Question: Publicly Available Whole Genome Or Exome Sequence Of A Quartet?
4
gravatar for Matt Shirley
7.2 years ago by
Matt Shirley8.8k
Cambridge, MA
Matt Shirley8.8k wrote:

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.

exome genome • 3.0k views
ADD COMMENTlink written 7.2 years ago by Matt Shirley8.8k
6
gravatar for Khader Shameer
7.2 years ago by
Manhattan, NY
Khader Shameer17k wrote:

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

ADD COMMENTlink written 7.2 years ago by Khader Shameer17k
1

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

ADD REPLYlink written 7.2 years ago by lh331k

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.

ADD REPLYlink written 7.2 years ago by Matt Shirley8.8k

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

ADD REPLYlink written 7.2 years ago by Greg Tyrelle70
2
gravatar for Greg Tyrelle
7.2 years ago by
Greg Tyrelle70
Netherlands
Greg Tyrelle70 wrote:

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

ADD COMMENTlink written 7.2 years ago by Greg Tyrelle70

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.

ADD REPLYlink written 7.2 years ago by Matt Shirley8.8k
0
gravatar for Larry_Parnell
7.2 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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

ADD COMMENTlink written 7.2 years ago by Larry_Parnell16k

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.

ADD REPLYlink written 7.2 years ago by Matt Shirley8.8k
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