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:
...
- 9,452
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 ...
- 2,159
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.
...
- 535
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%, ...
- 4,825
5
votes
Accepted
Searching for gene expression data by cell line
Try the Gene Expression Omnibus - it looks like they have some datasets.
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 ...
- 13.5k
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 ...
- 236
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 ...
- 9,452
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, ...
- 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, ...
- 1,563
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:/...
- 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 ...
- 2,739
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 ...
- 19.5k
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 ...
- 560
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 ...
- 4,692
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 ...
- 13.5k
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 ...
- 13.5k
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 ...
- 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. ...
- 1,059
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 ...
- 146
3
votes
Important genes beyond PAM50 for breast cancer classification
There is a CSV table in this paper with 33 sets of genes.
- 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
- 1,621
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 ...
- 2,294
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....
- 131
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, ...
- 4,692
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 ...
- 2,159
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 ...
- 4,692
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 ...
- 1,816
2
votes
Use of heterozygous SNPs in cancer research: why?
I'm not sure what I'm talking about, but I guess one could re-phrase Konrad's answer in terms of information theory.
The information content of a message (a packet of bits) is inversely proportional ...
- 689
2
votes
Accepted
How to interpret fish plot in R
Author of the package here, stumbled across this today. The existing explanation is close, but not entirely correct.
Our paper describes it like this: "We first created a fish plot of an AML ...
- 530
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