Illumina vs. Agilent Exome enrichment - higher false positive rates

[markusl]

Hello,

We are sequencing whole exomes (human) using an Illumina HiSeq2000. We previously did sample prep and exome enrichment using the Agilent SureSelect Human All Exon Kit. Recently we switched to the Illumina sample prep and exome enrichment kits, however we observed a dramatic increase in false positive SNP calls (the analysis pipeline is the same).

Has anybody else compared Agilent and Illumina exome enrichments and observed similar problems?

Thanks for any comments.

markusl

[Rocketknight]

Seconding this question! I'm in a lab that's just starting to get involved with whole exome sequencing, and I haven't been able to find any quality comparisons of the different exome capture methods. Any advice/experiences people have had with them would be awesome.

[stanford_genome_tech]

Several major papers on this topic will be coming out shortly. Be on the lookout in Genome Biology as well as others for bakeoff studies.

[Heisman]

If you are going to analyze multiple, unrelated exomes, you can simply filter out variants that appear in more than X % of the exomes. Granted, you won't get any information from those specific bases, so you have to consider if that is worthwhile (ie, if you are studying a rare Mendelian disease you will probably be fine; if you are studying other more common things and intend to do association tests of some sort then you probably don't want to filter out the common variants.

[markusl]

Yes, analyzing multiple samples could help. However we also would be interested if the sample prep method from illumina is somewhat more errorprone compared to Agilent - in that case it would be better to stay with Agilent. Then we have less problems downstream.

Thanks for any replies so far...

markusl

[Michael.James.Clark]

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.1975.html

Ask and ye shall receive.

In particular note the comparisons between exome-seq and WGS in the end. Not a substantially higher false positive rate in either.

[Rocketknight]

I love when two papers get published on exactly the topic I need just as I decide I need to research it. Thanks to both of you!

[Rocketknight]

Quick question. I'm still trying to decide between the three exome capture methods. Am I right in thinking that the Illumina kit offers substantially higher throughput (assuming we don't have access to robotics, etc.) because it supports multiplexing before the enrichment protocol? Or is this also possible with the Agilent and Nimblegen kits?

[prathima]

I am sharing a publication link on Performance comparison of four exome capture systems for deep sequencing. This is might be useful as a very quick reference, I guess. Thanks to the authors.


https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-449

Please do share if any further useful information is available.

[Geneus]

I am sharing a publication link on Performance comparison of four exome capture systems for deep sequencing. This is might be useful as a very quick reference, I guess. Thanks to the authors.


https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-449

Please do share if any further useful information is available.

I've been hearing good things as of late about IDT's exome kit (not tested in the above comparison)...maybe someone might want to comment?