Prenatal diagnosis of chromosomal abnormalities using optical genome mapping vs chromosomal microarray

Optical genome mapping (OGM) is the next-generation cytogenomic technology (Supplementary Material). Emerging studies and commentaries demonstrate that OGM is able to detect the majority of structural variations in a single assay with high concordance with standard-of-care methods.1Mantere T. Neveling K. Pebrel-Richard C. et al.Optical genome mapping enables constitutional chromosomal aberration detection.Am J Hum Genet. 2021; 108: 1409-1422Abstract Full Text Full Text PDF PubMed Google Scholar, 2Dremsek P. Schwarz T. Weil B. Malashka A. Laccone F. Neesen J. Optical genome mapping in routine human genetic diagnostics-its advantages and limitations.Genes (Basel). 2021; 12: 1958Crossref Scopus (21) Google Scholar, 3Sahajpal N.S. Barseghyan H. Kolhe R. Hastie A. Chaubey A. Optical genome mapping as a next-generation cytogenomic tool for detection of structural and copy number variations for prenatal genomic analyses.Genes (Basel). 2021; 12: 398Crossref PubMed Scopus (42) Google Scholar However, the application and evaluation of OGM in prenatal diagnosis remains limited.4Sahajpal N.S. Mondal A.K. Fee T. et al.Clinical validation and diagnostic utility of optical genome mapping in prenatal diagnostic testing.J Mol Diagn. 2023; 25: 234-246Abstract Full Text Full Text PDF Google Scholar,5Zhang Q. Wang Y. Xu Y. et al.Optical genome mapping for detection of chromosomal aberrations in prenatal diagnosis.Acta Obstet Gynecol Scand. 2023; 102: 1053-1062Crossref Scopus (0) Google Scholar Furthermore, no prospective study evaluating its application in prenatal setting has been reported. This study aimed to evaluate the feasibility, efficacy, and incremental yield of OGM compared with chromosomal microarray analysis (CMA) and karyotyping for routine prenatal diagnosis. We conducted a prospective back-to-back comparison study. A total of 200 consecutive singleton fetuses with soft markers (including increased nuchal translucency [≥3.0 mm], nasal bone hypoplasia and mild ventriculomegaly [10–15 mm]) and structural anomalies were included. OGM and CMA plus karyotyping were performed in each sample in parallel. Triploidies, aneuploidies, copy number variations (CNVs) and microscopic-balanced translocations and inversions were detected and analyzed in blinded fashion. The pathogenicity of CNVs was evaluated and classified based on American College of Medical Genetics and Genomics guidelines.6Riggs E.R. Andersen E.F. Cherry A.M. et al.Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).Genet Med. 2020; 22: 245-257Abstract Full Text Full Text PDF PubMed Scopus (738) Google Scholar Small (<50 kb) insertions, deletions, duplications and submicroscopic translocations, and inversions that beyond the detection range of CMA and karyotyping were validated by long-range polymerase chain reaction plus Sanger sequencing, multiplex ligation-dependent probe amplification, or fluorescence in situ hybridization. Overall, the detection rates of chromosome aberrations using OGM and CMA plus karyotyping were 20.5% (41/200) and 19.5% (39/200), respectively (Table). The 41 cases with chromosome aberrations identified by OGM consisted of 1 with triploidy, 22 with aneuploidies, 15 with pathogenic or likely pathogenic (P/LP) CNVs and 3 with balanced translocations (Supplementary Table 1). Compared with CMA plus karyotyping, OGM provided an additional detection of 1 case with pathogenic intragenic duplication (Supplementary Figure) and 2 cases with cryptic-balanced translocations (1 translocation resulted in the disruption of OMIM gene associated with dominant disorders) (Supplementary Table 2) but failed to identify 1 case with pericentric inversion of chromosome 9. The overall sensitivity, specificity, positive and negative predictive value of OGM to detect triploidies, aneuploidies, P/LP CNVs >50 kb, and microscopic–balanced chromosomal rearrangements were 97.4%, 100%, 100%, and 99.4%, respectively. In addition, OGM added information of location and orientation for 8 CNVs, revealing 6 tandem directed duplications and 2 cryptic unbalanced translocations (Supplementary Table 1). The location and orientation added by OGM might help interpret the effect of CNVs precisely and assist reproductive counseling. Moreover, OGM identified 8 (4.0%, 8/200) D4Z4 repeat contractions combined with 4qA haplotype that might cause facioscapulohumeral muscular dystrophy type1 (FSHD1) (Supplementary Table 3). The penetrance of FSHD1 increases with age and with shorter repeat counts, varying extensively.7Wohlgemuth M. Lemmers R.J. Jonker M. et al.A family-based study into penetrance in facioscapulohumeral muscular dystrophy type 1.Neurology. 2018; 91: e444-e454Crossref PubMed Scopus (0) Google ScholarTableResults of optical genome mapping, chromosomal microarray analysis, and karyotyping in 200 fetuses with ultrasound abnormalitiesVariationOGM, n (%)Standard-of-care, n (%)SensitivityaTaking CMA plus karyotyping as gold standard of OGMSpecificityaTaking CMA plus karyotyping as gold standard of OGMCMAKaryotypingTotalAberrations within the detection range of CMA or karyotyping Triploidy1bTriploidy and 1 case of aneuploidy was detected by manual inspection (0.5%)1 (0.5%)1 (0.5%)1 (0.5%)100.0%100.0% Aneuploidy22bTriploidy and 1 case of aneuploidy was detected by manual inspection (11.0%)22 (11.0%)22 (11.0%)22 (11.0%)100.0%100.0%Standard type––21 (10.5%)–––Translocation type––1 (0.5%)––– P/LP CNV14 (7.0%)14 (7.0%)2 (1.0%)14 (7.0%)100.0%100%Deletion10 (5.0%)10 (5.0%)2 (1.0%)10 (5.0%)100.0%100.0%Tandem-directed duplication1 (0.5%)–––––Unbalanced translocation1 (0.5 %)–0 (0.0%)–––Duplication unclassifiedcPathogenic or likely pathogenic duplications only called by OGM CNV algorithm, not by OGM SV algorithm2 (1.0 %)––––– Microscopic-balanced translocation and inversion1 (0.5 %)–2 (1.0%)–50.0%100.0%Balanced translocation1 (0.5%)–1 (0.5%)–100.0%100.0%Inversion0d1 case with inv(9)(p12q21) was undetected by OGM (0.0%)–1 (0.5%)–0.0%100.0% Total38 (19.0%)37 (18.5%)27 (13.5%)39 (19.5%)97.4%100.0%Additional findings of OGM P/LP CNVeP/LP CNV beyond the detection range of CMA.1 (0.5%)––––– Cryptic-balanced translocation2 (1.0%)––––– D4Z4 repeat contraction (4qA)8 (4.0%)–––––CMA, chromosomal microarray analysis; N, number of cases with variation; OGM, optical genome mapping; P/LP CNV, pathogenic or likely pathogenic copy number variation.Hu. Prenatal diagnosis of chromosomal abnormalities using optical genome mapping vs chromosomal microarray. Am J Obstet Gynecol 2023.a Taking CMA plus karyotyping as gold standardb Triploidy and 1 case of aneuploidy was detected by manual inspectionc Pathogenic or likely pathogenic duplications only called by OGM CNV algorithm, not by OGM SV algorithmd 1 case with inv(9)(p12q21) was undetected by OGMe P/LP CNV beyond the detection range of CMA. Open table in a new tab CMA, chromosomal microarray analysis; N, number of cases with variation; OGM, optical genome mapping; P/LP CNV, pathogenic or likely pathogenic copy number variation. Hu. Prenatal diagnosis of chromosomal abnormalities using optical genome mapping vs chromosomal microarray. Am J Obstet Gynecol 2023. Compared with CMA and karyotyping, OGM had an advantage in uncovering exonic CNVs and cryptic chromosomal rearrangements but might fail to identify inversions with breakpoints located in segmental duplication regions. In addition, OGM revealed the location and orientation of duplication segments, refined breakpoints of structural variations, and identified specific repeat contraction disorders. Our results suggest that OGM has the potential to be an alternative technology to CMA and karyotyping in prenatal diagnosis.