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A recent manuscript  documented the "index switching" of multiplexed samples on the Illumina platforms. This issue is distinct from the "cross-talk"/"sample bleeding" issue we previously identified . Illumina has released a white paper  ("Effects of Index Misassignment on Multiplexing and Downstream Analysis") that addresses "index switching"/"index hopping."
We are in the process of evaluating Illumina's recommendations and will follow up with the community regarding the implementation of mitigation strategies.
In the meantime, until we can provide further information, we recommend to avoid multiplexing samples together when index switching from one sample to another at a level of up to 2% could cause a biologically misleading false positive result. If you are uncertain about your multiplexing design please consult with the CGRB staff.
Please be advised that we have observed cases in which the Illumina HiSeq and MiSeq platforms have incorrectly assigned an index (“barcode”) to a sequence from an adjacent cluster on the flow cell. This “sample bleeding”  results in sequences (including PhiX clusters that have no index read) that are mis-binned into the incorrect FASTQ file during the demultiplexing step. Sample bleeding occurs due to characteristics of the Illumina hardware/software and is not related to biological cross-contamination. Anecdotally, sample bleeding has been observed to occur in less than 0.1% of sequences using single indexes and in less than 0.001% of sequences using dual indices.
Experiments using rare sequences in a sample to indicate the presence of a novel sequence may be impacted, e.g., such as in identifying the presence of a transcript in an RNA-seq experiment via a few reads or identifying novel sequence in a genome based on contigs with very low coverage.
The following may help mitigate the sample bleeding issue:
 “Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform” (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393298/)
Please be advised that we have observed cases in which the (unsupported) mixing of indexing kits in a single lane on the HiSeq and MiSeq platforms (e.g., dual and single indexed samples in the same lane) have resulted in unintended binning, i.e., sequences may be mis-binned (mis-assigned) into the incorrect FASTQ file during the demultiplexing step.
This mis-binning can occur as both the HiSeq 3000 and MiSeq demultiplexing step allows for a 1 base mismatch in the index read by default. Indexes that are close in base composition may be mis-binned due to sequencing error when allowing for this 1 base mismatch.
This unintended binning issue can be mitigated by re-demultiplexing a lane allowing for a 0 base mismatch in the index reads, i.e., indices must be perfectly matched to be “binned.”
Please contact Matthew if you have questions or require re-demultiplexing of a lane that may be affected by this issue.
Illumina samples can be barcoded or indexed using two different techniques: