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Schmidt RJ, Steeves M, Bayrak-Toydemir P, Benson KA, Coe BP, Conlin LK, Ganapathi M, Garcia J, Gollob MH, Jobanputra V, Luo M, Ma D, Maston G, McGoldrick K, Palculict TB, Pesaran T, Pollin TI, Qian E, Rehm HL, Riggs ER, Schilit SLP, Sergouniotis PI, Tvrdik T, Watkins N, Zec L, Zhang W, Lebo MS. Recommendations for risk allele evidence curation, classification, and reporting from the ClinGen Low Penetrance/Risk Allele Working Group. Genet Med 2024; 26:101036. [PMID: 38054408 PMCID: PMC10939896 DOI: 10.1016/j.gim.2023.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE Genetic variants at the low end of the penetrance spectrum have historically been challenging to interpret because their high population frequencies exceed the disease prevalence of the associated condition, leading to a lack of clear segregation between the variant and disease. There is currently substantial variation in the classification of these variants, and no formal classification framework has been widely adopted. The Clinical Genome Resource Low Penetrance/Risk Allele Working Group was formed to address these challenges and promote harmonization within the clinical community. METHODS The work presented here is the product of internal and community Likert-scaled surveys in combination with expert consensus within the Working Group. RESULTS We formally recognize risk alleles and low-penetrance variants as distinct variant classes from those causing highly penetrant disease that require special considerations regarding their clinical classification and reporting. First, we provide a preferred terminology for these variants. Second, we focus on risk alleles and detail considerations for reviewing relevant studies and present a framework for the classification these variants. Finally, we discuss considerations for clinical reporting of risk alleles. CONCLUSION These recommendations support harmonized interpretation, classification, and reporting of variants at the low end of the penetrance spectrum.
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Affiliation(s)
- Ryan J Schmidt
- Children's Hospital Los Angeles, Keck School of Medicine of USC, Los Angeles, CA.
| | | | - Pinar Bayrak-Toydemir
- Department of Pathology, University of Utah Molecular Genetics and Genomics, ARUP Laboratories, Salt Lake City, UT
| | - Katherine A Benson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Ireland
| | - Bradley P Coe
- Department of Pathology & Lab Medicine, BC Children's & BC Women's Hospitals, Vancouver, Canada
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | | | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, Toronto General Hospital and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Vaidehi Jobanputra
- New York Genome Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Deqiong Ma
- DNA diagnostic lab, Department of Genetics, School of Medicine, Yale University, New Haven, CT
| | | | | | | | | | - Toni I Pollin
- University of Maryland School of Medicine, Baltimore, MD
| | - Emily Qian
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Heidi L Rehm
- Center for Genomics Medicine, Massachusetts General Hospital, Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Erin R Riggs
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA
| | - Samantha L P Schilit
- Mass General Brigham, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA
| | | | - Tatiana Tvrdik
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Nicholas Watkins
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Matthew S Lebo
- Mass General Brigham, Brigham and Woman's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, MA.
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2
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Walsh N, Cooper A, Dockery A, O'Byrne JJ. Variant reclassification and clinical implications. J Med Genet 2024; 61:207-211. [PMID: 38296635 DOI: 10.1136/jmg-2023-109488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Genomic technologies have transformed clinical genetic testing, underlining the importance of accurate molecular genetic diagnoses. Variant classification, ranging from benign to pathogenic, is fundamental to these tests. However, variant reclassification, the process of reassigning the pathogenicity of variants over time, poses challenges to diagnostic legitimacy. This review explores the medical and scientific literature available on variant reclassification, focusing on its clinical implications.Variant reclassification is driven by accruing evidence from diverse sources, leading to variant reclassification frequency ranging from 3.6% to 58.8%. Recent studies have shown that significant changes can occur when reviewing variant classifications within 1 year after initial classification, illustrating the importance of early, accurate variant assignation for clinical care.Variants of uncertain significance (VUS) are particularly problematic. They lack clear categorisation but have influenced patient treatment despite recommendations against it. Addressing VUS reclassification is essential to enhance the credibility of genetic testing and the clinical impact. Factors affecting reclassification include standardised guidelines, clinical phenotype-genotype correlations through deep phenotyping and ancestry studies, large-scale databases and bioinformatics tools. As genomic databases grow and knowledge advances, reclassification rates are expected to change, reducing discordance in future classifications.Variant reclassification affects patient diagnosis, precision therapy and family screening. The exact patient impact is yet unknown. Understanding influencing factors and adopting standardised guidelines are vital for precise molecular genetic diagnoses, ensuring optimal patient care and minimising clinical risk.
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Affiliation(s)
- Nicola Walsh
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland
| | - Aislinn Cooper
- Next Generation Sequencing Lab, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Adrian Dockery
- Next Generation Sequencing Lab, Mater Misericordiae University Hospital, Dublin, Ireland
| | - James J O'Byrne
- National Centre for Inherited Metabolic Disorders, Mater Misericordiae University Hospital, Dublin, Ireland
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3
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Ghaedi H, Davey SK, Feilotter H. Variant Classification Discordance: Contributing Factors and Predictive Models. J Mol Diagn 2024; 26:115-126. [PMID: 38008287 DOI: 10.1016/j.jmoldx.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/04/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023] Open
Abstract
An ever-growing catalog of human variants is hosted in the ClinVar database. In this database, submissions on a variant are combined into a multisubmitter record; and in the case of discordance in variant classification between submitters, the record is labeled as conflicting. The current study used ClinVar data to identify characteristics that would make variants more likely to be associated with the conflict class of variants. Furthermore, the Extreme Gradient Boosting algorithm was used to train classifier models to provide prediction of classification discordance for single submission variants in ClinVar database. Population allele frequency, the gene harboring the variant, variant type, consequence on protein, variant deleteriousness score, first submitter identity, and submission count were associated with conflict in variant classification. Using such features, the optimized classifier showed accuracy on the test set of 88% with the weighted average of precision, recall, and f1-score of 0.84, 0.88, and 0.85, respectively. There were pronounced associations between variant classification discordance and allele frequency, gene type, and the identity of the first submitter. The study provides the predicted discordance status for single-submitter variants deposited in ClinVar. This approach can be used to assess whether single-submitter variants are likely to be supported, or in conflict with, future entries; this knowledge may help laboratories with clinical variant assessment.
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Affiliation(s)
- Hamid Ghaedi
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Scott K Davey
- Division of Cancer Biology and Genetics, Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Kingston, Ontario, Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.
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4
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Liu S, Zhong M, Huang Y, Zhang Q, Chen T, Xu X, Peng W, Wang X, Feng X, Kang L, Lu Y, Cheng J, Bu F, Yuan H. Quantitative thresholds for variant enrichment in 13,845 cases: improving pathogenicity classification in genetic hearing loss. Genome Med 2023; 15:116. [PMID: 38111038 PMCID: PMC10726519 DOI: 10.1186/s13073-023-01271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines recommend using variant enrichment among cases as "strong" evidence for pathogenicity per the PS4 criterion. However, quantitative support for PS4 thresholds from real-world Mendelian case-control cohorts is lacking. METHODS To address this gap, we evaluated and established PS4 thresholds using data from the Chinese Deafness Genetics Consortium. A total of 9,050 variants from 13,845 patients with hearing loss (HL) and 6,570 ancestry-matched controls were analyzed. Positive likelihood ratio and local positive likelihood ratio values were calculated to determine the thresholds corresponding to each strength of evidence across three variant subsets. RESULTS In subset 1, consisting of variants present in both cases and controls with an allele frequency (AF) in cases ≥ 0.0005, an odds ratio (OR) ≥ 6 achieved strong evidence, while OR ≥ 3 represented moderate evidence. For subset 2, which encompassed variants present in both cases and controls with a case AF < 0.0005, and subset 3, comprising variants found only in cases and absent from controls, we defined the PS4_Supporting threshold (OR > 2.27 or allele count ≥ 3) and the PS4_Moderate threshold (allele count ≥ 6), respectively. Reanalysis applying the adjusted PS4 criteria changed the classification of 15 variants and enabled diagnosis of an additional four patients. CONCLUSIONS Our study quantified evidence strength thresholds for variant enrichment in genetic HL cases, highlighting the importance of defining disease/gene-specific thresholds to improve the precision and accuracy of clinical genetic testing.
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Affiliation(s)
- Sihan Liu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Mingjun Zhong
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Huang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Qian Zhang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Ting Chen
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Wan Peng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaolu Wang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Lu Kang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Lu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Jing Cheng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Fengxiao Bu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
| | - Huijun Yuan
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
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Flowers M, Dickson A, Miller MJ, Spector E, Enns GM, Baudet H, Pasquali M, Racacho L, Sadre-Bazzaz K, Wen T, Fogarty M, Fernandez R, Weaver MA, Feigenbaum A, Graham BH, Mao R. Specifications of the ACMG/AMP guidelines for ACADVL variant interpretation. Mol Genet Metab 2023; 140:107668. [PMID: 37549443 PMCID: PMC10811274 DOI: 10.1016/j.ymgme.2023.107668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a relatively common inborn error of metabolism, but due to difficulty in accurately predicting affected status through newborn screening, molecular confirmation of the causative variants by sequencing of the ACADVL gene is necessary. Although the ACMG/AMP guidelines have helped standardize variant classification, ACADVL variant classification remains disparate due to a phenotype that can be nonspecific, the possibility of variants that produce late-onset disease, and relatively high carrier frequency, amongst other challenges. Therefore, an ACADVL-specific variant curation expert panel (VCEP) was created to facilitate the specification of the ACMG/AMP guidelines for VLCADD. We expect these guidelines to help streamline, increase concordance, and expedite the classification of ACADVL variants.
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Affiliation(s)
- May Flowers
- Invitae Corporation, San Francisco, CA 94103, USA
| | - Alexa Dickson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elaine Spector
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gregory Mark Enns
- Division of Medical Genetics, Department of Pediatrics, Lucile Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Heather Baudet
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Marzia Pasquali
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA
| | - Lemuel Racacho
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta T3B6A8, Canada
| | | | - Ting Wen
- ARUP Laboratories, Salt Lake City, UT 84108, USA
| | | | - Raquel Fernandez
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Annette Feigenbaum
- Department of Pediatrics, Division of Genetics, Rady Children's Hospital and The University of California, San Diego, CA 92123, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA.
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6
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Levy M, Bazak L, Lev-El N, Greenberg R, Kropach N, Basel-Salmon L, Maya I. Potential Founder Variants in COL4A4 Identified in Bukharian Jews Linked to Autosomal Dominant and Autosomal Recessive Alport Syndrome. Genes (Basel) 2023; 14:1854. [PMID: 37895203 PMCID: PMC10606019 DOI: 10.3390/genes14101854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Alport syndrome is a hereditary disorder caused by pathogenic variants in the COL4A gene, which can be inherited in an autosomal recessive, dominant, or X-linked pattern. In the Bukharian Jewish population, no founder pathogenic variant has been reported in COL4A4. METHODS The cohort included 38 patients from 22 Bukharian Jewish families with suspected Alport syndrome who were referred the nephrogenetics clinic between 2012 and 2022. The study collected demographic, clinical, and genetic data from electronic medical records, which were used to evaluate the molecular basis of the disease using Sanger sequencing, and next-generation sequencing. RESULTS Molecular diagnosis was confirmed in 20/38 patients, with each patient having at least one of the three disease-causing COL4A4 variants detected: c.338G A (p.Gly1008Arg), and c.871-6T>C. In addition, two patients were obligate carriers. Overall, there were 17 heterozygotes, 2 compound heterozygotes, and 3 homozygotes. Each variant was detected in more than one unrelated family. All patients had hematuria with/without proteinuria at referral, and the youngest patient with proteinuria (age 5 years) was homozygous for the c.338G>A variant. End-stage renal disease was diagnosed in two patients at the age of 38 years, a compound heterozygote for c.338G>A and c.871-6T>C. Hearing deterioration was detected in three patients, the youngest aged 40 years, all of whom were heterozygous for c.338G>A. CONCLUSION This study unveils three novel disease-causing variants, c.3022G>A, c.871-6T>C, and c.338G>A, in the COL4A4 gene that are recurrent among Jews of Bukharian ancestry, and cause Alport syndrome in both dominant and recessive autosomal inheritance patterns.
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Affiliation(s)
- Michal Levy
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
| | - Lily Bazak
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Noa Lev-El
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Rotem Greenberg
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Nesia Kropach
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva 4920235, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Felsenstein Medical Research Center, Petach Tikva 4920235, Israel
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
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7
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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8
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Arendt ML, Dobson JM. Sarcoma Predisposition in Dogs with a Comparative View to Human Orthologous Disease. Vet Sci 2023; 10:476. [PMID: 37505880 PMCID: PMC10385400 DOI: 10.3390/vetsci10070476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Sarcomas are malignant tumors arising from the embryonic mesodermal cell lineage. This group of cancers covers a heterogenous set of solid tumors arising from soft tissues or bone. Many features such as histology, biological behavior and molecular characteristics are shared between sarcomas in humans and dogs, suggesting that human sarcoma research can be informative for canine disease, and that dogs with sarcomas can serve as relevant translational cancer models, to aid in the understanding of human disease and cancer biology. In the present paper, risk factors for the development of sarcoma in dogs are reviewed, with a particular focus on recent advances in clinical genetics, and on the identification of simple and complex genetic risk factors with a comparison with what has been found in human orthologous disease.
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Affiliation(s)
- Maja L Arendt
- Department of Veterinary Clinical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Jane M Dobson
- Queens Veterinary School Hospital, University of Cambridge, Cambridge CB3 0ES, UK
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9
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Sharo AG, Zou Y, Adhikari AN, Brenner SE. ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden. Genome Med 2023; 15:51. [PMID: 37443081 PMCID: PMC10347827 DOI: 10.1186/s13073-023-01199-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Curated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines. METHODS Using archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6 years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD. RESULTS While the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar's lower false-positive rate. CONCLUSIONS Considering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.
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Affiliation(s)
- Andrew G. Sharo
- Biophysics Graduate Group, University of California, Berkeley, CA 94720 USA
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Ecology and Evolutionary Biology, University of California, 124 Biomed Building, 1156 High St., Santa Cruz, CA 95064 USA
| | - Yangyun Zou
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720 USA
- Currently at: Department of Clinical Research, Yikon Genomics Company, Ltd., Shanghai, China
| | - Aashish N. Adhikari
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720 USA
- Currently at: Illumina, Foster City, CA 94404 USA
| | - Steven E. Brenner
- Biophysics Graduate Group, University of California, Berkeley, CA 94720 USA
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720 USA
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10
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Maron JL, Kingsmore S, Gelb BD, Vockley J, Wigby K, Bragg J, Stroustrup A, Poindexter B, Suhrie K, Kim JH, Diacovo T, Powell CM, Trembath A, Guidugli L, Ellsworth KA, Reed D, Kurfiss A, Breeze JL, Trinquart L, Davis JM. Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder. JAMA 2023; 330:161-169. [PMID: 37432431 PMCID: PMC10336625 DOI: 10.1001/jama.2023.9350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/12/2023] [Indexed: 07/12/2023]
Abstract
Importance Genomic testing in infancy guides medical decisions and can improve health outcomes. However, it is unclear whether genomic sequencing or a targeted neonatal gene-sequencing test provides comparable molecular diagnostic yields and times to return of results. Objective To compare outcomes of genomic sequencing with those of a targeted neonatal gene-sequencing test. Design, Setting, and Participants The Genomic Medicine for Ill Neonates and Infants (GEMINI) study was a prospective, comparative, multicenter study of 400 hospitalized infants younger than 1 year of age (proband) and their parents, when available, suspected of having a genetic disorder. The study was conducted at 6 US hospitals from June 2019 to November 2021. Exposure Enrolled participants underwent simultaneous testing with genomic sequencing and a targeted neonatal gene-sequencing test. Each laboratory performed an independent interpretation of variants guided by knowledge of the patient's phenotype and returned results to the clinical care team. Change in clinical management, therapies offered, and redirection of care was provided to families based on genetic findings from either platform. Main Outcomes and Measures Primary end points were molecular diagnostic yield (participants with ≥1 pathogenic variant or variant of unknown significance), time to return of results, and clinical utility (changes in patient care). Results A molecular diagnostic variant was identified in 51% of participants (n = 204; 297 variants identified with 134 being novel). Molecular diagnostic yield of genomic sequencing was 49% (95% CI, 44%-54%) vs 27% (95% CI, 23%-32%) with the targeted gene-sequencing test. Genomic sequencing did not report 19 variants found by the targeted neonatal gene-sequencing test; the targeted gene-sequencing test did not report 164 variants identified by genomic sequencing as diagnostic. Variants unidentified by the targeted genomic-sequencing test included structural variants longer than 1 kilobase (25.1%) and genes excluded from the test (24.6%) (McNemar odds ratio, 8.6 [95% CI, 5.4-14.7]). Variant interpretation by laboratories differed by 43%. Median time to return of results was 6.1 days for genomic sequencing and 4.2 days for the targeted genomic-sequencing test; for urgent cases (n = 107) the time was 3.3 days for genomic sequencing and 4.0 days for the targeted gene-sequencing test. Changes in clinical care affected 19% of participants, and 76% of clinicians viewed genomic testing as useful or very useful in clinical decision-making, irrespective of a diagnosis. Conclusions and Relevance The molecular diagnostic yield for genomic sequencing was higher than a targeted neonatal gene-sequencing test, but the time to return of routine results was slower. Interlaboratory variant interpretation contributes to differences in molecular diagnostic yield and may have important consequences for clinical management.
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Affiliation(s)
- Jill L. Maron
- Women and Infants Hospital of Rhode Island, Providence
| | - Stephen Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jerry Vockley
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, California
- Department of Pediatrics, University of California San Diego, San Diego
| | - Jennifer Bragg
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Annemarie Stroustrup
- Division of Neonatology, Department of Pediatrics, Cohen Children’s Medical Center at Northwell Health, New Hyde Park, New York, New York
| | - Brenda Poindexter
- Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Kristen Suhrie
- Indiana University School of Medicine, Department of Pediatrics and Medical and Molecular Genetics, Indianapolis
| | - Jae H. Kim
- Perinatal Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Thomas Diacovo
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cynthia M. Powell
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Andrea Trembath
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | | | - Dallas Reed
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Anne Kurfiss
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Janis L. Breeze
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Ludovic Trinquart
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Jonathan M. Davis
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
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11
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Zukin E, Culver JO, Liu Y, Yang Y, Ricker CN, Hodan R, Sturgeon D, Kingham K, Chun NM, Rowe-Teeter C, Singh K, Zell JA, Ladabaum U, McDonnell KJ, Ford JM, Parmigiani G, Braun D, Kurian AW, Gruber SB, Idos GE. Clinical implications of conflicting variant interpretations in the cancer genetics clinic. Genet Med 2023; 25:100837. [PMID: 37057674 PMCID: PMC10416421 DOI: 10.1016/j.gim.2023.100837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
PURPOSE The aim of this study was to describe the clinical impact of commercial laboratories issuing conflicting classifications of genetic variants. METHODS Results from 2000 patients undergoing a multigene hereditary cancer panel by a single laboratory were analyzed. Clinically significant discrepancies between the laboratory-provided test reports and other major commercial laboratories were identified, including differences between pathogenic/likely pathogenic and variant of uncertain significance (VUS) classifications, via review of ClinVar archives. For patients carrying a VUS, clinical documentation was assessed for evidence of provider awareness of the conflict. RESULTS Fifty of 975 (5.1%) patients with non-negative results carried a variant with a clinically significant conflict, 19 with a pathogenic/likely pathogenic variant reported in APC or MUTYH, and 31 with a VUS reported in CDKN2A, CHEK2, MLH1, MSH2, MUTYH, RAD51C, or TP53. Only 10 of 28 (36%) patients with a VUS with a clinically significant conflict had a documented discussion by a provider about the conflict. Discrepant counseling strategies were used for different patients with the same variant. Among patients with a CDKN2A variant or a monoallelic MUTYH variant, providers were significantly more likely to make recommendations based on the laboratory-reported classification. CONCLUSION Our findings highlight the frequency of variant interpretation discrepancies and importance of clinician awareness. Guidance is needed on managing patients with discrepant variants to support accurate risk assessment.
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Affiliation(s)
- Elyssa Zukin
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA; University of California, Irvine, Irvine, CA
| | - Julie O Culver
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Yuxi Liu
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Yunqi Yang
- Dana-Farber Cancer Institute, Boston, MA
| | - Charité N Ricker
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Rachel Hodan
- Stanford University School of Medicine, Stanford, CA
| | - Duveen Sturgeon
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - Kerry Kingham
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Uri Ladabaum
- Stanford University School of Medicine, Stanford, CA
| | - Kevin J McDonnell
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - James M Ford
- Stanford University School of Medicine, Stanford, CA
| | - Giovanni Parmigiani
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Danielle Braun
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - Stephen B Gruber
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - Gregory E Idos
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA.
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12
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Zhang K, Lin G, Han Y, Peng R, Li J. Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient-Parent Trio Sample: Pilot Study for Neurodevelopmental Disorder de Novo Variants. J Mol Diagn 2023; 25:378-387. [PMID: 37208049 DOI: 10.1016/j.jmoldx.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 05/21/2023] Open
Abstract
To date, there has been no systematic analysis for the clinical laboratory in detecting technically challenging variants using the trio-based exome sequencing (ES) approach. Here, we present an interlaboratory pilot proficiency testing study that used synthetic patient-parent specimens to assess the detection of challenging variants with de novo dominant inheritance modes for neurodevelopmental disorders using various trio-based ES. In total, 27 clinical laboratories that performed diagnostic exome analyses participated in the survey. One of the 26 challenging variants was identified by all laboratories, whereas all 26 variants were identified by only nine laboratories. The lack of identification of mosaic variants was often due to the bioinformatics analysis that excluded the variant. For missing intended heterozygous variants, probable root causes were related to the technical bioinformatics pipeline and variant interpretation and reporting. For each missing variant, there may be more than one probable reason from the different laboratories. There was considerable variation in interlaboratory performance for detecting challenging variants using trio-based ES. This finding may have important implications for the design and validation of tests for different variant types in clinical laboratories, especially for technically challenging variants, and necessary workflow modification can potentially improve trio-based ES performance.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.
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13
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Ratajska A, Vigeland MD, Wirgenes KV, Krohg‐Sørensen K, Paus B. The use of segregation analysis in interpretation of sequence variants in SMAD3: A case report. Mol Genet Genomic Med 2022; 11:e2107. [PMID: 36495030 PMCID: PMC9938750 DOI: 10.1002/mgg3.2107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND While representing a significant improvement, the introduction of next-generation sequencing in genetic diagnosis also prompted new challenges. Despite widely recognized consensus guidelines for the interpretation of sequence variants, many variants remain unclassified or are discordantly interpreted. In heritable thoracic aortic aneurysms with dissection (HTAAD), most cases are caused by a heterozygous, private missense mutation, possibly contributing to the relatively common reports of variants with uncertain significance in this group. Segregation analysis necessitates advanced likelihood-based methods typically inaccessible to non-experts and is hampered by reduced penetrance, possible phenocopies, and non-availability of DNA from deceased relatives. METHODS In this report, challenges in variant interpretation and the use of segregation analyses were illustrated in two families with a suspected HTAAD disorder. The R package segregatr, a novel implementation of full-likelihood Bayes factor (FLB), was performed to explore the cosegregation of the variants in these families. CONCLUSION Using the R package segregatr, cosegregation in the reported families concluded with strong and supporting evidence for pathogenicity. Surveillance of families in a multidisciplinary team enabling systematic phenotype description for standardized segregation analysis with a robust calculation method may be imperative for reliable variant interpretation in HTAAD.
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Affiliation(s)
| | - Magnus D. Vigeland
- Department of Medical GeneticsOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Katrine Verena Wirgenes
- Department of Medical GeneticsOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Kirsten Krohg‐Sørensen
- Institute of Clinical MedicineUniversity of OsloOsloNorway,Department of Thoracic SurgeryOslo University HospitalOsloNorway
| | - Benedicte Paus
- Department of Medical GeneticsOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
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14
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Davidson AL, Kondrashova O, Leonard C, Wood S, Tudini E, Hollway GE, Pearson JV, Newell F, Spurdle AB, Waddell N. Analysis of hereditary cancer gene variant classifications from ClinVar indicates a need for regular reassessment of clinical assertions. Hum Mutat 2022; 43:2054-2062. [PMID: 36095262 DOI: 10.1002/humu.24468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/22/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
The clinical classification of variants may change with new information, however, there is limited guidance on how often significant changes in variant classification occur. We used ClinVar to examine how variant classification changes over time. We developed a custom parser and accessed variant data from ClinVar between January 2015 and July 2021. The ClinVar-assigned "aggregate" classification of variants in 121 hereditary cancer genes was harmonized across releases to align to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology terms. Aggregate classification categories were grouped as: benign/likely benign (B/LB); likely pathogenic/pathogenic (LP/P); variant of uncertain significance (VUS); conflicting interpretations of pathogenicity (Conflicting); or Other. We profiled changes in aggregate variant classification between consecutive semi-annual ClinVar releases. The proportion of variants that changed aggregate classification between semi-annual ClinVar releases ranged from 0.6% to 6.4%. The most frequent changes were "VUS to conflicting," "other to LP/P," and "B/LB to Conflicting." A limited number of variants changed aggregate classification from "LP/P to B/LB," or vice versa. Our analysis indicates need for regular reassessment of clinical variant interpretations. The parser developed for this project will facilitate extraction of relevant interpretation data from ClinVar.
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Affiliation(s)
- Aimee L Davidson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Emma Tudini
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Australian Genomics, Melbourne, Victoria, Australia
| | - Georgina E Hollway
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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15
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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16
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Burdon KP, Graham P, Hadler J, Hulleman JD, Pasutto F, Boese EA, Craig JE, Fingert JH, Hewitt AW, Siggs OM, Whisenhunt K, Young TL, Mackey DA, Dubowsky A, Souzeau E. Specifications of the ACMG/AMP variant curation guidelines for myocilin: Recommendations from the clingen glaucoma expert panel. Hum Mutat 2022; 43:2170-2186. [PMID: 36217948 PMCID: PMC9771967 DOI: 10.1002/humu.24482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/02/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023]
Abstract
The standardization of variant curation criteria is essential for accurate interpretation of genetic results and clinical care of patients. The variant curation guidelines developed by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) in 2015 are widely used but are not gene specific. To address this issue, the Clinical Genome Resource (ClinGen) Variant Curation Expert Panels (VCEP) have been tasked with developing gene-specific variant curation guidelines. The Glaucoma VCEP was created to develop rule specifications for genes associated with primary glaucoma, including myocilin (MYOC), the most common cause of Mendelian glaucoma. Of the 28 ACMG/AMP criteria, the Glaucoma VCEP adapted 15 rules to MYOC and determined 13 rules not applicable. Key specifications included determining minor allele frequency thresholds, developing an approach to counting probands and segregations, and reviewing functional assays. The rules were piloted on 81 variants and led to a change in classification in 40% of those that were classified in ClinVar, with functional evidence influencing the classification of 18 variants. The standardized variant curation guidelines for MYOC provide a framework for the consistent application of the rules between laboratories, to improve MYOC genetic testing in the management of glaucoma.
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Affiliation(s)
- Kathryn P. Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Patricia Graham
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Centre for Ophthalmology and Vision Sciences, Lions Eye Institute, University of Western Australia, Perth, WA, Australia
| | - Johanna Hadler
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA, Australia
- SA Pathology, Adelaide, SA, Australia
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Francesca Pasutto
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erin A. Boese
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA, Australia
| | - John H. Fingert
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Owen M. Siggs
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kristina Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Terri L. Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David A. Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Centre for Ophthalmology and Vision Sciences, Lions Eye Institute, University of Western Australia, Perth, WA, Australia
| | | | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA, Australia
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17
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Mighton C, Shickh S, Aguda V, Krishnapillai S, Adi-Wauran E, Bombard Y. From the patient to the population: Use of genomics for population screening. Front Genet 2022; 13:893832. [PMID: 36353115 PMCID: PMC9637971 DOI: 10.3389/fgene.2022.893832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/26/2022] [Indexed: 10/22/2023] Open
Abstract
Genomic medicine is expanding from a focus on diagnosis at the patient level to prevention at the population level given the ongoing under-ascertainment of high-risk and actionable genetic conditions using current strategies, particularly hereditary breast and ovarian cancer (HBOC), Lynch Syndrome (LS) and familial hypercholesterolemia (FH). The availability of large-scale next-generation sequencing strategies and preventive options for these conditions makes it increasingly feasible to screen pre-symptomatic individuals through public health-based approaches, rather than restricting testing to high-risk groups. This raises anew, and with urgency, questions about the limits of screening as well as the moral authority and capacity to screen for genetic conditions at a population level. We aimed to answer some of these critical questions by using the WHO Wilson and Jungner criteria to guide a synthesis of current evidence on population genomic screening for HBOC, LS, and FH.
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Affiliation(s)
- Chloe Mighton
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Vernie Aguda
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Centre for Medical Education, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Suvetha Krishnapillai
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Ella Adi-Wauran
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
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18
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Inoue Y, Machida O, Kita Y, Yamamoto T. Need for revision of the ACMG/AMP guidelines for interpretation of X-linked variants. Intractable Rare Dis Res 2022; 11:120-124. [PMID: 36200025 PMCID: PMC9437996 DOI: 10.5582/irdr.2022.01067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
The guidelines provided by American College of Medical Genetics and Genomics (ACMG) and the Association of Molecular Pathology (AMP) (ACMG/AMP guidelines) suggest a framework for the classification of clinical variants. However, the interpretations can be inconsistent, with each definition sometimes proving to be ambiguous. In particular, there can be difficulty with interpretation of variants related to the X-linked recessive trait. To confirm whether there are biases in the interpretation of inherited traits, we reanalyzed variants reported prior to the release of the ACMG/AMP guidelines. As expected, the interpretation ratio as pathogenic or likely pathogenic was significantly lower for variants related to the X-linked recessive trait. Evaluation of variants related to the X-linked recessive trait, hence, need to consider whether the variant is identified only in males in accordance with the X-linked recessive trait. The ACMG/AMP guidelines should be revised to eliminate the bias revealed in this study.
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Affiliation(s)
- Yoko Inoue
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Osamu Machida
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yosuke Kita
- Department of Psychology, Faculty of Letters, Keio University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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19
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Drackley A, Brew C, Wlodaver A, Spencer S, Leuer K, Rathbun P, Charrow J, Wieneke X, Lee Yap K, Ing A. Utility and Outcomes of the 2019 American College of Medical Genetics and Genomics-Clinical Genome Resource Guidelines for Interpretation of Copy Number Variants with Borderline Classifications at an Academic Clinical Diagnostic Laboratory. J Mol Diagn 2022; 24:1100-1111. [PMID: 35868509 DOI: 10.1016/j.jmoldx.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
In 2019, American College of Medical Genetics and Genomics and the Clinical Genome Resource published updated technical standards for the interpretation and reporting of copy number variants (CNVs), introducing a semiquantitative classification system that aims to foster greater standardization and consistency between laboratories. Evaluation of these guidelines' performance will inform laboratories about the impact of their implementation into clinical practice. A total of 145 difficult-to-classify CNVs, originally assessed by an academic molecular diagnostic laboratory, were re-interpreted/classified according to the American College of Medical Genetics and Genomics-Clinical Genome Resource guidelines. Classifications between interpretation systems were then compared. The concordance rate was 60.7%, and significantly more variants of uncertain significance were obtained when using the guidelines (n = 98) versus the laboratory's classification system (n = 49; P < 0.001). The concordance rate was presumably impacted by the intentionally unclear nature of the selected variants. The difference in variant of uncertain significance rate was largely due to laboratory-specific practices for variant interpretation and reporting, as well as differences in utilization of general population data. Laboratory-specific policies and practices may need to be addressed for true standardization to be achieved. Challenges to consistent guideline utilization are centered around the general lack of high-quality curated data available for CNV interpretations and the inherent subjectivity in the selection of evidence criteria and application of evidence points. Multiple aspects of the guidelines were highlighted as potential opportunities for subsequent refinements to further improve classification standardization.
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Affiliation(s)
- Andy Drackley
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Casey Brew
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alissa Wlodaver
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Sara Spencer
- Department of Obstetrics and Gynecology, Northwestern Medicine, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Katrin Leuer
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Pamela Rathbun
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joel Charrow
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Xuwen Wieneke
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Alexander Ing
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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20
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Rahimzadeh V, Friedman JM, de Wert G, Knoppers BM. Exome/Genome-Wide Testing in Newborn Screening: A Proportionate Path Forward. Front Genet 2022; 13:865400. [PMID: 35860465 PMCID: PMC9289115 DOI: 10.3389/fgene.2022.865400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Population-based newborn screening (NBS) is among the most effective public health programs ever launched, improving health outcomes for newborns who screen positive worldwide through early detection and clinical intervention for genetic disorders discovered in the earliest hours of life. Key to the success of newborn screening programs has been near universal accessibility and participation. Interest has been building to expand newborn screening programs to also include many rare genetic diseases that can now be identified by exome or genome sequencing (ES/GS). Significant declines in sequencing costs as well as improvements to sequencing technologies have enabled researchers to elucidate novel gene-disease associations that motivate possible expansion of newborn screening programs. In this paper we consider recommendations from professional genetic societies in Europe and North America in light of scientific advances in ES/GS and our current understanding of the limitations of ES/GS approaches in the NBS context. We invoke the principle of proportionality—that benefits clearly outweigh associated risks—and the human right to benefit from science to argue that rigorous evidence is still needed for ES/GS that demonstrates clinical utility, accurate genomic variant interpretation, cost effectiveness and universal accessibility of testing and necessary follow-up care and treatment. Confirmatory or second-tier testing using ES/GS may be appropriate as an adjunct to conventional newborn screening in some circumstances. Such cases could serve as important testbeds from which to gather data on relevant programmatic barriers and facilitators to wider ES/GS implementation.
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Affiliation(s)
- Vasiliki Rahimzadeh
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, United States
- *Correspondence: Vasiliki Rahimzadeh,
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Guido de Wert
- Department of Health, Ethics and Society, Maastricht University, Maastricht, Netherlands
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21
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Vears DF, Elferink M, Kriek M, Borry P, van Gassen KL. The patient with 41 reports: Analysis of laboratory exome sequencing reporting of a "virtual patient". Genet Med 2022; 24:1306-15. [PMID: 35389343 DOI: 10.1016/j.gim.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Few studies have systematically analyzed the structure and content of laboratory exome sequencing reports from the same patient. METHODS We merged 8 variants from patients into "normal" exomes to create virtual patient-parent trios. We provided laboratories worldwide with the data and patient phenotype information (developmental delay, dysmorphic features, and cardiac hypertrophy). Laboratories analyzed the data and issued a diagnostic exome report. Reports were scored using a coding matrix developed from existing guidelines. RESULTS In total, 41 laboratories representing 17 countries issued reports. Reporting of quality control statistics and technical information was poor (46.3%). Although 75.6% of the reports clearly stated the classification of all reported variants, few reports listed extensive evidence supporting variant classification. Only 53.1% of laboratories that reported unsolicited or secondary findings gave advice regarding health-related follow-up and 20.5% gave advice regarding cascade testing for relatives. Of the 147 variants reported, 105 (71.4%) were classified in agreement with classifications based on American College of Medical Genetics and Genomics/Association for Molecular Pathology and Association for Clinical Genomic Science guidelines. Concordance was higher for known pathogenic variants (86.3%) than for novel unpublished variants (56.8%). CONCLUSION The considerable variability identified in the components that laboratories included in their reports and their classification of variants suggests that existing guidelines are not being used consistently with significant implications for patient care.
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22
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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23
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Glazer AM, Davogustto G, Shaffer CM, Vanoye CG, Desai RR, Farber-Eger EH, Dikilitas O, Shang N, Pacheco JA, Yang T, Muhammad A, Mosley JD, Van Driest SL, Wells QS, Shaffer LL, Kalash OR, Wada Y, Bland S, Yoneda ZT, Mitchell DW, Kroncke BM, Kullo IJ, Jarvik GP, Gordon AS, Larson EB, Manolio TA, Mirshahi T, Luo JZ, Schaid D, Namjou B, Alsaied T, Singh R, Singhal A, Liu C, Weng C, Hripcsak G, Ralston JD, McNally EM, Chung WK, Carrell DS, Leppig KA, Hakonarson H, Sleiman P, Sohn S, Glessner J, Denny J, Wei WQ, George AL, Shoemaker MB, Roden DM. Arrhythmia Variant Associations and Reclassifications in the eMERGE-III Sequencing Study. Circulation 2022; 145:877-891. [PMID: 34930020 PMCID: PMC8940719 DOI: 10.1161/circulationaha.121.055562] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Sequencing Mendelian arrhythmia genes in individuals without an indication for arrhythmia genetic testing can identify carriers of pathogenic or likely pathogenic (P/LP) variants. However, the extent to which these variants are associated with clinically meaningful phenotypes before or after return of variant results is unclear. In addition, the majority of discovered variants are currently classified as variants of uncertain significance, limiting clinical actionability. METHODS The eMERGE-III study (Electronic Medical Records and Genomics Phase III) is a multicenter prospective cohort that included 21 846 participants without previous indication for cardiac genetic testing. Participants were sequenced for 109 Mendelian disease genes, including 10 linked to arrhythmia syndromes. Variant carriers were assessed with electronic health record-derived phenotypes and follow-up clinical examination. Selected variants of uncertain significance (n=50) were characterized in vitro with automated electrophysiology experiments in HEK293 cells. RESULTS As previously reported, 3.0% of participants had P/LP variants in the 109 genes. Herein, we report 120 participants (0.6%) with P/LP arrhythmia variants. Compared with noncarriers, arrhythmia P/LP carriers had a significantly higher burden of arrhythmia phenotypes in their electronic health records. Fifty-four participants had variant results returned. Nineteen of these 54 participants had inherited arrhythmia syndrome diagnoses (primarily long-QT syndrome), and 12 of these 19 diagnoses were made only after variant results were returned (0.05%). After in vitro functional evaluation of 50 variants of uncertain significance, we reclassified 11 variants: 3 to likely benign and 8 to P/LP. CONCLUSIONS Genome sequencing in a large population without indication for arrhythmia genetic testing identified phenotype-positive carriers of variants in congenital arrhythmia syndrome disease genes. As the genomes of large numbers of people are sequenced, the disease risk from rare variants in arrhythmia genes can be assessed by integrating genomic screening, electronic health record phenotypes, and in vitro functional studies. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier; NCT03394859.
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Affiliation(s)
| | | | | | | | | | | | | | - Ning Shang
- Columbia University Irving Medical Center, New York NY
| | | | - Tao Yang
- Vanderbilt University Medical Center, Nashville TN
| | | | | | | | | | | | | | - Yuko Wada
- Vanderbilt University Medical Center, Nashville TN
| | - Sarah Bland
- Vanderbilt University Medical Center, Nashville TN
| | | | | | | | | | - Gail P. Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | | | | | | | | | - Bahram Namjou
- Cincinnati Children’s Hospital Medical Center, Cincinnati OH
| | - Tarek Alsaied
- Cincinnati Children’s Hospital Medical Center, Cincinnati OH
| | | | | | - Cong Liu
- Columbia University Irving Medical Center, New York NY
| | - Chunhua Weng
- Columbia University Irving Medical Center, New York NY
| | | | - James D. Ralston
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | | | | | | | | | | | | | | | | | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville TN
| | | | | | - Dan M. Roden
- Vanderbilt University Medical Center, Nashville TN
- Correspondence should be addressed to Dan M. Roden, MD, Vanderbilt University Medical Center, 2215B Garland Ave, 1285 MRBIV, Nashville, TN 37232,
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24
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Zhang K, Lin G, Han D, Han Y, Peng R, Li J. Adaptation of ACMG-ClinGen Technical Standards for Copy Number Variant Interpretation Concordance. Front Genet 2022; 13:829728. [PMID: 35360839 PMCID: PMC8960312 DOI: 10.3389/fgene.2022.829728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
This study aimed to evaluate inter-laboratory classification concordance for copy number variants (CNVs) with a semiquantitative point-based scoring metric recommended by the American College of Medical Genetics and Genomics (ACMG) and Clinical Genome Resources (ClinGen). A total of 234 CNVs distributed by the National Center of Clinical Laboratories (NCCLs), and 72 CNVs submitted by different laboratories, were distributed to nine clinical laboratories performing routine clinical CNV testing in China and independently classified across laboratories. The overall inter-laboratory complete classification concordance rate of the 234 distributed CNVs increased from 18% (41/234) to 76% (177/234) using the scoring metric compared to the laboratory's previous method. The overall inter-laboratory complete classification concordance rate of the 72 submitted CNVs was 65% (47/72) using the scoring metrics. The 82 variants that initially did not reach complete concordance classification and 1 additional CNV deletion were reviewed; 34 reached complete agreement, and the overall post-review complete concordance rate was 85% (260/306). Additionally, the overall percentage of classification discordance possibly impacting medical management [i.e., pathogenic (P) or likely pathogenic (LP) vs. variant of uncertain significance (VUS)] was 11% (35/306). The causes of initial and final discordance in the classification were identified. The ACMG-ClinGen framework has promoted consistency in interpreting the clinical significance of CNVs. Continuous training among laboratories, further criteria and additional clarification of the standards, sharing classifications and supporting evidence through public database, and ongoing work for dosage sensitive genes/regions curation will be beneficial for harmonization of CNVs classification.
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25
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Zouk H, Yu W, Oza A, Hawley M, Vijay Kumar PK, Koch C, Mahanta LM, Harley JB, Jarvik GP, Karlson EW, Leppig KA, Myers MF, Prows CA, Williams MS, Weiss ST, Lebo MS, Rehm HL. Reanalysis of eMERGE phase III sequence variants in 10,500 participants and infrastructure to support the automated return of knowledge updates. Genet Med 2022; 24:454-462. [PMID: 34906510 PMCID: PMC10128874 DOI: 10.1016/j.gim.2021.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The clinical genomics knowledgebase is dynamic with variant classifications changing as newly identified cases, additional population data, and other evidence become available. This is a challenge for the clinical laboratory because of limited resource availability for variant reassessment. METHODS Throughout the Electronic Medical Records and Genomics phase III program, clinical sites associated with the Mass General Brigham/Broad sequencing center received automated, real-time notifications when reported variants were reclassified. In this study, we summarized the nature of these reclassifications and described the proactive reassessment framework we used for the Electronic Medical Records and Genomics program data set to identify variants most likely to undergo reclassification. RESULTS Reanalysis of 1855 variants led to the reclassification of 2% (n = 45) of variants, affecting 0.6% (n = 67) of participants. Of these reclassifications, 78% (n = 35) were high-impact changes affecting reportability, with 8 variants downgraded from likely pathogenic/pathogenic to variants of uncertain significance (VUS) and 27 variants upgraded from VUS to likely pathogenic/pathogenic. Most upgraded variants (67%) were initially classified as VUS-Favor Pathogenic, highlighting the benefit of VUS subcategorization. The most common reason for reclassification was new published case data and/or functional evidence. CONCLUSION Our results highlight the importance of periodic sequence variant reevaluation and the need for automated approaches to advance routine implementation of variant reevaluations in clinical practice.
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Affiliation(s)
- Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Andrea Oza
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Megan Hawley
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Prathik K Vijay Kumar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - John B Harley
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH; US Department of Veteran Affairs Medical Center, Cincinnati, OH
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH
| | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Scott T Weiss
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
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26
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Benet-Pagès A, Rosenbloom KR, Nassar LR, Lee CM, Raney BJ, Clawson H, Schmelter D, Casper J, Gonzalez JN, Perez G, Lee BT, Zweig AS, James Kent W, Haeussler M, Kuhn RM. Variant Interpretation: UCSC Genome Browser Recommended Track Sets. Hum Mutat 2022; 43:998-1011. [PMID: 35088925 PMCID: PMC9288501 DOI: 10.1002/humu.24335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 11/11/2022]
Abstract
The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anna Benet-Pagès
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Medical Genetics Center (MGZ), Munich, Germany
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Luis R Nassar
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Daniel Schmelter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Gerardo Perez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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R Hamre J, Klimov DK, McCoy MD, Jafri MS. Machine learning-based prediction of drug and ligand binding in BCL-2 variants through molecular dynamics. Comput Biol Med 2022; 140:105060. [PMID: 34920365 DOI: 10.1016/j.compbiomed.2021.105060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/13/2021] [Accepted: 11/20/2021] [Indexed: 12/13/2022]
Abstract
Venetoclax is a BH3 (BCL-2 Homology 3) mimetic used to treat leukemia and lymphoma by inhibiting the anti-apoptotic BCL-2 protein thereby promoting apoptosis of cancerous cells. Acquired resistance to Venetoclax via specific variants in BCL-2 is a major problem for the successful treatment of cancer patients. Replica exchange molecular dynamics (REMD) simulations combined with machine learning were used to define the average structure of variants in aqueous solution to predict changes in drug and ligand binding in BCL-2 variants. The variant structures all show shifts in residue positions that occlude the binding groove, and these are the primary contributors to drug resistance. Correspondingly, we established a method that can predict the severity of a variant as measured by the inhibitory constant (Ki) of Venetoclax by measuring the structure deviations to the binding cleft. In addition, we also applied machine learning to the phi and psi angles of the amino acid backbone to the ensemble of conformations that demonstrated a generalizable method for drug resistant predictions of BCL-2 proteins that elucidates changes where detailed understanding of the structure-function relationship is less clear.
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Affiliation(s)
- John R Hamre
- School of Systems Biology, George Mason University, Manassas, VA, USA.
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, VA, USA.
| | - Matthew D McCoy
- Innovation Center for Biomedical Informatics, Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA.
| | - M Saleet Jafri
- School of Systems Biology, George Mason University, Fairfax, VA and Center for Biomedical Technology and Engineering, University of Maryland School of Medicine, Baltimore, MD, USA.
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Harrison SM, Austin-Tse CA, Kim S, Lebo M, Leon A, Murdock D, Radhakrishnan A, Shirts BH, Steeves M, Venner E, Gibbs RA, Jarvik GP, Rehm HL. Harmonizing variant classification for return of results in the All of Us Research Program. Hum Mutat 2021; 43:1114-1121. [PMID: 34923710 PMCID: PMC9206690 DOI: 10.1002/humu.24317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 11/18/2022]
Abstract
The All of Us Research Program (AoURP) is a historic effort to accelerate research and improve healthcare by generating and collating data from one million people in the United States. Participants will have the option to receive results from their genome analysis, including actionable findings in 59 gene‐disorder pairs for which disorder‐associated variants are recommended for return by the American College of Medical Genetics and Genomics. To ensure consistent reporting across the AoURP, in a prelaunch study the four participating clinical laboratories shared all variant classifications in the 59 genes of interest from their internal databases. Of the 11,813 unique variants classified by at least two of the four laboratories, classifications were concordant with regard to reportability for 99.1% (11,711), with only 0.9% (102) having reportability differences. Through variant reassessment, data sharing, and discussion of rationale, participating laboratories resolved all 102 reportable differences. These approaches will be maintained during routine AoU reporting to ensure continuous classification harmonization and consistent reporting within AoURP.
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Affiliation(s)
| | - Christina A Austin-Tse
- Laboratory for Molecular Medicine, Mass General Brigham, Boston, Massachusetts, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Serra Kim
- Color Health, Burlingame, California, USA
| | - Matthew Lebo
- Laboratory for Molecular Medicine, Mass General Brigham, Boston, Massachusetts, USA
| | | | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Brian H Shirts
- University of Washington Medical Center, Seattle, Washington, USA
| | - Marcie Steeves
- Laboratory for Molecular Medicine, Mass General Brigham, Boston, Massachusetts, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Gail P Jarvik
- University of Washington Medical Center, Seattle, Washington, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Lazarte J, Hegele RA. Lamin A/C missense variants: from discovery to functional validation. NPJ Genom Med 2021; 6:102. [PMID: 34862397 DOI: 10.1038/s41525-021-00266-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/28/2021] [Indexed: 01/09/2023] Open
Abstract
Rare variants in the LMNA gene encoding nuclear lamin A/C are causal for more than a dozen diverse mendelian disorders. Defining the functional consequences of LMNA variants has been challenging given the pleiotropy of gene functions and potential pathogenic mechanisms. It is essential to develop trustworthy, scalable and rapidly deployable in vitro assays of function to enable timely assessment of missense variants that are being uncovered by high throughout next-generation sequencing.
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Frone MN, Stewart DR, Savage SA, Khincha PP. Quantification of Discordant Variant Interpretations in a Large Family-Based Study of Li-Fraumeni Syndrome. JCO Precis Oncol 2021; 5:PO.21.00320. [PMID: 34805717 PMCID: PMC8594664 DOI: 10.1200/po.21.00320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/22/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The use of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines has improved germline variant classification concordance, but discrepancies persist, sometimes directly affecting medical management. We evaluated variant discordance between and within families with germline TP53 variants in the National Cancer Institute's Li-Fraumeni syndrome longitudinal cohort study. MATERIALS AND METHODS Germline TP53 genetic testing results were obtained from 421 individuals in 140 families. A discordant test result was defined as a report of pathogenicity that differed between two clinical testing laboratories, between a testing laboratory and the ClinVar database, or between either the laboratory or ClinVar database and variant classification by internal study review. RESULTS There were 141 variants in 140 families (one family had two different TP53 variants). Fifty-four families had discordant interpretations (54 of 140, 39%). Sixteen families had discordant classifications leading to clinically important differences in medical management (16 of 140, 11%). Interfamilial discordance was observed between four families (two different variants). Intrafamilial discordance was observed within six families. One family experienced both intrafamilial and interfamilial discordance. CONCLUSION This large single-gene study found discordant germline TP53 variant interpretations in 39% of families studied; 11% had a variant with the potential to significantly affect medical management. This finding is especially concerning in patients with Li-Fraumeni syndrome because of their exceedingly high risks of multiple cancers and intensive cancer screening and risk-reducing recommendations. Centralized data sharing, gene-specific variant curation guidelines, and provider education for consistent variant interpretation are essential for optimal patient care.
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Affiliation(s)
- Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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31
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Eric V, Yi V, Murdock D, Kalla SE, Wu TJ, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei WQ, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny D, Gibbs RA. Neptune: an environment for the delivery of genomic medicine. Genet Med 2021; 23:1838-1846. [PMID: 34257418 PMCID: PMC8487966 DOI: 10.1038/s41436-021-01230-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/13/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. METHODS We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. RESULTS Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. CONCLUSION Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .
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Affiliation(s)
- Venner Eric
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Victoria Yi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sara E Kalla
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Cohen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, NY, USA
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Stark Z, Foulger RE, Williams E, Thompson BA, Patel C, Lunke S, Snow C, Leong IUS, Puzriakova A, Daugherty LC, Leigh S, Boustred C, Niblock O, Rueda-Martin A, Gerasimenko O, Savage K, Bellamy W, Lin VSK, Valls R, Gordon L, Brittain HK, Thomas ERA, Taylor Tavares AL, McEntagart M, White SM, Tan TY, Yeung A, Downie L, Macciocca I, Savva E, Lee C, Roesley A, De Fazio P, Deller J, Deans ZC, Hill SL, Caulfield MJ, North KN, Scott RH, Rendon A, Hofmann O, McDonagh EM. Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution. Am J Hum Genet 2021; 108:1551-1557. [PMID: 34329581 PMCID: PMC8456155 DOI: 10.1016/j.ajhg.2021.06.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/27/2021] [Indexed: 02/02/2023] Open
Abstract
Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Rebecca E Foulger
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Eleanor Williams
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bryony A Thompson
- University of Melbourne, Melbourne, VIC 3010, Australia; Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Catherine Snow
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ivone U S Leong
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Arina Puzriakova
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Louise C Daugherty
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher Boustred
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Olivia Niblock
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Antonio Rueda-Martin
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Oleg Gerasimenko
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kevin Savage
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - William Bellamy
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Victor San Kho Lin
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Roman Valls
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Lavinia Gordon
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Helen K Brittain
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ellen R A Thomas
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Guy's and St Thomas's NHS Trust, London SE1 9RS, UK
| | | | - Meriel McEntagart
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; St George's University Hospitals NHS Trust, London SW17 0QT, UK
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lilian Downie
- University of Melbourne, Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ivan Macciocca
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ain Roesley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Paul De Fazio
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Jane Deller
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Zandra C Deans
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Sue L Hill
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Mark J Caulfield
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kathryn N North
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Augusto Rendon
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Oliver Hofmann
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ellen M McDonagh
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Open Targets and European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
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Davieson CD, Joyce KE, Sharma L, Shovlin CL. DNA variant classification-reconsidering "allele rarity" and "phenotype" criteria in ACMG/AMP guidelines. Eur J Med Genet 2021; 64:104312. [PMID: 34411772 DOI: 10.1016/j.ejmg.2021.104312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/12/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
Recent guidance suggested modified DNA variant pathogenicity assignments based on genome-wide allele rarity. Different a priori probabilities of pathogenicity operate where patients already have clinical diagnoses, and are found to have a very rare variant in a gene known to cause their disease, compared to predictive testing of a clinically unaffected individual. We tested new recommendations from the ClinGen Sequence Variant Interpretation Working Group for ClinVar-listed, loss-of-function variants meeting the very strong evidence of pathogenicity criterion [PVS1] in genes for 3 specific diseases where causal gene identification can modify clinical care of an individual- Von Willebrand disease, cystic fibrosis and hereditary haemorrhagic telangiectasia. Across these diseases, current rules leave 20/1,278 (1.6%) of loss-of-function variants as variants of uncertain significance (VUS that may not be reported to clinicians), and 207/1,278 (17.2%) as likely pathogenic. Applying the new ClinGen rule enabling PVS1 and the allele rarity criterion PM2 to delineate likely pathogenicity still left 8/1,278 (0.9%) as VUS (reflecting non-PVS1 calls by the submitters), and the majority of null alleles meeting PVS1 as merely likely pathogenic. We favour an approach whereby, for PVS1 variants in patients who personally meet the phenotypic PP4 criterion for a disease where casual variants are commonly family-specific, that PM2 is upgraded to permit a pathogenic call. Of 1,278 ClinVar-listed frameshift, nonsense and canonical splice site variants that met PVS1 in the 3 conditions, 16.0% (204/1,278) would be newly designated as pathogenic, avoiding misinterpretation outside of clinical genetics communities. We suggest further discussion around variant assessment across different clinical applications, potentially guided by PP4 alerts to distinguish personal versus family phenotypic history.
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Affiliation(s)
- Connor D Davieson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Katie E Joyce
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Lakshya Sharma
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claire L Shovlin
- National Heart and Lung Institute, Imperial College London, London, UK; Imperial College Healthcare NHS Trust, London, UK.
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Lund AM, Wibrand F, Skogstrand K, Bækvad-Hansen M, Gregersen N, Andresen BS, Hougaard DM, Dunø M, Olsen RKJ. Use of Molecular Genetic Analyses in Danish Routine Newborn Screening. Int J Neonatal Screen 2021; 7:ijns7030050. [PMID: 34449524 PMCID: PMC8395600 DOI: 10.3390/ijns7030050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 12/20/2022] Open
Abstract
Historically, the analyses used for newborn screening (NBS) were biochemical, but increasingly, molecular genetic analyses are being introduced in the workflow. We describe the application of molecular genetic analyses in the Danish NBS programme and show that second-tier molecular genetic testing is useful to reduce the false positive rate while simultaneously providing information about the precise molecular genetic variant and thus informing therapeutic strategy and easing providing information to parents. When molecular genetic analyses are applied as second-tier testing, valuable functional data from biochemical methods are available and in our view, such targeted NGS technology should be implemented when possible in the NBS workflow. First-tier NGS technology may be a promising future possibility for disorders without a reliable biomarker and as a general approach to increase the adaptability of NBS for a broader range of genetic diseases, which is important in the current landscape of quickly evolving new therapeutic possibilities. However, studies on feasibility, sensitivity, and specificity are needed as well as more insight into what views the general population has towards using genetic analyses in NBS. This may be sensitive to some and could have potentially negative consequences for the NBS programme.
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Affiliation(s)
- Allan Meldgaard Lund
- Center for Inherited Metabolic Disorders, Departments of Clinical Genetics and Pediatrics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Correspondence: ; Fax: +45-35454072
| | - Flemming Wibrand
- Metabolic Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Marie Bækvad-Hansen
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (N.G.); (R.K.J.O.)
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark;
| | - David M. Hougaard
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Morten Dunø
- Molecular Genetics Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
| | - Rikke Katrine Jentoft Olsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (N.G.); (R.K.J.O.)
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Trost B, Loureiro LO, Scherer SW. Discovery of genomic variation across a generation. Hum Mol Genet 2021; 30:R174-R186. [PMID: 34296264 PMCID: PMC8490016 DOI: 10.1093/hmg/ddab209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Over the past 30 years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared with the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA—approximately 30 megabase pairs (Mb)—being ‘structurally variable’, mostly in the form of indels and copy number changes. Additional large-scale variations include balanced inversions (average of 18 Mb) and complex, difficult-to-resolve alterations. Collectively, ~1% of an individual’s genome will differ from the human reference sequence. When comparing across a generation, fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child’s genome. Driven by increasingly higher-resolution and higher-throughput sequencing technologies, newer and more accurate databases of genetic variation (for instance, more comprehensive structural variation data and phasing of combinations of variants along chromosomes) of worldwide populations will emerge to underpin the next era of discovery in human molecular genetics.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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Giles HH, Hegde MR, Lyon E, Stanley CM, Kerr ID, Garlapow ME, Eggington JM. The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy. Annu Rev Genomics Hum Genet 2021; 22:285-307. [PMID: 33900788 DOI: 10.1146/annurev-genom-121620-082709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clinical genetic variant classification science is a growing subspecialty of clinical genetics and genomics. The field's continued improvement is essential for the success of precision medicine in both germline (hereditary) and somatic (oncology) contexts. This review focuses on variant classification for DNA next-generation sequencing tests. We first summarize current limitations in variant discovery and definition, and then describe the current five- and four-tier classification systems outlined in dominant standards and guideline publications for germline and somatic tests, respectively. We then discuss measures of variant classification discordance and the field's bias for positive results, as well as considerations for panel size and population screening in the context of estimates of positive predictive value thatincorporate estimated variant classification imperfections. Finally, we share opinions on the current state of variant classification from some of the authors of the most widely used standards and guideline publications and from other domain experts.
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Affiliation(s)
- Hunter H Giles
- Center for Genomic Interpretation, Sandy, Utah 84092, USA; , ,
| | - Madhuri R Hegde
- PerkinElmer Genomics, Waltham, Massachusetts 02450, USA; .,Department of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Elaine Lyon
- HudsonAlpha Clinical Services Lab, Huntsville, Alabama 35806, USA;
| | - Christine M Stanley
- C2i Genomics, Cambridge, Massachusetts 02139, USA.,Variantyx, Framingham, Massachusetts 01701, USA;
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Mighton C, Smith AC, Mayers J, Tomaszewski R, Taylor S, Hume S, Agatep R, Spriggs E, Feilotter HE, Semenuk L, Wong H, Lazo de la Vega L, Marshall CR, Axford MM, Silver T, Charames GS, Di Gioacchino V, Watkins N, Foulkes WD, Clavier M, Hamel N, Chong G, Lamont RE, Parboosingh J, Karsan A, Bosdet I, Young SS, Tucker T, Akbari MR, Speevak MD, Vaags AK, Lebo MS, Lerner-Ellis J. Data sharing to improve concordance in variant interpretation across laboratories: results from the Canadian Open Genetics Repository. J Med Genet 2021; 59:571-578. [PMID: 33875564 DOI: 10.1136/jmedgenet-2021-107738] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study aimed to identify and resolve discordant variant interpretations across clinical molecular genetic laboratories through the Canadian Open Genetics Repository (COGR), an online collaborative effort for variant sharing and interpretation. METHODS Laboratories uploaded variant data to the Franklin Genoox platform. Reports were issued to each laboratory, summarising variants where conflicting classifications with another laboratory were noted. Laboratories could then reassess variants to resolve discordances. Discordance was calculated using a five-tier model (pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), benign (B)), a three-tier model (LP/P are positive, VUS are inconclusive, LB/B are negative) and a two-tier model (LP/P are clinically actionable, VUS/LB/B are not). We compared the COGR classifications to automated classifications generated by Franklin. RESULTS Twelve laboratories submitted classifications for 44 510 unique variants. 2419 variants (5.4%) were classified by two or more laboratories. From baseline to after reassessment, the number of discordant variants decreased from 833 (34.4% of variants reported by two or more laboratories) to 723 (29.9%) based on the five-tier model, 403 (16.7%) to 279 (11.5%) based on the three-tier model and 77 (3.2%) to 37 (1.5%) based on the two-tier model. Compared with the COGR classification, the automated Franklin classifications had 94.5% sensitivity and 96.6% specificity for identifying actionable (P or LP) variants. CONCLUSIONS The COGR provides a standardised mechanism for laboratories to identify discordant variant interpretations and reduce discordance in genetic test result delivery. Such quality assurance programmes are important as genetic testing is implemented more widely in clinical care.
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Affiliation(s)
- Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | | | - Justin Mayers
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | | | - Sherryl Taylor
- Alberta Precision Laboratories, Edmonton, Alberta, Canada.,Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Stacey Hume
- Alberta Precision Laboratories, Edmonton, Alberta, Canada.,Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ron Agatep
- Shared Health, Winnipeg, Manitoba, Canada.,Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Elizabeth Spriggs
- Shared Health, Winnipeg, Manitoba, Canada.,Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Harriet E Feilotter
- Kingston Health Sciences Centre, Kingston, Ontario, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Laura Semenuk
- Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Henry Wong
- Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Lorena Lazo de la Vega
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christian R Marshall
- Genome Diagnostics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Michelle M Axford
- Genome Diagnostics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Talia Silver
- Genome Diagnostics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - William D Foulkes
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady David Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Marcos Clavier
- Lady David Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nancy Hamel
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - George Chong
- Lady David Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Ryan E Lamont
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Jillian Parboosingh
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sean S Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Mohammad Reza Akbari
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada .,Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Gorin MB, Ahn J. Using Molecular Diagnostics for Inherited Retinal Dystrophies: The 6 “I”s That Are Necessary to Diagnose 2 Eyes Genetically. Ophthalmology Science 2021; 1:100018. [PMID: 36246004 PMCID: PMC9559090 DOI: 10.1016/j.xops.2021.100018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Woerner AC, Gallagher RC, Vockley J, Adhikari AN. The Use of Whole Genome and Exome Sequencing for Newborn Screening: Challenges and Opportunities for Population Health. Front Pediatr 2021; 9:663752. [PMID: 34350142 PMCID: PMC8326411 DOI: 10.3389/fped.2021.663752] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/07/2021] [Indexed: 01/01/2023] Open
Abstract
Newborn screening (NBS) is a population-based program with a goal of reducing the burden of disease for conditions with significant clinical impact on neonates. Screening tests were originally developed and implemented one at a time, but newer methods have allowed the use of multiplex technologies to expand additions more rapidly to standard panels. Recent improvements in next-generation sequencing are also evolving rapidly from first focusing on individual genes, then panels, and finally all genes as encompassed by whole exome and genome sequencing. The intersection of these two technologies brings the revolutionary possibility of identifying all genetic disorders in newborns, allowing implementation of therapies at the optimum time regardless of symptoms. This article reviews the history of newborn screening and early studies examining the use of whole genome and exome sequencing as a screening tool. Lessons learned from these studies are discussed, along with technical, ethical, and societal challenges to broad implementation.
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Affiliation(s)
- Audrey C Woerner
- Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Renata C Gallagher
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Aashish N Adhikari
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States.,Artificial Intelligence Lab, Illumina Inc, Foster City, CA, United States
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