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Old 04-04-2017, 09:14 AM   #1
GenoMax
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Default HiSeq 4000 index swaps

I was recently made aware of a potential problem that supposedly can result in index misassignments with HiSeq 4000 (under certain experimental conditions). James Hadfield wrote about this a few months back. This may be generally applicable for all ExAmp chemistry instruments.

Since I have not seen this discussed here/elsewhere online I wanted to see if people have seen this in your data.

Last edited by GenoMax; 04-04-2017 at 09:17 AM.
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Old 04-09-2017, 07:58 PM   #2
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Here's a preprint about it: http://www.biorxiv.org/content/early/2017/04/09/125724
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Old 04-12-2017, 03:40 AM   #3
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There's also this thread.
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Old 04-12-2017, 04:22 AM   #4
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Quote:
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There's also this thread.
Thanks for the reminder @ginger.
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Old 04-12-2017, 05:07 AM   #5
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Anyone doing significant multiplexing should be using dual indicies, which reduces this problem dramatically (making swapped reads go to Undetermined while demultiplexing).

Interested to see if this is a problem in our novaseq runs...will update if I note something.
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Old 04-12-2017, 05:23 AM   #6
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That's dual indexes using the same index at both ends.
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Old 04-12-2017, 09:33 AM   #7
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It is great that the Biorxiv manuscript from the Weissman lab has hopefully identified the cause of the problem which has been reported previously for some cases (the agent being "free barcoded primers" present in the library).
However, the scary index-swapping rates were seemingly generated from low-quality library preps with high primer contamination. I am aware that for their specific application (single-cell SMRT-seq) one can't be choosy with regards to the library quality. For any other application these libraries should have failed the QC. The free primers could and should have been easily drastically reduced by an additional magnetic bead cleanup for their first experiment. It is nice that we get to benefit from this mishap now.

I have posted my thoughts here: http://dnatech.genomecenter.ucdavis....ignment-issue/

Obviously these data ask for caution for any multiplexed sequencing projects and for protocol adjustments.
To some degree the manuscript shows: Ugly things can happen if one sequences really ugly libraries.
How relevant is this to the sequencing of high-quality and clean libraries? The observed linear correlation between between primer spike-ins and artifact rate indicates, to me, that there is no reason to panic.

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Old 04-12-2017, 12:32 PM   #8
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Good post, DNATECH. People are definitely overstating things on twitter, "10% reads misassigned on HS4000" without noting the caveats--this type of swap only happens when the primer contains indices, the paper used highly multiplexed samples where the read count per sample was low and the number of other samples that could contribute to crosstalk was high, and the prep (as you noted) lended itself to this issue.

I think it is also important to note that other forms of index swapping can occur (PCR of pooled libraries, for example).
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Old 04-12-2017, 04:24 PM   #9
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Treating final PCR reactions (for library preps using Nextera, NEBNext line of kits, 10X Genomics and some other mentioned in DNATECH blog) with ExoSAP-IT or ssDNA nucleases such as Exonuclease1 should digest remaining PCR primers and can be adapted as an add-on before bead clean up.

Edit: Exonuclease VII also can be used to cleave primers and single stranded region of adapters.

Last edited by nucacidhunter; 05-14-2017 at 07:30 PM. Reason: Added more information
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Old 04-13-2017, 08:21 AM   #10
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nucacidhunter, this is definitely worth a try! (Is seemingly clean - according to BA - good enough?)

I agree SNPsaurus the problem is more complex.

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Treating final PCR reactions (for library preps using Nextera, NEBNext line of kits, 10X Genomics and some other mentioned in DNATECH blog) with ExoSAP-IT or ssDNA nucleases such as Exonuclease1 should digest remaining PCR primers and can be adapted as an add-on before bead clean up.
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Old 04-13-2017, 10:36 AM   #11
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Treatment of PCR products with Exo I/EXOSAP/Antarctic Phosphatase for primer removal is an old trick and works very well.
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Old 04-13-2017, 04:42 PM   #12
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Quote:
Originally Posted by DNATECH View Post
(Is seemingly clean - according to BA - good enough?)
It depends on:
1- Primer length that should be long enough not to blend with lower marker of the Chip or Tape. A 50 base long primer would blend with HSD5000 Tape lower marker but not with HSD1000 one
2- Sensitivity of Chip or Tape that should be high sensitivity type capable of detecting low concentrations

It should also be possible to Exo treat the library pool rather than treating each individual library
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Old 04-18-2017, 02:13 AM   #13
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Illumina’s white paper on index misassignment:

https://www.illumina.com/content/dam...inkId=36607862
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Old 04-18-2017, 03:33 AM   #14
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Quote:
Originally Posted by nucacidhunter View Post
Illumina’s white paper on index misassignment:

https://www.illumina.com/content/dam...inkId=36607862
Thank you @nucacidhunter.
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Old 04-18-2017, 11:15 AM   #15
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1.5% index hopping with no adapters spiked in. Does that mean anything?
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Old 04-18-2017, 06:15 PM   #16
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Quote:
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1.5% index hopping with no adapters spiked in. Does that mean anything?
I think 1.5% hopping is from the libraries in the pool and not the spiked-in adapters.
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Old 04-18-2017, 06:16 PM   #17
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Makes me wonder if single molecule consensus is out of the question, since it would seem that the mitigation strategy requires defined barcode sequences.
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Old 04-18-2017, 07:56 PM   #18
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It shows that PCR-free libraries can hide a larger amount of adapters and adapter dimers somehow entangled in the y-adapters. We have several times seen surprises with (on the BA) clean looking PCR-free libraries in this regard.

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1.5% index hopping with no adapters spiked in. Does that mean anything?
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Old 05-31-2017, 02:34 AM   #19
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Quote:
Originally Posted by ECO View Post
Anyone doing significant multiplexing should be using dual indicies, which reduces this problem dramatically (making swapped reads go to Undetermined while demultiplexing).

Interested to see if this is a problem in our novaseq runs...will update if I note something.
I wonder if there is any update on this.
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