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Index Switching on Illumina platforms

I recently came across this manuscript from the Weissman (Stanford) group, in with the authors describe a problem on the more recent Illumia platforms (HiSeq 3000/4000/X), which can lead to contaminations between multiplexed samples.

Has anyone else observed this effect?

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Yeah, it’s pretty common, but usually not to the extent observed in that paper:
Illumina index hopping white paper

It’s something that needs to be corrected for in any analysis investigating public sequences. Usually a read count filter (eg, >3 raw reads) is sufficient to catch indexing errors, but low yield samples (eg, tissue, rare sorts, etc) can be trickier.

See also: http://dnatech.genomecenter.ucdavis.edu/2017/04/11/update-on-barcode-mis-assignment-issue/

More follow-up: http://biorxiv.org/content/early/2017/05/25/142356