Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions

Abstract

Copy-number variations (CNV), loss of heterozygosity (LOH), and uniparental disomy (UPD) are large genomic aberrations leading to many common inherited diseases, cancers, and other complex diseases. An integrated tool to identify these aberrations is essential in understanding diseases and in designing clinical interventions. Previous discovery methods based on whole-genome sequencing (WGS) require very high depth of coverage on the whole genome scale, and are cost-wise inefficient. Another approach, whole exome genome sequencing (WEGS), is limited to discovering variations within exons. Thus, we are lacking efficient methods to detect genomic aberrations on the whole genome scale using next-generation sequencing technology. Here we present a method to identify genome-wide CNV, LOH and UPD for the human genome via selectively sequencing a small portion of genome termed Selected Target Regions (SeTRs). In our experiments, the SeTRs are covered by 99.73%~99.95% with sufficient depth. Our developed bioinformatics pipeline calls genome-wide CNVs with high confidence, revealing 8 credible events of LOH and 3 UPD events larger than 5M from 15 individual samples. We demonstrate that genome-wide CNV, LOH and UPD can be detected using a cost-effective SeTRs sequencing approach, and that LOH and UPD can be identified using just a sample grouping technique, without using a matched sample or familial information.

Classification of Uniparental Isodisomy Patterns That Cause Autosomal Recessive Disorders: Proposed Mechanisms of Different Proportions and Parental Origin in Each Pattern

“…Accurate diagnosis provided by SNP array is the standard strategy today, and knowing that there are 3 patterns of the mechanisms of UPiD that produce AR disorders is important in order to correctly interpret the test results. Recent innovation has been impressive and SNP arrays may be superseded by next-generation sequencing in the near future [Wang et al, 2014].…”

Application of Molecular Karyotyping in Acute Myeloid Leukemia: A Review

“…In contrast to array CGH which only permits the identification of CNVs, SNP array facilitates simultaneous evaluation of DNA copy number alterations and genotyping information for detection of CN-LOH [21]. Prior to interrogation of genomic loci, DNA is subjected to restriction digestion and the fragmented DNA is hybridized on a slide which contains oligonucleotide probes.…”

“…On the other hand, CN-LOH happens when a genomic region originated from one parent and the loss of the other concurrent allele [21] [23]. Duplication of maternal (unimaternal) and loss of paternal and vice versa, results in CN-LOH without affecting the diploid copy number.…”

Techniques for detecting chromosomal aberrations in myelodysplastic syndromes

“…They found that SeTRs are covered by 99.73%∼99.95% with adequate depth. This new technique can identify chromosomal aberrations exempt from using a matched sample or familial information [ 112 ]. Furthermore, another study has found that NGS is highly-sensitive for accurate testing and quantification of various RUNX1 abnormalities with subsequent personalized monitoring of disease progression and therapeutic efficacy [ 113 ].…”