Journal: Genome Research

Article Title: Unraveling the hidden complexity of cancer through long-read sequencing

doi: 10.1101/gr.280041.124

Figure Lengend Snippet: Summary of software tools for analyzing long reads in cancer

Article Snippet: A more specific study comparing optical maps of breast cancer cell line SKBR3 with long-read whole-genome sequencing (LR-WGS) found that 74% of insertions and 80% of deletions detected with Bionano can be confirmed with PacBio and ONT, but lower concordance for inversions and duplications ( ).

Techniques: Software, Variant Assay, Sequencing, Methylation, DNA Methylation Assay, RNA modification

Journal: medRxiv

Article Title: Single cell long read whole genome sequencing reveals somatic transposon activity in human brain

doi: 10.1101/2024.11.11.24317113

Figure Lengend Snippet: Overall metrics of genomic data obtained in scWGS experiments of studied brains A) . Breadth of coverage for each of the analyzed cell types, including long-read ONT sequencing and short-read scWGS Illumina sequencing of the same dMDA single-cell DNA. For single cells, analyzed regions are limited to >=5x depth of coverage, while for bulk all covered regions are included. B) Mosaic SNV detected in long- read scWGS and bulk ONT MSA1 sample located within an exon of LRRK2 - a gene important in monogenic Parkinson’s disease. C) SVs (insertions and deletions) detected across the 3 studied brains in long-read scWGS and bulk ONT samples. The first category shows all bulk variants across the genome, while the remaining 4 categories are limited to regions covered >=5x in single cell-samples and variants from those regions in corresponding bulk. D) Mosaic deletion detected in long-read MSA1 ONT single cell samples as well as in low frequency in corresponding long-read ONT bulk tissue sample. The deletion overlaps ACTL6A gene, encoding actin-related protein associated with Non-Specific Syndromic Intellectual Disability and Torticollis. E) A comparison of variant allele frequency (VAF) in long-read ONT bulk samples and the ratio of single cells where the variant is detected to the total number of single cells covering the variant locus in long-read ONT scWGS experiments. High VAF population variants were removed. Most of the remaining variants are mosaic in bulk, as represented by the heatmap concentration in the lower half of the chart.

Article Snippet: To summarize, we demonstrated the utility of long-read single cell whole genome sequencing using Oxford nanopore to study SNV, InDel and SV mutations across 18 single cells derived from 3 brains.

Techniques: Sequencing, Illumina Sequencing, Comparison, Variant Assay, Concentration Assay