Previously, I introduced the idea that the $1000 genome has not been achieved because it is defined in simplistic terms that ignore many aspects of data completeness and verification. In that analysis, I cited a recent perspective by Robasky, Lewis, and Church  to present concepts related to the need to verify results and the general ways in which this is done. In this and the next few posts I will dig deeper into the elements of sequence data uncertainty and discuss ... Read more
Getting an accurate genome sequence requires that you collect the data at least twice argue Robasky, Lewis, and Church in their recent opinion piece in Nat. Rev. Genetics .
The DNA sequencing world kicked off 2014 with an audacious start. Andrew Pollack ran an article in the New York Times implying that 100,000 genomes will be the new norm in human genome sequencing projects . The article focused on a collaboration between Regeneron and Geisinger Health in which they plan to sequence the exomes (the ~2% of the genome that encodes proteins and some non-coding RNA) of 100,000 individuals ... Read more
We kick off 2014 with Finchtalk’s traditional post on the annual database issue from Nucleic Acids Research (NAR). Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by NAR grew from 1512 to 1552. In the leadoff introduction  the authors summarize this year’s issue and the status of the NAR index. The 21st issue includes 185 articles with 58 new databases and 123 updates. In the 1552 database repository, 193 had their URLs corrected and 24 were removed because they were deemed obsolete. ... Read more
I've heard you have to sing loud if you want to change the world.
Cloning DNA – lyrics by Sandra Porter, sung to the tune of Surfin' USA
If everybody had a plasmid, across the U.S.A.,
then everybody'd be cloning, with their DNA
You'd see them wearing their goggles.
and their lab coats, too
multicolored gloves on, ... Read more
In simple Mendelian genetics, a single change in one gene can produce a large change in mortality. The National Human Genome Research Institute (NHGRI) will be funding genomics studies on Mendelian traits using a similar strategy.
NHGRI will fund a small number of centers, dominant centers you might say, and look for large changes. The sequencing centers that will benefit are the Broad Institute, Washington University, and Baylor College of Medicine. For the next four years, the big three will be dividing $86 million a year according to a press ... Read more
This morning I attended a "bloggers-only" conference call with Dr. Eric Green and the folks from the NIH Human Genome Research Institute (NHGRI) to hear about NHGRI's new strategic plan. The new plan represents a shift away from viewing the genome through a lens marked "for research use only" and towards the goal of making the genome useful as a clinical tool. As a consequence, we will see a greater emphasis on funding activities that support clinical work. For example, it's not always clear how variations in the genome are related to disease. NHGRI might fund projects that help sort and ... Read more
One of my hobbies lately has been to get either RNA seq or microarray data from GEO and do quick analyses. Not only is this fun, I can find good examples to use for teaching biology.
One of these fun examples comes from some Arabidopsis data. In this experiment, some poor little seedlings were taken out of their happy semi-liquid culture tubes and allowed to dry out. This simulated drought situation isn't exactly dust bowls and hollow-eyed farmers, but the plants don't know that and most likely respond in a similar way. ... Read more