ArticleBioinformatics (Oxford, England)2017
HYSYS: have you swapped your samples?
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Clinicopathologic and molecular predictors of survival in BRCA-deficient tubo-ovarian high-grade serous carcinoma.Nature communications · 2026Article
- Beyond BRCA deficiency: Clinical and molecular predictors of survival in patients with BRCA-deficient tubo-ovarian high-grade serous carcinoma.Research square · 2025Article
- BeyondmedRxiv : the preprint server for health sciences · 2025Article
- PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.GigaScience · 2025Article
- ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection.GigaScience · 2024Article
- Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow.BMC bioinformatics · 2023Article
- Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer.Nature genetics · 2023Article
- The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer.Nature genetics · 2022Article
- Quality control of large genome datasets.HGG advances · 2022Article
- Computational analysis of cancer genome sequencing data.Nature reviews. Genetics · 2022Review
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Improving data quality in observational research studies: Report of the Cure Glomerulonephropathy (CureGN) network.Contemporary clinical trials communications · 2021Article
- Detecting sample swaps in diverse NGS data types using linkage disequilibrium.Nature communications · 2020Article
- Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches.Genome medicine · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: The application of a genomics assay to samples from a cohort is a frequently applied experimental design in cancer genomics studies. The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly-multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur that cause a DNA sample to be labelled incorrectly. However, there is a paucity of methods in the literature to identify such swaps specifically in cancer studies. Results: Here, we introduce a simple method, HYSYS, to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous SNPs between samples. The method is motivated by the observation that homozygous germline population variants rarely change in the disease and are not affected by loss of heterozygosity. Our tools include visualization and a testing framework to flag possible sample swaps. We demonstrate the utility of this approach on a small cohort. Availability and Implementation: http://github.com/PapenfussLab/HaveYouSwappedYourSamples. Contact: papenfuss@wehi.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.
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