User: Collin

gravatar for Collin
Collin420
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420
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United States
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2 years ago
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Posts by Collin

<prev • 47 results • page 1 of 5 • next >
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Comment: C: How to identify if certain recurrent SNPs in a given cancer are associated with
... I would imagine you will need to group somatic mutations together in a reasonable way. Otherwise you will be restricted to certain highly prevalent driver genes which have very highly recurrent hotspots, such as V600 in BRAF or G12 in KRAS. Or based on this comment ("So the first step would be to id ...
written 4 days ago by Collin420
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Comment: C: cosmic database genes
... I've been told from some prominent cancer geneticists that "if I can't find a link in a few steps of a gene to cancer than I haven't done enough background research on the gene yet." The point was the need for rigorous association based on data. The sequencing of cancers represent an observed endpoi ...
written 5 days ago by Collin420
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Comment: C: cosmic database genes
... I think there needs to be more clarification of COSMIC and the Cancer gene census (CGC) to avoid over interpretation. The CGC is a manually curated list of **genes** containing mutations that have a driving role in cancer. COSMIC contains somatic mutations from cancer sequencing studies, as such the ...
written 6 days ago by Collin420
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Comment: C: Input file requirements for hg38
... The issue is that the precomputed scores are annotated against the transcript chosen in the BED file I provide. So I really do have to provide updated data files for all of them together for it to work. Our lab has updated some of the score information for hg38, but it hasn't been made yet into a fo ...
written 4 weeks ago by Collin420
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Answer: A: Input file requirements for hg38
... The trained classifier would work, but the pipeline for fetching and computing features for you would not. This is because as you kind of suspected the pre-computed scores are based on information from hg19. Likewise the gene annotation in the BED file are also based on hg19 coordinates. I recommend ...
written 4 weeks ago by Collin420
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Answer: A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
... One option may be to look at the BRCA exchange (http://brcaexchange.org/ ) since it's curated by an expert panel. It's supported by the Global Alliance for Genomics and Health, and is a non-paid database. Although I'm not sure if it meets all of your needed criteria. ...
written 9 weeks ago by Collin420
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Comment: C: MuSic Tools !!!
... If you are talking about using MuSiC from analyzing significantly mutated genes in cancer, then you should be aware that MuSiC has elevated false positives due to how their statistical model handles mutational heterogeneity (PMIDs: 27911828 (includes a method comparison), 23770567). This is particul ...
written 10 weeks ago by Collin420 • updated 10 weeks ago by genomax37k
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Comment: C: Exploring cancer mutation data portals
... Are you solely interested in tools that just visualize/download publicly available data sets? What about resources where you can actually submit your own mutations and annotate, analyze, and visualize? ...
written 6 months ago by Collin420
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Comment: C: Genes responsible for cancers
... Tumorportal will only contain genes that are driven by small somatic mutations. This completely leaves out copy number alterations (although they do show copy number on their visual plots) and fusion genes. The cancer gene census from COSMIC, however, doesn't provide that great of breakdown on what ...
written 6 months ago by Collin420
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Comment: C: Statistical test for finding driver mutations.
... If you have your H1 be P != Pg, then you are assuming a two-sided statistical test. You can still have a H1 be P > Pg, which is a one sided statistical test. A one sided test is used, generally, because you are trying to identify cancer drivers. Cancer driver mutations would be more advantageous ...
written 7 months ago by Collin420

Latest awards to Collin

Appreciated 9 weeks ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 12 months ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 19 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 20 months ago, asked a question with at least 3 up-votes. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Scholar 20 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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