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Friedman CE, Fayer S, Pendyala S, Chien WM, Loiben A, Tran L, Chao LS, McKinstry A, Ahmed D, Farris SD, Stempien-Otero A, Jonlin EC, Murry CE, Starita LM, Fowler DM, Yang KC. Multiplexed Functional Assessments of MYH7 Variants in Human Cardiomyocytes. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004377. [PMID: 38362799 PMCID: PMC11196868 DOI: 10.1161/circgen.123.004377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Pathogenic autosomal-dominant missense variants in MYH7 (myosin heavy chain 7), which encodes the sarcomeric protein (β-MHC [beta myosin heavy chain]) expressed in cardiac and skeletal myocytes, are a leading cause of hypertrophic cardiomyopathy and are clinically actionable. However, ≈75% of MYH7 missense variants are of unknown significance. While human-induced pluripotent stem cells (hiPSCs) can be differentiated into cardiomyocytes to enable the interrogation of MYH7 variant effect in a disease-relevant context, deep mutational scanning has not been executed using diploid hiPSC derivates due to low hiPSC gene-editing efficiency. Moreover, multiplexable phenotypes enabling deep mutational scanning of MYH7 variant hiPSC-derived cardiomyocytes are unknown. METHODS To overcome these obstacles, we used CRISPRa On-Target Editing Retrieval enrichment to generate an hiPSC library containing 113 MYH7 codon variants suitable for deep mutational scanning. We first established that β-MHC protein loss occurs in a hypertrophic cardiomyopathy human heart with a pathogenic MYH7 variant. We then differentiated the MYH7 missense variant hiPSC library to cardiomyocytes for multiplexed assessment of β-MHC variant abundance by massively parallel sequencing and hiPSC-derived cardiomyocyte survival. RESULTS Both the multiplexed assessment of β-MHC abundance and hiPSC-derived cardiomyocyte survival accurately segregated all known pathogenic variants from synonymous variants. Functional data were generated for 4 variants of unknown significance and 58 additional MYH7 missense variants not yet detected in patients. CONCLUSIONS This study leveraged hiPSC differentiation into disease-relevant cardiomyocytes to enable multiplexed assessments of MYH7 missense variants for the first time. Phenotyping strategies used here enable the application of deep mutational scanning to clinically actionable genes, which should reduce the burden of variants of unknown significance on patients and clinicians.
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Affiliation(s)
- Clayton E. Friedman
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Shawn Fayer
- Dept of Genome Sciences, Univ of Washington; Seattle, WA
| | | | - Wei-Ming Chien
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS; Seattle, WA
| | - Alexander Loiben
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Linda Tran
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Leslie S. Chao
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Ashley McKinstry
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Dania Ahmed
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Stephen D. Farris
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS; Seattle, WA
| | - April Stempien-Otero
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Erica C. Jonlin
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
| | - Charles E. Murry
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Dept of Laboratory Medicine & Pathology, Univ of Washington; Seattle, WA
- Dept of Bioengineering, Univ of Washington; Seattle, WA
| | - Lea M. Starita
- Dept of Genome Sciences, Univ of Washington; Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Douglas M. Fowler
- Dept of Genome Sciences, Univ of Washington; Seattle, WA
- Dept of Bioengineering, Univ of Washington; Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Kai-Chun Yang
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS; Seattle, WA
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Aw AJ, Spence JP, Song YS. A SIMPLE AND FLEXIBLE TEST OF SAMPLE EXCHANGEABILITY WITH APPLICATIONS TO STATISTICAL GENOMICS. Ann Appl Stat 2024; 18:858-881. [PMID: 38784669 PMCID: PMC11115382 DOI: 10.1214/23-aoas1817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
In scientific studies involving analyses of multivariate data, basic but important questions often arise for the researcher: Is the sample exchangeable, meaning that the joint distribution of the sample is invariant to the ordering of the units? Are the features independent of one another, or perhaps the features can be grouped so that the groups are mutually independent? In statistical genomics, these considerations are fundamental to downstream tasks such as demographic inference and the construction of polygenic risk scores. We propose a non-parametric approach, which we call the V test, to address these two questions, namely, a test of sample exchangeability given dependency structure of features, and a test of feature independence given sample exchangeability. Our test is conceptually simple, yet fast and flexible. It controls the Type I error across realistic scenarios, and handles data of arbitrary dimensions by leveraging large-sample asymptotics. Through extensive simulations and a comparison against unsupervised tests of stratification based on random matrix theory, we find that our test compares favorably in various scenarios of interest. We apply the test to data from the 1000 Genomes Project, demonstrating how it can be employed to assess exchangeability of the genetic sample, or find optimal linkage disequilibrium (LD) splits for downstream analysis. For exchangeability assessment, we find that removing rare variants can substantially increase the p -value of the test statistic. For optimal LD splitting, the V test reports different optimal splits than previous approaches not relying on hypothesis testing. Software for our methods is available in R (CRAN: flintyR) and Python (PyPI: flintyPy).
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Affiliation(s)
- Alan J Aw
- Department of Statistics, University of California, Berkeley
| | | | - Yun S Song
- Department of Statistics and Computer Science Division, University of California, Berkeley
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3
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Xu W, Plummer L, Seminara SB, Balasubramanian R, Lippincott MF. How human genetic context can inform pathogenicity classification: FGFR1 variation in idiopathic hypogonadotropic hypogonadism. Hum Genet 2023; 142:1611-1619. [PMID: 37805574 PMCID: PMC10977353 DOI: 10.1007/s00439-023-02601-w] [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: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
Precision medicine requires precise genetic variant interpretation, yet many disease-associated genes have unresolved variants of unknown significance (VUS). We analyzed variants in a well-studied gene, FGFR1, a common cause of Idiopathic Hypogonadotropic Hypogonadism (IHH) and examined whether regional genetic enrichment of missense variants could improve variant classification. FGFR1 rare sequence variants (RSVs) were examined in a large cohort to (i) define regional genetic enrichment, (ii) determine pathogenicity based on the American College of Medical Genetics/Association for Molecular Pathology (ACMG/AMP) variant classification framework, and (iii) characterize the phenotype of FGFR1 variant carriers by variant classification. A total of 143 FGFR1 RSVs were identified in 175 IHH probands (n = 95 missense, n = 48 protein-truncating variants). FGFR1 missense RSVs showed regional enrichment across biologically well-defined domains: D1, D2, D3, and TK domains and linker regions (D2-D3, TM-TK). Using these defined regions of enrichment to augment the ACMG/AMP classification reclassifies 37% (20/54) of FGFR1 missense VUS as pathogenic or likely pathogenic (PLP). Non-proband carriers of FGFR1 missense VUS variants that were reclassified as PLP were more likely to express IHH or IHH-associated phenotypes [anosmia or delayed puberty] than non-proband carriers of FGFR1 missense variants that remained as VUS (76.9% vs 34.7%, p = 0.035). Using the largest cohort of FGFR1 variant carriers, we show that integration of regional genetic enrichment as moderate evidence for pathogenicity improves the classification of VUS and that reclassified variants correlated with phenotypic expressivity. The addition of regional genetic enrichment to the ACMG/AMP guidelines may improve clinical variant interpretation.
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Affiliation(s)
- Wanxue Xu
- Reproductive Endocrine Unit of the Department of Medicine, Harvard Reproductive Endocrine Sciences Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Lacey Plummer
- Reproductive Endocrine Unit of the Department of Medicine, Harvard Reproductive Endocrine Sciences Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Stephanie B Seminara
- Reproductive Endocrine Unit of the Department of Medicine, Harvard Reproductive Endocrine Sciences Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ravikumar Balasubramanian
- Reproductive Endocrine Unit of the Department of Medicine, Harvard Reproductive Endocrine Sciences Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Margaret F Lippincott
- Reproductive Endocrine Unit of the Department of Medicine, Harvard Reproductive Endocrine Sciences Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
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4
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Rodgers-Fouche L, Arora S, Ricker C, Li D, Farooqi M, Balaguer F, Dominguez-Valentin M, Guillem JG, Kanth P, Liska D, Melson J, Mraz KA, Shirts BH, Vilar E, Katona BW, Hodan R. Exploring Stakeholders' Perspectives on Implementing Universal Germline Testing for Colorectal Cancer: Findings From a Clinical Practice Survey. JCO Precis Oncol 2023; 7:e2300440. [PMID: 37897815 PMCID: PMC10860957 DOI: 10.1200/po.23.00440] [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: 08/13/2023] [Revised: 08/24/2023] [Accepted: 09/13/2023] [Indexed: 10/30/2023] Open
Abstract
PURPOSE New guidelines recommend considering germline genetic testing for all patients with colorectal cancer (CRC). However, there is a lack of data on stakeholders' perspectives on the advantages and barriers of implementing universal germline testing (UGT). This study assessed the perspectives of members of the Collaborative Group of the Americas on Inherited Gastrointestinal Cancer (CGA-IGC) regarding the implementation of UGT for patients with CRC, including readiness, logistics, and barriers. METHODS A cross-sectional survey was sent to 317 active members of CGA-IGC. The survey included sections on demographics, clinical practice specialty, established institutional practices for testing, and questions pertaining to support of and barriers to implementing UGT for patients with CRC. RESULTS Eighty CGA-IGC members (25%) participated, including 42 genetic counselors (53%) and 14 gastroenterologists (18%). Forty-seven (59%) reported an academic medical center as their primary work setting, and most participants (56%) had more than 10 years of clinical practice. Although most participants (73%) supported UGT, 54% indicated that changes in practice would be required before adopting UGT, and 39% indicated that these changes would be challenging to implement. There was support for both genetics and nongenetics providers to order genetic testing, and a majority (57%) supported a standardized multigene panel rather than a customized gene panel. Key barriers to UGT implementation included limited genetics knowledge among nongenetics providers, time-consuming processes for obtaining consent, ordering tests, disclosing results, and lack of insurance coverage. CONCLUSION This study demonstrates wide support among hereditary GI cancer experts for implementation of UGT for patients with CRC. However, alternative service delivery models using nongenetics providers should be considered to address the logistical barriers to UGT implementation, particularly the growing demand for genetic testing.
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Affiliation(s)
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Charité Ricker
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Dan Li
- Department of Gastroenterology, Kaiser Permanente Medical Center, Santa Clara, CA
| | - Maheen Farooqi
- Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Jose G. Guillem
- Department of Surgery, University of North Carolina, Chapel Hill, NC
| | - Priyanka Kanth
- Department of Gastroenterology, MedStar Georgetown University Hospital, Washington, DC
| | - David Liska
- Department of Colorectal Surgery, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH
| | - Joshua Melson
- Division of Gastroenterology, University of Arizona Cancer Center, Tucson, AZ
| | | | - Brian H. Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryson W. Katona
- Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Rachel Hodan
- Cancer Genetics, Stanford Health Care, Palo Alto, CA
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5
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Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM, Hurles ME. An Atlas of Variant Effects to understand the genome at nucleotide resolution. Genome Biol 2023; 24:147. [PMID: 37394429 PMCID: PMC10316620 DOI: 10.1186/s13059-023-02986-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 07/04/2023] Open
Abstract
Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for precision medicine and comprehension of genome function. A solution lies in experimental assessment of the functional effect of variants, which can reveal their biological and clinical impact. However, variant effect assays have generally been undertaken reactively for individual variants only after and, in most cases long after, their first observation. Now, multiplexed assays of variant effect can characterise massive numbers of variants simultaneously, yielding variant effect maps that reveal the function of every possible single nucleotide change in a gene or regulatory element. Generating maps for every protein encoding gene and regulatory element in the human genome would create an 'Atlas' of variant effect maps and transform our understanding of genetics and usher in a new era of nucleotide-resolution functional knowledge of the genome. An Atlas would reveal the fundamental biology of the human genome, inform human evolution, empower the development and use of therapeutics and maximize the utility of genomics for diagnosing and treating disease. The Atlas of Variant Effects Alliance is an international collaborative group comprising hundreds of researchers, technologists and clinicians dedicated to realising an Atlas of Variant Effects to help deliver on the promise of genomics.
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Affiliation(s)
- Douglas M. Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA USA
- Department of Bioengineering, University of Washington, Seattle, WA USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | | | - Anna L. Gloyn
- Department of Pediatrics & Department of Genetics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
- Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Debora S. Marks
- Broad Institute of MIT and Harvard, Cambridge, MA USA
- Department of Systems Biology, Harvard Medical School, Cambridge, USA
| | - Lara A. Muffley
- Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - James T. Neal
- Broad Institute of MIT and Harvard, Cambridge, MA USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA USA
| | - Frederick P. Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada
| | - Alan F. Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA USA
- Department of Bioengineering, University of Washington, Seattle, WA USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
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6
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Alix T, Chéry C, Josse T, Bronowicki JP, Feillet F, Guéant-Rodriguez RM, Namour F, Guéant JL, Oussalah A. Predictors of the utility of clinical exome sequencing as a first-tier genetic test in patients with Mendelian phenotypes: results from a referral center study on 603 consecutive cases. Hum Genomics 2023; 17:5. [PMID: 36740706 PMCID: PMC9899384 DOI: 10.1186/s40246-023-00455-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Clinical exome sequencing (CES) provides a comprehensive and effective analysis of relevant disease-associated genes in a cost-effective manner compared to whole exome sequencing. Although several studies have focused on the diagnostic yield of CES, no study has assessed predictors of CES utility among patients with various Mendelian phenotypes. We assessed the effectiveness of CES as a first-level genetic test for molecular diagnosis in patients with a Mendelian phenotype and explored independent predictors of the clinical utility of CES. RESULTS Between January 2016 and December 2019, 603 patients (426 probands and 177 siblings) underwent CES at the Department of Molecular Medicine of the University Hospital of Nancy. The median age of the probands was 34 years (IQR, 12-48), and the proportion of males was 46.9% (200/426). Adults and children represented 64.8% (276/426) and 35.2% (150/426), respectively. The median test-to-report time was 5.6 months (IQR, 4.1-7.2). CES revealed 203 pathogenic or likely pathogenic variants in 160 patients, corresponding to a diagnostic yield of 37.6% (160/426). Independent predictors of CES utility were criteria strongly suggestive of an extreme phenotype, including pediatric presentation and patient phenotypes associated with an increased risk of a priori probability of a monogenic disorder, the inclusion of at least one family member in addition to the proband, and a CES prescription performed by an expert in the field of rare genetic disorders. CONCLUSIONS Based on a large dataset of consecutive patients with various Mendelian phenotypes referred for CES as a first-tier genetic test, we report a diagnostic yield of ~ 40% and several independent predictors of CES utility that might improve CES diagnostic efficiency.
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Affiliation(s)
- Tom Alix
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Céline Chéry
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Thomas Josse
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Pierre Bronowicki
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Gastroenterology and Liver Diseases, University Hospital of Nancy, 54000 Nancy, France
| | - François Feillet
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Rosa-Maria Guéant-Rodriguez
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Farès Namour
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Louis Guéant
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
| | - Abderrahim Oussalah
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
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Corcuff M, Garibal M, Desvignes JP, Guien C, Grattepanche C, Collod-Béroud G, Ménoret E, Salgado D, Béroud C. Protein domains provide a new layer of information for classifying human variations in rare diseases. FRONTIERS IN BIOINFORMATICS 2023; 3:1127341. [PMID: 36896423 PMCID: PMC9990413 DOI: 10.3389/fbinf.2023.1127341] [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: 12/19/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Introduction: Using the ACMG-AMP guidelines for the interpretation of sequence variants, it remains difficult to meet the criterion associated with the protein domain, PM1, which is assigned in only about 10% of cases, whereas the criteria related to variant frequency, PM2/BA1/BS1, is reported in 50% of cases. To improve the classification of human missense variants using protein domains information, we developed the DOLPHIN system (https://dolphin.mmg-gbit.eu). Methods: We used Pfam alignments of eukaryotes to define DOLPHIN scores to identify protein domain residues and variants that have a significant impact. In parallel, we enriched gnomAD variants frequencies for each domains' residue. These were validated using ClinVar data. Results: We applied this method to all potential human transcripts' variants, resulting in 30.0% being assigned a PM1 label, whereas 33.2% were eligible for a new benign support criterion, BP8. We also showed that DOLPHIN provides an extrapolated frequency for 31.8% of the variants, compared to the original frequency available in gnomAD for 7.6% of them. Discussion: Overall, DOLPHIN allows a simplified use of the PM1 criterion, an expanded application of the PM2/BS1 criteria and the creation of a new BP8 criterion. DOLPHIN could facilitate the classification of amino acid substitutions in protein domains that cover nearly 40% of proteins and represent the sites of most pathogenic variants.
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Affiliation(s)
- Mélanie Corcuff
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | - Marc Garibal
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | | | - Céline Guien
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | - Coralie Grattepanche
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | | | - Estelle Ménoret
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | - David Salgado
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | - Christophe Béroud
- Aix Marseille University, INSERM, MMG, Bioinformatics & Genetics, Marseille, France.,Laboratoire de Génétique Médicale, APHM Hôpital d'Enfants de la Timone, Marseille, France
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8
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Kotan LD. Comparative Analyses of Turkish Variome and Widely Used Genomic Variation Databases for the Evaluation of Rare Sequence Variants in Turkish Individuals: Idiopathic Hypogonadotropic Hypogonadism as a Disease Model. J Clin Res Pediatr Endocrinol 2022; 14:293-301. [PMID: 35438269 PMCID: PMC9422916 DOI: 10.4274/jcrpe.galenos.2022.2022-3-11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 12/01/2022] Open
Abstract
Objective With the increasing use of whole-exome sequencing, one of the challenges in identifying the causal allele for a Mendelian disease is the lack of availability of population-specific human genetic variation reference databases. The people of Turkey were not represented in GnomAD or other publicly available large databases until recently, when the first comprehensive genomic variation database, Turkish Variome (TRV), was published. The aim of this study was to evaluate whether TRV or other publicly available large genomic variation databases can reliably be used for rare disease variant evaluation in Turkish individuals. Methods Sixty non-disease-causing, non-synonymous variants (minor allele frequencies >1%) were identified in 58 genes that are known to be associated with idiopathic hypogonadotropic hypogonadism from a large Turkish patient cohort. The allelic frequencies of these variants were then compared with those in various public genomic variation databases, including TRV. Results Our cohort variants showed the highest correlations with those in the TRV, Iranome, and The Greater Middle East Variome, in decreasing order. Conclusion These results suggest that the TRV is the appropriate database to use for rare genomic variant evaluations in the Turkish population. Our data also suggest that variomes from geographic neighborhoods may serve as substitute references for populations devoid of their own genomic variation databases.
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Affiliation(s)
- Leman Damla Kotan
- Çukurova University Faculty of Medicine, Department of
Pediatric Endocrinology, Adana, Turkey
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9
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Burke W, Parens E, Chung WK, Berger SM, Appelbaum PS. The Challenge of Genetic Variants of Uncertain Clinical Significance : A Narrative Review. Ann Intern Med 2022; 175:994-1000. [PMID: 35436152 PMCID: PMC10555957 DOI: 10.7326/m21-4109] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic tests expand diagnostic and screening opportunities but also identify genetic variants of uncertain clinical significance (VUSs). Only a minority of VUSs are likely to prove pathogenic when later reassessed, but resolution of the uncertainty is rarely timely. That uncertainty adds complexity to clinical decision making and can result in harms and costs to patients and the health care system, including the time-consuming analysis required to interpret a VUS and the potential for unnecessary treatment and adverse psychological effects. Current efforts to improve variant interpretation will help reduce the scope of the problem, but the high prevalence of rare and novel variants in the human genome points to VUSs as an ongoing challenge. Additional strategies can help mitigate the potential harms of VUSs, including testing protocols that limit identification or reporting of VUSs, subclassification of VUSs according to the likelihood of pathogenicity, routine family-based evaluation of variants, and enhanced counseling efforts. All involve tradeoffs, and the appropriate balance of measures is likely to vary for different test uses and clinical settings. Cross-specialty deliberation and public input could contribute to systematic and broadly supported policies for managing VUSs.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
| | | | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara M. Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul S. Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
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10
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Warren JT, Di Paola J. Genetics of inherited thrombocytopenias. Blood 2022; 139:3264-3277. [PMID: 35167650 PMCID: PMC9164741 DOI: 10.1182/blood.2020009300] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/04/2022] [Indexed: 01/19/2023] Open
Abstract
The inherited thrombocytopenia syndromes are a group of disorders characterized primarily by quantitative defects in platelet number, though with a variety demonstrating qualitative defects and/or extrahematopoietic findings. Through collaborative international efforts applying next-generation sequencing approaches, the list of genetic syndromes that cause thrombocytopenia has expanded significantly in recent years, now with over 40 genes implicated. In this review, we focus on what is known about the genetic etiology of inherited thrombocytopenia syndromes and how the field has worked to validate new genetic discoveries. We highlight the important role for the clinician in identifying a germline genetic diagnosis and strategies for identifying novel causes through research-based endeavors.
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Affiliation(s)
- Julia T Warren
- Division of Hematology-Oncology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Jorge Di Paola
- Division of Hematology-Oncology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
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11
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Abstract
[Figure: see text].
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Affiliation(s)
- Tuuli Lappalainen
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,New York Genome Center, New York, NY, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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12
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Roggenbuck J, Rich KA, Vicini L, Palettas M, Schroeder J, Zaleski C, Lincoln T, Drury L, Glass JD. Amyotrophic Lateral Sclerosis Genetic Access Program: Paving the Way for Genetic Characterization of ALS in the Clinic. NEUROLOGY-GENETICS 2021; 7:e615. [PMID: 34386583 PMCID: PMC8356701 DOI: 10.1212/nxg.0000000000000615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
Objective To report the frequency of amyotrophic lateral sclerosis (ALS) genetic variants in a nationwide cohort of clinic-based patients with ALS with a family history of ALS (fALS), dementia (dALS), or both ALS and dementia (fALS/dALS). Methods A multicenter, prospective cohort of 573 patients with fALS, dALS, or fALS/dALS, underwent genetic testing in the ALS Genetic Access Program (ALS GAP), a clinical program for clinics of the Northeast ALS Consortium. Patients with dALS underwent C9orf72 hexanucleotide repeat expansion (HRE) testing; those with fALS or fALS/dALS underwent C9orf72 HRE testing, followed by sequencing of SOD1, FUS, TARDBP, TBK1, and VCP. Results A pathogenic (P) or likely pathogenic (LP) variant was identified in 171/573 (30%) of program participants. About half of patients with fALS or fALS/dALS (138/301, 45.8%) had either a C9orf72 HRE or a P or LP variant identified in SOD1, FUS, TARDBP, TBK1, or VCP. The use of a targeted, 5-gene sequencing panel resulted in far fewer uncertain test outcomes in familial cases compared with larger panels used in other in clinic-based cohorts. Among dALS cases 11.8% (32/270) were found to have the C9orf72 HRE. Patients of non-Caucasian geoancestry were less likely to test positive for the C9orf72 HRE, but were more likely to test positive on panel testing, compared with those of Caucasian ancestry. Conclusions The ALS GAP program provided a genetic diagnosis to ∼1 in 3 participants and may serve as a model for clinical genetic testing in ALS.
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Affiliation(s)
- Jennifer Roggenbuck
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Kelly A Rich
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Leah Vicini
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Marilly Palettas
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Joceyln Schroeder
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Christina Zaleski
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Tara Lincoln
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Luke Drury
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
| | - Jonathan D Glass
- Department of Internal Medicine (J.R.) and Department of Neurology (J.R., K.A.R.), The Ohio State University Wexner Medical Center, Columbus; The Ohio State University Wexner Medical Center (L.V.), College of Medicine, Columbus; Department of Biomedical Informatics (M.P.), The Ohio State University, Center for Biostatistics, Columbus; PreventionGenetics, LLC (J.S., C.Z., T.L., L.D.), Marshfield, WI; The Northeast ALS Consortium (NEALS) (T.L.); and Emory ALS Center (J.D.G.), Emory University School of Medicine, Atlanta, GA
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13
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Abstract
Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA;
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14
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Wu D, Luo X, Feurstein S, Kesserwan C, Mohan S, Pineda-Alvarez DE, Godley LA. How I curate: applying American Society of Hematology-Clinical Genome Resource Myeloid Malignancy Variant Curation Expert Panel rules for RUNX1 variant curation for germline predisposition to myeloid malignancies. Haematologica 2020; 105:870-887. [PMID: 32165484 PMCID: PMC7109758 DOI: 10.3324/haematol.2018.214221] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/21/2019] [Indexed: 01/30/2023] Open
Abstract
The broad use of next-generation sequencing and microarray platforms in research and clinical laboratories has led to an increasing appreciation of the role of germline mutations in genes involved in hematopoiesis and lineage differentiation that contribute to myeloid neoplasms. Despite implementation of the American College of Medical Genetics and Genomics and Association for Molecular Pathology 2015 guidelines for sequence variant interpretation, the number of variants deposited in ClinVar, a genomic repository of genotype and phenotype data, and classified as having uncertain significance or being discordantly classified among clinical laboratories remains elevated and contributes to indeterminate or inconsistent patient care. In 2018, the American Society of Hematology and the Clinical Genome Resource co-sponsored the Myeloid Malignancy Variant Curation Expert Panel to develop rules for classifying gene variants associated with germline predisposition to myeloid neoplasia. Herein, we demonstrate application of our rules developed for the RUNX1 gene to variants in six examples to show how we would classify them within the proposed framework.
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Affiliation(s)
- David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Simone Feurstein
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, Chicago, IL
| | - Chimene Kesserwan
- Albert Einstein College of Medicine, Department of Pathology, New York, NY
| | - Shruthi Mohan
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC
| | | | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, Chicago, IL .,Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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15
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Makhnoon S, Peterson SK. Variant of Uncertain Significance-Related Uncertainty in Breast Cancer Genomics. CURRENT BREAST CANCER REPORTS 2020. [DOI: 10.1007/s12609-020-00351-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Exploring the effect of ascertainment bias on genetic studies that use clinical pedigrees. Eur J Hum Genet 2019; 27:1800-1807. [PMID: 31296927 DOI: 10.1038/s41431-019-0467-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/09/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
Recent studies have reported novel cancer risk associations with incidentally tested genes on cancer risk panels using clinically ascertained cohorts. Clinically ascertained pedigrees may have unknown ascertainment biases for both patients and relatives. We used a method to assess gene and variant risk and ascertainment bias based on comparing the number of observed disease instances in a pedigree given the sex and ages of individuals with those expected given established population incidence. We assessed the performance characteristics of the method by simulating families with varying genetic risk and proportion of individuals genotyped. We implemented this method using SEER cancer incidence data to assess clinical ascertainment bias in a set of 42 pedigrees with clinical testing ordered for either breast/ovarian cancer or colorectal/endometrial cancer at the University of Washington and negative sequencing results. In addition to expected biases consistent with the stated testing purpose, there were trends suggesting increased colorectal and endometrial cancer in pedigrees tested for breast cancer risk and trends suggesting increased breast cancer in families tested for colon cancer risk. There was no observed selection bias for prostate cancer in this set of families. This analysis illustrates that clinically ascertained data sets may have subtle biases. In the future, researchers seeking to explore risk associations with clinical data sets could assess potential ascertainment bias by comparing incidence of disease in families that test negative under given ordering criteria to expected population disease frequencies. Failure to assess for ascertainment bias increases the risk of false genetic associations.
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17
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Swaminathan A, Shirts BH, Chen AT. Incorporating user feedback in the design of a genetics analysis tool: A two-part approach. J Biomed Inform 2019; 95:103204. [PMID: 31075532 DOI: 10.1016/j.jbi.2019.103204] [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: 08/07/2018] [Revised: 04/21/2019] [Accepted: 05/05/2019] [Indexed: 11/28/2022]
Abstract
While general usability assessment models for websites have been developed for a wide variety of contexts, research literature on incorporating user feedback in the design of online scientific tools is lacking. In this article, we present an approach that we developed and illustrate how it was used to elicit user feedback of the AnalyzeMyVariant tool, which enables geneticists to use family pedigree data to calculate pathogenicity likelihood ratios for variants of unknown significance. We reviewed existing usability literature and developed a survey instrument emphasizing concepts of importance to online, data-driven, scientific tools. The items on the survey instrument were grouped in four categories: usability, quality, privacy and security, and satisfaction. We performed a two-part evaluation using the survey and a semi-structured interview protocol. The survey instrument was used to collect data about the use experience of AnalyzeMyVariant from 57 genetic experts and trainees who were recruited via email invitations. We also conducted semi-structured interviews with six genetics experts to explore work contexts in which users might use the tool and further delve into issues faced in tool use. Interviews were inductively coded and major themes identified using the constant comparative method. We found that the needs of genetics professionals vary for research- and clinically-focused work. These differences can inform the design of tools to serve their needs. The major contribution of this work is the description of a two-part method to elicit user feedback to inform the design of online, data-driven, scientific tools, which focuses on constructs of particular relevance to these tools such as usability, quality, privacy, security, and satisfaction. The survey instrument that we developed, coupled with contextual interviews, may serve as an example that can be used by others conducting usability studies of similar tools. In addition, our results emphasize the importance of considering contextual factors such as background knowledge, situational factors, and the intended application of results, in the usability evaluation of scientific software. It is our hope that this two-part approach might be adapted to assess the usability of other online scientific tools and facilitate the design of tools to meet the needs of their target audiences.
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Affiliation(s)
- Aarti Swaminathan
- Biomedical Informatics and Medical Education, UW Medicine South Lake Union, 850 Republican Street, Box 358047, Seattle, WA 98109, USA
| | - Brian H Shirts
- University of Washington, Department of Laboratory Medicine, Box 357110, 1959 NE Pacific Street, NW120, Seattle, WA 98195-7110, USA.
| | - Annie T Chen
- Biomedical Informatics and Medical Education, UW Medicine South Lake Union, 850 Republican Street, Box 358047, Seattle, WA 98109, USA.
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18
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Krumm N, Shirts BH. Technical, Biological, and Systems Barriers for Molecular Clinical Decision Support. Clin Lab Med 2019; 39:281-294. [PMID: 31036281 DOI: 10.1016/j.cll.2019.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-enabled or molecular clinical decision support (CDS) systems provide unique advantages for the clinical use of genomic data; however, their implementation is complicated by technical, biological, and systemic barriers. This article reviews the substantial technical progress that has been made in the past decade and finds that the underlying biological limitations of genomics as well as systemic barriers to adoption of molecular CDS have been comparatively underestimated. A hybrid consultative CDS system, which integrates a genomics consultant into an active CDS system, may provide an interim path forward.
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Affiliation(s)
- Niklas Krumm
- Department of Laboratory Medicine, University of Washington, Box 357110, 1959 Northeast Pacific Street, NW120, Seattle, WA 98195-7110, USA.
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Box 357110, 1959 Northeast Pacific Street, NW120, Seattle, WA 98195-7110, USA
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19
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The effects of genomic germline variant reclassification on clinical cancer care. Oncotarget 2019; 10:417-423. [PMID: 30728895 PMCID: PMC6355179 DOI: 10.18632/oncotarget.26501] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
The last two decades have provided an astounding amount of novel information about the human genome. Translating germline genomic data into clinically actionable findings is reliant on the annotation and laboratory classification of specific variants. Variant classification helps providers and patients determine if genomic findings can inform clinical management. In germline hereditary cancer predisposition testing, variants of uncertain significance (VUS) are routinely misunderstood. By definition, they cannot be classified by the testing laboratory as either problematic mutations or benign variants. Many VUS undergo category reclassifications over time (from months to years after initial classification) as more information is known about normal human genomic diversity, especially among underrepresented minority populations. When VUS are reclassified, it has been shown that they are often downgraded. Likewise, some variants originally thought to be actionable mutations are downgraded to VUS or benign variants. Rarely but importantly, VUS may be reclassified in a manner that increases their initial clinical significance. Here, we discuss the insights gained from the study of variant reclassification. We provide a case series to highlight the potential impact that variant reclassifications can have on individual and family cancer management, risk counseling, and screening.
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20
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Tsai GJ, Garrett LT, Makhnoon S, Bowen DJ, Burke W, Shirts BH. Patient goals, motivations, and attitudes in a patient-driven variant reclassification study. J Genet Couns 2018; 28:558-569. [PMID: 31163102 DOI: 10.1002/jgc4.1052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/12/2018] [Accepted: 07/27/2018] [Indexed: 01/12/2023]
Abstract
Family studies to reclassify clinically ascertained variants of uncertain significance (VUS) can impact risk assessment, medical management, and psychological outcomes for patients and their families. There are limited avenues for patients and their families to actively participate in VUS reclassification, and access to family studies at most commercial laboratories is restricted by multiple factors. To explore patient attitudes about participation in family studies for VUS reclassification, we conducted semistructured pre- and post-participation telephone interviews with 38 participants in a family-based VUS reclassification study that utilized a patient-driven approach for family ascertainment and recruitment. Participants had VUS from multigene panel testing performed at multiple clinical laboratories for cancer or other disease risk. Inductive thematic analysis of transcribed interviews highlighted four major themes: (a) Participants' study goals were driven by the desire to resolve uncertainty related to the VUS, (b) Participants had mixed reactions to the VUS reclassification outcomes of the study, (c) Personal, public, and familial knowledge increased through study participation and (d) Participants used study participation to actively cope with the uncertainty of a VUS. As personalized genomic medicine becomes more prevalent, clinicians, clinical laboratories, and researchers could consider creating more opportunities for active partnership with patients and families, who are motivated to contribute data to familial VUS studies.
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Affiliation(s)
- Ginger J Tsai
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Sukh Makhnoon
- Institute of Public Health Genomics, University of Washington, Seattle, Washington
| | - Deborah J Bowen
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
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21
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Outcomes of 92 patient-driven family studies for reclassification of variants of uncertain significance. Genet Med 2018; 21:1435-1442. [PMID: 30374176 DOI: 10.1038/s41436-018-0335-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/28/2018] [Indexed: 01/30/2023] Open
Abstract
PURPOSE Family studies are an important but underreported source of information for reclassification of variants of uncertain significance (VUS). We evaluated outcomes of a patient-driven framework that offered familial VUS reclassification analysis to any adult with any clinically ascertained VUS from any laboratory in the United States. METHODS With guidance from FindMyVariant.org, participants recruited their own relatives for study participation. We genotyped relatives, calculated quantitative cosegregation likelihood ratios, and evaluated variant classifications using Tavtigian's unified framework for Bayesian analysis with American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria. We report participation and VUS reclassification rates from the 50 families enrolled for at least one year and reclassification results for 112 variants from the larger 92-family cohort. RESULTS For the 50-family cohort, 6.7 relatives per family were invited to participate and 67% of relatives returned samples for genotyping. Sixty-one percent of VUS were reclassified, 84% of which were classified as benign or likely benign. Genotyping relatives identified a de novo variant, phase variants, and relatives with phenotypes highly specific for or incompatible with specific classifications. CONCLUSIONS Motivated families can contribute to successful VUS reclassification at substantially higher rates than those previously published. Clinical laboratories could consider offering family studies to all patients with VUS.
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22
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle
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23
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Makhnoon S, Garrett LT, Burke W, Bowen DJ, Shirts BH. Experiences of patients seeking to participate in variant of uncertain significance reclassification research. J Community Genet 2018; 10:189-196. [PMID: 30027524 DOI: 10.1007/s12687-018-0375-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/10/2018] [Indexed: 01/29/2023] Open
Abstract
Patients' understanding of a genetic variant of unknown clinical significance (VUS) is likely to influence beliefs about risk implications, consequent medical decisions, and other actions such as involvement in research. We interviewed 26 self-selected participants with a clinically identified VUS before they enrolled into a VUS reclassification study. Semi-structured interviews addressed topics including motivation to get genetic test, experience with the VUS result, affective responses to receiving VUS, and perceived effect of VUS and reclassification on medical care. We found that family and personal history of disease were the most prevalent motivators for getting a genetic test. Participants demonstrated mixed understanding of VUS. Most expressed negative effect on learning of their VUS result and uncertainty about its impact on clinical management. Most expected reclassification efforts to benefit their family members but not themselves. Some expressed distrust of their providers following a VUS result. Participation in the VUS reclassification study appeared to be motivated by four factors for patients with VUS-negative effect about VUS, uncertainty about its impact on clinical management, concern for family members' well-being, and to advance science. Perhaps the direct acknowledgement and appraisal of uncertainty as a means of coping was missing in some pre-test counseling experienced by our participants and thus they were not psychologically prepared for atypical VUS results. The finding of VUS-induced provider distrust suggests a need for careful consideration of appropriate pre- and post-test counseling about VUS.
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Affiliation(s)
- Sukh Makhnoon
- Institute of Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Lauren Thomas Garrett
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific Street, NW120, Seattle, WA, 98195-7110, USA
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
| | - Deborah J Bowen
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific Street, NW120, Seattle, WA, 98195-7110, USA.
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24
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Tonelli MR. Clinical judgement in precision medicine. J Eval Clin Pract 2018; 24:646-648. [PMID: 29464829 DOI: 10.1111/jep.12892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/18/2017] [Accepted: 01/23/2018] [Indexed: 01/30/2023]
Abstract
Precision medicine, which aims to individualize care based upon the unique combination of genetic, environmental, and lifestyle features in particular patients, will require an evolution in clinical decision making. Practitioners of precision medicine will need to utilize an expanded body of medical knowledge derived from a wide variety of sources. Clinical judgement in the case-based reasoning necessary for individualizing care will involve understanding and utilizing methodological approaches not commonly invoked in medicine, including mechanistic and qualitative research results. Instead of searching for an answer in the published literature, precision medicine demands clinical judgement that finds the reasons for clinical decisions within, not without, the patient.
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Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, Fowler DM. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nat Genet 2018; 50:874-882. [PMID: 29785012 PMCID: PMC5980760 DOI: 10.1038/s41588-018-0122-z] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes requires generalizable, scalable assays. We describe variant abundance by massively parallel sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single-amino-acid variants of PTEN and TPMT, proteins in which functional variants are clinically actionable. We identify 1,138 PTEN and 777 TPMT variants that result in low protein abundance, and may be pathogenic or alter drug metabolism, respectively. We observe selection for low-abundance PTEN variants in cancer, and show that p.Pro38Ser, which accounts for ~10% of PTEN missense variants in melanoma, functions via a dominant-negative mechanism. Finally, we demonstrate that VAMP-seq is applicable to other genes, highlighting its generalizability.
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Affiliation(s)
- Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melissa A Chiasson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Vanessa E Gray
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Arineh Khechaduri
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jennifer N Dines
- Department of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Ronald J Hause
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Smita Bhatia
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Genetic Networks Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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Daly AK, Rettie AE, Fowler DM, Miners JO. Pharmacogenomics of CYP2C9: Functional and Clinical Considerations. J Pers Med 2017; 8:E1. [PMID: 29283396 PMCID: PMC5872075 DOI: 10.3390/jpm8010001] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023] Open
Abstract
CYP2C9 is the most abundant CYP2C subfamily enzyme in human liver and the most important contributor from this subfamily to drug metabolism. Polymorphisms resulting in decreased enzyme activity are common in the CYP2C9 gene and this, combined with narrow therapeutic indices for several key drug substrates, results in some important issues relating to drug safety and efficacy. CYP2C9 substrate selectivity is detailed and, based on crystal structures for the enzyme, we describe how CYP2C9 catalyzes these reactions. Factors relevant to clinical response to CYP2C9 substrates including inhibition, induction and genetic polymorphism are discussed in detail. In particular, we consider the issue of ethnic variation in pattern and frequency of genetic polymorphisms and clinical implications. Warfarin is the most well studied CYP2C9 substrate; recent work on use of dosing algorithms that include CYP2C9 genotype to improve patient safety during initiation of warfarin dosing are reviewed and prospects for their clinical implementation considered. Finally, we discuss a novel approach to cataloging the functional capabilities of rare 'variants of uncertain significance', which are increasingly detected as more exome and genome sequencing of diverse populations is conducted.
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Affiliation(s)
- Ann K Daly
- Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Douglas M Fowler
- Department of Genome Sciences and Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - John O Miners
- Department of Clinical Pharmacology, Flinders University School of Medicine, Adelaide 5042, Australia.
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