Date of Award
Thesis - Open Access
Whole-genome sequencing (WGS) is being increasingly utilized for the diagnosis of neurological disease. The advent of next-generation sequencing (NGS) has replaced Sanger sequencing due to its ability to sequence millions of fragments in parallel, in real-time. It’s application in targeted gene panels and whole-exome sequencing (WES) has revolutionized standard investigation practices of neurodevelopmental diseases (NDDs). WGS utilizes NGS technology in order to sequence beyond the exome and into the remaining 98-99% of the genetic code comprising the genome. In addition to increased coverage, WGS allows for the detection of novel gene variants, copy number variants (CNVs) and single nucleotide variants (SNVs) that are not traditionally picked up by WES. Furthermore, RNA sequencing (RNA-Seq) of the blood used in conjunction with WGS may have the ability to validate WGS findings by analyzing gene expression in addition to identifying novel RNA species within the transcriptome. The objective of this retrospective study was to measure the diagnostic yield of trio-based WGS and RNA-Seq against that of negative or inconclusive WES in a patient cohort comprised of complex neurological phenotypes. Whole genome sequencing was performed by Medical Neurogenetics LLC, a CLIA-certified laboratory in Atlanta, Georgia. This laboratory utilized the Illumina NovaSeq 6000 Sequencing System, with a goal of 30x coverage of 99% of mapped genome regions. Alignment and variant interpretation was performed by Dragen v2.2 and CNV analysis by Dragen v2.5. Variants were assessed in accordance with current ACMG criteria. WGS with complementary RNA-Seq resulted in 7 solved patient cases, providing a 31.8% yield. This phenotypically complex cohort was comprised of a spectrum of neurological conditions with suspected underlying genetic mechanisms. The use of WGS in conjunction with RNA-Seq resulted in a markedly increased diagnostic yield over that of preceding WES and conventional first-tier tests which included chromosomal microarray, targeted gene panels, and metabolic testing. Thus, proving its efficacy in the clinical setting.
Blake, Bianca, "The Efficacy of Whole-Genome Sequencing in the Diagnosis Of Complex Neurological Phenotypes" (2020). Human Genetics Theses. 80.