Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Pan-cancer analysis of systematic batch effects on somatic sequence variations.

BMC bioinformatics - 11 Apr 2017

Choi Ji-Hye, Hong Seong-Eui, Woo Hyun Goo

Abstract excerpt

BACKGROUND: The Cancer Genome Atlas (TCGA) is a comprehensive database that includes multi-layered cancer genome profiles. Large-scale collection of data inevitably generates batch effects introduced by differences in processing at various stages from sample collection to data generation. However, batch effects on the sequence variation and its characteristics have not been studied extensively. RESULTS: We...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Databases, Genetic
Share to Genomics
Share to Mutation

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Neoplasms

Share to Reproducibility of Results

Share to Sequence Analysis, DNA

Source

Open in PubMed Open full text

Identifiers

PMID: 28399795
DOI: 10.1186/s12859-017-1627-7
PMCID: PMC5387285

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 6 Sept 2026. Manifest publication-graph-cohort-2026-09-06.1.

Source receipt: pubmed, retrieved 6 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 10 closest

Pan-cancer analysis of systematic batch effects on somatic sequence variations.PMID 28399795Read ↗

Substantial Batch Effects in TCGA Exome Sequences Undermine Pan-Cancer Analysis of Germline VariantsSemantic proximity Read ↗

Pan-cancer analysis reveals technical artifacts in TCGA germline variant callsSemantic proximity Read ↗

Pan-Cancer Analysis Reveals Technical Artifacts in TCGA Germline Variant CallsSemantic proximity Read ↗

Standard operating procedure for somatic variant refinement of tumor sequencing dataSemantic proximity Read ↗

Identifying and mitigating batch effects in whole genome sequencing data.Semantic proximity Read ↗

Enhancing sensitivity and controlling false discovery rate in somatic indel discoverySemantic proximity Read ↗

Cleaning clinical genomic data: Simple identification and removal of recurrently miscalled variants in single genomesSemantic proximity Read ↗

Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies.Semantic proximity Read ↗

Impact of Variant-level Batch Effects on Identification of Genetic Risk Factors in Large Sequencing StudiesSemantic proximity Read ↗

Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.