Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing

Abstract

The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing. The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing. Clinically recognized pregnancy loss and fetal anomaly (including birth defects and genetic disorders) occur in approximately 15% to 25% and 3% to 5% of pregnancies, respectively; and represent a major public health concern, requiring morphologic examination, biochemical screening, genetic counseling, invasive genetic testing, and appropriate perinatal management.1Jacobs P.A. Hassold T. Chromosome abnormalities: origin and etiology in abortions and livebirths.in: Vogel F. Sperling K. Human Genetics. Springer-Verlag, Berlin, Germany1987: 233-244Crossref Google Scholar, 2Rydberg C. Tunón K. 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Cytogenetic analysis of miscarriages from couples with recurrent miscarriage: a case-control study.Hum Reprod. 2002; 17: 446-451Crossref PubMed Scopus (386) Google Scholar Therefore, medical associations, including the International Society of Ultrasound and Obstetrics and Gynecology, the American College of Obstetrics and Gynecology, and the American College of Medical Genetics and Genomics, recommend that prenatal genetic testing be offered to all pregnant women, irrespective of the gestation and maternal age.7Rose N.C. Kaimal A.J. Dugoff L. Norton M.E. American College of Obstetricians and GynecologistsScreening for fetal chromosomal abnormalities: ACOG practice bulletin, number 226.Obstet Gynecol. 2020; 136: e48-e69Crossref PubMed Scopus (213) Google Scholar, 8Salomon L.J. Alfirevic Z. Audibert F. Kagan K.O. Paladini D. Yeo G. Raine-Fenning N. ISUOG Clinical Standards CommitteeISUOG consensus statement on the impact of non-invasive prenatal testing (NIPT) on prenatal ultrasound practice.Ultrasound Obstet Gynecol. 2014; 44: 122-123Crossref PubMed Scopus (86) Google Scholar, 9Gregg A.R. Skotko B.G. Benkendorf J.L. Monaghan K.G. Bajaj K. Best R.G. Klugman S. Watson M.S. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics.Genet Med. 2016; 18: 1056-1065Abstract Full Text Full Text PDF PubMed Scopus (488) Google Scholar Typically, noninvasive prenatal screening is offered to pregnant women as early as 10 to 12 weeks of gestation,10Van Opstal D. Srebniak M.I. Cytogenetic confirmation of a positive NIPT result: evidence-based choice between chorionic villus sampling and amniocentesis depending on chromosome aberration.Expert Rev Mol Diagn. 2016; 16: 513-520Crossref PubMed Scopus (40) Google Scholar and invasive diagnostic testing is to the of the screening or in that an ultrasound morphologic invasive testing chorionic villus sampling or and either 10 to weeks or weeks of screening and diagnostic Gynecol Clin 2017; 44: Full Text Full Text PDF PubMed Scopus Google Scholar prenatal diagnostic testing has been offered the using karyotyping, which of structural variations that aneuploidies, and balanced and and number variations a resolution of approximately to 10 S. and Obstet Gynecol. PubMed Scopus Google Scholar In the fluorescence in situ hybridization analysis and was for of the chromosomes and using The clinical of FISH in prenatal Diagn. PubMed Scopus Google Scholar The diagnostic with cytogenetic methods 3% in with positive biochemical screening, in maternal and to in with structural D. Klugman S. T. Simpson J.L. K. L. Chromosomal microarray karyotyping for prenatal J Med. PubMed Scopus Google Scholar In the chromosomal microarray the to detect and with a resolution of approximately to and was by American College of Obstetrics and and International Society of Ultrasound and Obstetrics and as the in with an Dugoff L. J.A. and the use of genetic diagnostic in and Gynecol. 2016; PubMed Scopus Google G. N. D. M.D. of prenatal chromosomal study and and Obstet Gynecol. PubMed Scopus Google Scholar detect balanced SVs or the of an diagnostic of to in with structural G. D. N. in fetal anomalies and diagnostic rates and of the and PubMed Scopus Google Scholar with the in has been evaluated as a diagnostic and has an diagnostic of to in with structural G. D. N. in fetal anomalies and diagnostic rates and of the and PubMed Scopus Google Scholar However, is to the of and detect several classes of and has a of it is in a cytogenetic G. D. N. in fetal anomalies and diagnostic rates and of the and PubMed Scopus Google Scholar the current diagnostic workflow on multiple that are simultaneously or in a leading to and to reach a clinical is This the of that the potential to replace multiple and the diagnostic in of In genome mapping (OGM) is a technology with a resolution standard-of-care methods, and it can detect all classes of SVs in a single The is on imaging a specific that the genome the are to to a genome which can be with a reference genome to The and of the the of classes of including deletions, duplications, and including and an and to several that OGM is 100% concordant with in several including T. K. C. G. T. F. D. S. D. D. C. L. Optical genome mapping chromosomal J Hum Genet. Full Text Full Text PDF PubMed Scopus Google Scholar K. T. S. G. D. of by genome J Hum Genet. Full Text Full Text PDF PubMed Scopus Google Scholar and S. L. K. A.R. D. of structural in by genome Med. PubMed Scopus Google Scholar in either or the potential of OGM in prenatal diagnostic testing has been Optical genome mapping as a for of structural and number variations for prenatal PubMed Scopus Google Scholar the of the technology for a in a clinical for prenatal in clinical validation study in a Clinical OGM was with methods FISH, and which included and and of for the and of OGM for prenatal diagnostic testing with methods, with the and and recommend OGM as a in prenatal This validation study included the analysis of 114 samples (including and samples that were received in the clinical laboratory for cytogenetic analysis with karyotyping, FISH, and/or CMA. 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Alfirevic Z. Audibert F. Kagan K.O. Paladini D. Yeo G. Raine-Fenning N. ISUOG Clinical Standards CommitteeISUOG consensus statement on the impact of non-invasive prenatal testing (NIPT) on prenatal ultrasound practice.Ultrasound Obstet Gynecol. 2014; 44: 122-123Crossref PubMed Scopus (86) Google Scholar, 9Gregg A.R. Skotko B.G. Benkendorf J.L. Monaghan K.G. Bajaj K. Best R.G. Klugman S. Watson M.S. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics.Genet Med. 2016; 18: 1056-1065Abstract Full Text Full Text PDF PubMed Scopus (488) Google Scholar, Opstal D. Srebniak M.I. Cytogenetic confirmation of a positive NIPT result: evidence-based choice between chorionic villus sampling and amniocentesis depending on chromosome aberration.Expert Rev Mol Diagn. 2016; 16: 513-520Crossref PubMed Scopus (40) Google Scholar, screening and diagnostic Gynecol Clin 2017; 44: Full Text Full Text PDF PubMed Scopus Google Scholar, S. and Obstet Gynecol. PubMed Scopus Google Scholar, The clinical of FISH in prenatal Diagn. PubMed Scopus Google Scholar, D. Klugman S. T. Simpson J.L. K. L. Chromosomal microarray karyotyping for prenatal J Med. PubMed Scopus Google Scholar, Dugoff L. J.A. and the use of genetic diagnostic in and Gynecol. 2016; PubMed Scopus Google Scholar, G. N. D. M.D. of prenatal chromosomal study and and Obstet Gynecol. PubMed Scopus Google Scholar, G. D. N. in fetal anomalies and diagnostic rates and of the and PubMed Scopus Google Scholar, T. K. C. G. T. F. D. S. D. D. C. L. Optical genome mapping chromosomal J Hum Genet. Full Text Full Text PDF PubMed Scopus Google Scholar, K. T. S. G. D. of by genome J Hum Genet. Full Text Full Text PDF PubMed Scopus Google Scholar, S. L. K. A.R. D. of structural in by genome Med. 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The the in the the was not is in the the reference is The chromosome a from to a of 1 and a a of with by the and from to a of The chromosome was from the and by the the of and represent a which is with the karyotyping as the chromosome was detected in of This study included samples with and samples with These samples were analyzed with the to detect and was not in the of the the were and was The of was from the in the and the genome of the In a a is to a of a is to a of with a of the genome In the triploid the is to approximately and as to and The is from the number of and in the of is approximately and the of is approximately and In addition, samples with regions, from to 64 and with approximately of the genome were included in the The of the as the current can detect The the and the to detect the In the as the in the genome of the the SVs were as either or with each with a its the The of were by a in a in the with the in the the were evaluated and detected by the using the The with approximately was analyzed the and the 10 regions, of approximately of with The of the not in as the were concordant with detected with CMA. an of of the genome is as by in a of samples the is demonstrates that the can be to detect in the However, it is that be detected with the and a is to detect in In to additional SVs were for in samples. the 43 64 SVs that were determined to be clinically reportable (including of 64 26 with were in with The included and confirmation of additional is the of the all of the additional and in and for The were for that included prenatal and 10 of The 101 aberrations detected with and CMA in the prenatal were to the OGM was concordant in 101 of 101 101 3 4 isochromosomes, 4 regions, and 1 chromosome were and were not by the OGM has and has been to detect additional with methods, the samples were for and were and SVs were for SVs were detected with OGM in with CMA the 101 analyzed in OGM was to a 100% positive and of samples were in to and the of of the mapping to and These samples included deletions, duplications, and OGM detected in each a 100% and and In addition, the additional detected with OGM in were and were to be the The were to the of the The was evaluated for the and with the analysis the genome was detected to to and and to the the and were detected from 25% to 5% and were detected to The was by the but a was to the were detected in with 5% determined as the for and and for and genome with the medical associations, such as International Society of Ultrasound and Obstetrics and Gynecology, American College of Obstetrics and Gynecology, and American College of Medical Genetics and Genomics, recommend that prenatal genetic testing be offered to all pregnant women of and maternal age.7Rose N.C. Kaimal A.J. Dugoff L. Norton M.E. American College of Obstetricians and GynecologistsScreening for fetal chromosomal abnormalities: ACOG practice bulletin, number 226.Obstet Gynecol. 2020; 136: e48-e69Crossref PubMed Scopus (213) Google Scholar, 8Salomon L.J. Alfirevic Z. Audibert F. Kagan K.O. Paladini D. Yeo G. Raine-Fenning N. ISUOG Clinical Standards CommitteeISUOG consensus statement on the impact of non-invasive prenatal testing (NIPT) on prenatal ultrasound practice.Ultrasound Obstet Gynecol. 2014; 44: 122-123Crossref PubMed Scopus (86) Google Scholar, 9Gregg A.R. Skotko B.G. Benkendorf J.L. Monaghan K.G. Bajaj K. Best R.G. Klugman S. Watson M.S. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics.Genet Med. 2016; 18: 1056-1065Abstract Full Text Full Text PDF PubMed Scopus (488) Google Scholar prenatal diagnostic testing is a positive noninvasive prenatal screening in with ultrasound or in the methods for prenatal diagnostic testing karyotyping, FISH, and which are either simultaneously or in a to a cytogenetic Optical genome mapping as a for of structural and number variations for prenatal PubMed Scopus Google Scholar The for multiple methods is from the as of samples in our were with methods, all methods FISH, and This is each technology the of of classes or is by analysis or resolution the limitations of current methods, has been a in and OGM for prenatal diagnostic testing, as it all classes of SVs in a single the of our validation study as Clinical for a and the and of OGM with a 100% to in the prenatal workflow using cultured amniocytes is and standardized for the OGM The samples in study were cultured in and the was using with However, with the of of the from the which included of the of using approximately 1 for was The samples cultured in from to several to the were for was to the of the and the amniocentesis was leading to in were with in for several which be that for However, all samples cultured in and from as low as to the and with and In addition, the as for not the of the for OGM analysis These the of using OGM from a for prenatal diagnostic testing, as the of in is the in cytogenetic laboratories for analysis and does not to the in the of analyzed in study the to the and in for the OGM for and OGM with 100% positive and in 101 of 101 genetic aberrations in prenatal samples. 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