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Tong L, Wang X, Wang H, Yang R, Li X, Yin X. Functional analysis of a novel nonsense PPP1R12A variant in a Chinese family with infantile epilepsy. BMC Med Genomics 2024; 17:236. [PMID: 39334371 PMCID: PMC11429181 DOI: 10.1186/s12920-024-02009-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Defects in PPP1R12A can lead to genitourinary and/or brain malformation syndrome (GUBS). GUBS is primarily characterized by neurological or genitourinary system abnormalities, but a few reported cases are associated with neonatal seizures. Here, we report a case of a female newborn with neonatal seizures caused by a novel variant in PPP1R12A, aiming to enhance the clinical and variant data of genetic factors related to epilepsy in early life. METHODS Whole-exome and Sanger sequencing were used for familial variant assessment, and bioinformatics was employed to annotate the variant. A structural model of the mutant protein was simulated using molecular dynamics (MD), and the free binding energy between PPP1R12A and PPP1CB was analyzed. A mutant plasmid was constructed, and mutant protein expression was analyzed using western blotting (WB), and the interaction between the mutant and PPP1CB proteins using co-immunoprecipitation (Co-IP) experiments. RESULTS The patient experienced tonic-clonic seizures on the second day after birth. Genetic testing revealed a heterozygous variant in PPP1R12A, NM_002480.3:c.2533 C > T (p.Arg845Ter). Both parents had the wild-type gene. MD suggested that loss of the C-terminal structure in the mutant protein altered its structural stability and increased the binding energy with PPP1CB, indicating unstable protein-protein interactions. On WB, a low-molecular-weight band was observed, indicating that the protein was truncated. Co-IP indicated that the mutant protein no longer interacted with PPP1CB, indicating an effect on the structural stability of the myosin phase complex. CONCLUSION The PPP1R12A c.2533 C > T variant may explain the neonatal seizures in the present case. The findings of this study expand the spectrum of PPP1R12A variants and highlight the potential significance of truncated proteins in the pathogenesis of GUBS.
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Affiliation(s)
- Ling Tong
- Department of Neonatology, Anhui Women and Children's Medical Center, No. 15, Yimin Street, Hefei, 230001, Anhui, China
| | - Xinxin Wang
- Department of Neonatology, Anhui Women and Children's Medical Center, No. 15, Yimin Street, Hefei, 230001, Anhui, China
| | - Huiqin Wang
- Department of Neonatology, Anhui Women and Children's Medical Center, No. 15, Yimin Street, Hefei, 230001, Anhui, China
| | - Rong Yang
- Department of Neonatology, Anhui Women and Children's Medical Center, No. 15, Yimin Street, Hefei, 230001, Anhui, China
| | - Xiaoyan Li
- Department of Neonatology, Anhui Women and Children's Medical Center, No. 15, Yimin Street, Hefei, 230001, Anhui, China
| | - Xiaoguang Yin
- Department of Neonatology, Anhui Women and Children's Medical Center, No. 15, Yimin Street, Hefei, 230001, Anhui, China.
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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, de Dunnen J, Hassanin E, Lin WL, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau E, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Large-scale application of ClinGen-InSiGHT APC-specific ACMG/AMP variant classification criteria leads to substantial reduction in VUS. Am J Hum Genet 2024:S0002-9297(24)00337-9. [PMID: 39357517 DOI: 10.1016/j.ajhg.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 10/04/2024] Open
Abstract
Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUSs), APC-specific variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) based on the criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). A streamlined algorithm using the APC-specific criteria was developed and applied to assess all APC variants in ClinVar and the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) international reference APC Leiden Open Variation Database (LOVD) variant database, which included a total of 10,228 unique APC variants. Among the ClinVar and LOVD variants with an initial classification of (likely) benign or (likely) pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUSs were reclassified into clinically meaningful classes, the vast majority as (likely) benign. The total number of VUSs was reduced by 37%. In 24 out of 37 (65%) promising APC variants that remained VUS despite evidence for pathogenicity, a data-mining-driven work-up allowed their reclassification as (likely) pathogenic. These results demonstrated that the application of APC-specific criteria substantially reduced the number of VUSs in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalizable model for other gene- or disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUSs that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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Affiliation(s)
- Xiaoyu Yin
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia; Department of Medicine, University of Melbourne, Parkville, VIC, Australia; Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - Xuemei Shi
- Greenwood Genetic Center, Greenwood, SC, USA
| | - Elisabet Ognedal
- Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Valeria Vasta
- Northwest Genomics Center, Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marta Pineda
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, the Netherlands; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Deborah Ritter
- Baylor College of Medicine, Houston, TX, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Johan de Dunnen
- Departments of Human Genetics & Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Emadeldin Hassanin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | | | - Margareta Nordling
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | | | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Emily Nadeau
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | | | - Carli Tops
- Departments of Human Genetics & Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, and Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Ian M Frayling
- Polyposis Registry, St Mark's Hospital, London, UK; Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, Cardiff University, Cardiff, UK; National Centre for Colorectal Disease, St Vincent's University Hospital, Dublin, Ireland
| | - Gabriel Capellá
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, the Netherlands; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Andrew Latchford
- Polyposis Registry, St Mark's Hospital, London, UK; Department of Surgery and Cancer, Imperial College, London, UK
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA; Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany; Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Sharon E Plon
- Baylor College of Medicine, Houston, TX, USA; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Marc S Greenblatt
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Finlay A Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia; Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, the Netherlands; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, the Netherlands; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.
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Rowlands CF, Garrett A, Allen S, Durkie M, Burghel GJ, Robinson R, Callaway A, Field J, Frugtniet B, Palmer-Smith S, Grant J, Pagan J, McDevitt T, McVeigh TP, Hanson H, Whiffin N, Jones M, Turnbull C. The PS4-likelihood ratio calculator: flexible allocation of evidence weighting for case-control data in variant classification. J Med Genet 2024; 61:983-991. [PMID: 39227160 DOI: 10.1136/jmg-2024-110034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/05/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND The 2015 American College of Medical Genetics/Association of Molecular Pathology (ACMG/AMP) variant classification framework specifies that case-control observations can be scored as 'strong' evidence (PS4) towards pathogenicity. METHODS We developed the PS4-likelihood ratio calculator (PS4-LRCalc) for quantitative evidence assignment based on the observed variant frequencies in cases and controls. Binomial likelihoods are computed for two models, each defined by prespecified OR thresholds. Model 1 represents the hypothesis of association between variant and phenotype (eg, OR≥5) and model 2 represents the hypothesis of non-association (eg, OR≤1). RESULTS PS4-LRCalc enables continuous quantitation of evidence for variant classification expressed as a likelihood ratio (LR), which can be log-converted into log LR (evidence points). Using PS4-LRCalc, observed data can be used to quantify evidence towards either pathogenicity or benignity. Variants can also be evaluated against models of different penetrance. The approach is applicable to balanced data sets generated for more common phenotypes and smaller data sets more typical in very rare disease variant evaluation. CONCLUSION PS4-LRCalc enables flexible evidence quantitation on a continuous scale for observed case-control data. The converted LR is amenable to incorporation into the now widely used 2018 updated Bayesian ACMG/AMP framework.
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Affiliation(s)
- Charlie F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Alice Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Sophie Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NEY Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rachel Robinson
- The Leeds Genetics Laboratory, NEY Genomic Laboratory Hub, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alison Callaway
- Wessex Genetics Laboratory Service, University Hospital Southampton NHS Foundation Trust, Salisbury, UK
| | - Joanne Field
- Genomics and Molecular Medicine Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Bethan Frugtniet
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Sheila Palmer-Smith
- Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Jonathan Grant
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, G51 4TF, UK
| | - Judith Pagan
- South East Scotland Clinical Genetics, Western General Hospital, Edinburgh, UK
| | - Trudi McDevitt
- CHI Crumlin Department of Clinical Genetics, Dublin, Ireland
| | | | - Helen Hanson
- Peninsula Regional Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford, UK
- Program in Medical and Population Genetics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
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Bergquist T, Stenton SL, Nadeau EAW, Byrne AB, Greenblatt MS, Harrison SM, Tavtigian SV, O'Donnell-Luria A, Biesecker LG, Radivojac P, Brenner SE, Pejaver V. Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.611902. [PMID: 39345488 PMCID: PMC11429929 DOI: 10.1101/2024.09.17.611902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Purpose We previously developed an approach to calibrate computational tools for clinical variant classification, updating recommendations for the reliable use of variant impact predictors to provide evidence strength up to Strong . A new generation of tools using distinctive approaches have since been released, and these methods must be independently calibrated for clinical application. Method Using our local posterior probability-based calibration and our established data set of ClinVar pathogenic and benign variants, we determined the strength of evidence provided by three new tools (AlphaMissense, ESM1b, VARITY) and calibrated scores meeting each evidence strength. Results All three tools reached the Strong level of evidence for variant pathogenicity and Moderate for benignity, though sometimes for few variants. Compared to previously recommended tools, these yielded at best only modest improvements in the tradeoffs of evidence strength and false positive predictions. Conclusion At calibrated thresholds, three new computational predictors provided evidence for variant pathogenicity at similar strength to the four previously recommended predictors (and comparable with functional assays for some variants). This calibration broadens the scope of computational tools for application in clinical variant classification. Their new approaches offer promise for future advancement of the field.
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5
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Richardson ME, Holdren M, Brannan T, de la Hoya M, Spurdle AB, Tavtigian SV, Young CC, Zec L, Hiraki S, Anderson MJ, Walker LC, McNulty S, Turnbull C, Tischkowitz M, Schon K, Slavin T, Foulkes WD, Cline M, Monteiro AN, Pesaran T, Couch FJ. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants. Am J Hum Genet 2024:S0002-9297(24)00332-X. [PMID: 39317201 DOI: 10.1016/j.ajhg.2024.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/26/2024] Open
Abstract
The ClinGen Hereditary Breast, Ovarian, and Pancreatic Cancer (HBOP) Variant Curation Expert Panel (VCEP) is composed of internationally recognized experts in clinical genetics, molecular biology, and variant interpretation. This VCEP made specifications for the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) guidelines for the ataxia telangiectasia mutated (ATM) gene according to the ClinGen protocol. These gene-specific rules for ATM were modified from the ACMG/AMP guidelines and were tested against 33 ATM variants of various types and classifications in a pilot curation phase. The pilot revealed a majority agreement between the HBOP VCEP classifications and the ClinVar-deposited classifications. Six pilot variants had conflicting interpretations in ClinVar, and re-evaluation with the VCEP's ATM-specific rules resulted in four that were classified as benign, one as likely pathogenic, and one as a variant of uncertain significance (VUS) by the VCEP, improving the certainty of interpretations in the public domain. Overall, 28 of the 33 pilot variants were not VUS, leading to an 85% classification rate. The ClinGen-approved, modified rules demonstrated value for improved interpretation of variants in ATM.
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Affiliation(s)
| | - Megan Holdren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | | | | | | | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shannon McNulty
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | - Katherine Schon
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | - Thomas Slavin
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - William D Foulkes
- Departments of Human Genetics, McGill University, Montreal, QC, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Mail Stop: Genomics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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6
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Ranola JMO, Horton C, Pesaran T, Fayer S, Starita LM, Shirts BH. Assigning credit where it is due: an information content score to capture the clinical value of multiplexed assays of variant effect. BMC Bioinformatics 2024; 25:295. [PMID: 39243022 PMCID: PMC11380199 DOI: 10.1186/s12859-024-05920-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 09/03/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND A variant can be pathogenic or benign with relation to a human disease. Current classification categories from benign to pathogenic reflect a probabilistic summary of the current understanding. A primary metric of clinical utility for multiplexed assays of variant effect (MAVE) is the number of variants that can be reclassified from uncertain significance (VUS). However, a gap in this measure of utility is that it underrepresents the information gained from MAVEs. The aim of this study was to develop an improved quantification metric for MAVE utility. We propose adopting an information content approach that includes data that does not reclassify variants will better reflect true information gain. We adopted an information content approach to evaluate the information gain, in bits, for MAVEs of BRCA1, PTEN, and TP53. Here, one bit represents the amount of information required to completely classify a single variant starting from no information. RESULTS BRCA1 MAVEs produced a total of 831.2 bits of information, 6.58% of the total missense information in BRCA1 and a 22-fold increase over the information that only contributed to VUS reclassification. PTEN MAVEs produced 2059.6 bits of information which represents 32.8% of the total missense information in PTEN and an 85-fold increase over the information that contributed to VUS reclassification. TP53 MAVEs produced 277.8 bits of information which represents 6.22% of the total missense information in TP53 and a 3.5-fold increase over the information that contributed to VUS reclassification. CONCLUSIONS An information content approach will more accurately portray information gained through MAVE mapping efforts than by counting the number of variants reclassified. This information content approach may also help define the impact of guideline changes that modify the information definitions used to classify groups of variants.
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Affiliation(s)
| | | | | | - Shawn Fayer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | - Brian H Shirts
- Brotman Baty Institute, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA.
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7
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Parsons MT, de la Hoya M, Richardson ME, Tudini E, Anderson M, Berkofsky-Fessler W, Caputo SM, Chan RC, Cline MS, Feng BJ, Fortuno C, Gomez-Garcia E, Hadler J, Hiraki S, Holdren M, Houdayer C, Hruska K, James P, Karam R, Leong HS, Martins A, Mensenkamp AR, Monteiro AN, Nathan V, O'Connor R, Pedersen IS, Pesaran T, Radice P, Schmidt G, Southey M, Tavtigian S, Thompson BA, Toland AE, Turnbull C, Vogel MJ, Weyandt J, Wiggins GAR, Zec L, Couch FJ, Walker LC, Vreeswijk MPG, Goldgar DE, Spurdle AB. Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel. Am J Hum Genet 2024; 111:2044-2058. [PMID: 39142283 PMCID: PMC11393667 DOI: 10.1016/j.ajhg.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
The ENIGMA research consortium develops and applies methods to determine clinical significance of variants in hereditary breast and ovarian cancer genes. An ENIGMA BRCA1/2 classification sub-group, formed in 2015 as a ClinGen external expert panel, evolved into a ClinGen internal Variant Curation Expert Panel (VCEP) to align with Food and Drug Administration recognized processes for ClinVar contributions. The VCEP reviewed American College of Medical Genetics and Genomics/Association of Molecular Pathology (ACMG/AMP) classification criteria for relevance to interpreting BRCA1 and BRCA2 variants. Statistical methods were used to calibrate evidence strength for different data types. Pilot specifications were tested on 40 variants and documentation revised for clarity and ease of use. The original criterion descriptions for 13 evidence codes were considered non-applicable or overlapping with other criteria. Scenario of use was extended or re-purposed for eight codes. Extensive analysis and/or data review informed specification descriptions and weights for all codes. Specifications were applied to pilot variants with pre-existing ClinVar classification as follows: 13 uncertain significance or conflicting, 14 pathogenic and/or likely pathogenic, and 13 benign and/or likely benign. Review resolved classification for 11/13 uncertain significance or conflicting variants and retained or improved confidence in classification for the remaining variants. Alignment of pre-existing ENIGMA research classification processes with ACMG/AMP classification guidelines highlighted several gaps in the research processes and the baseline ACMG/AMP criteria. Calibration of evidence strength was key to justify utility and strength of different data types for gene-specific application. The gene-specific criteria demonstrated value for improving ACMG/AMP-aligned classification of BRCA1 and BRCA2 variants.
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Affiliation(s)
- Michael T Parsons
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, 28040 Madrid Spain
| | | | - Emma Tudini
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | | | - Sandrine M Caputo
- Department of Genetics, Institut Curie, and Paris Sciences Lettres Research University, 75005 Paris, France
| | | | - Melissa S Cline
- UC Santa Cruz Genomics Institute, Genomics, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Bing-Jian Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Encarna Gomez-Garcia
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Johanna Hadler
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Megan Holdren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Claude Houdayer
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics, FHU G4 Génomique, F-76000 Rouen, France
| | | | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rachid Karam
- Ambry Genetics Corporation, Aliso Viejo, CA 92656, USA
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | | | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Vaishnavi Nathan
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Tina Pesaran
- Ambry Genetics Corporation, Aliso Viejo, CA 92656, USA
| | - Paolo Radice
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sean Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84132, USA
| | - Bryony A Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Clare Turnbull
- Translational Genetics Team, Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Maartje J Vogel
- Department of Human Genetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jamie Weyandt
- Ambry Genetics Corporation, Aliso Viejo, CA 92656, USA
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
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8
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Davidson AL, Michailidou K, Parsons MT, Fortuno C, Bolla MK, Wang Q, Dennis J, Naven M, Abubakar M, Ahearn TU, Alonso MR, Andrulis IL, Antoniou AC, Auvinen P, Behrens S, Bermisheva MA, Bogdanova NV, Bojesen SE, Brüning T, Byers HJ, Camp NJ, Campbell A, Castelao JE, Cessna MH, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Collée JM, Czene K, Dörk T, Eriksson M, Evans DG, Fasching PA, Figueroa JD, Flyger H, Gago-Dominguez M, García-Closas M, Glendon G, González-Neira A, Grassmann F, Gronwald J, Guénel P, Hadjisavvas A, Haeberle L, Hall P, Hamann U, Hartman M, Ho PJ, Hooning MJ, Hoppe R, Howell A, Jakubowska A, Khusnutdinova EK, Kristensen VN, Li J, Lim J, Lindblom A, Liu J, Lophatananon A, Mannermaa A, Mavroudis DA, Mensenkamp AR, Milne RL, Muir KR, Newman WG, Obi N, Panayiotidis MI, Park SK, Park-Simon TW, Peterlongo P, Radice P, Rashid MU, Rhenius V, Saloustros E, Sawyer EJ, Schmidt MK, Seibold P, Shah M, Southey MC, Teo SH, Tomlinson I, Torres D, Truong T, van de Beek I, van der Hout AH, Wendt CC, Dunning AM, Pharoah PDP, Devilee P, Easton DF, James PA, Spurdle AB. Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset. Am J Hum Genet 2024; 111:2059-2069. [PMID: 39096911 PMCID: PMC11393698 DOI: 10.1016/j.ajhg.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 08/05/2024] Open
Abstract
Co-observation of a gene variant with a pathogenic variant in another gene that explains the disease presentation has been designated as evidence against pathogenicity for commonly used variant classification guidelines. Multiple variant curation expert panels have specified, from consensus opinion, that this evidence type is not applicable for the classification of breast cancer predisposition gene variants. Statistical analysis of sequence data for 55,815 individuals diagnosed with breast cancer from the BRIDGES sequencing project was undertaken to formally assess the utility of co-observation data for germline variant classification. Our analysis included expected loss-of-function variants in 11 breast cancer predisposition genes and pathogenic missense variants in BRCA1, BRCA2, and TP53. We assessed whether co-observation of pathogenic variants in two different genes occurred more or less often than expected under the assumption of independence. Co-observation of pathogenic variants in each of BRCA1, BRCA2, and PALB2 with the remaining genes was less frequent than expected. This evidence for depletion remained after adjustment for age at diagnosis, study design (familial versus population-based), and country. Co-observation of a variant of uncertain significance in BRCA1, BRCA2, or PALB2 with a pathogenic variant in another breast cancer gene equated to supporting evidence against pathogenicity following criterion strength assignment based on the likelihood ratio and showed utility in reclassification of missense BRCA1 and BRCA2 variants identified in BRIDGES. Our approach has applicability for assessing the value of co-observation as a predictor of variant pathogenicity in other clinical contexts, including for gene-specific guidelines developed by ClinGen Variant Curation Expert Panels.
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Affiliation(s)
- Aimee L Davidson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Marc Naven
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA
| | - M Rosario Alonso
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, 70210 Kuopio, Finland; Institute of Clinical Medicine, Oncology, University of Eastern Finland, 70210 Kuopio, Finland; Department of Oncology, Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina A Bermisheva
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany; Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany; N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk 223040, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark; Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, 44789 Bochum, Germany
| | - Helen J Byers
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS) Foundation, Complejo Hospitalario Universitario de Santiago, SERGAS, 36312 Vigo, Spain
| | - Melissa H Cessna
- Department of Pathology, Intermountain Health, Murray, UT, USA; Intermountain Biorepository, Intermountain Health, Murray, UT, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA
| | - Georgia Chenevix-Trench
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA; Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH16 4UX, UK; Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Manuela Gago-Dominguez
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Fundación Pública Gallega de IDIS, Cancer Genetics and Epidemiology Group, Genomic Medicine Group, 15706 Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA; The Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden; Health and Medical University, Potsdam, Germany
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, 70-115 Szczecin, Poland
| | - Pascal Guénel
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussay, CESP, 94805 Villejuif, France
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus
| | - Lothar Haeberle
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden; Department of Oncology, Södersjukhuset, 118 83 Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City 117549, Singapore; Department of Surgery, National University Hospital and National University Health System, Singapore City 119228, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore City 119228, Singapore
| | - Peh Joo Ho
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City 117549, Singapore; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A(∗)STAR), Singapore City 138672, Singapore
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, the Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72074 Tübingen, Germany
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, 70-115 Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 171-252 Szczecin, Poland
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia; Federal State Budgetary Educational Institution of Higher Education, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0379 Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | - Jingmei Li
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A(∗)STAR), Singapore City 138672, Singapore
| | - Joanna Lim
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Jenny Liu
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City 117549, Singapore; Department of General Surgery, Ng Teng Fong General Hospital, Singapore City 609606, Singapore
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, 70210 Kuopio, Finland; Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210 Kuopio, Finland; Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Dimitrios A Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, 711 10 Heraklion, Greece
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, 6525 Nijmegen GA, the Netherlands
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Kenneth R Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - William G Newman
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Nadia Obi
- Institute for Occupational and Maritime Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Mihalis I Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Korea; Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul 03080, Korea; Cancer Research Institute, Seoul National University, Seoul 03080, Korea
| | | | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Paolo Radice
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), 20133 Milan, Italy
| | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore 54000, Pakistan
| | - Valerie Rhenius
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Emmanouil Saloustros
- Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia; Department of Surgery, Faculty of Medicine, University of Malaya, UM Cancer Research Institute, Kuala Lumpur 50603, Malaysia
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford OX3 7LF, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota 110231, Colombia
| | - Thérèse Truong
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussay, CESP, 94805 Villejuif, France
| | - Irma van de Beek
- Department of Clinical Genetics, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Annemieke H van der Hout
- Department of Genetics, University Medical Center Groningen, University Groningen, 9713 GZ Groningen, the Netherlands
| | - Camilla C Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 118 83 Stockholm, Sweden
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul D P Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90069, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul A James
- Parkville Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia.
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9
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Tejura M, Fayer S, McEwen AE, Flynn J, Starita LM, Fowler DM. Calibration of variant effect predictors on genome-wide data masks heterogeneous performance across genes. Am J Hum Genet 2024; 111:2031-2043. [PMID: 39173626 PMCID: PMC11393694 DOI: 10.1016/j.ajhg.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024] Open
Abstract
In silico variant effect predictions are available for nearly all missense variants but played a minimal role in clinical variant classification because they were deemed to provide only supporting evidence. Recently, the ClinGen Sequence Variant Interpretation (SVI) Working Group updated recommendations for variant effect prediction use. By analyzing control pathogenic and benign variants across all genes, they were able to compute evidence strength for predictor score intervals with some intervals generating moderate, strong, or even very strong evidence. However, this genome-wide approach could obscure heterogeneous predictor performance in different genes. We quantified the gene-by-gene performance of two top predictors, REVEL and BayesDel, by analyzing control variants in each predictor score interval in 3,668 disease-relevant genes. Approximately 10% of intervals had sufficient control variants for analysis, and ∼70% of these intervals exceeded the maximum number of incorrect predictions implied by the SVI recommendations. These trending discordant intervals arose owing to the divergence of the gene-specific distribution of predictions from the genome-wide distribution, suggesting that gene-specific calibration is needed in many cases. Approximately 22% of ClinVar missense variants of uncertain significance in genes we analyzed (REVEL = 100,629, BayesDel = 71,928) had predictions in trending discordant intervals. Thus, genome-wide calibrations could result in many variants receiving inappropriate evidence strength. To facilitate a review of the SVI's calibrations, we developed a web application enabling visualization of gene-specific predictions and trending concordant and discordant intervals.
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Affiliation(s)
- Malvika Tejura
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Shawn Fayer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Abbye E McEwen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jake Flynn
- University of Washington Interdisciplinary Data Science Group, Seattle, WA 98195, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
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10
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Zanti M, O'Mahony DG, Parsons MT, Dorling L, Dennis J, Boddicker NJ, Chen W, Hu C, Naven M, Yiangou K, Ahearn TU, Ambrosone CB, Andrulis IL, Antoniou AC, Auer PL, Baynes C, Bodelon C, Bogdanova NV, Bojesen SE, Bolla MK, Brantley KD, Camp NJ, Campbell A, Castelao JE, Cessna MH, Chang-Claude J, Chen F, Chenevix-Trench G, Conroy DM, Czene K, De Nicolo A, Domchek SM, Dörk T, Dunning AM, Eliassen AH, Evans DG, Fasching PA, Figueroa JD, Flyger H, Gago-Dominguez M, García-Closas M, Glendon G, González-Neira A, Grassmann F, Hadjisavvas A, Haiman CA, Hamann U, Hart SN, Hartman MBA, Ho WK, Hodge JM, Hoppe R, Howell SJ, Jakubowska A, Khusnutdinova EK, Ko YD, Kraft P, Kristensen VN, Lacey JV, Li J, Lim GH, Lindström S, Lophatananon A, Luccarini C, Mannermaa A, Martinez ME, Mavroudis D, Milne RL, Muir K, Nathanson KL, Nuñez-Torres R, Obi N, Olson JE, Palmer JR, Panayiotidis MI, Patel AV, Pharoah PDP, Polley EC, Rashid MU, Ruddy KJ, Saloustros E, Sawyer EJ, Schmidt MK, Southey MC, Tan VKM, Teo SH, Teras LR, Torres D, Trentham-Dietz A, Truong T, Vachon CM, Wang Q, Weitzel JN, Yadav S, Yao S, Zirpoli GR, Cline MS, Devilee P, Tavtigian SV, Goldgar DE, Couch FJ, Easton DF, Spurdle AB, Michailidou K. Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.04.24313051. [PMID: 39281752 PMCID: PMC11398439 DOI: 10.1101/2024.09.04.24313051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS, and previous findings indicate that case-control likelihood ratios (LRs) outperform odds ratios for variant classification. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyzed germline sequencing data of BRCA1 and BRCA2 from 96,691 female breast cancer cases and 303,925 unaffected controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observed 11,227 BRCA1 and BRCA2 variants, with 6,921 being coding, covering 23.4% of BRCA1 and BRCA2 VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control LR evidence was highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.4% specificity for BRCA1 and 92.2% sensitivity and 86.6% specificity for BRCA2. This approach provides case-control evidence for 785 unclassified variants, that can serve as a valuable element for clinical classification.
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Affiliation(s)
- Maria Zanti
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Denise G O'Mahony
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Michael T Parsons
- Public Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas J Boddicker
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Wenan Chen
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marc Naven
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristia Yiangou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Institute, Buffalo, NY, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul L Auer
- Division of Biostatistics, Data Science Institute and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Natalia V Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristen D Brantley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS) Foundation, Complejo Hospitalario Universitario de Santiago, SERGAS, Vigo, Spain
| | - Melissa H Cessna
- Department of Pathology and Intermountatin Biorepository, Intermountain Health, Salt Lake City, UT, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fei Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Georgia Chenevix-Trench
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Don M Conroy
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Cancer Genetics and Epidemiology Group, Genomic Medicine Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Felix Grassmann
- Institute for Clinical Research, Health and Medical University, Potsdam, Germany
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven N Hart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mikael B A Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City, Singapore
- Department of Surgery, National University Health System, Singapore City, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Selangor, Malaysia
| | - James M Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Sacha J Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Yon-Dschun Ko
- Department of Internal Medicine, Johanniter GmbH Bonn, Johanniter Krankenhaus, Bonn, Germany
| | - Peter Kraft
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Geok Hoon Lim
- Breast Department, KK Women's and Children's Hospital, Singapore City, Singapore
- Duke-NUS Medical School, Singapore City, Singapore
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Maria Elena Martinez
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Rocio Nuñez-Torres
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute for Occupational and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janet E Olson
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
- School of Medicine, Boston University, Boston, MA, USA
| | - Mihalis I Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Paul D P Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Eric C Polley
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | | | - Emmanouil Saloustros
- Division of Oncology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, the Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Veronique Kiak-Mien Tan
- Duke-NUS Medical School, Singapore City, Singapore
- Department of Breast Surgery, Singapore General Hospital, Singapore City, Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore City, Singapore
- SingHealth Duke-NUS Breast Centre, Singapore City, Singapore
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, UM Cancer Research Institute, Kuala Lumpur, Malaysia
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Amy Trentham-Dietz
- Carbone Cancer Center and Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Thérèse Truong
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Institute, Buffalo, NY, USA
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | | | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sean V Tavtigian
- Department of Oncological Services, University of Utah School of Medicine, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Amanda B Spurdle
- Public Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
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11
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Arlt A, Knaus A, Hsieh TC, Klinkhammer H, Bhasin MA, Hustinx A, Moosa S, Krawitz P, Ekure E. Next-generation phenotyping in Nigerian children with Cornelia de Lange syndrome. Am J Med Genet A 2024; 194:e63641. [PMID: 38725242 DOI: 10.1002/ajmg.a.63641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 08/10/2024]
Abstract
Next-generation phenotyping (NGP) can be used to compute the similarity of dysmorphic patients to known syndromic diseases. So far, the technology has been evaluated in variant prioritization and classification, providing evidence for pathogenicity if the phenotype matched with other patients with a confirmed molecular diagnosis. In a Nigerian cohort of individuals with facial dysmorphism, we used the NGP tool GestaltMatcher to screen portraits prior to genetic testing and subjected individuals with high similarity scores to exome sequencing (ES). Here, we report on two individuals with global developmental delay, pulmonary artery stenosis, and genital and limb malformations for whom GestaltMatcher yielded Cornelia de Lange syndrome (CdLS) as the top hit. ES revealed a known pathogenic nonsense variant, NM_133433.4: c.598C>T; p.(Gln200*), as well as a novel frameshift variant c.7948dup; p.(Ile2650Asnfs*11) in NIPBL. Our results suggest that NGP can be used as a screening tool and thresholds could be defined for achieving high diagnostic yields in ES. Training the artificial intelligence (AI) with additional cases of the same ethnicity might further increase the positive predictive value of GestaltMatcher.
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Affiliation(s)
- Annabelle Arlt
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Meghna Ahuja Bhasin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Ekanem Ekure
- Faculty of Clinical Sciences, Department of Pediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
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12
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Gilbert MA, Keefer-Jacques E, Jadhav T, Antfolk D, Ming Q, Valente N, Shaw GTW, Sottolano CJ, Matwijec G, Luca VC, Loomes KM, Rajagopalan R, Hayeck TJ, Spinner NB. Functional characterization of 2,832 JAG1 variants supports reclassification for Alagille syndrome and improves guidance for clinical variant interpretation. Am J Hum Genet 2024; 111:1656-1672. [PMID: 39043182 PMCID: PMC11339624 DOI: 10.1016/j.ajhg.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/15/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024] Open
Abstract
Pathogenic variants in the JAG1 gene are a primary cause of the multi-system disorder Alagille syndrome. Although variant detection rates are high for this disease, there is uncertainty associated with the classification of missense variants that leads to reduced diagnostic yield. Consequently, up to 85% of reported JAG1 missense variants have uncertain or conflicting classifications. We generated a library of 2,832 JAG1 nucleotide variants within exons 1-7, a region with a high number of reported missense variants, and designed a high-throughput assay to measure JAG1 membrane expression, a requirement for normal function. After calibration using a set of 175 known or predicted pathogenic and benign variants included within the variant library, 486 variants were characterized as functionally abnormal (n = 277 abnormal and n = 209 likely abnormal), of which 439 (90.3%) were missense. We identified divergent membrane expression occurring at specific residues, indicating that loss of the wild-type residue itself does not drive pathogenicity, a finding supported by structural modeling data and with broad implications for clinical variant classification both for Alagille syndrome and globally across other disease genes. Of 144 uncertain variants reported in patients undergoing clinical or research testing, 27 had functionally abnormal membrane expression, and inclusion of our data resulted in the reclassification of 26 to likely pathogenic. Functional evidence augments the classification of genomic variants, reducing uncertainty and improving diagnostics. Inclusion of this repository of functional evidence during JAG1 variant reclassification will significantly affect resolution of variant pathogenicity, making a critical impact on the molecular diagnosis of Alagille syndrome.
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Affiliation(s)
- Melissa A Gilbert
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Ernest Keefer-Jacques
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Tanaya Jadhav
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel Antfolk
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Qianqian Ming
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Nicolette Valente
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Grace Tzun-Wen Shaw
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher J Sottolano
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Grace Matwijec
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Vincent C Luca
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kathleen M Loomes
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tristan J Hayeck
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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Stawiński P, Płoski R. Genebe.net: Implementation and validation of an automatic ACMG variant pathogenicity criteria assignment. Clin Genet 2024; 106:119-126. [PMID: 38440907 DOI: 10.1111/cge.14516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
We present GeneBe, an online platform streamlining the automated application of American College of Medical Genetics and Genomics (ACMG), Association for Molecular Pathology (AMP), and the College of American Pathologists (CAP) criteria for assessment of pathogenicity of genetic variants. GeneBe utilizes automated algorithms that evaluate 17 criteria from 28, closely aligning with current guidelines and leveraging data from diverse sources, including ClinVar. The user-friendly web interface enables manual refinement of assignments for specific criteria based on site-collected data. Our algorithm demonstrates a high correlation (r = 0.90) of assigned pathogenicity scores compared to expert assessments from the ClinGen Evidence Repository and substantial concordance with ClinVar verdict assignments (κ = 0.69). Comparative analysis with other published tools reveals that GeneBe performs similarly to VarSome while being superior over TAPES and InterVar. In contrast to some other tools, GeneBe's web implementation is tracker-free and third-party request-free, safeguarding user privacy. Additionally, GeneBe offers an Application Programming Interface (API) for enhanced flexibility and integration into existing workflows and is provided free of charge for research purposes. GeneBe is available at https://genebe.net.
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Affiliation(s)
- Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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14
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Ma JG, O’Neill MJ, Richardson E, Thomson KL, Ingles J, Muhammad A, Solus JF, Davogustto G, Anderson KC, Benjamin Shoemaker M, Stergachis AB, Floyd BJ, Dunn K, Parikh VN, Chubb H, Perrin MJ, Roden DM, Vandenberg JI, Ng CA, Glazer AM. Multisite Validation of a Functional Assay to Adjudicate SCN5A Brugada Syndrome-Associated Variants. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004569. [PMID: 38953211 PMCID: PMC11335442 DOI: 10.1161/circgen.124.004569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Brugada syndrome is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in SCN5A. Interpreting the pathogenicity of SCN5A missense variants is challenging, and ≈79% of SCN5A missense variants in ClinVar are currently classified as variants of uncertain significance. Automated patch clamp technology enables high-throughput functional studies of ion channel variants and can provide evidence for variant reclassification. METHODS An in vitro SCN5A-Brugada syndrome automated patch clamp assay was independently performed at Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute. The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. Odds of pathogenicity values were derived from the experimental results according to ClinGen Sequence Variant Interpretation recommendations. The calibrated assay was then used to study SCN5A variants of uncertain significance observed in 4 families with Brugada syndrome and other arrhythmia phenotypes associated with SCN5A loss-of-function. RESULTS Variant channel parameters generated independently at the 2 research sites showed strong correlations, including peak INa density (R2=0.86). The assay accurately distinguished benign controls (24/25 concordant variants) from pathogenic controls (23/24 concordant variants). Odds of pathogenicity values were 0.042 for normal function and 24.0 for abnormal function, corresponding to strong evidence for both American College of Medical Genetics and Genomics/Association for Molecular Pathology benign and pathogenic functional criteria (BS3 and PS3, respectively). Application of the assay to 4 clinical SCN5A variants of uncertain significance revealed loss-of-function for 3/4 variants, enabling reclassification to likely pathogenic. CONCLUSIONS This validated high-throughput assay provides clinical-grade functional evidence to aid the classification of current and future SCN5A-Brugada syndrome variants of uncertain significance.
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Affiliation(s)
- Joanne G. Ma
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Inst
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | | | - Ebony Richardson
- Clinical Genomics Laboratory, Ctr for Population Genomics, Garvan Inst of Medical Rsrch, Darlinghurst, NSW & Australia & Murdoch Children’s Research Inst, Melbourne, Australia
| | - Kate L. Thomson
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Jodie Ingles
- Clinical Genomics Laboratory, Ctr for Population Genomics, Garvan Inst of Medical Rsrch, Darlinghurst, NSW & Australia & Murdoch Children’s Research Inst, Melbourne, Australia
| | | | - Joseph F. Solus
- Vanderbilt Ctr for Arrhythmia Research & Therapeutics (VanCART), Division of Clinical Pharmacology, Dept of Medicine, Nashville, TN
| | | | | | | | | | - Brendan J. Floyd
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Kyla Dunn
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Victoria N. Parikh
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Henry Chubb
- Stanford Ctr for Inherited Cardiovascular Disease, Stanford Univ School of Medicine, Stanford, CA
| | - Mark J. Perrin
- Dept of Genomic Medicine, Royal Melbourne Hospital, Victoria, Australia
| | - Dan M. Roden
- Depts of Pharmacology, and Biomedical Informatics, Vanderbilt Univ Medical Ctr, Nashville, TN
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Inst
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Inst
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Andrew M. Glazer
- Vanderbilt Ctr for Arrhythmia Research & Therapeutics (VanCART), Division of Clinical Pharmacology, Dept of Medicine, Nashville, TN
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15
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Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau EAW, Greenblatt MS, Harrison SM, Tavtigian SV, Radivojac P, Brenner SE, O'Donnell-Luria A. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations. Genet Med 2024; 26:101213. [PMID: 39030733 DOI: 10.1016/j.gim.2024.101213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024] Open
Abstract
PURPOSE To investigate the number of rare missense variants observed in human genome sequences by ACMG/AMP PP3/BP4 evidence strength, following the ClinGen-calibrated PP3/BP4 computational recommendations. METHODS Missense variants from the genome sequences of 300 probands from the Rare Genomes Project with suspected rare disease were analyzed using computational prediction tools that were able to reach PP3_Strong and BP4_Moderate evidence strengths (BayesDel, MutPred2, REVEL, and VEST4). The numbers of variants at each evidence strength were analyzed across disease-associated genes and genome-wide. RESULTS From a median of 75.5 rare (≤1% allele frequency) missense variants in disease-associated genes per proband, a median of one reached PP3_Strong, 3-5 PP3_Moderate, and 3-5 PP3_Supporting. Most were allocated BP4 evidence (median 41-49 per proband) or were indeterminate (median 17.5-19 per proband). Extending the analysis to all protein-coding genes genome-wide, the number of variants reaching PP3_Strong score thresholds increased approximately 2.6-fold compared with disease-associated genes, with a median per proband of 1-3 PP3_Strong, 8-16 PP3_Moderate, and 10-17 PP3_Supporting. CONCLUSION A small number of variants per proband reached PP3_Strong and PP3_Moderate in 3424 disease-associated genes. Although not the intended use of the recommendations, this was also observed genome-wide. Use of PP3/BP4 evidence as recommended from calibrated computational prediction tools in the clinical diagnostic laboratory is unlikely to inappropriately contribute to the classification of an excessive number of variants as pathogenic or likely pathogenic by ACMG/AMP rules.
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Affiliation(s)
- Sarah L Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Timothy Bergquist
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emily A W Nadeau
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Ambry Genetics, Aliso Viejo, CA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Steven E Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, (redundant), Berkeley, CA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
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Xiao D, Shi C, Zhang Y, Li S, Ye Y, Yuan G, Miu T, Ma H, Diao S, Su C, Li Z, Li H, Zhuang G, Wang Y, Lu F, Gu X, Zhou W, Xiao X, Huang W, Wei T, Hao H. Using metabolic abnormalities of carriers in the neonatal period to evaluate the pathogenicity of variants of uncertain significance in methylmalonic acidemia. Front Genet 2024; 15:1403913. [PMID: 39076170 PMCID: PMC11284102 DOI: 10.3389/fgene.2024.1403913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/28/2024] [Indexed: 07/31/2024] Open
Abstract
Objective To accurately verify the pathogenicity of variants of uncertain significance (VUS) in MUT and MMACHC genes through mass spectrometry and silico analysis. Methods This multicenter retrospective study included 35 participating units (ClinicalTrials.gov ID: NCT06183138). A total of 3,071 newborns (within 7 days of birth) were sorted into carrying pathogenic/likely pathogenic (P/LP) variants and carrying VUS, non-variant groups. Differences in metabolites among the groups were calculated using statistical analyses. Changes in conservatism, free energy, and interaction force of MMUT and MMACHC variants were analyzed using silico analysis. Results The percentage of those carrying VUS cases was 68.15% (659/967). In the MMUT gene variant, we found that C3, C3/C2, and C3/C0 levels in those carrying the P/LP variant group were higher than those in the non-variant group (p < 0.000). The conservative scores of those carrying the P/LP variant group were >7. C3, C3/C0, and C3/C2 values of newborns carrying VUS (c.1159A>C and c.1286A>G) were significantly higher than those of the non-variant group and the remaining VUS newborns (p < 0.005). The conservative scores of c.1159A>C and c.1286A>G calculated by ConSurf analysis were 9 and 7, respectively. Unfortunately, three MMA patients with c.1159A>C died during the neonatal period; their C3, C3/C0, C3/C2, and MMA levels were significantly higher than those of the controls. Conclusion Common variants of methylmalonic acidemia in the study population were categorized as VUS. In the neonatal period, the metabolic biomarkers of those carrying the P/LP variant group of the MUT gene were significantly higher than those in the non-variant group. If the metabolic biomarkers of those carrying VUS are also significantly increased, combined with silico analysis the VUS may be elevated to a likely pathogenic variant. The results also suggest that mass spectrometry and silico analysis may be feasible screening methods for verifying the pathogenicity of VUS in other inherited metabolic diseases.
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Affiliation(s)
- Dongfan Xiao
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Congcong Shi
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yinchun Zhang
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sitao Li
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuhao Ye
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Guilong Yuan
- Neonates Department, Nanhai Maternity and Child Healthcare Hospital of Foshan, Foshan, China
| | - Taohan Miu
- Neonatology Departmen, Heyuan Women and Children’s Hospital and Health Institute, Heyuan, China
| | - Haiyan Ma
- Department of Neonatology, Zhuhai Women and Children’s Hospital, Zhuhai, China
| | - Shiguang Diao
- Department of Neonatology, Yuebei People’s Hospital, Shaoguan, China
| | - Chaoyun Su
- Department of Neonatology, Maoming Huazhou People’s Hospital, Huazhou, China
| | - Zhitao Li
- Guangzhou Baiyun District Maternal and Child Health Hospital, Guangzhou, China
| | - Haiyan Li
- Department of Pediatrics, Huidong County Maternal and Child Health Hospital, Huidong, China
| | - Guiying Zhuang
- Department of Neonatology, The Maternal and Child Healthcare Hospital of Huadu, Guangzhou, China
| | - Yuanli Wang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, Qinzhou, China
| | - Feiyan Lu
- Huizhou Huiyang District Maternal and Child Health Hospital, Huizhou, China
| | - Xia Gu
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhou
- Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xin Xiao
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiben Huang
- Department of Neonatology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Tao Wei
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Hu Hao
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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17
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Xue H, Yu A, Chen L, Guo Q, Zhang L, Lin N, Chen X, Xu L, Huang H. Prenatal genetic diagnosis of fetuses with dextrocardia using whole exome sequencing in a tertiary center. Sci Rep 2024; 14:16266. [PMID: 39009665 PMCID: PMC11251054 DOI: 10.1038/s41598-024-67164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
To evaluate the genetic etiology of fetal dextrocardia, associated ultrasound anomalies, and perinatal outcomes, we investigated the utility of whole exome sequencing (WES) for prenatal diagnosis of dextrocardia. Fetuses with dextrocardia were prospectively collected between January 2016 and December 2022. Trio-WES was performed on fetuses with dextrocardia, following normal karyotyping and/or chromosomal microarray analysis (CMA) results. A total of 29 fetuses with dextrocardia were collected, including 27 (93.1%) diagnosed with situs inversus totalis and 2 (6.9%) with situs inversus partialis. Cardiac malformations were present in nine cases, extra-cardiac anomalies were found in seven cases, and both cardiac and extra-cardiac malformations were identified in one case. The fetal karyotypes and CMA results of 29 cases were normal. Of the 29 cases with dextrocardia, 15 underwent WES, and the other 14 cases refused. Of the 15 cases that underwent WES, clinically relevant variants were identified in 5/15 (33.3%) cases, including the diagnostic variants DNAH5, DNAH11, LRRC56, PEX10, and ZIC3, which were verified by Sanger sequencing. Of the 10 cases with non-diagnostic results via WES, eight (80%) chose to continue the pregnancies. Of the 29 fetuses with dextrocardia, 10 were terminated during pregnancy, and 19 were live born. Fetal dextrocardia is often accompanied by cardiac and extra-cardiac anomalies, and fetal dextrocardia accompanied by situs inversus is associated with a high risk of primary ciliary dyskinesia. Trio-WES is recommended following normal karyotyping and CMA results because it can improve the diagnostic utility of genetic variants of fetal dextrocardia, accurately predict fetal prognosis, and guide perinatal management and the reproductive decisions of affected families.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
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18
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Villani RM, McKenzie ME, Davidson AL, Spurdle AB. Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease. Am J Hum Genet 2024; 111:1301-1315. [PMID: 38815586 PMCID: PMC11267523 DOI: 10.1016/j.ajhg.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024] Open
Abstract
To date, clinical genetic testing for Mendelian disease variants has focused heavily on exonic coding and intronic gene regions. This multi-step study was undertaken to provide an evidence base for selecting and applying computational approaches for use in clinical classification of 5' cis-regulatory region variants. Curated datasets of clinically reported disease-causing 5' cis-regulatory region variants and variants from matched genomic regions in population controls were used to calibrate six bioinformatic tools as predictors of variant pathogenicity. Likelihood ratio estimates were aligned to code weights following ClinGen recommendations for application of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) classification scheme. Considering code assignment across all reference dataset variants, performance was best for CADD (81.2%) and REMM (81.5%). Optimized thresholds provided moderate evidence toward pathogenicity (CADD, REMM) and moderate (CADD) or supporting (REMM) evidence against pathogenicity. Both sensitivity and specificity of prediction were improved when further categorizing variants based on location in an EPDnew-defined promoter region. Combining predictions (CADD, REMM, and location in a promoter region) increased specificity at the expense of sensitivity. Importantly, the optimal CADD thresholds for assigning ACMG/AMP codes PP3 (≥10) and BP4 (≤8) were vastly different from recommendations for protein-coding variants (PP3 ≥25.3; BP4 ≤22.7); CADD <22.7 would incorrectly assign BP4 for >90% of reported disease-causing cis-regulatory region variants. Our results demonstrate the need to consider a tiered approach and tailored score thresholds to optimize bioinformatic impact prediction for clinical classification of 5' cis-regulatory region variants.
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Affiliation(s)
- Rehan M Villani
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Maddison E McKenzie
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Aimee L Davidson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; University of Queensland, Brisbane, Queensland, Australia.
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19
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Waters AJ, Brendler-Spaeth T, Smith D, Offord V, Tan HK, Zhao Y, Obolenski S, Nielsen M, van Doorn R, Murphy JE, Gupta P, Rowlands CF, Hanson H, Delage E, Thomas M, Radford EJ, Gerety SS, Turnbull C, Perry JRB, Hurles ME, Adams DJ. Saturation genome editing of BAP1 functionally classifies somatic and germline variants. Nat Genet 2024; 56:1434-1445. [PMID: 38969833 PMCID: PMC11250367 DOI: 10.1038/s41588-024-01799-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/14/2024] [Indexed: 07/07/2024]
Abstract
Many variants that we inherit from our parents or acquire de novo or somatically are rare, limiting the precision with which we can associate them with disease. We performed exhaustive saturation genome editing (SGE) of BAP1, the disruption of which is linked to tumorigenesis and altered neurodevelopment. We experimentally characterized 18,108 unique variants, of which 6,196 were found to have abnormal functions, and then used these data to evaluate phenotypic associations in the UK Biobank. We also characterized variants in a large population-ascertained tumor collection, in cancer pedigrees and ClinVar, and explored the behavior of cancer-associated variants compared to that of variants linked to neurodevelopmental phenotypes. Our analyses demonstrated that disruptive germline BAP1 variants were significantly associated with higher circulating levels of the mitogen IGF-1, suggesting a possible pathological mechanism and therapeutic target. Furthermore, we built a variant classifier with >98% sensitivity and specificity and quantify evidence strengths to aid precision variant interpretation.
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Affiliation(s)
| | | | | | | | | | - Yajie Zhao
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Charlie F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Helen Hanson
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | | | | | - Elizabeth J Radford
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, NHS England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - John R B Perry
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
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20
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Houge G, Bratland E, Aukrust I, Tveten K, Žukauskaitė G, Sansovic I, Brea-Fernández AJ, Mayer K, Paakkola T, McKenna C, Wright W, Markovic MK, Lildballe DL, Konecny M, Smol T, Alhopuro P, Gouttenoire EA, Obeid K, Todorova A, Jankovic M, Lubieniecka JM, Stojiljkovic M, Buisine MP, Haukanes BI, Lorans M, Roomere H, Petit FM, Haanpää MK, Beneteau C, Pérez B, Plaseska-Karanfilska D, Rath M, Fuhrmann N, Ferreira BI, Stephanou C, Sjursen W, Maver A, Rouzier C, Chirita-Emandi A, Gonçalves J, Kuek WCD, Broly M, Haer-Wigman L, Thong MK, Tae SK, Hyblova M, den Dunnen JT, Laner A. Comparison of the ABC and ACMG systems for variant classification. Eur J Hum Genet 2024; 32:858-863. [PMID: 38778080 PMCID: PMC11219933 DOI: 10.1038/s41431-024-01617-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.
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Affiliation(s)
- Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Eirik Bratland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Gabrielė Žukauskaitė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ivona Sansovic
- Department of Medical and Laboratory Genetics, Endocrinology and Diabetology, Childrens' Hospital Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBERER), Santiago de Compostela, Spain
| | - Karin Mayer
- Center for Human Genetics and Laboratory Diagnostics, MVZ Martinsried GmbH, Martinsried, Germany
| | - Teija Paakkola
- Nordlab Wellbeing Service Group, Genetics Laboratory, Oulu, Finland
| | - Caoimhe McKenna
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - William Wright
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - Milica Keckarevic Markovic
- Center for Applied and Forensic Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dorte L Lildballe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michal Konecny
- Laboratory of Genomic Medicine, GHC GENETICS SK, Bratislava, Slovakia
- Department of Biology, Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Thomas Smol
- Institut de Genetique Medicale-CHU Lille, Lille, France
| | - Pia Alhopuro
- HUS Diagnostic Center, Laboratory of Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Katharina Obeid
- Molecular Diagnostics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Albena Todorova
- Genetic Medico-Diagnostic Laboratory "Genica" and Genome Center Bulgaria, Sofia, Bulgaria
| | - Milena Jankovic
- Neurology Clinic UCCS, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marie-Pierre Buisine
- Molecular Oncogenetics, Department of Biochemistry and Molecular Biology, Lille University Hospital, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, CANTHER, Lille, France
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Marie Lorans
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Hanno Roomere
- Department of laboratory genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - François M Petit
- Department of Oncopharmacology, Centre Antoine Lacassagne, Nice, France
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland
| | - Claire Beneteau
- CHU Bordeaux, Service de Génétique Médicale, F-33000, Bordeaux, France
| | - Belén Pérez
- Genetics Department of CEDEM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Matthias Rath
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Nico Fuhrmann
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Bibiana I Ferreira
- GENELAB by ABC, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Coralea Stephanou
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, Ljubljana, Slovenia
| | - Cécile Rouzier
- Department of Medical Genetics, National Centre for Mitocondrial Diseases, CHU de NICE, Université Côte d'Azur, Nice, France
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Adela Chirita-Emandi
- Department of Microscopic Morphology Genetics Discipline, Center of Genomic Medicine, "Victor Babes" University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - João Gonçalves
- Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Wei Cheng David Kuek
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Kent Ridge, Singapore
| | - Martin Broly
- Laboratory of Rare and Autoinflammatory Genetic Diseases, Department of Genetics-LBM, Montpellier University Hospital, Montpellier, France
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Meow-Keong Thong
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok-Kun Tae
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Laner
- Medizinisch Genetisches Zentrum (MGZ) München, Munich, Germany
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21
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. Genet Med 2024; 26:101199. [PMID: 38944749 DOI: 10.1016/j.gim.2024.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA.
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, Orange, CA
| | - Daniel G Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, TX
| | | | | | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA; Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA
| | - Heidi L Rehm
- Program in 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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22
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579012. [PMID: 38370830 PMCID: PMC10871197 DOI: 10.1101/2024.02.05.579012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Seth I. Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, 111 Michigan Ave, NW, Washington, DC, 20010, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, 200 South Manchester Ave. St 206E, Orange, CA, 92868, USA
| | - Daniel G. Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Megan H. Hawley
- Clinical Operations, Invitae, 485F US-1 Suite 110, Iselin, NJ, 08830, USA
| | - E. Andres Rivera-Munoz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza T605, Houston, TX, 77030, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | | | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA, 98195, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
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23
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Rastogi R, Chung R, Li S, Li C, Lee K, Woo J, Kim DW, Keum C, Babbi G, Martelli PL, Savojardo C, Casadio R, Chennen K, Weber T, Poch O, Ancien F, Cia G, Pucci F, Raimondi D, Vranken W, Rooman M, Marquet C, Olenyi T, Rost B, Andreoletti G, Kamandula A, Peng Y, Bakolitsa C, Mort M, Cooper DN, Bergquist T, Pejaver V, Liu X, Radivojac P, Brenner SE, Ioannidis NM. Critical assessment of missense variant effect predictors on disease-relevant variant data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597828. [PMID: 38895200 PMCID: PMC11185644 DOI: 10.1101/2024.06.06.597828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity of missense variants is necessary to evaluate their clinical and research utility and suggest directions for future improvement. Here, as part of the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, we assess missense variant effect predictors (or variant impact predictors) on an evaluation dataset of rare missense variants from disease-relevant databases. Our assessment evaluates predictors submitted to the CAGI6 Annotate-All-Missense challenge, predictors commonly used by the clinical genetics community, and recently developed deep learning methods for variant effect prediction. To explore a variety of settings that are relevant for different clinical and research applications, we assess performance within different subsets of the evaluation data and within high-specificity and high-sensitivity regimes. We find strong performance of many predictors across multiple settings. Meta-predictors tend to outperform their constituent individual predictors; however, several individual predictors have performance similar to that of commonly used meta-predictors. The relative performance of predictors differs in high-specificity and high-sensitivity regimes, suggesting that different methods may be best suited to different use cases. We also characterize two potential sources of bias. Predictors that incorporate allele frequency as a predictive feature tend to have reduced performance when distinguishing pathogenic variants from very rare benign variants, and predictors supervised on pathogenicity labels from curated variant databases often learn label imbalances within genes. Overall, we find notable advances over the oldest and most cited missense variant effect predictors and continued improvements among the most recently developed tools, and the CAGI Annotate-All-Missense challenge (also termed the Missense Marathon) will continue to assess state-of-the-art methods as the field progresses. Together, our results help illuminate the current clinical and research utility of missense variant effect predictors and identify potential areas for future development.
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24
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Liu X, Lei M, Xue Y, Li H, Yin J, Li D, Shu J, Cai C. Multi-dimensional Insight into the Coexistence of Pathogenic Genes for ADAR1 and TSC2: Careful Consideration is Essential for Interpretation of ADAR1 Variants. Biochem Genet 2024; 62:1811-1826. [PMID: 37740860 DOI: 10.1007/s10528-023-10488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/06/2023] [Indexed: 09/25/2023]
Abstract
Aicardi-Goutières syndrome 6 (AGS6) is a serious auto-immunization-associated acute neurologic decompensation. AGS6 manifests as acute onset of severe generalized dystonia of limbs and developmental regression secondary to febrile illness mostly. Dyschromatosis symmetrica hereditaria (DSH), as pigmentary genodermatosis, is a characterized mixture of hyperpigmented and hypopigmented macules. Both AGS6 and DSH are associated with ADAR1 pathogenic variants. To explore the etiology of a proband with developmental regression with mixture of hyperpigmentation and hypopigmentation macules, we used the trio-WES. Later, to clarify the association between variants and diseases, we used guidelines of ACMG for variants interpretation and quantitative Real-time PCR for verifying elevated expression levels of interferon-stimulated genes, separately. By WES, we detected 2 variants in ADAR1 and a variant in TSC2, respectively, were NM_001111.5:c.1096_1097del, NM_001111.5:c.518A>G, and NM_000548.5:c.1864C>T. Variants interpretation suggested that these 3 variants were both pathogenic. Expression levels of interferon-stimulated genes also elevated as expected. We verified the co-occurrence of pathogenic variants of ADAR1 and TSC2 in AGS6 patients with DSH. Our works contributed to the elucidation of ADAR1 pathogenic mechanism, given the specific pathogenic mechanism of ADAR1, and it is necessary to consider with caution when variants were found in ADAR1.
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Affiliation(s)
- Xiangyu Liu
- Graduate College of Tianjin Medical University, Tianjin, 300070, China
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China
| | - Meifang Lei
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Yan Xue
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Beichen District, No. 238 Longyan Road, Tianjin, 300134, China
| | - Hong Li
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Jing Yin
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China
- Department of Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China
| | - Dong Li
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China.
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China.
| | - Jianbo Shu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China.
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Beichen District, No. 238 Longyan Road, Tianjin, 300134, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Chunquan Cai
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, 300134, China.
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Beichen District, No. 238 Longyan Road, Tianjin, 300134, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
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25
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Richardson ME, Holdren M, Brannan T, de la Hoya M, Spurdle AB, Tavtigian SV, Young CC, Zec L, Hiraki S, Anderson MJ, Walker LC, McNulty S, Turnbull C, Tischkowitz M, Schon K, Slavin T, Foulkes WD, Cline M, Monteiro AN, Pesaran T, Couch FJ. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.28.24307502. [PMID: 38854136 PMCID: PMC11160822 DOI: 10.1101/2024.05.28.24307502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP) Variant Curation Expert Panel (VCEP) is composed of internationally recognized experts in clinical genetics, molecular biology and variant interpretation. This VCEP made specifications for ACMG/AMP guidelines for the ataxia telangiectasia mutated (ATM) gene according to the Food and Drug Administration (FDA)-approved ClinGen protocol. These gene-specific rules for ATM were modified from the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) guidelines and were tested against 33 ATM variants of various types and classifications in a pilot curation phase. The pilot revealed a majority agreement between the HBOP VCEP classifications and the ClinVar-deposited classifications. Six pilot variants had conflicting interpretations in ClinVar and reevaluation with the VCEP's ATM-specific rules resulted in four that were classified as benign, one as likely pathogenic and one as a variant of uncertain significance (VUS) by the VCEP, improving the certainty of interpretations in the public domain. Overall, 28 the 33 pilot variants were not VUS leading to an 85% classification rate. The ClinGen-approved, modified rules demonstrated value for improved interpretation of variants in ATM.
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Affiliation(s)
| | - Megan Holdren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | | | | | | | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shannon McNulty
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Marc Tischkowitz
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Katherine Schon
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Thomas Slavin
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - William D Foulkes
- Departments of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Mail Stop: Genomics, University of California, Santa Cruz, CA, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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26
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Cooper S, Obolenski S, Waters AJ, Bassett AR, Coelho MA. Analyzing the functional effects of DNA variants with gene editing. CELL REPORTS METHODS 2024; 4:100776. [PMID: 38744287 PMCID: PMC11133854 DOI: 10.1016/j.crmeth.2024.100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/01/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Continual advancements in genomics have led to an ever-widening disparity between the rate of discovery of genetic variants and our current understanding of their functions and potential roles in disease. Systematic methods for phenotyping DNA variants are required to effectively translate genomics data into improved outcomes for patients with genetic diseases. To make the biggest impact, these approaches must be scalable and accurate, faithfully reflect disease biology, and define complex disease mechanisms. We compare current methods to analyze the function of variants in their endogenous DNA context using genome editing strategies, such as saturation genome editing, base editing and prime editing. We discuss how these technologies can be linked to high-content readouts to gain deep mechanistic insights into variant effects. Finally, we highlight key challenges that need to be addressed to bridge the genotype to phenotype gap, and ultimately improve the diagnosis and treatment of genetic diseases.
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Affiliation(s)
- Sarah Cooper
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, UK
| | - Sofia Obolenski
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Andrew J Waters
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Andrew R Bassett
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, UK.
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27
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Brock DC, Wang M, Hussain HMJ, Rauch DE, Marra M, Pennesi ME, Yang P, Everett L, Ajlan RS, Colbert J, Porto FBO, Matynia A, Gorin MB, Koenekoop RK, Lopez I, Sui R, Zou G, Li Y, Chen R. Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases. Hum Mol Genet 2024; 33:945-957. [PMID: 38453143 PMCID: PMC11102593 DOI: 10.1093/hmg/ddae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T>A, p.Ile143Thr) and RHO (c.631C>G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.
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Affiliation(s)
- Daniel C Brock
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Hafiz Muhammad Jafar Hussain
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - David E Rauch
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Lesley Everett
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Radwan S Ajlan
- Department of Ophthalmology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS 66160, United States
| | - Jason Colbert
- Department of Ophthalmology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS 66160, United States
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Rua dos Otoni, 735/507 - Santa Efigênia, Belo Horizonte, MG 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Av. Francisco Sales, 1111 - Santa Efigênia, Belo Horizonte, MG 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, R. Santa Catarina, 941 - Lourdes, Belo Horizonte, MG 30180070, Brazil
| | - Anna Matynia
- College of Optometry, University of Houston, 4401 Martin Luther King Boulevard, Houston, TX 77004, United States
| | - Michael B Gorin
- Jules Stein Eye Institute, University of California Los Angeles, 100 Stein Plaza, Los Angeles, CA 90095, United States
- Department of Ophthalmology, University of California Los Angeles David Geffen School of Medicine, 10833 Le Conte Ave, Los Angeles, CA 90095, United States
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, 5252 Boul de Maisonneuve ouest, Montreal, QC H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, 5252 Boul de Maisonneuve ouest, Montreal, QC H4A 3S5, Canada
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, WC67+HW Dongcheng, Beijing 100005, China
| | - Gang Zou
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, F4RJ+43 Xixia District, Yinchuan, Ningxia, China
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
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28
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Lee CL, Chuang CK, Chiu HC, Chang YH, Tu YR, Lo YT, Lin HY, Lin SP. Application of whole exome sequencing in the diagnosis of muscular disorders: a study of Taiwanese pediatric patients. Front Genet 2024; 15:1365729. [PMID: 38818036 PMCID: PMC11137626 DOI: 10.3389/fgene.2024.1365729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Background Muscular dystrophies and congenital myopathies encompass various inherited muscular disorders that present diagnostic challenges due to clinical complexity and genetic heterogeneity. Methods This study aimed to investigate the use of whole exome sequencing (WES) in diagnosing muscular disorders in pediatric patients in Taiwan. Out of 161 pediatric patients suspected to have genetic/inherited myopathies, 115 received a molecular diagnosis through conventional tests, single gene testing, and gene panels. The remaining 46 patients were divided into three groups: Group 1 (multiplex ligation-dependent probe amplification-negative Duchenne muscular dystrophy) with three patients (6.5%), Group 2 (various forms of muscular dystrophies) with 21 patients (45.7%), and Group 3 (congenital myopathies) with 22 patients (47.8%). Results WES analysis of these groups found pathogenic variants in 100.0% (3/3), 57.1% (12/21), and 68.2% (15/22) of patients in Groups 1 to 3, respectively. WES had a diagnostic yield of 65.2% (30 patients out of 46), detecting 30 pathogenic or potentially pathogenic variants across 28 genes. Conclusion WES enables the diagnosis of rare diseases with symptoms and characteristics similar to congenital myopathies and muscular dystrophies, such as muscle weakness. Consequently, this approach facilitates targeted therapy implementation and appropriate genetic counseling.
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Chih-Kuang Chuang
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- College of Medicine, Fu-Jen Catholic University, Taipei, Taiwan
| | - Huei-Ching Chiu
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ya-Hui Chang
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yuan-Rong Tu
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yun-Ting Lo
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Shuan-Pei Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
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Levy M, Lifshitz S, Goldenberg-Fumanov M, Bazak L, Goldstein RJ, Hamiel U, Berger R, Lipitz S, Maya I, Shohat M. Exome sequencing in every pregnancy? Results of trio exome sequencing in structurally normal fetuses. Prenat Diagn 2024. [PMID: 38735835 DOI: 10.1002/pd.6585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
OBJECTIVE This study aimed to assess the detection rate of clinically significant results of prenatal exome sequencing (pES) in low-risk pregnancies and apparently normal fetuses in non-consanguineous couples. METHODS A retrospective analysis of pES conducted at a single center from January 2020 to September 2023 was performed. Genetic counseling was provided, and detailed medical histories were obtained. High-risk pregnancies were excluded due to major ultrasound anomalies, sonographic soft markers, abnormal maternal biochemical screening, or family history suggestive of monogenic diseases as well as cases with pathogenic and likely pathogenic (P/LP) chromosomal microarray results. Exome analysis focused on ∼2100 genes associated with Mendelian genetic disorders. Variant analysis and classification followed the American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS Among 1825 pES conducted, 1020 low-risk cases revealed 28 fetuses (2.7%) with potentially clinically significant variants indicating known monogenic diseases, primarily de novo dominant variants (64%). Among these 28 cases, 9 fetuses (0.9%) had the potential for severe phenotypes, including shortened lifespan and intellectual disability, and another 12 had the potential for milder phenotypes. Seven cases were reported with variants of uncertain significance (VUS) that, according to the ACMG criteria, leaned toward LP, constituting 0.7% of the entire cohort. Termination of pregnancy was elected in 13 out of 1020 cases (1.2%) in the cohort, including 7/9 in the severe phenotypes group, 2/12 in the milder phenotype group, and 4/7 in the VUS group. CONCLUSION The 2.7% detection rate highlights the significant contribution of pES in low-risk pregnancies. However, it necessitates rigorous analysis, and comprehensive genetic counseling before and after testing.
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Affiliation(s)
- Michal Levy
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Shira Lifshitz
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
| | | | - Lily Bazak
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
| | | | - Uri Hamiel
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Berger
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
| | - Shlomo Lipitz
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Idit Maya
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai Shohat
- The Genetic Institute of Maccabi Health Services, Rehovot, Israel
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Bioinformatics Unit, Cancer Research Center, Chaim Sheba Medical Center, Tel-Hashomer, Israel
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30
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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, den Dunnen JT, Hassanin E, Lyman Lin W, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau EAW, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306761. [PMID: 38746299 PMCID: PMC11092726 DOI: 10.1101/2024.05.03.24306761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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31
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Wang Y, Xu Y, Zhou C, Cheng Y, Qiao N, Shang Q, Xia L, Song J, Gao C, Qiao Y, Zhang X, Li M, Ma C, Fan Y, Peng X, Wu S, Lv N, Li B, Sun Y, Zhang B, Li T, Li H, Zhang J, Su Y, Li Q, Yuan J, Liu L, Moreno-De-Luca A, MacLennan AH, Gecz J, Zhu D, Wang X, Zhu C, Xing Q. Exome sequencing reveals genetic heterogeneity and clinically actionable findings in children with cerebral palsy. Nat Med 2024; 30:1395-1405. [PMID: 38693247 DOI: 10.1038/s41591-024-02912-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/06/2024] [Indexed: 05/03/2024]
Abstract
Cerebral palsy (CP) is the most common motor disability in children. To ascertain the role of major genetic variants in the etiology of CP, we conducted exome sequencing on a large-scale cohort with clinical manifestations of CP. The study cohort comprised 505 girls and 1,073 boys. Utilizing the current gold standard in genetic diagnostics, 387 of these 1,578 children (24.5%) received genetic diagnoses. We identified 412 pathogenic and likely pathogenic (P/LP) variants across 219 genes associated with neurodevelopmental disorders, and 59 P/LP copy number variants. The genetic diagnostic rate of children with CP labeled at birth with perinatal asphyxia was higher than the rate in children without asphyxia (P = 0.0033). Also, 33 children with CP manifestations (8.5%, 33 of 387) had findings that were clinically actionable. These results highlight the need for early genetic testing in children with CP, especially those with risk factors like perinatal asphyxia, to enable evidence-based medical decision-making.
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Affiliation(s)
- Yangong Wang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Yiran Xu
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Chongchen Zhou
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Ye Cheng
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
- Shanghai Center for Women and Children's Health, Shanghai, China
| | - Niu Qiao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Shang
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Xia
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Juan Song
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Chao Gao
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yimeng Qiao
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Ming Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Caiyun Ma
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yangyi Fan
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Xirui Peng
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Silin Wu
- Department of Neurosurgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai, China
| | - Nan Lv
- Rehabilitation Department, Henan Key Laboratory of Child Genetics and Metabolism, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingbing Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Yanyan Sun
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Bohao Zhang
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Tongchuan Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Hongwei Li
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Jin Zhang
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
- Shanghai Center for Women and Children's Health, Shanghai, China
| | - Yu Su
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Qiaoli Li
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Junying Yuan
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Lei Liu
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Alastair H MacLennan
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jozef Gecz
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Dengna Zhu
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoyang Wang
- Centre for Perinatal Medicine and Health, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Changlian Zhu
- Department of Pediatrics, Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China.
| | - Qinghe Xing
- Children's Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai, China.
- Shanghai Center for Women and Children's Health, Shanghai, China.
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32
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Innella G, Ferrari S, Miccoli S, Luppi E, Fortuno C, Parsons MT, Spurdle AB, Turchetti D. Clinical implications of VUS reclassification in a single-centre series from application of ACMG/AMP classification rules specified for BRCA1/2. J Med Genet 2024; 61:483-489. [PMID: 38160042 DOI: 10.1136/jmg-2023-109694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND BRCA1/2 testing is crucial to guide clinical decisions in patients with hereditary breast/ovarian cancer, but detection of variants of uncertain significance (VUSs) prevents proper management of carriers. The ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) BRCA1/2 Variant Curation Expert Panel (VCEP) has recently developed BRCA1/2 variant classification guidelines consistent with ClinGen processes, specified against the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular-Pathology) classification framework. METHODS The ClinGen-approved BRCA1/2-specified ACMG/AMP classification guidelines were applied to BRCA1/2 VUSs identified from 2011 to 2022 in a series of patients, retrieving information from the VCEP documentation, public databases, literature and ENIGMA unpublished data. Then, we critically re-evaluated carrier families based on new results and checked consistency of updated classification with main sources for clinical interpretation of BRCA1/2 variants. RESULTS Among 166 VUSs detected in 231 index cases, 135 (81.3%) found in 197 index cases were classified by applying BRCA1/2-specified ACMG/AMP criteria: 128 (94.8%) as Benign/Likely Benign and 7 (5.2%) as Pathogenic/Likely Pathogenic. The average time from the first report as 'VUS' to classification using this approach was 49.4 months. Considering that 15 of these variants found in 64 families had already been internally reclassified prior to this work, this study provided 121 new reclassifications among the 151 (80.1%) remaining VUSs, relevant to 133/167 (79.6%) families. CONCLUSIONS These results demonstrated the effectiveness of new BRCA1/2 ACMG/AMP classification guidelines for VUS classification within a clinical cohort, and their important clinical impact. Furthermore, they suggested a cadence of no more than 3 years for regular review of VUSs, which however requires time, expertise and resources.
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Affiliation(s)
- Giovanni Innella
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simona Ferrari
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Sara Miccoli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elena Luppi
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Michael T Parsons
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Daniela Turchetti
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA. Guidelines for releasing a variant effect predictor. ARXIV 2024:arXiv:2404.10807v1. [PMID: 38699161 PMCID: PMC11065047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released to date, and there is tremendous variability in their underlying algorithms and outputs, and in the ways in which the methodologies and predictions are shared. This leads to considerable challenges for end users in knowing which VEPs to use and how to use them. Here, to address these issues, we provide guidelines and recommendations for the release of novel VEPs. Emphasising open-source availability, transparent methodologies, clear variant effect score interpretations, standardised scales, accessible predictions, and rigorous training data disclosure, we aim to improve the usability and interpretability of VEPs, and promote their integration into analysis and evaluation pipelines. We also provide a large, categorised list of currently available VEPs, aiming to facilitate the discovery and encourage the usage of novel methods within the scientific community.
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Affiliation(s)
- Benjamin J. Livesey
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mafalda Dias
- Centre for Genomic Regulation (CRG),The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan Frazer
- Centre for Genomic Regulation (CRG),The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sushant Kumar
- Department of Medical Biophysics, University of Toronto; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rose Orenbuch
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Lara Muffley
- Department of Genome Sciences, University of Washington and the Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Julia Foreman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Ben Lehner
- Wellcome Sanger Institute, Cambridge, UK; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Frederick P. Roth
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alan F. Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington and the Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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Fortuno C, Michailidou K, Parsons M, Dolinsky JS, Pesaran T, Yussuf A, Mester JL, Hruska KS, Hiraki S, O’Connor R, Chan RC, Kim S, Tavtigian SV, Goldgar D, James PA, Spurdle AB. Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines. Hum Mol Genet 2024; 33:724-732. [PMID: 38271184 PMCID: PMC11000651 DOI: 10.1093/hmg/ddae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Since first publication of the American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) variant classification guidelines, additional recommendations for application of certain criteria have been released (https://clinicalgenome.org/docs/), to improve their application in the diagnostic setting. However, none have addressed use of the PS4 and PP4 criteria, capturing patient presentation as evidence towards pathogenicity. Application of PS4 can be done through traditional case-control studies, or "proband counting" within or across clinical testing cohorts. Review of the existing PS4 and PP4 specifications for Hereditary Cancer Gene Variant Curation Expert Panels revealed substantial differences in the approach to defining specifications. Using BRCA1, BRCA2 and TP53 as exemplar genes, we calibrated different methods proposed for applying the "PS4 proband counting" criterion. For each approach, we considered limitations, non-independence with other ACMG/AMP criteria, broader applicability, and variability in results for different datasets. Our findings highlight inherent overlap of proband-counting methods with ACMG/AMP frequency codes, and the importance of calibration to derive dataset-specific code weights that can account for potential between-dataset differences in ascertainment and other factors. Our work emphasizes the advantages and generalizability of logistic regression analysis over simple proband-counting approaches to empirically determine the relative predictive capacity and weight of various personal clinical features in the context of multigene panel testing, for improved variant interpretation. We also provide a general protocol, including instructions for data formatting and a web-server for analysis of personal history parameters, to facilitate dataset-specific calibration analyses required to use such data for germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Michael Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | | | - Tina Pesaran
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | | | | | | | | | - Raymond C Chan
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Serra Kim
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - David Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
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Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585809. [PMID: 38585983 PMCID: PMC10996540 DOI: 10.1101/2024.03.21.585809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Jie Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zara Shariff
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Stephen P. Plassmeyer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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Zucca S, Nicora G, De Paoli F, Carta MG, Bellazzi R, Magni P, Rizzo E, Limongelli I. An AI-based approach driven by genotypes and phenotypes to uplift the diagnostic yield of genetic diseases. Hum Genet 2024:10.1007/s00439-023-02638-x. [PMID: 38520562 DOI: 10.1007/s00439-023-02638-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/27/2023] [Indexed: 03/25/2024]
Abstract
Identifying disease-causing variants in Rare Disease patients' genome is a challenging problem. To accomplish this task, we describe a machine learning framework, that we called "Suggested Diagnosis", whose aim is to prioritize genetic variants in an exome/genome based on the probability of being disease-causing. To do so, our method leverages standard guidelines for germline variant interpretation as defined by the American College of Human Genomics (ACMG) and the Association for Molecular Pathology (AMP), inheritance information, phenotypic similarity, and variant quality. Starting from (1) the VCF file containing proband's variants, (2) the list of proband's phenotypes encoded in Human Phenotype Ontology terms, and optionally (3) the information about family members (if available), the "Suggested Diagnosis" ranks all the variants according to their machine learning prediction. This method significantly reduces the number of variants that need to be evaluated by geneticists by pinpointing causative variants in the very first positions of the prioritized list. Most importantly, our approach proved to be among the top performers within the CAGI6 Rare Genome Project Challenge, where it was able to rank the true causative variant among the first positions and, uniquely among all the challenge participants, increased the diagnostic yield of 12.5% by solving 2 undiagnosed cases.
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Affiliation(s)
- S Zucca
- enGenome Srl, 27100, Pavia, Italy
| | - G Nicora
- enGenome Srl, 27100, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | | | - M G Carta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - R Bellazzi
- enGenome Srl, 27100, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - P Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.
- University of Pavia, 27100, Pavia, Italy.
| | - E Rizzo
- enGenome Srl, 27100, Pavia, Italy
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Allen S, Loong L, Garrett A, Torr B, Durkie M, Drummond J, Callaway A, Robinson R, Burghel GJ, Hanson H, Field J, McDevitt T, McVeigh TP, Bedenham T, Bowles C, Bradshaw K, Brooks C, Butler S, Del Rey Jimenez JC, Hawkes L, Stinton V, MacMahon S, Owens M, Palmer-Smith S, Smith K, Tellez J, Valganon-Petrizan M, Waskiewicz E, Yau M, Eccles DM, Tischkowitz M, Goel S, McRonald F, Antoniou AC, Morris E, Hardy S, Turnbull C. Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey. J Med Genet 2024; 61:305-312. [PMID: 38154813 PMCID: PMC10982625 DOI: 10.1136/jmg-2023-109645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/28/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND National and international amalgamation of genomic data offers opportunity for research and audit, including analyses enabling improved classification of variants of uncertain significance. Review of individual-level data from National Health Service (NHS) testing of cancer susceptibility genes (2002-2023) submitted to the National Disease Registration Service revealed heterogeneity across participating laboratories regarding (1) the structure, quality and completeness of submitted data, and (2) the ease with which that data could be assembled locally for submission. METHODS In May 2023, we undertook a closed online survey of 51 clinical scientists who provided consensus responses representing all 17 of 17 NHS molecular genetic laboratories in England and Wales which undertake NHS diagnostic analyses of cancer susceptibility genes. The survey included 18 questions relating to 'next-generation sequencing workflow' (11), 'variant classification' (3) and 'phenotypical context' (4). RESULTS Widely differing processes were reported for transfer of variant data into their local LIMS (Laboratory Information Management System), for the formatting in which the variants are stored in the LIMS and which classes of variants are retained in the local LIMS. Differing local provisions and workflow for variant classifications were also reported, including the resources provided and the mechanisms by which classifications are stored. CONCLUSION The survey responses illustrate heterogeneous laboratory workflow for preparation of genomic variant data from local LIMS for centralised submission. Workflow is often labour-intensive and inefficient, involving multiple manual steps which introduce opportunities for error. These survey findings and adoption of the concomitant recommendations may support improvement in laboratory dataflows, better facilitating submission of data for central amalgamation.
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Affiliation(s)
- Sophie Allen
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Lucy Loong
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Alice Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NEY Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - James Drummond
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Rachel Robinson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Helen Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Joanne Field
- Genomics and Molecular Medicine Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Trudi McDevitt
- Department of Clinical Genetics, CHI at Crumlin, Dublin, Ireland
| | - Terri P McVeigh
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Tina Bedenham
- West Midlands, Oxford and Wessex Genomic Laboratory Hub, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christopher Bowles
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Kirsty Bradshaw
- East Midlands and East of England Genomics Laboratory, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Claire Brooks
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Samantha Butler
- Central and South Genomic Laboratory Hub, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Lorraine Hawkes
- South East Genomics Laboratory Hub, Guy's Hospital, London, UK
| | - Victoria Stinton
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Suzanne MacMahon
- Centre for Molecular Pathology, Institute of Cancer Research Sutton, Sutton, UK
- Department of Molecular Diagnostics, The Royal Marsden NHS Foundation Trust, London, UK
| | - Martina Owens
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sheila Palmer-Smith
- Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Kenneth Smith
- South West Genomic Laboratory Hub, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - James Tellez
- North East and Yorkshire Genomic Laboratory Hub, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mikel Valganon-Petrizan
- Centre for Molecular Pathology, Institute of Cancer Research Sutton, Sutton, UK
- Department of Molecular Diagnostics, The Royal Marsden NHS Foundation Trust, London, UK
| | - Erik Waskiewicz
- Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Michael Yau
- South East Genomics Laboratory Hub, Guy's Hospital, London, UK
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Shilpi Goel
- NHS England, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Fiona McRonald
- NHS England, National Disease Registration Service, London, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Eva Morris
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Steven Hardy
- NHS England, National Disease Registration Service, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
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Kim HH, Kim DW, Woo J, Lee K. Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders. Hum Genomics 2024; 18:28. [PMID: 38509596 PMCID: PMC10956189 DOI: 10.1186/s40246-024-00595-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND In the process of finding the causative variant of rare diseases, accurate assessment and prioritization of genetic variants is essential. Previous variant prioritization tools mainly depend on the in-silico prediction of the pathogenicity of variants, which results in low sensitivity and difficulty in interpreting the prioritization result. In this study, we propose an explainable algorithm for variant prioritization, named 3ASC, with higher sensitivity and ability to annotate evidence used for prioritization. 3ASC annotates each variant with the 28 criteria defined by the ACMG/AMP genome interpretation guidelines and features related to the clinical interpretation of the variants. The system can explain the result based on annotated evidence and feature contributions. RESULTS We trained various machine learning algorithms using in-house patient data. The performance of variant ranking was assessed using the recall rate of identifying causative variants in the top-ranked variants. The best practice model was a random forest classifier that showed top 1 recall of 85.6% and top 3 recall of 94.4%. The 3ASC annotates the ACMG/AMP criteria for each genetic variant of a patient so that clinical geneticists can interpret the result as in the CAGI6 SickKids challenge. In the challenge, 3ASC identified causal genes for 10 out of 14 patient cases, with evidence of decreased gene expression for 6 cases. Among them, two genes (HDAC8 and CASK) had decreased gene expression profiles confirmed by transcriptome data. CONCLUSIONS 3ASC can prioritize genetic variants with higher sensitivity compared to previous methods by integrating various features related to clinical interpretation, including features related to false positive risk such as quality control and disease inheritance pattern. The system allows interpretation of each variant based on the ACMG/AMP criteria and feature contribution assessed using explainable AI techniques.
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Affiliation(s)
- Ho Heon Kim
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Dong-Wook Kim
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Junwoo Woo
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Kyoungyeul Lee
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea.
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Bhasin MA, Knaus A, Incardona P, Schmid A, Holtgrewe M, Elbracht M, Krawitz PM, Hsieh TC. Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis. Genes (Basel) 2024; 15:370. [PMID: 38540429 PMCID: PMC10969976 DOI: 10.3390/genes15030370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/03/2024] [Accepted: 03/13/2024] [Indexed: 06/14/2024] Open
Abstract
Genomic variant prioritization is crucial for identifying disease-associated genetic variations. Integrating facial and clinical feature analyses into this process enhances performance. This study demonstrates the integration of facial analysis (GestaltMatcher) and Human Phenotype Ontology analysis (CADA) within VarFish, an open-source variant analysis framework. Challenges related to non-open-source components were addressed by providing an open-source version of GestaltMatcher, facilitating on-premise facial analysis to address data privacy concerns. Performance evaluation on 163 patients recruited from a German multi-center study of rare diseases showed PEDIA's superior accuracy in variant prioritization compared to individual scores. This study highlights the importance of further benchmarking and future integration of advanced facial analysis approaches aligned with ACMG guidelines to enhance variant classification.
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Affiliation(s)
- Meghna Ahuja Bhasin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Pietro Incardona
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Alexander Schmid
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Manuel Holtgrewe
- CUBI—Core Unit Bioinformatics, Berlin Institute of Health, 10117 Berlin, Germany;
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, 52062 Aachen, Germany;
| | - Peter M. Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
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40
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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41
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Hu C, Huang H, Na J, Lumby C, Abozaid M, Holdren MA, Rao TJ, Karam R, Pesaran T, Weyandt JD, Csuy CM, Seelaus CA, Young CC, Fulk K, Heidari Z, Morais Lyra PC, Couch RE, Persons B, Polley EC, Gnanaolivu RD, Boddicker NJ, Monteiro ANA, Yadav S, Domchek SM, Richardson ME, Couch FJ. Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain. Am J Hum Genet 2024; 111:584-593. [PMID: 38417439 PMCID: PMC10940015 DOI: 10.1016/j.ajhg.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/01/2024] Open
Abstract
Variants of uncertain significance (VUSs) in BRCA2 are a common result of hereditary cancer genetic testing. While more than 4,000 unique VUSs, comprised of missense or intronic variants, have been identified in BRCA2, the few missense variants now classified clinically as pathogenic or likely pathogenic are predominantly located in the region encoding the C-terminal DNA binding domain (DBD). We report on functional evaluation of the influence of 462 BRCA2 missense variants affecting the DBD on DNA repair activity of BRCA2 using a homology-directed DNA double-strand break repair assay. Of these, 137 were functionally abnormal, 313 were functionally normal, and 12 demonstrated intermediate function. Comparisons with other functional studies of BRCA2 missense variants yielded strong correlations. Sequence-based in silico prediction models had high sensitivity, but limited specificity, relative to the homology-directed repair assay. Combining the functional results with clinical and genetic data in an American College of Medical Genetics (ACMG)/Association for Molecular Pathology (AMP)-like variant classification framework from a clinical testing laboratory, after excluding known splicing variants and functionally intermediate variants, classified 431 of 442 (97.5%) missense variants (129 as pathogenic/likely pathogenic and 302 as benign/likely benign). Functionally abnormal variants classified as pathogenic by ACMG/AMP rules were associated with a slightly lower risk of breast cancer (odds ratio [OR] 5.15, 95% confidence interval [CI] 3.43-7.83) than BRCA2 DBD protein truncating variants (OR 8.56, 95% CI 6.03-12.36). Overall, functional studies of BRCA2 variants using validated assays substantially improved the variant classification yield from ACMG/AMP models and are expected to improve clinical management of many individuals found to harbor germline BRCA2 missense VUS.
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Affiliation(s)
- Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Huaizhi Huang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Jie Na
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA
| | - Carolyn Lumby
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Mohamed Abozaid
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Megan A Holdren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Tara J Rao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | | | | | | | | | | | | | - Kelly Fulk
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | | | - Ronan E Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Benjamin Persons
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Eric C Polley
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Rohan D Gnanaolivu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA
| | - Nicholas J Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA
| | | | - Siddhartha Yadav
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Susan M Domchek
- Division of Hematology Oncology, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA; Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA.
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Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau E, Greenblatt MS, Harrison S, Tavtigian S, Radivojac P, Brenner SE, O’Donnell-Luria A. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.05.24303807. [PMID: 38496501 PMCID: PMC10942508 DOI: 10.1101/2024.03.05.24303807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Purpose To investigate the number of rare missense variants observed in human genome sequences by ACMG/AMP PP3/BP4 evidence strength, following the calibrated PP3/BP4 computational recommendations. Methods Missense variants from the genome sequences of 300 probands from the Rare Genomes Project with suspected rare disease were analyzed using computational prediction tools able to reach PP3_Strong and BP4_Moderate evidence strengths (BayesDel, MutPred2, REVEL, and VEST4). The numbers of variants at each evidence strength were analyzed across disease-associated genes and genome-wide. Results From a median of 75.5 rare (≤1% allele frequency) missense variants in disease-associated genes per proband, a median of one reached PP3_Strong, 3-5 PP3_Moderate, and 3-5 PP3_Supporting. Most were allocated BP4 evidence (median 41-49 per proband) or were indeterminate (median 17.5-19 per proband). Extending the analysis to all protein-coding genes genome-wide, the number of PP3_Strong variants increased approximately 2.6-fold compared to disease-associated genes, with a median per proband of 1-3 PP3_Strong, 8-16 PP3_Moderate, and 10-17 PP3_Supporting. Conclusion A small number of variants per proband reached PP3_Strong and PP3_Moderate in 3,424 disease-associated genes, and though not the intended use of the recommendations, also genome-wide. Use of PP3/BP4 evidence as recommended from calibrated computational prediction tools in the clinical diagnostic laboratory is unlikely to inappropriately contribute to the classification of an excessive number of variants as Pathogenic or Likely Pathogenic by ACMG/AMP rules.
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Affiliation(s)
- Sarah L. Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Timothy Bergquist
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Leslie G. Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alicia B. Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Emily Nadeau
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Marc S. Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Steven Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Sean Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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43
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Lee JY, Oh SH, Keum C, Lee BL, Chung WY. Clinical application of prospective whole-exome sequencing in the diagnosis of genetic disease: Experience of a regional disease center in South Korea. Ann Hum Genet 2024; 88:101-112. [PMID: 37795942 DOI: 10.1111/ahg.12530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
INTRODUCTION Next-generation sequencing helps clinicians diagnose patients with suspected genetic disorders. The current study aimed to investigate the diagnostic yield and clinical utility of prospective whole-exome sequencing (WES) in rare diseases. METHODS WES was performed in 92 patients who presented with clinical symptoms suggestive of genetic disorders. The WES data were analyzed using an in-house developed software. The patients' phenotypic characteristics were classified according to the human phenotype ontology. RESULTS WES detected 64 variants, 13 were classified as pathogenic, 26 as likely pathogenic, and 25 as variants of uncertain significance. In 57 patients with these variants, 30 were identified as causal variants. The diagnostic yield was higher in patients with abnormalities in joint mobility and skin morphology than in those with cerebellar hypoplasia/atrophy, epilepsy, global developmental delay, dysmorphic features/facial dysmorphisms, and chronic kidney disease/abnormal renal morphology. CONCLUSION In this study, a WES-based variant interpretation system was employed to provide a definitive diagnosis for 28.3% of the patients suspected of having genetic disorders. WES is particularly useful for diagnosing rare diseases with symptoms that affect more than one system, when targeted genetic panels are difficult to employ.
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Affiliation(s)
- Ja Young Lee
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, South Korea
| | - Seung-Hwan Oh
- Department of Laboratory Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | | | - Bo Lyun Lee
- Department of Pediatrics, Inje University College of Medicine, Busan, South Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Inje University College of Medicine, Busan, South Korea
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Jain S, Bakolitsa C, Brenner SE, Radivojac P, Moult J, Repo S, Hoskins RA, Andreoletti G, Barsky D, Chellapan A, Chu H, Dabbiru N, Kollipara NK, Ly M, Neumann AJ, Pal LR, Odell E, Pandey G, Peters-Petrulewicz RC, Srinivasan R, Yee SF, Yeleswarapu SJ, Zuhl M, Adebali O, Patra A, Beer MA, Hosur R, Peng J, Bernard BM, Berry M, Dong S, Boyle AP, Adhikari A, Chen J, Hu Z, Wang R, Wang Y, Miller M, Wang Y, Bromberg Y, Turina P, Capriotti E, Han JJ, Ozturk K, Carter H, Babbi G, Bovo S, Di Lena P, Martelli PL, Savojardo C, Casadio R, Cline MS, De Baets G, Bonache S, Díez O, Gutiérrez-Enríquez S, Fernández A, Montalban G, Ootes L, Özkan S, Padilla N, Riera C, De la Cruz X, Diekhans M, Huwe PJ, Wei Q, Xu Q, Dunbrack RL, Gotea V, Elnitski L, Margolin G, Fariselli P, Kulakovskiy IV, Makeev VJ, Penzar DD, Vorontsov IE, Favorov AV, Forman JR, Hasenahuer M, Fornasari MS, Parisi G, Avsec Z, Çelik MH, Nguyen TYD, Gagneur J, Shi FY, Edwards MD, Guo Y, Tian K, Zeng H, Gifford DK, Göke J, Zaucha J, Gough J, Ritchie GRS, Frankish A, Mudge JM, Harrow J, Young EL, Yu Y, Huff CD, Murakami K, Nagai Y, Imanishi T, Mungall CJ, Jacobsen JOB, Kim D, Jeong CS, Jones DT, Li MJ, Guthrie VB, Bhattacharya R, Chen YC, Douville C, Fan J, Kim D, Masica D, Niknafs N, Sengupta S, Tokheim C, Turner TN, Yeo HTG, Karchin R, Shin S, Welch R, Keles S, Li Y, Kellis M, Corbi-Verge C, Strokach AV, Kim PM, Klein TE, Mohan R, Sinnott-Armstrong NA, Wainberg M, Kundaje A, Gonzaludo N, Mak ACY, Chhibber A, Lam HYK, Dahary D, Fishilevich S, Lancet D, Lee I, Bachman B, Katsonis P, Lua RC, Wilson SJ, Lichtarge O, Bhat RR, Sundaram L, Viswanath V, Bellazzi R, Nicora G, Rizzo E, Limongelli I, Mezlini AM, Chang R, Kim S, Lai C, O’Connor R, Topper S, van den Akker J, Zhou AY, Zimmer AD, Mishne G, Bergquist TR, Breese MR, Guerrero RF, Jiang Y, Kiga N, Li B, Mort M, Pagel KA, Pejaver V, Stamboulian MH, Thusberg J, Mooney SD, Teerakulkittipong N, Cao C, Kundu K, Yin Y, Yu CH, Kleyman M, Lin CF, Stackpole M, Mount SM, Eraslan G, Mueller NS, Naito T, Rao AR, Azaria JR, Brodie A, Ofran Y, Garg A, Pal D, Hawkins-Hooker A, Kenlay H, Reid J, Mucaki EJ, Rogan PK, Schwarz JM, Searls DB, Lee GR, Seok C, Krämer A, Shah S, Huang CV, Kirsch JF, Shatsky M, Cao Y, Chen H, Karimi M, Moronfoye O, Sun Y, Shen Y, Shigeta R, Ford CT, Nodzak C, Uppal A, Shi X, Joseph T, Kotte S, Rana S, Rao A, Saipradeep VG, Sivadasan N, Sunderam U, Stanke M, Su A, Adzhubey I, Jordan DM, Sunyaev S, Rousseau F, Schymkowitz J, Van Durme J, Tavtigian SV, Carraro M, Giollo M, Tosatto SCE, Adato O, Carmel L, Cohen NE, Fenesh T, Holtzer T, Juven-Gershon T, Unger R, Niroula A, Olatubosun A, Väliaho J, Yang Y, Vihinen M, Wahl ME, Chang B, Chong KC, Hu I, Sun R, Wu WKK, Xia X, Zee BC, Wang MH, Wang M, Wu C, Lu Y, Chen K, Yang Y, Yates CM, Kreimer A, Yan Z, Yosef N, Zhao H, Wei Z, Yao Z, Zhou F, Folkman L, Zhou Y, Daneshjou R, Altman RB, Inoue F, Ahituv N, Arkin AP, Lovisa F, Bonvini P, Bowdin S, Gianni S, Mantuano E, Minicozzi V, Novak L, Pasquo A, Pastore A, Petrosino M, Puglisi R, Toto A, Veneziano L, Chiaraluce R, Ball MP, Bobe JR, Church GM, Consalvi V, Cooper DN, Buckley BA, Sheridan MB, Cutting GR, Scaini MC, Cygan KJ, Fredericks AM, Glidden DT, Neil C, Rhine CL, Fairbrother WG, Alontaga AY, Fenton AW, Matreyek KA, Starita LM, Fowler DM, Löscher BS, Franke A, Adamson SI, Graveley BR, Gray JW, Malloy MJ, Kane JP, Kousi M, Katsanis N, Schubach M, Kircher M, Mak ACY, Tang PLF, Kwok PY, Lathrop RH, Clark WT, Yu GK, LeBowitz JH, Benedicenti F, Bettella E, Bigoni S, Cesca F, Mammi I, Marino-Buslje C, Milani D, Peron A, Polli R, Sartori S, Stanzial F, Toldo I, Turolla L, Aspromonte MC, Bellini M, Leonardi E, Liu X, Marshall C, McCombie WR, Elefanti L, Menin C, Meyn MS, Murgia A, Nadeau KCY, Neuhausen SL, Nussbaum RL, Pirooznia M, Potash JB, Dimster-Denk DF, Rine JD, Sanford JR, Snyder M, Cote AG, Sun S, Verby MW, Weile J, Roth FP, Tewhey R, Sabeti PC, Campagna J, Refaat MM, Wojciak J, Grubb S, Schmitt N, Shendure J, Spurdle AB, Stavropoulos DJ, Walton NA, Zandi PP, Ziv E, Burke W, Chen F, Carr LR, Martinez S, Paik J, Harris-Wai J, Yarborough M, Fullerton SM, Koenig BA, McInnes G, Shigaki D, Chandonia JM, Furutsuki M, Kasak L, Yu C, Chen R, Friedberg I, Getz GA, Cong Q, Kinch LN, Zhang J, Grishin NV, Voskanian A, Kann MG, Tran E, Ioannidis NM, Hunter JM, Udani R, Cai B, Morgan AA, Sokolov A, Stuart JM, Minervini G, Monzon AM, Batzoglou S, Butte AJ, Greenblatt MS, Hart RK, Hernandez R, Hubbard TJP, Kahn S, O’Donnell-Luria A, Ng PC, Shon J, Veltman J, Zook JM. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 2024; 25:53. [PMID: 38389099 PMCID: PMC10882881 DOI: 10.1186/s13059-023-03113-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/17/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. RESULTS Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. CONCLUSIONS Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
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Hall HN, Parry D, Halachev M, Williamson KA, Donnelly K, Campos Parada J, Bhatia S, Joseph J, Holden S, Prescott TE, Bitoun P, Kirk EP, Newbury-Ecob R, Lachlan K, Bernar J, van Heyningen V, FitzPatrick DR, Meynert A. Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia. J Med Genet 2024; 61:250-261. [PMID: 38050128 PMCID: PMC7615962 DOI: 10.1136/jmg-2023-109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. METHODS Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. RESULTS Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5' non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. CONCLUSION Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia.
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Affiliation(s)
- Hildegard Nikki Hall
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - David Parry
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
- Illumina United Kingdom, Edinburgh, UK
| | - Mihail Halachev
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kathleen A Williamson
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kevin Donnelly
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jose Campos Parada
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Shipra Bhatia
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jeffrey Joseph
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
| | - Simon Holden
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Trine E Prescott
- Department of Medical Genetics, Telemark Hospital, Skien, Norway
| | - Pierre Bitoun
- Consultations de Génétique médicale, Service de Pédiatrie, CHU Paris-Nord, Hôpital Jean Verdier, Bondy, France
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Katherine Lachlan
- University Hospital Southampton, NHS Foundation Trust Wessex Clinical Genetics Service, Southampton, UK
| | - Juan Bernar
- Department of Genetics, Hospital Ruber Internacional, Madrid, Spain
| | - Veronica van Heyningen
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
- Institute of Ophthalmology, University College London, London, UK
| | - David R FitzPatrick
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Alison Meynert
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
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Garcia ABDM, Viola GD, Corrêa BDS, Fischer TDS, Pinho MCDF, Rodrigues GM, Ashton-Prolla P, Rosset C. An overview of actionable and potentially actionable TSC1 and TSC2 germline variants in an online Database. Genet Mol Biol 2024; 46:e20230132. [PMID: 38373162 PMCID: PMC10876083 DOI: 10.1590/1678-4685-gmb-2023-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/26/2023] [Indexed: 02/21/2024] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by loss of function germline variants in the TSC1 or TSC2 tumor suppressor genes. Genetic testing for the detection of pathogenic variants in either TSC1 or TSC2 was implemented as a diagnostic criterion for TSC. However, TSC molecular diagnosis can be challenging due to the absence of variant hotspots and the high number of variants described. This review aimed to perform an overview of TSC1/2 variants submitted in the ClinVar database. Variants of uncertain significance (VUS), missense and single nucleotide variants were the most frequent in clinical significance (37-40%), molecular consequence (37%-39%) and variation type (82%-83%) categories in ClinVar in TSC1 and TSC2 variants, respectively. Frameshift and nonsense VUS have potential for pathogenic reclassification if further functional and segregation studies were performed. Indeed, there were few functional assays deposited in the database and literature. In addition, we did not observe hotspots for variation and many variants presented conflicting submissions regarding clinical significance. This study underscored the importance of disseminating molecular diagnostic results in a public database to render the information largely accessible and promote accurate diagnosis. We encourage the performance of functional studies evaluating the pathogenicity of TSC1/2 variants.
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Affiliation(s)
- Arthur Bandeira de Mello Garcia
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Guilherme Danielski Viola
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Taís da Silveira Fischer
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Maria Clara de Freitas Pinho
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Centro Universitário CESUCA, Cachoeirinha, RS, Brazil
| | - Grazielle Motta Rodrigues
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
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Spier I, Yin X, Richardson M, Pineda M, Laner A, Ritter D, Boyle J, Mur P, Hansen TVO, Shi X, Mahmood K, Plazzer JP, Ognedal E, Nordling M, Farrington SM, Yamamoto G, Baert-Desurmont S, Martins A, Borras E, Tops C, Webb E, Beshay V, Genuardi M, Pesaran T, Capellá G, Tavtigian SV, Latchford A, Frayling IM, Plon SE, Greenblatt M, Macrae FA, Aretz S. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel. Genet Med 2024; 26:100992. [PMID: 37800450 PMCID: PMC10922469 DOI: 10.1016/j.gim.2023.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
PURPOSE The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. METHODS Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. RESULTS The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). CONCLUSION The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
| | - Xiaoyu Yin
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia.
| | | | - Marta Pineda
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | | | - Deborah Ritter
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Julie Boyle
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Australia; Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia
| | | | - Margareta Nordling
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, the University of Edinburgh, Edinburgh, United Kingdom
| | - Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | | | | | | | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, and Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Gabriel Capellá
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sean V Tavtigian
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Andrew Latchford
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Department of Surgery and Cancer, Imperial College, London, United Kingdom
| | - Ian M Frayling
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, Cardiff University, United Kingdom
| | - Sharon E Plon
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Marc Greenblatt
- Larner College of Medicine, University of Vermont, Burlington, VT
| | - Finlay A Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
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Asatryan B, Murray B, Gasperetti A, McClellan R, Barth AS. Unraveling Complexities in Genetically Elusive Long QT Syndrome. Circ Arrhythm Electrophysiol 2024; 17:e012356. [PMID: 38264885 DOI: 10.1161/circep.123.012356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Genetic testing has become standard of care for patients with long QT syndrome (LQTS), providing diagnostic, prognostic, and therapeutic information for both probands and their family members. However, up to a quarter of patients with LQTS do not have identifiable Mendelian pathogenic variants in the currently known LQTS-associated genes. This absence of genetic confirmation, intriguingly, does not lessen the severity of LQTS, with the prognosis in these gene-elusive patients with unequivocal LQTS mirroring genotype-positive patients in the limited data available. Such a conundrum instigates an exploration into the causes of corrected QT interval (QTc) prolongation in these cases, unveiling a broad spectrum of potential scenarios and mechanisms. These include multiple environmental influences on QTc prolongation, exercise-induced repolarization abnormalities, and the profound implications of the constantly evolving nature of genetic testing and variant interpretation. In addition, the rapid advances in genetics have the potential to uncover new causal genes, and polygenic risk factors may aid in the diagnosis of high-risk patients. Navigating this multifaceted landscape requires a systematic approach and expert knowledge, integrating the dynamic nature of genetics and patient-specific influences for accurate diagnosis, management, and counseling of patients. The role of a subspecialized expert cardiogenetic clinic is paramount in evaluation to navigate this complexity. Amid these intricate aspects, this review outlines potential causes of gene-elusive LQTS. It also provides an outline for the evaluation of patients with negative and inconclusive genetic test results and underscores the need for ongoing adaptation and reassessment in our understanding of LQTS, as the complexities of gene-elusive LQTS are increasingly deciphered.
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Affiliation(s)
- Babken Asatryan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Brittney Murray
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alessio Gasperetti
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rebecca McClellan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andreas S Barth
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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Horton C, Hoang L, Zimmermann H, Young C, Grzybowski J, Durda K, Vuong H, Burks D, Cass A, LaDuca H, Richardson ME, Harrison S, Chao EC, Karam R. Diagnostic Outcomes of Concurrent DNA and RNA Sequencing in Individuals Undergoing Hereditary Cancer Testing. JAMA Oncol 2024; 10:212-219. [PMID: 37924330 PMCID: PMC10625669 DOI: 10.1001/jamaoncol.2023.5586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 11/06/2023]
Abstract
Importance Personalized surveillance, prophylaxis, and cancer treatment options for individuals with hereditary cancer predisposition are informed by results of germline genetic testing. Improvements to genomic technology, such as the availability of RNA sequencing, may increase identification of individuals eligible for personalized interventions by improving the accuracy and yield of germline testing. Objective To assess the cumulative association of paired DNA and RNA testing with detection of disease-causing germline genetic variants and resolution of variants of uncertain significance (VUS). Design, Setting, and Participants Paired DNA and RNA sequencing was performed on individuals undergoing germline testing for hereditary cancer indication at a single diagnostic laboratory from March 2019 through April 2020. Demographic characteristics, clinical data, and test results were curated as samples were received, and changes to variant classification were assessed over time. Data analysis was performed from May 2020 to June 2023. Main Outcomes and Measures Main outcomes were increase in diagnostic yield, decrease in VUS rate, the overall results by variant type, the association of RNA evidence with variant classification, and the corresponding predicted effect on cancer risk management. Results A total of 43 524 individuals were included (median [range] age at testing, 54 [2-101] years; 37 373 female individuals [85.7%], 6224 male individuals [14.3%], and 2 individuals of unknown sex [<0.1%]), with 43 599 tests. A total of 2197 (5.0%) were Ashkenazi Jewish, 1539 (3.5%) were Asian, 3077 (7.1%) were Black, 2437 (5.6%) were Hispanic, 27 793 (63.7%) were White, and 2049 (4.7%) were other race, and for 4507 individuals (10.3%), race and ethnicity were unknown. Variant classification was impacted in 549 individuals (1.3%). Medically significant upgrades were made in 97 individuals, including 70 individuals who had a variant reclassified from VUS to pathogenic/likely pathogenic (P/LP) and 27 individuals who had a novel deep intronic P/LP variant that would not have been detected using DNA sequencing alone. A total of 93 of 545 P/LP splicing variants (17.1%) were dependent on RNA evidence for classification, and 312 of 439 existing splicing VUS (71.1%) were resolved by RNA evidence. Notably, the increase in positive rate (3.1%) and decrease in VUS rate (-3.9%) was higher in Asian, Black, and Hispanic individuals combined compared to White individuals (1.6%; P = .02; and -2.5%; P < .001). Conclusions and Relevance Findings of this diagnostic study demonstrate that the ability to perform RNA sequencing concurrently with DNA sequencing represents an important advancement in germline genetic testing by improving detection of novel variants and classification of existing variants. This expands the identification of individuals with hereditary cancer predisposition and increases opportunities for personalization of therapeutics and surveillance.
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Affiliation(s)
| | | | | | | | | | | | - Huy Vuong
- Ambry Genetics, Aliso Viejo, California
| | | | | | | | | | | | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, California
- University of California, Irvine, School of Medicine
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