Publicly Available Whole Genome Or Exome Sequence Of A Quartet?

Question

[Matt Shirley]

Does anyone know of a publicly available quartet with either whole genome or exome sequence? Preferably aligned reads, or just the unmapped reads would be fine. I've looked through 1000 genomes, hoping that there would be a pedigree with a quartet, but there are only trios. There are some papers on quartet-based analysis of exome sequence, but no public data sets.

Answer 1

[Khader Shameer]

There is a quartet dataset (genome) at EBI-ENA.

"Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing"

Manuscript here, dataset here

[lh3]

+1. But use data with cautious. The only mappers/SNP callers that work with CG data are the CGAtools and the RTG investigator.

[Matt Shirley]

Thanks. I'm not familiar with the EBI, but I was able to apply for access through dbGaP. Even though we have more and more public sequences coming out, it is still difficult to find large pedigrees. This really helps me.

[Greg Tyrelle]

Interesting, I couldn't see any way to download the files associated with that experiment from ENA. There are no FTP or Aspera links.

Answer 2

[Greg Tyrelle]

If the data you are looking for does not need to include effected individuals, Complete Genomics has sequenced a 3 generation 17 member family (CEPH). Files here:

ftp://ftp2.completegenomics.com/Pedigree_1463/ASM_Build37_2.0.0

[Matt Shirley]

This is a good answer, but I was really looking for exome sequence. I know this is kind of a subtle difference, but the data handling and analysis is a bit different. Thanks.

Answer 3

[Larry_Parnell]

I'd search for data from the West family. Here's a news story.

[Matt Shirley]

Thanks. I liked the article, but it seems the data are still private. Not surprising, considering that this is a healthy family, and that the father paid for all the sequencing out of pocket.