So You Just Got Your Genome Sequenced...
January 29, 2018 9:17 PM Subscribe
I downloaded my DNA from ancestry.com as a 17.3MB .txt file.* I want to run the data through other engines and see what I find. What's accurate? What's secure? What's informative or educational? What's free?
*The raw data looks something like this:
*The raw data looks something like this:
rsID chromosome position allele1 allele2 rs4477212 1 72017 A A rs3094315 1 742429 A A rs3131972 1 742584 G G rs12124819 1 766409 G GI am running High Sierra and Win10.
Best answer: DNALand is free, with a focus on ancestry. Promethease isn't free, but it's not expensive, with a focus on health.
posted by holgate at 9:34 PM on January 29, 2018 [2 favorites]
posted by holgate at 9:34 PM on January 29, 2018 [2 favorites]
Best answer: The Genetic Geologist has a pretty extensive list of apps that let you get the maximum information from your results.
DNA Geek offers a summary of some of the other sites that you can transfer your records, most useful if you are looking to find other people with related DNA.
posted by metahawk at 9:52 PM on January 29, 2018
DNA Geek offers a summary of some of the other sites that you can transfer your records, most useful if you are looking to find other people with related DNA.
posted by metahawk at 9:52 PM on January 29, 2018
Best answer: I have had my genetic information analyzed for drug interactions, and while it has proven novel, and slightly interesting there have been plenty of inaccuracies with it. The technology is still quite in its infancy though.
This, a million times. Please take any "DNA info" with this HUGE GRAIN OF SALT.
posted by kuanes at 4:46 AM on January 30, 2018 [6 favorites]
This, a million times. Please take any "DNA info" with this HUGE GRAIN OF SALT.
posted by kuanes at 4:46 AM on January 30, 2018 [6 favorites]
Best answer: Gedmatch.com is free and has great Facebook groups and bloggers writing about it.
posted by jgirl at 6:39 AM on January 30, 2018 [1 favorite]
posted by jgirl at 6:39 AM on January 30, 2018 [1 favorite]
Response by poster: Please take any "DNA info" with this HUGE GRAIN OF SALT.
A huge cubic crystal of pure NaCl, thanks. But, am I right in assuming that, since it's my DNA fingerprint in a file, it's not likely to morph—the text file would be applicable/valid five, ten, twenty years from now, when the accuracy of the technology advances?
posted by not_on_display at 5:37 PM on January 30, 2018
A huge cubic crystal of pure NaCl, thanks. But, am I right in assuming that, since it's my DNA fingerprint in a file, it's not likely to morph—the text file would be applicable/valid five, ten, twenty years from now, when the accuracy of the technology advances?
posted by not_on_display at 5:37 PM on January 30, 2018
Some quick notes:
1) You didn't actually get your genome sequenced at ancestry. You got a handful of positions (probably 500k) in your DNA genotyped on a SNP array. This is an important distinction, as it's a much smaller pool of information that you're working with. That said, at all but the level of hardcore genome scientist, there's probably no appreciable difference in terms of the interpretations that you can receive at this point in time.
2) You're right - the genotypes at those positions will not change! However as technology improves and more people get actual sequences done (exomes or whole genomes), you'll find that there is more "missing" information in your file. Some of it can be imputed, but for lots of it, you'll just have no information from this test. (great layman's introduction to imputation here: https://dna.land/impute-info) Using your example, positions 1: 72017 and 1:742429 were genotyped, but what about the 670k bases in between?
3) Promethease is probably your best bet. For 10 bucks, you get some nice interpretations in a decent interface. It's worth it, if you're curious, but do not expect any, y'know, actually actionable information. :)
posted by chrisamiller at 9:15 PM on January 30, 2018 [4 favorites]
1) You didn't actually get your genome sequenced at ancestry. You got a handful of positions (probably 500k) in your DNA genotyped on a SNP array. This is an important distinction, as it's a much smaller pool of information that you're working with. That said, at all but the level of hardcore genome scientist, there's probably no appreciable difference in terms of the interpretations that you can receive at this point in time.
2) You're right - the genotypes at those positions will not change! However as technology improves and more people get actual sequences done (exomes or whole genomes), you'll find that there is more "missing" information in your file. Some of it can be imputed, but for lots of it, you'll just have no information from this test. (great layman's introduction to imputation here: https://dna.land/impute-info) Using your example, positions 1: 72017 and 1:742429 were genotyped, but what about the 670k bases in between?
3) Promethease is probably your best bet. For 10 bucks, you get some nice interpretations in a decent interface. It's worth it, if you're curious, but do not expect any, y'know, actually actionable information. :)
posted by chrisamiller at 9:15 PM on January 30, 2018 [4 favorites]
Response by poster: Thanks, ↑chrisamiller (and everyone) thanks for the reminders that none of the info is "actionable". But, as far as bits of the sequence to take with my grains of salt, which kinds of predictions/attributes would you say need the least salt? Like if I saw XYZ was likely, could I tell my doc, hey, look at my XYZ genes, what would you say?
Would they also prescribe salt?
posted by not_on_display at 5:25 PM on January 31, 2018
Would they also prescribe salt?
posted by not_on_display at 5:25 PM on January 31, 2018
Promethease will give you a magnitude for each SNP, indicating how serious it may be. Just be aware that the vast majority of the SNPs from direct-to-consumer tests are NOT validated.
I ran my 23andMe data through Promethease in December, and it flagged a SNP that is pathogenic for a very serious hereditary cancer syndrome (magnitude was 5.8 on Promethease). I spent about 6 weeks panicking, messaged my doctor about it (no response), and ended up paying another $200 for the Hereditary Cancer Test through Color Genomics, which actually sequences 30 genes. It identified no mutations, meaning the 23andMe data had a false positive.
We're talking GIANT grains of salt. Maybe even salt mines.
posted by fluffymag at 8:55 AM on February 2, 2018 [3 favorites]
I ran my 23andMe data through Promethease in December, and it flagged a SNP that is pathogenic for a very serious hereditary cancer syndrome (magnitude was 5.8 on Promethease). I spent about 6 weeks panicking, messaged my doctor about it (no response), and ended up paying another $200 for the Hereditary Cancer Test through Color Genomics, which actually sequences 30 genes. It identified no mutations, meaning the 23andMe data had a false positive.
We're talking GIANT grains of salt. Maybe even salt mines.
posted by fluffymag at 8:55 AM on February 2, 2018 [3 favorites]
Perfect timing -- I just got my data (via the FaceBook "Genes For Good" project) this week!
posted by wenestvedt at 11:12 AM on February 9, 2018 [1 favorite]
posted by wenestvedt at 11:12 AM on February 9, 2018 [1 favorite]
This thread is closed to new comments.
I have had my genetic information analyzed for drug interactions, and while it has proven novel, and slightly interesting there have been plenty of inaccuracies with it. The technology is still quite in its infancy though. The only really useful bit is being able to prove to my dentist that my body processes novocaine faster than average, and to re-up me during procedures.
posted by furnace.heart at 9:28 PM on January 29, 2018