search

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
Other
101 stars 67 forks source link

Germline Mutation Data #451

Closed yangyangclover closed 4 years ago

yangyangclover commented 4 years ago

What data file(s) does this issue pertain to?

germline mutation data/SNP

What release are you using?

V12

Put your question or report your issue here.

I am trying to perform an association study between SV signature cluster and germline gene mutation. However, it seems the SNP data is controlled. I am wondering if I can access those data or if there are some processed files about germline gene mutation statistics across patients.

jharenza commented 4 years ago

Hi @yangyangclover! The germline data is controlled due to the possibility of patient identification, and as such, we cannot release it on a public platform at this time. However, if there are a minimal number of variants you are looking for, and/or specific SNPs you are interested in, we can determine whether we can pre-filter and release just those specific variants. For example, with #431 we will release a binary matrix of whether or not putative deleterious germline variants exist in TP53, SUFU, and/or PTCH1 in medulloblastoma patients.

Do you have some more information on exactly what variants you are interested in or would this be more of a discovery effort? If discovery, you are more than welcome to request access to these data via the CBTTC here, but this may also be beyond the scope the OpenPBTA paper, in which we are largely focusing on somatic variation across the pediatric brain tumors. Either way, happy to help!

yangyangclover commented 4 years ago

Thank you @jharenza , if it possible to release BRCA1, BRCA2, TP53 germline mutation data? We found some SV mutation may be related to defective homologous recombination-based DNA damage repair, so we wanna see if BRCA1/BRCA2 is the cause.

jharenza commented 4 years ago

@yangyangclover - Per our conversation about subjectiveness of germline filtering and potential to miss/over-assign pathogenicity of TP53 variants when they are of uncertain significance, @jaclyn-taroni and I decided to not filter/release the germline data with our lack of expertise in this area. I think in your analysis, you can instead use the mutational signatures and look for mutational signature 3 in those patients.