A Novel Somatic Variant in HEY2 Unveils an Alternative Splicing Isoform Linked to Ventricular Septal Defect
Sign Up to like & getrecommendations! Published in 2019 at "Pediatric Cardiology"
DOI: 10.1007/s00246-019-02099-y
Abstract: Congenital heart defects (CHDs) are the leading cause of death in infants under 1 year of age. Aberrations in the expression and function of cardiac transcription factors (TFs) are a major contributor to CHDs. Despite the… read more here.
Keywords: hey2; novel somatic; ventricular septal; variant hey2 ... See more keywords
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Sign Up to like & getrecommendations! Published in 2018 at "Genetics in Medicine"
DOI: 10.1038/s41436-018-0278-z
Abstract: PurposeFollowing automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been… read more here.
Keywords: somatic variant; operating procedure; manual review; standard operating ... See more keywords
SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-69772-8
Abstract: It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble… read more here.
Keywords: consensus approach; somatic variant; performance; approach ... See more keywords
Genome-wide somatic variant calling using localized colored de Bruijn graphs
Sign Up to like & getrecommendations! Published in 2018 at "Communications Biology"
DOI: 10.1038/s42003-018-0023-9
Abstract: Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by jointly analyzing reads from tumor and… read more here.
Keywords: colored bruijn; genome wide; variant; lancet ... See more keywords
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
Halvade somatic: Somatic variant calling with Apache Spark
Sign Up to like & getrecommendations! Published in 2022 at "GigaScience"
DOI: 10.1093/gigascience/giab094
Abstract: Abstract Background The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the… read more here.
Keywords: halvade somatic; somatic variant; sequencing data; apache spark ... See more keywords
Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data
Sign Up to like & getrecommendations! Published in 2019 at "BMC Medical Genomics"
DOI: 10.1186/s12920-019-0636-y
Abstract: The application of next-generation sequencing in cancer has revealed the genomic landscape of many tumour types and is nowadays routinely used in research and clinical settings. Multiple algorithms have been developed to detect somatic variation… read more here.
Keywords: sequencing data; somatic variant; torrent; deep sequencing ... See more keywords
Evidence for a Dual-Pathway, 2-Hit Genetic Model for Focal Cortical Dysplasia and Epilepsy
Sign Up to like & getrecommendations! Published in 2022 at "Neurology: Genetics"
DOI: 10.1212/nxg.0000000000000652
Abstract: Background and Objectives The 2-hit model of genetic disease is well established in cancer, yet has only recently been reported to cause brain malformations associated with epilepsy. Pathogenic germline and somatic variants in genes in… read more here.
Keywords: hit model; somatic variant; epilepsy; model ... See more keywords
The Somatic Curation and Interpretation Across Laboratories (SOCIAL) project-current state of solid-tumour variant interpretation for molecular pathology in Canada.
Sign Up to like & getrecommendations! Published in 2019 at "Current oncology"
DOI: 10.3747/co.26.5281
Abstract: Background Practices in somatic variant interpretation and classification vary between Canadian clinical molecular diagnostic laboratories, and understanding of current practices and perspectives is limited. To define gaps and future directions, including consensus guideline development, the… read more here.
Keywords: classification; interpretation; pathology; somatic variant ... See more keywords
Somatic variant analysis of linked-reads sequencing data with Lancet
Sign Up to like & getrecommendations! Published in 2019 at "F1000Research"
DOI: 10.7490/f1000research.1117597.1
Abstract: Summary: We present a new version of the popular somatic variant caller, Lancet, that supports the analysis of linked-reads sequencing data. By seamlessly integrating barcodes and haplotype read assignments within the colored De Bruijn graph… read more here.
Keywords: sequencing data; reads sequencing; lancet; somatic variant ... See more keywords