DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac828
Abstract: Abstract Motivation Somatic mutations are usually called by analyzing the DNA sequence of a tumor sample in conjunction with a matched normal. However, a matched normal is not always available, for instance, in retrospective analysis… read more here.
Keywords: somatic variant; wgs samples; deepsom; matched normal ... See more keywords
DNA methylation and miRNA expression in colon adenomas compared with matched normal colon mucosa and carcinomas
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Experimental Pathology"
DOI: 10.1111/iep.12432
Abstract: Dysregulation of DNA methylation patterns and non‐coding RNA, including miRNAs, has been implicated in colon cancer, and these changes may occur early in the development of carcinoma. In this study, the role of epigenetics as… read more here.
Keywords: methylation; adenomas; dna methylation; expression ... See more keywords
Refined variant calling pipeline on RNA-seq data of breast cancer cell lines without matched-normal samples
Sign Up to like & getrecommendations! Published in 2025 at "BMC Research Notes"
DOI: 10.1186/s13104-025-07140-3
Abstract: RNA-seq delivers valuable insights both to transcriptional patterns and mutational landscapes for transcribed genes. However, as tumour cell lines frequently lack their matched-normal counterpart, variant calling without the paired normal sample is still challenging. In… read more here.
Keywords: cancer; cell lines; rna seq; cell ... See more keywords