Batch bias while merging TrueSeq PCR-free and Nano data

hudja · 09-30-2016, 01:34 PM

Hi All,

We are starting a new sequencing project of human DNA samples. Part of our sample was already sequenced using Illumina TrueSeq PCR-free kit. Now, it turned out that part of the new samples does not qualify for PCR-free protocol and we were suggested to switch them to TrueSeq Nano protocol. In addition, we have been advised that PCR-free protocol could have a big failure rate during library prep currently, up to 15%. The issue seems to be connected to changes in kit chemistry and affects many labs worldwide.

However, I am a little bit worried about the possible extent of batch bias arising when processing/merging data from two different protocols (PCR-free and Nano). Does anybody here have this kind of experience?

Thank you in advance!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
TrueSeq PCR free POOR LIGATION efficiencies	Degraz	Illumina/Solexa	3	04-08-2015 06:03 AM
TruSeq DNA PCR-free vs NANO DNA kit	mbk0asis	Illumina/Solexa	8	05-17-2014 09:15 AM
PCR-Free Libraries & Bioinformatic PCR Duplicate detection?	aeonsim	Bioinformatics	3	10-23-2013 02:36 PM
The NEXTflex™ PCR-Free DNA Sequencing Kit Reduces Bias in NGS Library Prep	Bioo Scientific	Vendor Forum	10	12-20-2012 08:10 AM
bias in merging sequence data?	quinne5	RNA Sequencing	0	11-01-2012 10:17 AM

09-30-2016, 01:34 PM	#1
hudja Junior Member Location: planet Earth Join Date: Sep 2016 Posts: 1	Batch bias while merging TrueSeq PCR-free and Nano data Hi All, We are starting a new sequencing project of human DNA samples. Part of our sample was already sequenced using Illumina TrueSeq PCR-free kit. Now, it turned out that part of the new samples does not qualify for PCR-free protocol and we were suggested to switch them to TrueSeq Nano protocol. In addition, we have been advised that PCR-free protocol could have a big failure rate during library prep currently, up to 15%. The issue seems to be connected to changes in kit chemistry and affects many labs worldwide. However, I am a little bit worried about the possible extent of batch bias arising when processing/merging data from two different protocols (PCR-free and Nano). Does anybody here have this kind of experience? Thank you in advance!