Illumina published a white paper today on the barcode mis-assignment issue (Illumina calls it somewhat euphemistically “barcode hopping”).
In contrast to the Sinha et al. paper, which only presented data for libraries with NextSeq adapter sequences, the white paper shows that the issue is also relevant for TruSeq style adapters. The conclusions are fairly similar to the ones drawn in our last newsletter.
The major take home message is that clean sequencing libraries are of highest importance when sequencing on the HiSeq 4000, HiSeq 3000, and HiSeq X Ten. For the majority of applications the “barcode hopping” between clean libraries will be minimal and will have minimal or no impact on the data analysis.
To be able to provide the best possible data we are implementing the protocol modifications laid out in our last newsletter which are also suggested in the white paper.
content/dam/illumina- marketing/documents/products/ whitepapers/index-hopping- white-paper-770-2017-004.pdf? linkId=36607862
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Edits (04/20 &21/2017):
Megan Molteni wrote an article for the interested public on the topic: https://www.wired.com/2017/04/geneticists-fear-illuminas-sequencers-may-distort-results/
James Hadfield provides a comprehensive summary of the discussion here: http://enseqlopedia.com/2017/04/update-illumina-index-swapping/