Diagnostic Utility of Low-Pass Whole Genome Sequencing in Prenatal Detection of Chromosomal Abnormalities in an Indian Cohort

Abstract

ObjectiveThis study evaluates the diagnostic utility of low-pass whole genome sequencing (LP-WGS) for the detection of chromosomal abnormalities in Amniotic fluid samples (AFS), Chorionic villi samples (CVS) and Product of conception (POC) samples from India. MethodsA total of 1508 prenatal samples including - AFS, CVS and POC were analyzed using LP-WGS at either low-resolution ([~]0.5-1X) or high-resolution ([~]5X). CNV analysis was performed using StrandNGS v4.2 and Variant Intelligence Applications (VIA) v7.0. Copy number variants (CNVs) were classified according to ACMG guidelines with the support from publicly available databases. ResultsAmong 1508 samples analysed, chromosomal abnormalities were identified in 168 cases resulting in a diagnostic yield of 11.1%. The detection rate was significantly higher in first-trimester samples (44.0%) compared to second-trimester samples (8.2%). Based on clinical indications, abnormalities were detected in 10.1% of cases with ultrasound abnormalities, 4.0% of cases with positive maternal serum screening, and 35.8% of cases flagged as high-risk by non-invasive prenatal testing (NIPT). The commonly assessed ultrasound markers were more prevalent in negative cases than in those with clinical findings highlighting their limited predictive value in isolation. Aneuploidies accounted for 71% of the detected abnormalities which included 10 mosaic aneuploidies, followed by cytoband-level CNVs (25%). Polyploidy and haploidy were detected in 2.38% of cases, while in 1.6% of the cases gene-level CNVs were detected. CNVs lower than 500kbp, including few gene level CNVs, were detected in the high resolution workflow while the low resolution workflow was effective for events >500Kbp. We detected a mosaic gain of chromosome 13 and chromosome X in a POC sample and mosaic gain of chromosome 21 in an AFS sample which was not detected in QF-PCR due to its technical limitation. The most frequently observed chromosomal abnormality was Down syndrome, followed by Turner syndrome, Edwards syndrome, triple X, trisomy 16, Patau syndrome and 22q11.21 deletion/duplication syndrome. Turner syndrome was the most frequent observation in POC samples. In 12 cases, multiple CNVs were detected, with concurrent gain and loss events suggesting potential underlying balanced translocations in parents, as supported by literature on recurrent cytoband involvement. Concordance analysis performed on a subset of samples showed a 100% concordance with whole exome sequencing (WES) and a partially reduced concordance of 98% with QF-PCR possibly due to lower sensitivity of detecting mosaic events by QF-PCR. Unlike QF-PCR, LP-WGS test could detect mosaic CNV, cytoband-level CNVs and trisomies involving chromosomes not routinely targeted by the assay, such as trisomy 19, 16, 10, 17, 4, 5, 2, frequently associated with first trimester miscarriages. ConclusionsLP-WGS is a robust, accurate, cost effective tool for prenatal detection of chromosomal abnormality. It offers a high diagnostic yield with rapid turnaround time, and the ability to detect a broad spectrum of abnormalities. It has the potential to detect chromosomal anomalies associated with first trimester miscarriage, mosaic copy number variants and possible unbalanced translocation events. These findings support its utility as a first-line method in prenatal diagnostics.