Lists of somatic mutations from WGS

Jane M · 05-02-2019, 07:47 AM

Dear all,

I am looking for lists of somatic mutations from cohorts of patient (>=50 patients).
There are some discussions about this search (https://www.biostars.org/p/217812/), but I did not identify a good resource/way to get that: I tried using icgc website but -to me- it is unclear if the data are WES or WGS. Also trying using COSMIC (V88_38_NONCODINGVARIANTS.csv) gave weird numbers of somatic mutations per sample...
Thus, I am currently trying to identify publications where the authors released the list of somatic mutations they identified in genomes.
Up to now, I could identify only one such a publication: Zhang et al., Nature Genetics, 2018: A global transcriptional network connecting noncoding mutations to changes in tumor gene expression

Most publications unfortunately do not give this information, they show summaries, hotspots, drivers, or only coding mutations. It should be more systematic in the future, as data reproducibility and availability is of growing interest.

Could you please indicate such publications if you know some of them?
Such a collection might be a useful resource for several of us.

Thank you in advance
Jane

colindaven · 05-08-2019, 05:58 AM

You're right, these full VCFs are rare. I think a lot of the problems are due to data privacy. You can get them from the TCGA archive but that takes a lot of time to gain access.

I don't do a lot in this area but you might look at this small open set:

https://www.nature.com/articles/sdata201610

Jane M · 05-10-2019, 01:13 AM

Thank you for your feedback.
The concept of this pilot study is very interesting but it seems that 3 years later, there was no new development unfortunately.
The principle of data privacy is crucial, but providing somatic mutations from a patient tumor may not be intrusive. It is not like providing germline mutations or SNPs...

I am still looking for this kind of data. If someone has clues for me, it would be very nice.

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05-02-2019, 07:47 AM	#1
Jane M Senior Member Location: Paris Join Date: Aug 2011 Posts: 239	Lists of somatic mutations from WGS Dear all, I am looking for lists of somatic mutations from cohorts of patient (>=50 patients). There are some discussions about this search (https://www.biostars.org/p/217812/), but I did not identify a good resource/way to get that: I tried using icgc website but -to me- it is unclear if the data are WES or WGS. Also trying using COSMIC (V88_38_NONCODINGVARIANTS.csv) gave weird numbers of somatic mutations per sample... Thus, I am currently trying to identify publications where the authors released the list of somatic mutations they identified in genomes. Up to now, I could identify only one such a publication: Zhang et al., Nature Genetics, 2018: A global transcriptional network connecting noncoding mutations to changes in tumor gene expression Most publications unfortunately do not give this information, they show summaries, hotspots, drivers, or only coding mutations. It should be more systematic in the future, as data reproducibility and availability is of growing interest. Could you please indicate such publications if you know some of them? Such a collection might be a useful resource for several of us. Thank you in advance Jane Last edited by Jane M; 05-02-2019 at 07:51 AM.

05-08-2019, 05:58 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	You're right, these full VCFs are rare. I think a lot of the problems are due to data privacy. You can get them from the TCGA archive but that takes a lot of time to gain access. I don't do a lot in this area but you might look at this small open set: https://www.nature.com/articles/sdata201610

05-10-2019, 01:13 AM	#3
Jane M Senior Member Location: Paris Join Date: Aug 2011 Posts: 239	Thank you for your feedback. The concept of this pilot study is very interesting but it seems that 3 years later, there was no new development unfortunately. The principle of data privacy is crucial, but providing somatic mutations from a patient tumor may not be intrusive. It is not like providing germline mutations or SNPs... I am still looking for this kind of data. If someone has clues for me, it would be very nice.