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Stanford team says Illumina-sequenced data could be compromised

April 10, 2017 11:15 PM UTC

A team led by Stanford University's Irv Weissman published a manuscript on Sunday describing a technical artifact in the HiSeq 4000 sequencer from Illumina Inc. (NASDAQ:ILMN) that attributed 5-10% of single cell RNA sequencing (RNAseq) reads to the wrong samples. The manuscript was shared on the bioRxiv preprint server before peer review. The study authors recommended researchers re-evaluate all single cell RNAseq data obtained using the platform's exclusion amplification (ExAmp) technology since its launch in 2015.

The Stanford team showed the HiSeq 4000 platform was prone to “spreading-of-signal” across single cell RNA samples that had been converted into complimentary DNA (cDNA), then multiplexed and sequenced in parallel. The method systematically assigned a fraction of sequences to the wrong samples, including control samples that contained sequencing reagents but lacked cDNA. ...