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- W3018638530 abstract "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." @default.
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- W3018638530 date "2020-04-22" @default.
- W3018638530 modified "2023-10-12" @default.
- W3018638530 title "Consistent RNA sequencing contamination in GTEx and other data sets" @default.
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- W3018638530 doi "https://doi.org/10.1038/s41467-020-15821-9" @default.
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