Detecting sample swaps in diverse NGS data types using linkage disequilibrium.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 32728101.
- Also identified by DOI 10.1038/s41467-020-17453-5 and PMC identifier 7391710.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
As the number of genomics datasets grows rapidly, sample mislabeling has become a high stakes issue. We present CrosscheckFingerprints (Crosscheck), a tool for quantifying sample-relatedness and detecting incorrectly paired sequencing datasets from different donors. Crosscheck outperforms similar methods and is effective even when data are sparse or from different assays. Application of Crosscheck to 8851 ENCODE ChIP-, RNA-, and DNase-seq datasets enabled us to identify and correct dozens of mislabeled samples and ambiguous metadata annotations, representing ~1% of ENCODE datasets.
Medical subject headings
- High-Throughput Nucleotide Sequencing
- Linkage Disequilibrium