There is a particular type of variation that genotype chips can never get at, the type of variation that most people will find most interesting: variation that is unique to you, or to your family. If you get sequenced now, about 200,000 single-base variants in your genome will never have been seen before, ever. These are likely to include changes that modify proteins in a unique way, that may make them act differently in your cells. A big proportion of indels and structural variants will be novel, and these can include strange and exotic things: genes that have been swapped around, jumbled up, fused together, or deleted entirely. There may well be stretches of DNA, hundreds of base pairs long or longer, that have never been observed in another human. Regardless of how "useful" these personal oddities are, to be able to look directly at new genomic discoveries that live inside you makes them invaluable.Read the rest here.
Genetic Future
Commentary on human genetics and evolution, direct-to-consumer genetic testing, and the personal genomics industry.
Search
Profile
Daniel MacArthur
I write about the genetic and evolutionary basis of human variation, and the companies trying to sell you information about your genome.
Daniel also blogs about personal genomics at Genomes Unzipped.
Subscribe via RSS.
Follow me on Twitter.
Recent Posts
- Genetic Future is moving
- One more step towards the end of recessive diseases
- New FireFox plugin for 23andMe customers
- Why you CAN have your $1000 genome - so long as you learn what to do with it
- Bioscience Resource Project critique of modern genomics: a missed opportunity
- Genomes Unzipped reader survey
- News from 23andMe: a bigger chip, a new subscription model and another discount drive
- Why I'm releasing my genetic data online
- Oddities of the odds ratio
- Genetic Future is moving to Wired
Recent Comments
- Dan Frost on Genetic Future is moving
- Neil on One more step towards the end of recessive diseases
- Daniel MacArthur on One more step towards the end of recessive diseases
- Neil on One more step towards the end of recessive diseases
- Daniel MacArthur on One more step towards the end of recessive diseases
- Moreno on One more step towards the end of recessive diseases
- Bob on One more step towards the end of recessive diseases
- Neil on One more step towards the end of recessive diseases
- Jonathan on One more step towards the end of recessive diseases
- Daniel MacArthur on One more step towards the end of recessive diseases
Archives
- January 2011
- December 2010
- November 2010
- October 2010
- September 2010
- August 2010
- July 2010
- June 2010
- May 2010
- April 2010
- March 2010
- February 2010
- January 2010
- December 2009
- November 2009
- October 2009
- September 2009
- August 2009
- July 2009
- June 2009
- May 2009
- April 2009
- March 2009
- February 2009
- January 2009
- December 2008
- November 2008
- October 2008
- September 2008
- August 2008
Blogs I read:
Consumer Genomics:
Genomic Science:
- Anthony Fejes
- David Dooling
- Dan Koboldt
- Luke Jostins
- Pathogenomics
- Jan Aerts
- Popgen Ramblings
- Adaptive Complexity
- Genomicron
Genetics/Evolution Blogs:
- Razib Khan
- John Hawks
- Gene Expression
- Eye on DNA
- Dienekes
- Yann Klimentidis
- European Genetics
- Discovering Biology in a Digital World
- The Genetic Genealogist
- business|bytes|genes|molecules
- Thomas Mailund
- John Halamka
General Science:
Corporate Blogs:
Skeptics:
« Announcing Genomes Unzipped, a new group blog on personal genomics | Main | How to interpret a genome-wide association study »
Why sequencing matters for personal genomics
Category: genomes unzipped • next-generation sequencing • personal genomics
Posted on: July 13, 2010 10:30 AM, by Daniel MacArthur
The first ever post on the new group blog I announced yesterday, Genomes Unzipped, is now live: it's Luke Jostins of Genetic Inference talking about the importance of sequencing for the future of personal genomics. Here's a taste:
Find more posts in: 
Life Science
Medicine & Health
Life ScienceMedicine & Health
Comments
Luke Jostins should note that the extremely low prior probabilities associated with true de novo variants make them very challenging to actually identify. At least with familial variants you have other individuals in the family tree which you can check against. But right now it's pretty hard to distinguish true de novos from sequencing error without a lot of confirmatory followup.
Posted by: asdf | July 18, 2010 5:04 AM
@asdf
That depends on what you mean by "identifying de novo mutations". The case I am talking about is more "identifying novel variants", i.e. finding mutations that have not been seen before in anyone else; with 30X of 2x100+bp read length this isn't that difficult. Yes, you can have an elevated FP rate, due to having a lower prior, but this can be overcome (at the expense of sensativity) using appropriate quality thresholds.
I expect what you are thinking about is identifying variants as de novo mutations from trio sequence - i.e. looking for all mutations that have arisen between the parents and the child. This is indeed difficult, but still not impossible, and with very up-to-date next gen stuff is very much possible.
Posted by: Luke | July 18, 2010 10:37 AM