Low Pass Whole Genome sequencing - a cost-effective new technique for the identification of aneuploidies and copy number variations: a study of 1372 clinical samples in an Indian cohort

BackgroundIdentification and confirmation of copy number variation is an important aspect of genetic testing for several prenatal scenarios, such as abnormal maternal serum screening, abnormal ultrasound findings, high risk results on non-invasive prenatal screening as well as postnatal settings such as developmental delay, intellectual disabilities, congenital anomalies and dysmorphism as well as in couples with recurrent miscarriages. Low pass whole genome sequencing (lpWGS) followed by copy number variation (CNV) analysis has shown identification of critical pathogenic/likely pathogenic variants comprehensively with great accuracy and cost-effectiveness. We validated this technique on retrospective routine clinical samples previously assessed by an orthogonal tests, either chromosomal microarray or karyotyping or fluorescence in situ hybridization in a diagnostic laboratory and evaluated its performance. Material and MethodsThe validation included 112 clinical samples which showed the following events: 14 aneuploidies, 70 copy number variations of size range (50 kb - 116 Mb), 11 mosaics aneuplodies, 4 mosaics CNVs and 4 triploidies. These validation samples were derived from 21 fetuses (6 chorionic villus biopsies and 15 amniotic fluid samples), 25 abortuses and 66 postnatal samples. The validation was performed at two different resolutions - 1Mb and 50Kb. We then assessed the overall yield of the lpWGS assay on 1,260 clinical samples that comprised 801 fetuses, 346 products of conception/intrauterine fetal demise/stillbirth and 113 postnatal cases. ResultsWe obtained 100% concordance in detecting full aneuploidies and copy number variations including mosaics and triploidy. The overall success rate of this assay that passed all quality parameters was 99.8%. (1235/1238). The overall diagnostic yield for pathogenic and likely pathogenic variants was 13.6% (168/1235), and specifically 7.3%, 28.8%, 15% for fetuses, products of conception/intrauterine fetal demise/stillbirth and post natal samples respectively. An additional 2.9% (36/1235) of overall samples showed CNVs that were classified as variants of unknown significance. ConclusionOverall, low pass whole genome sequencing is a sensitive and robust technique for identification of aneuploidies and copy number variations in a clinical setting.