SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Allele Distributions jkozubek Bioinformatics 3 05-13-2013 03:29 PM
allele counts in bam bair Bioinformatics 0 01-25-2012 10:04 AM

Reply
 
Thread Tools
Old 04-28-2014, 04:29 AM   #1
IonTom
Member
 
Location: Germany

Join Date: Apr 2014
Posts: 32
Default Allele Bias

What would you consider the lowest reasonable Allele frequency for a heterozygous germline SNP. Something like between 30% and 60% ?

Also for somatic mutations what would be the limit to a call it heterozygous,
and when would you start to label it as subclonal ?
IonTom is offline   Reply With Quote
Old 04-29-2014, 02:38 PM   #2
m_two
Member
 
Location: USA

Join Date: Mar 2010
Posts: 50
Default

Q: What would you consider the lowest reasonable Allele frequency for a heterozygous germline SNP. Something like between 30% and 60% ?

It's a dependent on the of coverage of that site. If you're dealing with tumor data, the combination of purity and ploidy can be a challenge.

Check out these options:

https://www.broadinstitute.org/gatk/...Genotyper.html

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106328/


Q: Also for somatic mutations what would be the limit to a call it heterozygous, and when would you start to label it as subclonal ?

Here are some tools and software that can help you attempt to answer this difficult question:
(Now you have to deal with tumor purity, ploidy, and heterogeneity)

http://bioinformatics.oxfordjournals...tt750.abstract
DeepSNV - Subclonal variant calling with multiple samples and prior knowledge
Bioinformatics (2014)doi: 10.1093/bioinformatics/btt750
http://bioinformatics.oxfordjournals...tt750.abstract

EXPANDS: expanding ploidy and allele frequency on nested subpopulations
http://bioinformatics.oxfordjournals...t/30/1/50.long
Bioinformatics. 2014 Jan 1;30(1):50-60. doi: 10.1093/bioinformatics/btt622. Epub 2013 Oct 30.

ESTIMATE:
https://sourceforge.net/projects/estimateproject/
:http://www.nature.com/ncomms/2013/13...comms3612.html

Absolute:
http://www.broadinstitute.org/cancer/cga/absolute
http://www.nature.com/nbt/journal/va.../nbt.2203.html

https://github.com/genome/sciclone

You should also consider the possibility that many of your low level somatic and germline predictions could be due to cross contamination from other samples. The dbSNP VCF file with 1000 Genomes GMAF/CAF can be a useful resource as well as the data from
http://evs.gs.washington.edu/EVS/
m_two is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:00 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO