Identifying structural variants using linked-read sequencing data

Abstract

Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (˜5-10) DNA molecules˜50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification -including two recent methods that also analyze linked-reads -on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes.

Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

“…Overall, the method combines the advantage of long‐read approach to the reliability of short‐read sequencing. This method has already shown its efficacy in SV detection (Elyanow, Wu, & Raphael, ; Zheng et al, ).…”

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

“…Furthermore, when a genome G derives from a diploid reference R we can not measure a set A(G) of adjacencies in G directly, but rather we can only measure an obfuscated version of the set A N (G) of novel adjacencies in G. That is, for every novel adjacency {j H , k ® H ® } À A N (G) we can only measure an unlabeled (i.e., with involved extremities missing the A/B labels) adjacency {j , k ® } (e.g., for a derived genome G shown in Figure 4 instead of measuring a novel adjacency {3 h A , 7 h B } À A N (G) we measure an unlabeled novel adjacency {3 h , 7 h }). There exist several methods capable of producing the unlabeled novel adjacencies both from a standard short-read bulk sequencing data [51,48,30,10,60] as well as from 3rd-generation sequencing technologies [49,16,52,66,50,27,17].…”

Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

“…Via a series of withincompartment molecular biology and subsequent standard steps of library construction and sequencing, barcoded short reads are produced that retain the long-range information of the long fragments of the initial DNA extract. Due to the combination of high base pair-level sequence accuracy and long-range information, 10x/Illumina data therefore support excellent SNP and small indel detection and phasing (Zheng et al 2016), as well as breakpoint detection of large events in cancer (Zheng et al 2016;Spies et al 2017;Elyanow et al 2017). For diploid genome reconstruction, 10x developed the de novo assembler, Supernova, which has been shown to produce whole human genome assemblies from 56-fold coverage 10x/Illumina data (Weisenfeld et al 2017;Zhang et al 2019a).…”