--- Log opened Sun Jul 09 00:00:44 2017
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01:06 < justanotheruser> https://blogs.fda.gov/fdavoice/index.php/2017/06/fda-working-to-lift-barriers-to-generic-drug-competition/
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03:22 < chris_99> Hi, i'm just wondering does anyone have any opinion on the dna testing services, that give ancestor info, does that work reasonably well? or if there are any papers relating to how they do it, a friend was curious about getting it done
03:33 < chris_99> also are there any full genome sequencing services out of interest, i guess that is a _lot_ dearer if there is
03:35 < abetusk> chris_99, I've used 23andMe and they successfully identified my mother and father.  I've used Ancestry but I don't know the efficacy wrt ancestry identification.  Veritas offers sub $1k whole genome sequencing services: https://www.veritasgenetics.com/mygenome.  Here's a list by George Church for a listing of sequencing services: http://arep.med.harvard.edu/gmc/genome_services.html
03:36 < abetusk> Genomix is listed as $200 30x whole genome but I think that service is pretty much vaporware at this point
03:36 < chris_99> oh cheers abetusk, sub $1 is better than i thought
03:36 < abetusk> $1k
03:36 < chris_99> ah
03:36 < chris_99> the ancestory is one i was looking at, as it's only ?80 compared to ?140 for 23andme
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03:36 < chris_99> did you compare 23andme to ancestory for differences in the ancestor stuff?
03:37 < abetusk> I think they're comparible.  I did a concordance between my father and mother's 23andme with my ancestry and it was high...presumably you could do the same concordance with the ancestry data
03:37 < abetusk> oh...sorry.  My genome is public but my folks aren't so I guess you can't do that test
03:37 < chris_99> gotcha
03:38 < abetusk> opensnp has a large pool. Maybe you get lucky and find a parent/child pair in there that has Ancestry
03:38 < chris_99> i guess the main difference between 23andme and ancestry, is that 23andme also look for potential diseases you'd be susceptable to right?
03:38 < abetusk> I haven't looked at 23andMe vs. Ancestry...you're welcome to look at mine (or others).  If you really want to know I could probably do something 'back of the envelope' quickly
03:39 < abetusk> 23andMe provides a genome report which Ancestry (afaik) doesn't.
03:39 < chris_99> but the genome report, would only be useful if you wanted to know disease info would it, or is it good for other stuff too?
03:39 < abetusk> but from what I understand the 'raw data' (the genotyping file) is similar.  For all I know they could be using the same sequencing service underneath
03:40 < abetusk> "more like to metabolize caffeine", "more  likely to be a sprinter"
03:40 < chris_99> oh gotcha
03:40 < abetusk> if you want "genome reports" there are a few open source options floating around out there
03:40 < chris_99> is it possible to see sample data for either 23andme or ancestry or is that not public data
03:40 < abetusk> OpenHumans I think even has a service that lets you link 23andMe/Ancestry data.
03:40 < chris_99> oh neat
03:42 < abetusk> yes: https://opensnp.org/, https://www.openhumans.org/members/, https://my.pgp-hms.org/public_genetic_data
03:42 < chris_99> cheers, i'll have a look, thanks!
03:42 < chris_99> also one other thing with https://www.veritasgenetics.com/mygenome you get the raw data right?
03:42 < abetusk> I think they provide a BAM and VCF
03:42 < abetusk> if you want something more complicated you'll have to assemble the BAM yourself
03:43 < chris_99> in laymans terms what's bam/vcf, i need to do a lot more reading
03:45 < abetusk> Short answer, BAM is a close approximation of what 'comes off the machine'...short fragment reads in a big pile.  One needs to reassemble the fragments into a contiguous sequence.  Doing a big long contiguous sequence of a's, c's, t's' and g's is inefficient so a "diff" file was created to store only the difference from some reference (nowadays something called 'hg19').
03:45 < abetusk> Raw ascii sequence compressed gives just under a 1Gb or two.  VCF is about 100Mb compressed or so.
03:46 < chris_99> oh neat, thanks a lot, that's very interesting, in how it's a diff
03:47 < abetusk> https://bioinformatics.stackexchange.com/questions/1/whats-the-most-efficient-format-to-store-dna-sequence
03:48 < chris_99> thanks i'll have a look through those and at the open data
03:48 < abetusk> you should also feel free to ask questions there for this type of 'getting started in genomics' questions.  I think a lot of people have the same questions as you.  There's also biostars.org but that's a bit more specialized now I guess.
03:48 < abetusk> I'm also happy to go more in depth into anything that I have knowledge of.
03:49 < chris_99> cool thanks :) i wont pester you for a bit now, i'll go through all the links you mentioned
03:50 < chris_99> $1k seems fairly affordable too, its better than i thought it'd be for a full sequence
03:50 < abetusk> It was $5k about 3 years ago.  I imagine it'll go down quickly
03:51 < chris_99> neat
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05:25 < kanzure> for veritas you have to request the data, it's an additional $100 on top of their price.
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05:31 < kanzure> "In September, Quake was named co-president of the Chan Zuckerberg BioHub, a new $600 million center funded by Silicon Valley's couple-in-chief. The BioHub's premier project is the Human Cell Atlas, made possible by inventions (from Quake and others) that let scientists study individual cells on chips."
05:31 < kanzure> zuck put stephen quake in charge? cool.
05:32 < kanzure> from https://www.wired.com/story/biologys-roiling-debate-over-publishing-preprint-research-early/
05:33 < abetusk> https://veritasgene.zendesk.com/hc/en-us/articles/230145447-Can-I-get-my-raw-data-
05:34 < kanzure> "Church confirmed the donation to MIT Technology Review, saying that Thiel told him he wanted to fund the "craziest thing" he was doing."
05:34 < abetusk> too bad there's no big initiative to fund a large pool of public genomes
05:35 < abetusk> $10M would get 10k genomes presumably
05:35 < kanzure> the 1000genome project wasn't big eough for you? :P
05:35 < abetusk> no
05:35 < abetusk> also no phenotypic data...or at least not much
05:41 < kanzure> .title https://news.ycombinator.com/item?id=14728226
05:41 < yoleaux> Verdi - Formally Verifying Distributed Systems (2016) | Hacker News
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06:22 < streety> the wired article kanzure posted mentioned https://www.nature.com/nature/journal/v536/n7616/full/nature19057.html
06:22 < streety> "Analysis of protein-coding genetic variation in 60,706 humans"
06:23 < streety> http://exac.broadinstitute.org/
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06:49 < chris_99> oh cheers kanzure just saw your message wrt veritas
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11:54 < kanzure> https://github.com/subzerocloud/pg-amqp-bridge
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--- Log closed Mon Jul 10 00:00:45 2017