False Positives In Disease Gene Hunting - Truseq Exome Enrichment Kit - A Call For Data

Question

[Zev.Kronenberg]

I am working on eliminating false positives while disease gene hunting. Often across searches (and across diseases) I find the same genes popping up as top candidates. We have multiple lines of evidence that these are false positives from biological and in silico data.

A neat paper highlights several of the genes that are common false positives.

Taxonomizing, sizing, and overcoming the incidentalome

I am looking for (healthy or sick) TruSeq Exome Enrichment Kit exomes. I plan on running the raw data through my pipeline and mixing them into my larger background.

Does anyone know where I can get raw reads from TruSeq Exome Enrichment Kits or variant calls?

Would anyone be willing to share these data for use a control?

[Khader Shameer]

Are you looking for fastq files or VCFs ?

[Zev.Kronenberg]

I will take either, but I really want them to be from the same capture array.

Answer 1

[Sean Davis]

You might take a look at the Exome Sequencing Project site. You can download VCF files from variant calls representing thousands of samples.

[Alex Paciorkowski]

The dataset at this site makes a big difference. >5400 exomes at present, and growing. If your variant of interest is present here, it's probably not disease causing. If it's absent from this dataset, then you've got a rare variant, and can probably justify moving forward with validation.

[Zev.Kronenberg]

Nice resource. I have browsed their SNVs, but never downloaded it. Downloading now.

[Zev.Kronenberg]

Do you know if there is a way to get individuals genotypes rather than allele frequencies?

[Sean Davis]

I don't believe there is a way to get individual genotypes; I imagine this is due to privacy concerns.

Answer 2

[Khader Shameer]

Have you checked ENA ?