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

Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors.

Bioinformatics (Oxford, England) - 15 May 2018

Mannakee Brian K, Balaji Uthra, Witkiewicz Agnieszka K, Gutenkunst Ryan N, Knudsen Erik S

Abstract excerpt

Motivation: Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts. Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, Mouse And Paralog EXterminator (MAPEX), to...

Read the complete abstract on PubMed

Topics

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

Share to Algorithms
Share to Genetic Variation

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Heterografts

Share to High-Throughput Nucleotide Sequencing

Share to Neoplasms

Share to Software

Source

Open in PubMed Open full text

Identifiers

PMID: 29325072
DOI: 10.1093/bioinformatics/bty010
PMCID: PMC5946891

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 6 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors.PMID 29325072Read ↗

Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumorsSemantic proximity Read ↗

pdxBlacklist: Identifying artefactual variants in patient-derived xenograft samplesSemantic proximity Read ↗

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence dataSemantic proximity Read ↗

Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis.Semantic proximity Read ↗

Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival.Semantic proximity Read ↗

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.Semantic proximity Read ↗

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelinesSemantic proximity Read ↗

FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures.Semantic proximity Read ↗

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts.Semantic proximity Read ↗

Bioinformatics workflows for genomic analysis of tumors from Patient Derived Xenografts (PDX): challenges and guidelinesSemantic proximity Read ↗

Computational modeling of human genetic variants in miceSemantic proximity Read ↗

Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaksSemantic proximity Read ↗

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