Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases

Abstract

This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders. This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders. Constitutional disorders—including birth defects and neurodevelopmental disorders—warrant genetic/genomic testing for accurate disease diagnosis and clinical management. Developmental disabilities, including attention-deficit/hyperactivity disorder, autism spectrum disorder, blindness, cerebral palsy, moderate to profound hearing loss, learning disability, intellectual disability, seizures, stuttering or stammering, and other developmental delays, affect about 17% of the pediatric population in the United States.1Zablotsky B. Black L.I. Maenner M.J. Schieve L.A. Danielson M.L. Bitsko R.H. Blumberg S.J. Kogan M.D. Boyle C.A. Prevalence and trends of developmental disabilities among children in the United States: 2009-2017.Pediatrics. 2019; 144: e20190811Crossref PubMed Scopus (599) Google Scholar Different classes of structural variations (SVs) in the genome, such as aneuploidies, translocations, inversions, interstitial deletions/duplications, repeated expansions/contractions, and complex rearrangements, contribute to a significant number of developmental disability cases.2Sudmant P.H. Rausch T. Gardner E.J. Handsaker R.E. Abyzov A. Huddleston J. et al.An integrated map of structural variation in 2,504 human genomes.Nature. 2015; 526: 75-81Crossref PubMed Scopus (1418) Google Scholar Before 2010, G-banded karyotype was the recommended genetic testing method for individuals with developmental disabilities to detect gross unbalanced rearrangements as well as balanced events with a diagnostic yield of approximately 5%.3Martin C.L. Ledbetter D.H. Chromosomal microarray testing for children with unexplained neurodevelopmental disorders.JAMA. 2017; 317: 2545-2546Crossref PubMed Scopus (15) Google Scholar,4Miller D.T. Adam M.P. Aradhya S. Biesecker L.G. Brothman A.R. Carter N.P. Church D.M. Crolla J.A. Eichler E.E. Epstein C.J. Faucett W.A. Feuk L. Friedman J.M. Hamosh A. Jackson L. Kaminsky E.B. Kok K. Krantz I.D. Kuhn R.M. Lee C. Ostell J.M. Rosenberg C. Scherer S.W. Spinner N.B. Stavropoulos D.J. Tepperberg J.H. Thorland E.C. Vermeesch J.R. Waggoner D.J. Watson M.S. Martin C.L. Ledbetter D.H. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.Am J Hum Genet. 2010; 86: 749-764Abstract Full Text Full Text PDF PubMed Scopus (2109) Google Scholar In the mid-2000s, chromosomal microarray analysis (CMA) was established as an effective clinical tool for the analysis of whole-genome copy number variations (CNVs) with a diagnostic yield of up to 15% to 20%.4Miller D.T. Adam M.P. Aradhya S. Biesecker L.G. Brothman A.R. Carter N.P. Church D.M. Crolla J.A. Eichler E.E. Epstein C.J. Faucett W.A. Feuk L. Friedman J.M. Hamosh A. Jackson L. Kaminsky E.B. Kok K. Krantz I.D. Kuhn R.M. Lee C. Ostell J.M. Rosenberg C. Scherer S.W. Spinner N.B. Stavropoulos D.J. Tepperberg J.H. Thorland E.C. Vermeesch J.R. Waggoner D.J. Watson M.S. Martin C.L. Ledbetter D.H. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.Am J Hum Genet. 2010; 86: 749-764Abstract Full Text Full Text PDF PubMed Scopus (2109) Google Scholar Subsequently, in 2010, CMA was recommended as the first-tier clinical diagnostic test by several medical organizations and societies [including the American College of Medical Genetics and Genomics (ACMG),5Manning M. Hudgins L. Professional Practice and Guidelines CommitteeArray-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities [published correction appears in Genet Med. 2020 Dec;22(12):2126].Genet Med. 2010; 12: 742-745Abstract Full Text Full Text PDF PubMed Scopus (465) Google Scholar the American Academy of Neurology,6Shevell M. Ashwal S. Donley D. Flint J. Gingold M. Hirtz D. Majnemer A. Noetzel M. Sheth R.D. Quality Standards Subcommittee of the American Academy of Neurology; Practice Committee of the Child Neurology SocietyPractice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society.Neurology. 2003; 60: 367-380Crossref PubMed Scopus (640) Google Scholar and the American Academy of Pediatrics7Hyman S.L. Levy S.E. Myers S.M. Identification, evaluation, and management of children with autism spectrum disorder.Pediatrics. 2020; 145: e20193447Crossref PubMed Scopus (194) Google Scholar,8Moeschler J.B. Shevell M. Committee on GeneticsComprehensive evaluation of the child with intellectual disability or global developmental delays.Pediatrics. 2014; 134: e903-e918Crossref PubMed Scopus (366) Google Scholar] for individuals with developmental disabilities and neurodevelopmental disorders. CMA several technical including to detect balanced structural rearrangements, and of and for J.M. Myers S.M. testing in neurodevelopmental PubMed Scopus Google Scholar In testing is recommended in the diagnostic for individuals with developmental disability and autism spectrum L. A. S.L. B. A. J. S. D. and recommendations for PubMed Scopus Google Scholar and analysis CMA is to detect repeated expansions for in genome to and and whole-genome for genetic testing of individuals with clinically developmental disorders. In a a diagnostic yield of approximately and is as a test a CMA test K. L.A. S. J. D. and genome for pediatric with congenital or intellectual an clinical of the American College of Medical Genetics and Genomics Med. Full Text Full Text PDF PubMed Scopus Google Scholar detection of with technical at in the genome of mapping of detect repeated expansions repeated expansions approximately S. D. A. B. K. C. A. K. A. J.H. a tool to variation in 2019; PubMed Scopus Google Scholar and whole-genome detect contractions of the of facioscapulohumeral dystrophy 1 such as analysis or for repeated and or a and a diagnostic yield with is to for individuals with developmental disability and for individuals with autism spectrum J.M. Myers S.M. testing in neurodevelopmental PubMed Scopus Google A. L. J. S. yield of in with neurodevelopmental J PubMed Scopus Google Scholar genome mapping (OGM) is an technology analysis of the M. M.S. A. Lee E.C. a for detection of structural with a utility in clinical Med. 2017; PubMed Scopus Google Scholar OGM is performed on the Saphyr system at a the The of the used to a of the compared with a genome to several classes of S. M. S. A. M. Structural variation detection and analysis using Bionano optical PubMed Scopus Google Scholar balanced and unbalanced events and and including of for the detection of to OGM also of repeated expansions in the FMR1 as well as repeated contractions with or of is the in L. S. J. D. L. K. optical mapping of in facioscapulohumeral dystrophy Genet. 2020; PubMed Scopus Google Scholar In several OGM concordance to standard-of-care (SOC) L. L. of optical genome mapping in clinical cytogenetic a Google W.A. D.M. of optical genome mapping in and Full Text Full Text PDF Google Scholar OGM and is clinically in the United for J.A. D. of optical genome mapping for the diagnosis of facioscapulohumeral Full Text Full Text PDF PubMed Scopus Google Scholar of and of and as well as analysis Genomics and of the OGM is to SOC test results to A. A. genome mapping as a tool for detection of structural and copy number variations for 12: PubMed Scopus Google D. S. Levy B. of optical genome mapping for of chromosomal structural for clinical evaluation of T. K. C. M. T. M. D. S. M. A. M. D. J.M. D. A. C. L. genome mapping constitutional chromosomal J Hum Genet. 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Adam M.P. Aradhya S. Biesecker L.G. Brothman A.R. Carter N.P. Church D.M. Crolla J.A. Eichler E.E. Epstein C.J. Faucett W.A. Feuk L. Friedman J.M. Hamosh A. Jackson L. Kaminsky E.B. Kok K. Krantz I.D. Kuhn R.M. Lee C. Ostell J.M. Rosenberg C. Scherer S.W. Spinner N.B. Stavropoulos D.J. Tepperberg J.H. Thorland E.C. Vermeesch J.R. Waggoner D.J. Watson M.S. Martin C.L. Ledbetter D.H. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.Am J Hum Genet. 2010; 86: 749-764Abstract Full Text Full Text PDF PubMed Scopus (2109) Google M. Hudgins L. Professional Practice and Guidelines CommitteeArray-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities [published correction appears in Genet Med. 2020 Dec;22(12):2126].Genet Med. 2010; 12: 742-745Abstract Full Text Full Text PDF PubMed Scopus (465) Google M. Ashwal S. Donley D. Flint J. Gingold M. Hirtz D. Majnemer A. Noetzel M. Sheth R.D. Quality Standards Subcommittee of the American Academy of Neurology; Practice Committee of the Child Neurology SocietyPractice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society.Neurology. 2003; 60: 367-380Crossref PubMed Scopus (640) Google S.L. Levy S.E. Myers S.M. Identification, evaluation, and management of children with autism spectrum disorder.Pediatrics. 2020; 145: e20193447Crossref PubMed Scopus (194) Google J.B. Shevell M. Committee on GeneticsComprehensive evaluation of the child with intellectual disability or global developmental delays.Pediatrics. 2014; 134: e903-e918Crossref PubMed Scopus (366) Google J.M. Myers S.M. testing in neurodevelopmental PubMed Scopus Google Scholar CMA by detection of and performed on negative first-tier methods to the detection of to in mapping to A. D. Rausch T. et of structural variation in human 2019; PubMed Scopus Google Scholar other a of the of current the SOC genetic testing several cytogenetic and testing to a genetic a and significant and to the and using a of a significant of M. C. Structural variant the and the of 2019; PubMed Scopus Google Scholar as the with and compared with SOC a study of OGM with technology by the Structural a of OGM for A. A.R. T. C. C. S. J. S.M. M. structural variation detection by genome mapping on PubMed Scopus Google Scholar OGM the to multiple SOC methods of ability to detect several classes of with and M. M.S. A. Lee E.C. a for detection of structural with a utility in clinical Med. 2017; PubMed Scopus Google S. M. S. A. M. Structural variation detection and analysis using Bionano optical PubMed Scopus Google Scholar 100% concordance between OGM and SOC D. S. Levy B. of optical genome mapping for of chromosomal structural for clinical evaluation of T. K. C. M. T. M. D. S. M. A. M. D. J.M. D. A. C. L. genome mapping constitutional chromosomal J Hum Genet. Full Text Full Text PDF PubMed Scopus Google Scholar the technical of OGM multiple sites with data In this samples of constitutional with clinical and chromosomal abnormalities were by The validity and technical of OGM were five in the United The of OGM is by a of and an of sites, is in with clinical cytogenetic testing by karyotype and chromosomal of this study was to and to and the of this The for OGM were and as the evaluation of samples in this study map of to the was at and was with of samples in this number of to the genome effective was to and was with of a of was for of were also and included in this study and were to successful for SOC is the established map to for the and of to effective the for In in a College of American the for the of the The regions by in and in were The of this was the of the of the in this the information. as an for the also provide relevant for the of such as testing is recommended for individuals with autism spectrum J.M. Myers S.M. testing in neurodevelopmental PubMed Scopus Google Scholar the diagnostic yield is to L. A. S.L. B. A. J. S. D. and recommendations for PubMed Scopus Google Scholar CMA is also recommended and in with to testing with testing. The authors tool for and to expansions in the of the FMR1 in this study with a clinical classification of or The SOC testing for was in 100% agreement the with with the is recommended to also the in the the of results from the the samples classified as SOC or the testing by OGM is for of individuals with an for to the SOC for testing is to to samples and were an of well established by OGM accurate and T. K. C. M. T. M. D. S. M. A. M. D. J.M. D. A. C. L. genome mapping constitutional chromosomal J Hum Genet. Full Text Full Text PDF PubMed Scopus Google A. D. Rausch T. et of structural variation in human 2019; PubMed Scopus Google M. C. Structural variant the and the of 2019; PubMed Scopus Google B. D. M.J. et human and integrated analysis of structural PubMed Scopus Google Scholar a was to clinically relevant On the basis of a variant population to and a the number of was to of the classified in the Bionano Access the of and The analysis of was by the ability to several such as an integrated to the of as well as to of genome for was in Bionano Access by a variant by by an American of Medical Genetics and or American of Medical or to the variant classification and The for for the samples of for technical concordance were with SOC detection and classification agreement to the SOC was 97.6% (364/373). for the in complex regions of the genome, the is by the analysis software to and the number

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