Archive for the ‘Seq and Ye Shall Find’
We are going to start hearing stories about people getting their entire genome sequenced. What might these stories miss?
One thing that they might do, is try to interpret the data the same way they did for companies like 23andMe and focus on common variants.
The real story is in the rare alleles. One in ten of us are very affected by these, and the sequencing tests reveal them as long as we are looking for them. Almost all common diseases have a rare allele component to [them]. What happened before is that we went through a fad. Scientists were looking where the light was in the common variants and they mostly ignored rare alleles.
(Hat tip: @DivaBiotech)
On April 24th and 25th in Cambridge, MA, the Boston Open Source Science Lab will be amplifying and sequencing genes for anyone with 40 bucks.
Together, we’ll use the polymerase chain reaction (PCR) to amplify a fragment of one of your genes and have the DNA sequenced. The event will be part of the Cambridge Science Festival and will run from 12 - 4 pm on April 24th and 25th.
I will provide primers that will enable us to amplify sections of several popular genes. If you have a particular gene of interest, please get in touch…
That sound you hear is hundreds of clinical geneticists’ panties getting in a wad. And maybe a few IP lawyers, too…
See you there, you DIY rascals you!
The GET Conference 2010 marks the last chance in history to collect everyone with a personal genome sequence on the same stage to share their experiences and discuss the important ways in which personal genomes will affect all of our lives in the coming years.
Tickets are pricey. This is a (long overdue, IMHO) fundraiser for PersonalGenomes.org:
We foresee a day when many individuals will want to get their own genome sequenced so that they may use this information to understand such things as their individual risk profiles for disease, their physical and biological characteristics, and their personal ancestries. To get to this point will require a critical mass of interested users, tools for obtaining and interpreting genome information, and supportive policy, research, and service communities.
ScienceDaily (Feb. 12, 2010) — Just because you don’t swallow the worm at the bottom of a bottle of mescal doesn’t mean you have avoided the essential worminess of the potent Mexican liquor, according to scientists from the Biodiversity Institute of Ontario (BIO) at the University of Guelph.
They have discovered that the liquid itself contains the DNA of the agave butterfly caterpillar — the famously tasty mescal “worm.”
“Showing that the DNA of a preserved specimen can be extracted from the preservative liquid introduces a range of important possibilities,” said Dr. Mehrdad Hajibaebi, a member of the research team. “We can develop inexpensive, high-throughput and non-invasive genetic analysis protocols for situations where the original tissue cannot be touched or when there is simply no sample left for analysis.”
In case you missed it:
The average sequencing consumables cost for these
three genomes was under $4,400 (table S5). The raw base and
variant call accuracy achieved compares favorably with other
reported human genome sequences (2–12).
FWIW, Quake, co-founder of Helicos, interpreted his sequence using Trait-o-matic, an open-source app developed in the Church lab that I and the rest of the PGP-10 are using to interrogate our genomes and about which I expect to have more to say in the near future.
Reid also took issue with the idea that CGI is a services business. “It’s not a services business — you can’t call us up and ask for services – we have a data business. This business is enabled by a dramatic new development in this industry. There is finally, for the first time, one organism, one type of data that can be produced in a standardized mechanism — it’s called a human genome.”
Reid draws a strong analogy to Google. “Google has one type of data called web documents, and produces one type of report called sorted list of documents, based on your query. We’re doing that for genomic data, taking the one type of data – the human genome — building a huge Google-like proprietary back end, that can take one input – human DNA – and produce one standardized output, a human genome report, a sorted list of variants. That is all about economies of scale.”