Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads

Abstract

Linked-read sequencing enables greatly improves haplotype assembly over standard paired-end analysis. The detection of mosaic single-nucleotide variants benefits from haplotype assembly when the model is informed by the mapping between constituent reads and linked reads. Samovar evaluates haplotype-discordant reads identified through linked-read sequencing, thus enabling phasing and mosaic variant detection across the entire genome. Samovar trains a random forest model to score candidate sites using a dataset that considers read quality, phasing, and linkedread characteristics. Samovar calls mosaic single-nucleotide variants (SNVs) within a single sample with accuracy comparable with what previously required trios or matched tumor/normal pairs and outperforms single-sample mosaic variant callers at minor allele frequency 5%-50% with at least 30X coverage. Samovar finds somatic variants in both tumor and normal whole-genome sequencing from 13 pediatric cancer cases that can be corroborated with high recall with whole exome sequencing. Samovar is available open-source at https://github.com/cdarby/samovar under the MIT license.

Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads

“…The subject of this paper however is calling mutations in absence of the matched normal sample, referred to as "tumour-only" calling. This problem has been studied for short read sequencing and, most relevant to this work, Darby et al 2019 introduced the idea of using haplotype phasing patterns for 10X Genomics Linked Reads.…”

“…In this paper, we explore the potential for using long read sequencing to perform tumour-only mutation calling. The advantage of long reads for this problem is that reads can often be assigned to individual haplotypes, transforming the problem of detecting somatic mutations from potentially small shifts in the variant allele fraction, into detecting the presence of two or more bases within a single haplotype, as proposed in the mosaic variant detection method by Darby et al (2019) for 10X Genomics linked reads. In this work we formalize the problem and use simulations to assess the applicability of this approach as a function of key experimental parameters (sequencing depth, tumour purity, sequencing error rate).…”

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity

“…Salmon version 0.13.1 was used to calculate TPM values as previously described [ 17 ]. In addition, the tumor was previously characterized via exome sequencing and found to have a mutation in H3-3A (NM_002107.4:c.83A > T:p.Lys28Met) [ 65 ]. The H3-3A K28M mutation had been clinically confirmed, likely via sanger sequencing, at the patient’s prior institution but we do not have access to those records.…”

Rabbit Biomodels of Human Diseases Developed Using New Genomic Technologies. Crispr/Cas9 (Review)

“…А если мозаицизм встречается только в популяции клеток зародышевой линии, индивидуум не будет иметь фенотипических проявлений, но его потомки унаследуют данный признак. Также возможно, что в случае индукции мозаицизма в раннем онтогенезе как соматические, так и клетки зародышевой линии будут мозаичны [17]. Существует множество возможных механизмов развития мозаицизма: соматические мутации, эпигенетические изменения, нарушения структуры и/или количества хромосом [13,102].…”