Genomic variant benchmark: if you cannot measure it, you cannot improve it
Genomic benchmark datasets are essential to driving the field of genomics and
bioinformatics. They provide a snapshot of the performances of sequencing technologies …
bioinformatics. They provide a snapshot of the performances of sequencing technologies …
Implementation of whole-genome and transcriptome sequencing into clinical cancer care
E Cuppen, O Elemento, R Rosenquist, S Nikic… - JCO Precision …, 2022 - ascopubs.org
PURPOSE The combination of whole-genome and transcriptome sequencing (WGTS) is
expected to transform diagnosis and treatment for patients with cancer. WGTS is a …
expected to transform diagnosis and treatment for patients with cancer. WGTS is a …
Detection of mosaic and population-level structural variants with Sniffles2
Calling structural variations (SVs) is technically challenging, but using long reads remains
the most accurate way to identify complex genomic alterations. Here we present Sniffles2 …
the most accurate way to identify complex genomic alterations. Here we present Sniffles2 …
JBrowse 2: a modular genome browser with views of synteny and structural variation
C Diesh, GJ Stevens, P Xie, T De Jesus Martinez… - Genome biology, 2023 - Springer
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced
visualization of complex structural variation and evolutionary relationships. It retains core …
visualization of complex structural variation and evolutionary relationships. It retains core …
Comprehensive structural variant detection: from mosaic to population-level
Abstract Long-read Structural Variation (SV) calling remains a challenging but highly
accurate way to identify complex genomic rearrangements. Here, we present Sniffles2 …
accurate way to identify complex genomic rearrangements. Here, we present Sniffles2 …
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
GRIDSS2 is the first structural variant caller to explicitly report single breakends—
breakpoints in which only one side can be unambiguously determined. By treating single …
breakpoints in which only one side can be unambiguously determined. By treating single …
Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv
Y Shiraishi, J Koya, K Chiba, A Okada… - Nucleic acids …, 2023 - academic.oup.com
We present our novel software, nanomonsv, for detecting somatic structural variations (SVs)
using tumor and matched control long-read sequencing data with a single-base resolution …
using tumor and matched control long-read sequencing data with a single-base resolution …
Unscrambling cancer genomes via integrated analysis of structural variation and copy number
Complex somatic genomic rearrangements and copy number alterations are hallmarks of
nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural …
nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural …
Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics
S Garg - Nature Communications, 2023 - nature.com
Cancer genomes are highly complex and heterogeneous. The standard short-read
sequencing and analytical methods are unable to provide the complete and precise base …
sequencing and analytical methods are unable to provide the complete and precise base …
Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram
Abstract Breakage-fusion-bridge (BFB) is a complex rearrangement that leads to tumor
malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out …
malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out …