Category: Personal genomics
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Free 23andMe genotyping
From OpenSNP: At the end of last year we announced that we’ve got some funding from the German WikiMedia foundation to get more people – who are willing to share their results – genotyped. We have now settled on a process that should allow us to perform the project without too many problems.Starting today, you can…
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Extraordinary mutations require extraordinary evidence
Over at Genomes Unzipped Dr. Daniel MacArthur has a review up of a paper in Science where he is first author (note for grad students and aspiring post-docs, Dr. MacArthur is starting a new lab, where he posted an ungated version of the paper). He hits all the salient points, so I will cover two…
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The Nanopore footnote?
The New York Times and Nature both have favorable reviews of Oxford Nanopore’s showy claims at Advances in Genome Biology and Technology. If you don’t know what I’m talking about, please see the twitter stream, or the post at Genomes Unzipped. A note of caution: look back at The New York Times reporting on Pacific…
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Update on the Afrikaner genotype
Since my original post on the Afrikaner genotype, I’ve gotten many responses. No genotypes yet though. At some point I need to organize how to pay for typing many individuals. Currently my intent is to pay for those who will allow their identities to be public so that people can confirm their genealogies. Other people…
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Socialized personal genomics?
Norway to bring cancer-gene tests to the clinic: Norway is set to become the first country to incorporate genome sequencing into its national health-care system. The Scandinavian nation, which has a population of 4.8 million, will use ‘next-generation’ DNA sequencers to trawl for mutations in tumours that might reveal which cancer treatments would be most…
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ChromoPainter & fineSTRUCTURE on a South Asian data set
Over at Harappa DNA Zack ran ChromoPainter/fineStructure on his South Asian data set and posted the results. The new method immediately makes a few things clear: 1) The “South Asians” in the HGDP data set that’s been used for so long are rather on the inbred side, and relatively genetically distinct as far as South Asian populations…
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Socialized medicine + personal genomics = ?
My own working assumption is that the demand side impulse toward mass adoption of human genomic technology in the USA is going to be dampened by fear of downside consequences, GINA notwithstanding. Rather, I assume that the more deregulated consumer environment in parts of Asia with very low fertility rates, as well as European states…
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Personal genomics and adoption
With DNA Testing, Suddenly They Are Family: Several companies provide tests that can confirm whether adoptees are related to individuals they already know. Others cast a wider net by plugging DNA results into databases that contain tens of thousands of genetic samples, provided mostly by people searching for their ancestral roots. The tests detect genetic…
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Genetic profiling: CSI edition
Apparently the national media is reporting that scientific genealogy may result in leads to a cold case. The principle is simple: apparently Y chromosomal material was matched to public genealogy databases. From this the researcher concluded that the perpetrator is probably a male line descendant of Robert Fuller of Salem, Massachusetts. Contrary to the urban…
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“Recreational genomics,” 4+ years on
In an exchange with Mark Shriver, I was pointed to this 2007 position paper in Science, The Science and Business of Genetic Ancestry Testing. It’s an interesting historical artifact. Much of the critique was aimed at AncestrybyDNA, but it can be generalized. Now that 23andMe has ~100,000 customers, have the things which they worried about…
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Reconstructing a generation unsampled
In the near future I will be analyzing the genotype of an individual where all four grandparents have been typed. But this got me thinking about my own situation: is there a way I could “reconstruct” my own grandparents? None of them are living. The easiest way to type them would be to obtain tissue…
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PGD:2010s::IVF:1980s
Get ready for PGD, the acronym for preimplantation genetic diagnosis. We don’t really talk about “test tube babies” anymore. It’s “IVF,” and as American as apple pie (OK, perhaps as Israeli as falafel). Here’s the Ngrams result: It’s just not that big of a deal anymore. But take a look at the order articles in The…
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23andMe controversies in the genetic genealogy community
A few readers have pointed me to controversies having to do with 23andMe’s “terms of use”. You can read about it over at Your Genetic Genealogist, who has two posts up on the issues. I think the crux is that the early enthusiasts for personal genomics in the genetic genealogy community can not support the revenue…
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Basque genetic distinctiveness (again)
With all the talk about Basques I decided to do my own analysis with Admixture. Dienekes gave me a copy of his IBS file, which has all the 1000 Genomes Spanish samples, including Basques. I merged it with the HGDP sample, which has French Basques (just “Basques” in the plots below) and French non-Basques. I…
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Would you have your fetus genetically tested?
There’s a variable in the GSS, GENESELF, which asks: Today, tests are being developed that make it possible to detect serious genetic defects before a baby is born. But so far, it is impossible either to treat or to correct most of them. If (you/your partner) were pregnant, would you want (her) to have a…
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Are you a caveman?
23andMe finally unveiled a Neanderthal Ancestry estimation feature. I’m at ~2.4 percent. What I’m curious about is the fact that out of the 45 “friends and family” who are surveyed, only two are at 3 percent. One of my them is my sibling who I found seems to have the Neandertal copy of a dystrophin…
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I pledge my full genome to the public domain
I expect to get my full genome sequenced in a few years, at the latest. When that happens, I’ll try and place it online at a public repository. Why? There’s something of a chicken and egg issue with the utility of genomes. The more you have out there, the more juice you can squeeze. I’m…
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Thoughts on the $1,000 genome, circa 2007
You’ve probably read Andrew Pollack’s DNA Sequencing Caught in Deluge of Data, by now. This section caught my eye: “The cost of sequencing a human genome — all three billion bases of DNA in a set of human chromosomes — plunged to $10,500 last July from $8.9 million in July 2007, according to the National…
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Congratulations to openSNP
For winning the API Binary Battle! The Nature News weblog has a moderately overwrought piece on the possibilities for crowd-sourcing in genetics. Interestingly they report that openSNP only has 50 genotypes. That’s lame. Though I haven’t poked around the site much since I initially loaded my data. I’ll have to spend some time this weekend…
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A consideration of Pacific Biosciences
I went to a seminar where a Pacific Biosciences representative was presenting recently. Along with others I arrived early because we thought it would be rather crowded. Not so much. Has the bubble burst? Zoom in to the last year….