Comments for Manuel Corpas' Blog

Comment on My Personal Exome Analysis (Part I): First Findings by cariaso

cariaso — Tue, 07 Feb 2012 04:46:54 +0000

processing just the exome yields 881 snpedia snps

pooling it with your 23andMe v2
http://files.snpedia.com/reports/genome_corpas_pool.html
pushes you up to 9591 snpedia snps

There are 2 which conflict between the two platforms
rs12344615 reported as (A;G) and (G;G)
rs2290272 reported as (C;T) and (T;T)

your v2 has 9241
so there are 350 genos with annotations which are new

These in particular occur in less than 10% of the HapMap and are likely to be the most interesting
rs11465702(A;G) 0.0%
rs12265684(C;G) 0.0%
rs12934561(C;T) 0.0%
rs2233682(A;G) 0.0%
rs2852464(C;G) 0.0%
rs3752472(C;T) 1.8%
rs12344615(G;G) 2.7%
rs7951(C;T) 4.7%
rs1052773(A;A) 5.3%
rs10409962(A;G) 6.2%
rs2326369(C;T) 6.2%
rs2522943(C;G) 7.7%
rs2229944(C;T) 8.0%
rs11852361(C;T) 8.8%
rs25489(A;G) 8.8%

Comment on My Personal Exome Now Publicly Released by My Personal Exome Analysis (Part I): First Findings « Manuel Corpas' Blog

My Personal Exome Analysis (Part I): First Findings « Manuel Corpas' Blog — Mon, 06 Feb 2012 10:56:20 +0000

[...] Exome Analysis (Part I): First Findings You may have read in a previous entry about the release of my raw personal exome data. Although users were not required to report back any finding derived from this data, my hope was [...]

Comment on Getting My Genome Sequencing Done (Part I) by Article: Getting My Genome Sequencing Done (Part I) « Manuel Corpas’ Blog « linkstream2

Tue, 31 Jan 2012 14:07:33 +0000

[...] Getting My Genome Sequencing Done (Part I) « Manuel Corpas’ Blog http://manuelcorpas.com/2011/07/12/getting-my-genome-sequencing-done-part-i/ [...]

Comment on My Personal Exome Now Publicly Released by Dan Gaston

Dan Gaston — Mon, 30 Jan 2012 14:46:17 +0000

Thanks Daniel for the info, I’ll definitely pass it along and keep that in mind as our project moves forward.

Comment on My Personal Exome Now Publicly Released by Daniel Swan

Daniel Swan — Mon, 30 Jan 2012 14:44:46 +0000

Dan, this is one reason we don’t include depth filters in our pipeline. No coverage is one thing, but I’m quite wary of throwing away low coverage variants – especially if the read quality and mapping quality is good. For trio analysis where we need to be confident about genotype calls we do filter by depth by proxy. We recommend to people to start with variants of 20x depth or higher first, but if nothing is found then we don’t discourage exploration of the lower coverage data for potential causal variants. It just implies that a little more confirmation is required, but to follow up a tranche of low-coverage variants of interest isn’t a terrible burden by other genotyping methods.

Comment on My Personal Exome Now Publicly Released by Dan Gaston

Dan Gaston — Mon, 30 Jan 2012 14:36:41 +0000

Thanks for the info, good to know. It has turned out oddly with two or three of our projects that the most likely causal variant was found in some random exome somewhere that had just not been captured at all so it is something we now pay attention to when we get our data back.

Comment on My Personal Exome Now Publicly Released by Daniel Swan

Daniel Swan — Mon, 30 Jan 2012 13:51:20 +0000

Dan, I can’t quote exact coverage figures because I don’t know what capture kit was used, but if we assume an Agilent SureSelect 50Mb kit, then mean target coverage is >37x for Manuel according to my analysis of the data. I think there are always going to be issues with biased capture. It’s easier to get this right for more focused targeted re-sequencing where the baits can be designed for more even coverage. We find most people ask for 50x mean target coverage for rare-disease studies.

Comment on How to be a Biohacker by admin

admin — Sat, 28 Jan 2012 14:43:11 +0000

George, have a look at the Computational Biology Wikiproject in Wikipedia. There you can have some general pointers.
Manuel

Comment on How to be a Biohacker by George

George — Sat, 28 Jan 2012 08:07:13 +0000

Cool thank you. I am developer and I wanna hack with bio, that was informative but can you provide more e.g. links, tools, books anything at all. Thanks.

Comment on My Personal Exome Now Publicly Released by Pepetideo

Pepetideo — Fri, 27 Jan 2012 15:42:39 +0000

It is not a problem… I am asking this because there are a discussion about your blog post on google plus and a person commented that that by placing it in CC3.0 SA would make the data more difficult to integrate into already existing public databases because it requires that the data be provided according to the same license you selected so it would be better to have the least restrictive license. I do not know enough on the subject to have an opinion on that :)