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Detecting sample swaps in diverse NGS data types using linkage disequilibrium

View ORCID ProfileNauman Javed, View ORCID ProfileYossi Farjoun, View ORCID ProfileTim Fennell, View ORCID ProfileCharles Epstein, Bradley E. Bernstein, View ORCID ProfileNoam Shoresh
doi: https://doi.org/10.1101/2020.03.15.992750
Nauman Javed
1Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
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  • ORCID record for Nauman Javed
Yossi Farjoun
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Tim Fennell
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Charles Epstein
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Bradley E. Bernstein
1Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Noam Shoresh
1Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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  • For correspondence: nshoresh@broadinstitute.org
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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.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 26, 2020.
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Detecting sample swaps in diverse NGS data types using linkage disequilibrium
Nauman Javed, Yossi Farjoun, Tim Fennell, Charles Epstein, Bradley E. Bernstein, Noam Shoresh
bioRxiv 2020.03.15.992750; doi: https://doi.org/10.1101/2020.03.15.992750
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Detecting sample swaps in diverse NGS data types using linkage disequilibrium
Nauman Javed, Yossi Farjoun, Tim Fennell, Charles Epstein, Bradley E. Bernstein, Noam Shoresh
bioRxiv 2020.03.15.992750; doi: https://doi.org/10.1101/2020.03.15.992750

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