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Consistent RNA sequencing contamination in GTEx and other data sets

Author

Listed:
  • Tim O. Nieuwenhuis

    (Johns Hopkins University SOM
    Johns Hopkins University SOM)

  • Stephanie Y. Yang

    (Johns Hopkins University SOM)

  • Rohan X. Verma

    (Johns Hopkins University SOM)

  • Vamsee Pillalamarri

    (Johns Hopkins University SOM)

  • Dan E. Arking

    (Johns Hopkins University SOM)

  • Avi Z. Rosenberg

    (Johns Hopkins University SOM)

  • Matthew N. McCall

    (University of Rochester Medical Center)

  • Marc K. Halushka

    (Johns Hopkins University SOM)

Abstract

A challenge of next generation sequencing is read contamination. We use Genotype-Tissue Expression (GTEx) datasets and technical metadata along with RNA-seq datasets from other studies to understand factors that contribute to contamination. Here we report, of 48 analyzed tissues in GTEx, 26 have variant co-expression clusters of four highly expressed and pancreas-enriched genes (PRSS1, PNLIP, CLPS, and/or CELA3A). Fourteen additional highly expressed genes from other tissues also indicate contamination. Sample contamination is strongly associated with a sample being sequenced on the same day as a tissue that natively expresses those genes. Discrepant SNPs across four contaminating genes validate the contamination. Low-level contamination affects ~40% of samples and leads to numerous eQTL assignments in inappropriate tissues among these 18 genes. This type of contamination occurs widely, impacting bulk and single cell (scRNA-seq) data set analysis. In conclusion, highly expressed, tissue-enriched genes basally contaminate GTEx and other datasets impacting analyses.

Suggested Citation

  • Tim O. Nieuwenhuis & Stephanie Y. Yang & Rohan X. Verma & Vamsee Pillalamarri & Dan E. Arking & Avi Z. Rosenberg & Matthew N. McCall & Marc K. Halushka, 2020. "Consistent RNA sequencing contamination in GTEx and other data sets," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15821-9
    DOI: 10.1038/s41467-020-15821-9
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