality is needed for clinical applications. Methods: We developed a quality-control procedure for rare variants which integrates different algorithms, filters, and experiments to increase the accuracy of variant calling. Using data from the TWB 2.0 custom Axiom array, we adopted an advanced normalization adjustment to prevent false calls caused by splitting the cluster and a rare het adjustment which decreases false calls in rare variants. The concordance of allelic frequencies from array data was compared to those from sequencing datasets of Taiwanese. Finally, genotyping results were used to detect familial hypercholesterolemia (FH), thrombophilia (TH), and maturity-onset diabetes of the young (MODY) to assess the performance in disease screening. All heterozygous calls were verified by Sanger sequencing or qPCR. The positive predictive value (PPV) of each step was estimated to evaluate the performance of our procedure. Results: We analyzed SNP array data from 43,433 individuals, which interrogated 267,247 rare variants. The advanced normalization and rare het adjustment methods adjusted genotyping calling of 168,134 variants (96.49%). We further removed 3916 probesets which were discordant in MAFs between the SNP array and sequencing data. The PPV for detecting pathogenic variants with 0.01%10,000 are available. The results demonstrated our procedure could perform correct genotype calling of rare variants. It provides a solution of pathogenic variant detection through SNP array. The approach brings tremendous promise for implementing precision medicine in medical practice.
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Affiliation(s)
- Ting-Hsuan Sun
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Hsuan Joni Shao
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chien-Lin Mao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Miao-Neng Hung
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yi-Yun Lo
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tai-Ming Ko
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Research Center for Biomedical Science and Engineering, National Tsing Hua University, Hsinchu, Taiwan
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