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Wolf SM, Green RC. Return of Results in Genomic Research Using Large-Scale or Whole Genome Sequencing: Toward a New Normal. Annu Rev Genomics Hum Genet 2023; 24:393-414. [PMID: 36913714 PMCID: PMC10497726 DOI: 10.1146/annurev-genom-101122-103209] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Genome sequencing is increasingly used in research and integrated into clinical care. In the research domain, large-scale analyses, including whole genome sequencing with variant interpretation and curation, virtually guarantee identification of variants that are pathogenic or likely pathogenic and actionable. Multiple guidelines recommend that findings associated with actionable conditions be offered to research participants in order to demonstrate respect for autonomy, reciprocity, and participant interests in health and privacy. Some recommendations go further and support offering a wider range of findings, including those that are not immediately actionable. In addition, entities covered by the US Health Insurance Portability and Accountability Act (HIPAA) may be required to provide a participant's raw genomic data on request. Despite these widely endorsed guidelines and requirements, the implementation of return of genomic results and data by researchers remains uneven. This article analyzes the ethical and legal foundations for researcher duties to offer adult participants their interpreted results and raw data as the new normal in genomic research.
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Affiliation(s)
- Susan M Wolf
- Law School and Medical School, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Robert C Green
- Genomes2People Research Program, Harvard Medical School, Mass General Brigham, Broad Institute, and Ariadne Labs, Boston, Massachusetts, USA;
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2
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Lynch MT, Maloney KA, Xu H, Perry JA, Center RG, Shuldiner AR, Mitchell BD. Associations of genome-wide and regional autozygosity with 96 complex traits in old order Amish. BMC Genomics 2023; 24:134. [PMID: 36941539 PMCID: PMC10029202 DOI: 10.1186/s12864-023-09208-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Autozygosity, the proportion of the genome that is homozygous by descent, has been associated with variation in multiple health-related traits impacting evolutionary fitness. Autozygosity (FROH) is typically measured from runs of homozygosity (ROHs) that arise when identical-by-descent (IBD) haplotypes are inherited from each parent. Population isolates with a small set of common founders have elevated autozygosity relative to outbred populations. METHODS In this study, we examined whether degree of autozygosity was associated with variation in 96 cardiometabolic traits among 7221 Old Order Amish individuals residing in Lancaster County, PA. We estimated the average length of an ROH segment to be 6350 KB, with each individual having on average 17.2 segments 1.5 KB or larger. Measurements of genome-wide and regional FROH were used as the primary predictors of trait variation in association analysis. RESULTS In genome-wide FROH analysis, we did not identify any associations that withstood Bonferroni-correction (p = 0.0005). However, on regional FROH analysis, we identified associations exceeding genome-wide thresholds for two traits: serum bilirubin levels, which were significantly associated with a region on chromosome 2 localized to a region surrounding UGT1A10 (p = 1 × 10- 43), and HbA1c levels, which were significantly associated with a region on chromosome 8 localized near CHRNB3 (p = 8 × 10- 10). CONCLUSIONS These analyses highlight the potential value of autozygosity mapping in founder populations.
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Affiliation(s)
- Megan T Lynch
- Department of Medicine Baltimore, University of Maryland School of Medicine, Maryland, MD, USA.
- University of Maryland School of Medicine, Program for Personalized and Genomic Medicine, Baltimore, MD, USA.
| | - Kristin A Maloney
- Department of Medicine Baltimore, University of Maryland School of Medicine, Maryland, MD, USA
- University of Maryland School of Medicine, Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Huichun Xu
- Department of Medicine Baltimore, University of Maryland School of Medicine, Maryland, MD, USA
- University of Maryland School of Medicine, Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - James A Perry
- Department of Medicine Baltimore, University of Maryland School of Medicine, Maryland, MD, USA
- University of Maryland School of Medicine, Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | | | | | - Braxton D Mitchell
- Department of Medicine Baltimore, University of Maryland School of Medicine, Maryland, MD, USA
- University of Maryland School of Medicine, Program for Personalized and Genomic Medicine, Baltimore, MD, USA
- Baltimore Veterans Administration Medical Center Geriatrics Research and Education Clinical Center, Baltimore, MD, USA
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Ehrenberg S, Walsh Vockley C, Heiman P, Ammous Z, Wenger O, Vockley J, Ghaloul-Gonzalez L. Natural history of propionic acidemia in the Amish population. Mol Genet Metab Rep 2022; 33:100936. [PMID: 36393899 PMCID: PMC9647228 DOI: 10.1016/j.ymgmr.2022.100936] [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: 07/13/2022] [Revised: 10/25/2022] [Accepted: 10/30/2022] [Indexed: 11/07/2022] Open
Abstract
Propionic acidemia (PA) in the Amish is caused by a homozygous pathogenic variant (c.1606A>G; p.Asn536Asp) in the PCCB gene. Amish patients can have borderline or normal newborn screening (NBS) results and symptoms can present at any time from early childhood to mid-adulthood. Early diagnosis and initiation of treatment for PA in the non-Amish population improves patient outcomes. Here, we present data from a retrospective chart review of Amish patients diagnosed with PA from three different medical centers in order to document its natural history in the Amish and determine the influence of treatment on outcomes in this population. A total of 38 patients with average current age 19.9 years (range 4y-45y), 57.9% males, were enrolled in the study. Fourteen patients (36.8%) were diagnosed with a positive newborn screening (NBS) while 24 patients (63.2%) had negative or inconclusive NBS or had no record of NBS in their charts. These 24 patients were diagnosed by screening after a family member was diagnosed with PA (14; 58.3%), following a hospitalization for metabolic acidosis (5; 20.8%), hospitalization for seizures (3; 12.5%) or via cord blood (2; 8.3%). The majority of patients were prescribed a protein restricted diet (32; 84.2%), including metabolic formula (29; 76.3%). Most were treated with carnitine (35; 92.1%), biotin (2; 76.3%) and/or Coenzyme Q10 (16; 42.1%). However, treatment adherence varied widely among patients, with 7 (24.1%) of the patients prescribed metabolic formula reportedly nonadherent. Cardiomyopathy was the most prevalent finding (22; 63.2%), followed by developmental delay/intellectual disability (15; 39.5%), long QT (14; 36.8%), seizures (12; 31.6%), failure to thrive (4; 10.5%), and basal ganglia strokes (3; 7.9%). No difference in outcome was obvious for those diagnosed by NBS and treated early with dietary and supplement management, especially for cardiomyopathy. However, this is a limited retrospective observational study. A prospective study with strict documentation of treatment adherence and universal screening for cardiomyopathy and long QT should be conducted to better study the impact of early detection and treatment. Additional treatment options such as liver transplantation and future therapies such as mRNA or gene therapy should be explored in this population.
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Affiliation(s)
- Sarah Ehrenberg
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA,Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA
| | - Catherine Walsh Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Paige Heiman
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA
| | | | - Olivia Wenger
- New Leaf Center, Mount Eaton, OH, USA,Department of Pediatrics, Akron Children's Hospital, 214 West Bowery Street, Akron, OH 44308, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Lina Ghaloul-Gonzalez
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA,Corresponding author at: Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Rangos Research Building, Pittsburgh, PA 15224, USA.
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Khan AT, Gogarten SM, McHugh CP, Stilp AM, Sofer T, Bowers ML, Wong Q, Cupples LA, Hidalgo B, Johnson AD, McDonald MLN, McGarvey ST, Taylor MR, Fullerton SM, Conomos MP, Nelson SC. Recommendations on the use and reporting of race, ethnicity, and ancestry in genetic research: Experiences from the NHLBI TOPMed program. CELL GENOMICS 2022; 2:100155. [PMID: 36119389 PMCID: PMC9481067 DOI: 10.1016/j.xgen.2022.100155] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
How race, ethnicity, and ancestry are used in genomic research has wide-ranging implications for how research is translated into clinical care and incorporated into public understanding. Correlation between race and genetic ancestry contributes to unresolved complexity for the scientific community, as illustrated by heterogeneous definitions and applications of these variables. Here, we offer commentary and recommendations on the use of race, ethnicity, and ancestry across the arc of genetic research, including data harmonization, analysis, and reporting. While informed by our experiences as researchers affiliated with the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, these recommendations are applicable to basic and translational genomic research in diverse populations with genome-wide data. Moving forward, considerable collaborative effort will be required to ensure that race, ethnicity, and ancestry are described and used appropriately to generate scientific knowledge that yields broad and equitable benefit.
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Affiliation(s)
- Alyna T. Khan
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | | | - Caitlin P. McHugh
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Michael L. Bowers
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew D. Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Merry-Lynn N. McDonald
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen T. McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - Matthew R.G. Taylor
- Department of Medicine, Adult Medical Genetics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Sarah C. Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
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Puffenberger EG. Mendelian disease research in the Plain populations of Lancaster County, Pennsylvania. Am J Med Genet A 2021; 185:3322-3333. [PMID: 34532947 DOI: 10.1002/ajmg.a.62489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 11/07/2022]
Abstract
Founder populations have long contributed to our knowledge of rare disease genes and phenotypes. From the pioneering work of Dr. Victor McKusick to today, research in these groups has shed light on rare recessive phenotypes, expanded the clinical spectrum of disease, and facilitated disease gene identification. Current clinical and research studies in these special groups augment the wealth of knowledge already gained, provide new insights into emerging problems such as variant interpretation and reduced penetrance, and contribute to the development of novel therapies for rare genetic diseases. Clinical developments over the past 30 years have altered the fundamental relationship with the Lancaster Plain communities: research has become more collaborative, and the knowledge imparted by these studies is now being harnessed to provide cutting-edge translational medicine to the very community of vulnerable individuals who need it most.
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Lynch MT, Maloney KA, Pollin TI, Streeten EA, Xu H, Shuldiner AR, Van Hout CV, Gonzaga-Jauregui C, Mitchell BD. The burden of pathogenic variants in clinically actionable genes in a founder population. Am J Med Genet A 2021; 185:3476-3484. [PMID: 34467620 DOI: 10.1002/ajmg.a.62472] [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: 03/31/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/10/2022]
Abstract
Founder populations may be enriched with certain genetic variants of high clinical impact compared to nonfounder populations due to bottleneck events and genetic drift. Using exome sequencing (ES), we quantified the load of pathogenic variants that may be clinically actionable in 6136 apparently healthy adults living in the Lancaster, PA Old Order Amish settlement. We focused on variants in 78 genes deemed clinically actionable by the American College of Medical Genetics and Genomics (ACMG) or Geisinger's MyCode Health Initiative. ES revealed 3191 total variants among these genes including 480 nonsynonymous variants. After quality control and filtering, we applied the ACMG/AMP guidelines for variant interpretation and classified seven variants, across seven genes, as either pathogenic or likely pathogenic. Through genetic drift, all seven variants, are highly enriched in the Amish compared to nonfounder populations. In total, 14.7% of Lancaster Amish individuals carry at least one of these variants, largely explained by the 13% who harbor a copy of a single variant in APOB. Other studies report combined frequencies of pathogenic/likely pathogenic (P/LP) variants in actionable genes between 2.0% and 6.2% in outbred populations. The Amish population harbors fewer actionable variants compared to similarly characterized nonfounder populations but have a higher frequency of each variant identified, offering opportunities for efficient and cost-effective targeted precision medicine.
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Affiliation(s)
- Megan T Lynch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin A Maloney
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Streeten
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Huichun Xu
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
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- Regeneron Genetics Center LLC, Tarrytown, New York, USA
| | | | | | | | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Administration Medical Center Geriatrics Research and Education Clinical Center, Baltimore, Maryland, USA
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