Which Personalized Genetics Service Is Interesting From A Bioinformaticians Perspective

Question

[Andra Waagmeester]

Some years back I read "The seven daughters of eve" by Bryan Sykes. A very interesting read. At that time they already offered some service to link your genes with one of the ancestral mothers described in this book. Ever since sending in some material has been on my to consider list. Recently 23andme has been a buzz word on twitter. Apparently you can have saliva send in to to be mapped to existing scientific knowledge. I am very much tempted to get the personalized genetics from my to consider list, to my to do list.

I would like to know if there are experiences good/bad with personalized genetics. How reliable are these personalized services? If so, do you get data back in such a way that you can do personalized bioinformatics with it?

Are there other reliable services overing personalized genetics except the two already mentioned?

Answer 1

[Neilfws]

Brief answers to some of your questions:

My own experience with 23andme has been good. Read about it here (1), here (2) and here (3). A Web search will bring up many other people who have blogged about their experience; I'd especially recommend the Genomes Unzipped team.

There's a lot of discussion on the Web regarding reliability, but precious little in the way of hard numbers. I'd assume it's as reliable as any genotyping lab with good QC in place. 23andme did have a sample mix-up a few months ago but it was rapidly identified, rectified and they were very open about it.

You can certainly obtain raw data with which to do bioinformatics. A file is made available for download, which looks like this (first few lines):

# rsid  chromosome      position        genotype
rs3094315       1       742429  AA
rs12562034      1       758311  GG
rs3934834       1       995669  CC
rs9442372       1       1008567 GG
rs3737728       1       1011278 GG
rs11260588      1       1011521 GG
rs6687776       1       1020428 CC

Again, dig around on the Web and you'll find people developing tools for the data. A good example is Promethease, which searches SNPedia using your data.

Other services: I only have direct experience with 23andme, so cannot comment.

Answer 2

[Bert Overduin]

I have no experience with this myself, but a friend of me told me last week he has good experiences with Family Tree DNA and I am considering to use them myself. Note that they are focussed on genealogical information rather than medical information. But as I am much more interested in the former than the latter, I think this will do fine for me.

Answer 3

[Mary]

I have also obtained 23andme data, and I've been having some fun with it. Mostly in excel, though, which I know makes everyone's heads here explode....

I use the SNPTips tool a lot. I also intended to use the Enlis browser for my analysis, but last I checked it wasn't set up for the v3 (current) 23andme chip yet. Someone I know also participated in the Dodecad project with the data.

There's a whole network of third-party support tools developing around the 23andme stuff: 23andyou. So I would say this is becoming something of a hacker's community and there's going to be more and more developed around this.

I have no financial relationship with any of the services or tool developer parties I'm mentioning here. Just trying to bring some stuff I know about to the discussion. And I also only have experience with 23andme data as well at this point.

Answer 4

[Jeroen Van Goey]

1. Colm O'Dushlaine, a bioinformatician working on statistical analyses of genome-wide association studies and next-generation sequencing datasets at the Broad Institute, has done several analysises on his raw 23andme data.

For example: Can we identify any SNPs, predicted to be damaging, in OMIM? This would point to any Mendelian traits/disorders?

wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz
 gunzip OmimVarLocusIdSNP.bcp.gz
 cut -f 1,9 OmimVarLocusIdSNP.bcp | gawk '{print "rs"$2,$1 }' | sort > snps_2_omim.txt

1. Interpretome supports raw data files from 23andme and Lumigenix. You can explore: how your genotype alters your response to prescription drugs, you can look up your genotype at all entries in the GWAS catalog, you can use a heuristic method to paint ancestry onto your chromosomes, etc.

2. David Pike, a combinatorial Mathematician who has worked on phylogenetic networks, has released some utilities to perform some advanced analysis of autosomal DNA results, with the objective of better pursueing genealogical research.