Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma

Abstract

Linked-read sequencing was developed to aid the detection of large structural variants (SVs) from short-read sequencing efforts. We performed a systematic evaluation to determine if linked-read exome sequencing provides more comprehensive and clinically relevant information than whole-exome sequencing (WES) when applied to the same set of multiple myeloma patient samples. We report that linked-read sequencing detected a higher number of SVs (n = 18,455) than WES (n = 4065). However, linked-read predictions were dominated by inversions (92.4%), leading to poor detection of other types of SVs. In contrast, WES detected 56.3% deletions, 32.6% insertions, 6.7% translocations, 3.3% duplications and 1.2% inversions. Surprisingly, the quantitative performance assessment suggested a higher performance for WES (AUC = 0.791) compared to linked-read sequencing (AUC = 0.766) for detecting clinically validated cytogenetic alterations. We also found that linked-read sequencing detected more short variants (n = 704) compared to WES (n = 109). WES detected somatic mutations in all MM-related genes while linked-read sequencing failed to detect certain mutations. The comparison of somatic mutations detected using linked-read, WES and RNA-seq revealed that WES and RNA-seq detected more mutations than linked-read sequencing. These data indicate that WES outperforms and is more efficient than linked-read sequencing for detecting clinically relevant SVs and MM-specific short variants.

Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield

“…Several linked-read-specific SV calling pipelines such as LinkedSV 8 have been developed in addition to LongRanger. Although linked-read sequencing has been previously reported to lead to the identification of SVs missed using short-read sequencing 8 , 21 , linked-read sequencing did not significantly improve the SV identification in our study nor in the studies done by others 21 , 22 . Nevertheless, due to the long phase block length with optimal DNA samples (typically 50–100 kb), linked-read sequencing has been suggested to have the potential to identify large SVs better than other long-read methods (read length typically 20–30 kb) 8 .…”

S100 Calcium Binding Protein Family Members Associate With Poor Patient Outcome and Response to Proteasome Inhibition in Multiple Myeloma

“…Exome 1 https://osf.io capture was performed with The SeqCap R EZ MedExome kit (Roche NimbleGen, Madison, WI, United States), SureSelect Clinical Research Exome kit, or SureSelect Human All Exon V5 kit (Agilent Technologies, Santa Clara, CA, United States) and exomes sequenced on a HiSeq R 1500 or 2500 instrument. Gene copy numbers were estimated from exome sequencing data as previously described (Sulonen et al, 2011;Kumar et al, 2021). Copy number variants (CNVs) were identified using the CopyCat tool 2 .…”

Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection

“…As an alternative to long-read sequencing as a means of capturing both SVs and SNVs, we have explored the synergy between short-read WGS and OGM not only for identifying both SVs and SNVs but also for enhancing SV detection. The studies comparing OGM to current long-read next-generation sequencing (NGS) technologies highlighted the differences between these two orthogonal methods [ 9 , 12 , 14 , 15 ]. Largely left out of the discussion was short-read NGS data and how they might integrate with OGM.…”