Evaluating the clinical utility of genome sequencing for cytogenetically balanced chromosomal abnormalities in prenatal diagnosis

Abstract

Introduction and Project Objectives: Balanced chromosomal abnormalities (BCAs) are changes in the localization or orientation of a chromosomal segment without visible gain or loss of genetic material. BCAs occur at a frequency of 1 in 500 newborns and are associated with an increased risk of multiple congenital anomalies and/or neurodevelopmental disorders, especially if it is a de novo mutation. As GS sequencing cost continues to be reduced, it is foreseeable that GS will become more affordable for clinical use in the near future. In order to judge the feasibility and clinical utility of GS in the evaluation of BCAs, the clinical implications will be examined. Methods: In this pilot project, we used short read genome sequencing (GS) to retrospectively re-sequence ten prenatal subjects with de novo BCAs and compared the performance of GS with the original karyotyping. To detect all chromosomal abnormalities, including cryptic genomic imbalances, GS data were analyzed by in-house bioinformatics pipeline customized for structural variants (SV) and copy number variants (CNV) detection. Results: GS characterized all BCAs found by conventional karyotyping with the added benefit of precise sub-band delineation. In nine out of ten cases in this study (90%), the conventional karyotype results were revised by at least one sub-band. By identifying BCA breakpoints at the nucleotide level using GS, we found disruption of OMIM genes in three cases and identified cryptic gain/loss at the breakpoints in two cases. Of these five cases, four cases reached a definitive genetic diagnosis and were classified as pathogenic under the ACMG pathogenicity framework while the other one case had a BCA interpreted as unknown clinical significance. The additional information gained from GS can change the interpretation of the BCAs and has the potential to improve the genetic counselling and perinatal management by providing a more specific genetic diagnosis. Conclusion: To conclude, the findings from this study demonstrated the advantages of GS over conventional karyotyping on the detection of BCAs. GS allows the precise detection of BCA breakpoints and cryptic genomic imbalances surrounding the regions of BCAs. This results in better evaluation on the risk of congenital anomalies in BCA on a caseby-case basis.