8 votes
Accepted

GRCh38 vcf file with common cancer mutations

Your question doesn't give enough information for a specific answer but this should do for a start. Get the VCF file describing all variants in Clinvar from NCBI: ...
terdon's user avatar
  • 10.1k
8 votes

GRCh38 vcf file with common cancer mutations

If you are looking for cancer mutations, the primary resource is COSMIC and they provide GRCh38 VCFs. The download page is here: http://cancer.sanger.ac.uk/cosmic/download It'll be up to you how you ...
burger's user avatar
  • 2,179
7 votes
Accepted

Database of copy number alterations in different cancer types

I don't know if there's a database that does exactly what you want, but there are some places that might help you figure this out, especially if you already have a list of CNAs/genes/regions in mind. ...
Jared Andrews's user avatar
5 votes
Accepted

Use of heterozygous SNPs in cancer research: why?

I’m no longer working in tumour sequencing so I’m by no means an expert. But in a nutshell, the reason is that, as indicated, homozygous SNPs aren’t informative: if your allelic fraction is 100%, ...
Konrad Rudolph's user avatar
5 votes
Accepted

Searching for gene expression data by cell line

Try the Gene Expression Omnibus - it looks like they have some datasets.
Kristoffer Vitting-Seerup's user avatar
5 votes
Accepted

Detecting structural variants with MinION data

There was a Structural Variant breakout session at the London Calling conference this year. Unfortunately I didn't attend that session, but MinION community members have access to Constance Donnell's ...
gringer's user avatar
  • 14.1k
5 votes

How can I use annotations to remove variants not relevant to cancer risk?

While your question is specific to cancerous germline mutations, I'd suggest you look at the COSMIC database of somatic mutations to include in your analysis. There are other factors to include in ...
A_Skelton73's user avatar
5 votes

Somatic tumor only variant calling?

I've been using the LoFreq* caller for exactly this. It is designed to find variants with very low frequency, so is well suited for this type of analysis. LoFreq* (i.e. LoFreq version 2) is a fast ...
terdon's user avatar
  • 10.1k
5 votes
Accepted

Somatic tumor only variant calling?

There is a recent paper that attempts to do this: ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. In this work, we describe the development, ...
GWW's user avatar
  • 752
5 votes

How to interpret fish plot in R

Each color is a clone (set of mutations) or an individual mutation (depends on how the input data was generated). This is a cancer with the bottleneck likely being induced by a treatment (e.g. UV, ...
story's user avatar
  • 1,573
4 votes

Using data mining of papers in order to derive genomic connections

There are many databases that have used publication scraping for oncogenic gene fusions. There are publications for the individual methods they used for their scraping and aggregation. COSMIC - http:/...
Bioathlete's user avatar
  • 2,574
4 votes

Why the t-test for a specific gene shows different value compared to differential analysis?

There is no reason your t-test should reproduce edgeR. In fact, edgeR exists because t-test is inappropriate. edgeR does the tests by pooling information from all genes, because with the low number ...
SmallChess's user avatar
  • 2,699
4 votes

How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?

There are plenty of tools to summarize long lists of GO terms by removing redundancy (which seems to be your concern), such as REVIGO (web) or rrvgo (R+Bioconductor). Disclaimer: I'm the author of the ...
ssayols's user avatar
  • 141
3 votes
Accepted

Why the t-test for a specific gene shows different value compared to differential analysis?

The $log(CPM)$ of any low-moderately expressed gene will be negative. There is nothing unexpected there. Your statistics are inappropriate for a variety of reasons. Firstly, a CPM is not a robust ...
Devon Ryan's user avatar
  • 19.6k
3 votes
Accepted

Is there a publicly available tumor-normal sample?

Please take a look at An open access pilot freely sharing cancer genomic data from participants in Texas Although I have not worked on this paper but author claimed that both tumor and normal data ...
Lot_to_learn's user avatar
3 votes

COSMIC Genotypes and Phenotypes

It seems like I was wrong and COSMIC does store information about cell lines. You need to download the files from Genotypes: Genotypes Files listing the SNP calls for each cell line ...
llrs's user avatar
  • 4,703
3 votes

GRCh38 vcf file with common cancer mutations

The trouble with looking for cancer-associated variants is that it can be difficult to tease out spurious effects (e.g. ethnicity) from causative variants. If you're interested in what genes are ...
gringer's user avatar
  • 14.1k
3 votes

Using data mining of papers in order to derive genomic connections

This existed as a closed silo, at least in 2015. Qiagen has a team of hired students and Post-Docs for collating research papers into their Knowledge Base, an extensive database that is integrated ...
gringer's user avatar
  • 14.1k
3 votes

How can I use annotations to remove variants not relevant to cancer risk?

I don't think it will be possible to do what you ask, right now with current knowledge. Selecting variants relevant to cancer risk is still an open problem and usually requires quite a lot of human ...
bernatgel's user avatar
  • 166
3 votes
Accepted

Tumor purity/contamination/admixture estimation

I have previously estimated tumour purity with the EXPANDS an inferred tumour heterogeneity program which is designed to calculate the number of clonal subpopulations in matched tumour/normal samples. ...
Matt Bashton's user avatar
  • 1,069
3 votes
Accepted

Survival analysis using CoxPH - Effect of covariates

Example 2 and 3 seem symmetric because they are forced to by the model. The Cox proportional hazard relies on the proportional hazards assumption. This basically means that the ratio of the hazards ...
pzivich's user avatar
  • 146
3 votes

Important genes beyond PAM50 for breast cancer classification

There is a CSV table in this paper with 33 sets of genes.
user66081's user avatar
  • 151
3 votes
Accepted

Is there any database about the abundance of proteins in urine of healthy patients?

If you have access to the UK Biobank dataset, then they have urine data for healthy individuals. https://www.nature.com/articles/s41588-020-00757-z
user438383's user avatar
  • 1,679
3 votes

How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?

It is totally acceptable in your main figure to display only a selected part of your GO term, as long as the reader is aware of this action (e.g., by including a legend specifying "selected ...
RomainL.'s user avatar
  • 145
2 votes

Tumor purity/contamination/admixture estimation

It's usually CNV callers that make use of Tumour/Normal WGS pairs to estimate purity. It can also be done with WES (exome) Tumour/Normal pairs. There are several tools out there, I have some ...
719016's user avatar
  • 2,324
2 votes

How to access the patient-derived xenografts (PDXs) repository?

I already see for links when I try to search. Take a look at them below. Also if you can be precise about kind of data are you trying to find, it would be better https://pdmr.cancer.gov/ http://cdt....
ivivek_ngs's user avatar
2 votes
Accepted

EMT/EMT-like processes in bioinformatics to study cancer progression

EMT describe cells' change in their state from being epithelial to the mesenchymal class. So, if a cancer cell line is gaining properties that allow it to move, it might reach the metastasis phase, ...
llrs's user avatar
  • 4,703
2 votes

Somatic tumor only variant calling?

All the popular variant calling tools such as Strelka, VarScan etc require a normal sample. Strelka and VarScan require a normal sample in somatic mode, but they both have a germline mode for ...
burger's user avatar
  • 2,179
2 votes

What would be a reasonable healthy data set/control group to compare with a cell line from TCGA?

In the TCGA datasets there is a variable (type) containing the information if the sample was from the tumor or from an adjacent region, which is usually considered as healthy. As this samples come ...
llrs's user avatar
  • 4,703
2 votes

Information about control data

Without control data from your subjects, I don't think there's really no way to distinguish somatic mutations from germ-line mutations. The best you can do is to screen out common variants, which are ...
heathobrien's user avatar
  • 1,816

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