detection of somatic mutations using RNA seq data for tumor samples paired with WES

SaraYones · 08-29-2017, 02:31 AM

i have WES data for normal and I have RNA seq only for tumor. I want to use the RNA seq data to detect somatic driver mutations and I want to pair it with the normal WES data in order to be able to effectively filter the false positive somatic mutations. Is there a way to do that ? I have read a few method papers that use RNA seq for detection of somatic mutations but it is either that the RNA seq has paired normal and tumor samples or the others use unpaired RNA seq data to detect somatic mutations but I haven't found any paper which paired tumor and normal samples using RNA seq and WES data so I don't know if thats possible or not.

Brian Bushnell · 08-29-2017, 10:53 AM

It's certainly possible, to an extent. Call variations in WES, call variations in RNA-seq, subtract WES mutations from RNA-seq mutations, and look at what's left. You'll miss a lot due to the uneven expression of RNA, but then, you miss 98% of mutations already with WES.

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08-29-2017, 02:31 AM	#1
SaraYones Junior Member Location: Uppsala, Sweden Join Date: Mar 2017 Posts: 4	detection of somatic mutations using RNA seq data for tumor samples paired with WES i have WES data for normal and I have RNA seq only for tumor. I want to use the RNA seq data to detect somatic driver mutations and I want to pair it with the normal WES data in order to be able to effectively filter the false positive somatic mutations. Is there a way to do that ? I have read a few method papers that use RNA seq for detection of somatic mutations but it is either that the RNA seq has paired normal and tumor samples or the others use unpaired RNA seq data to detect somatic mutations but I haven't found any paper which paired tumor and normal samples using RNA seq and WES data so I don't know if thats possible or not.

08-29-2017, 10:53 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	It's certainly possible, to an extent. Call variations in WES, call variations in RNA-seq, subtract WES mutations from RNA-seq mutations, and look at what's left. You'll miss a lot due to the uneven expression of RNA, but then, you miss 98% of mutations already with WES.