Obtaining the probability that zero, one, or two alleles are shared identical by descent (IBD) is useful for many reasons in a GWAS analysis. A while back I showed you how to visualize sample relatedness using R and ggplot2, which requires IBD estimates. Using plink --genome uses IBS and allele frequencies to infer IBD.

Human Genetics / Biostatistics Associate Professor (and my first statistics teacher) Dr. Chun Li will be giving a talk Wednesday on a new measure of R² for continuous, binary, ordinal, and survival outcomes.

As I mentioned in my recap of the ASHG 1000 genomes tutorial, I'm doing to be imputing some of my own data to 1000 genomes, and I'll try to post lessons learned along the way here under the 1000 genomes and imputation tags. I'm starting from a binary pedigree format file (plink's bed/bim/fam format) and the first thing in the 1000 genomes imputation cookbook is to store your data in Merlin format, one per chromosome.

If you missed the tutorial on the 1000 genomes project data last week at ASHG, you can now watch the tutorials on youtube and download the slides online at http://genome.gov/27542240.

As this year's ASHG meeting starts to wind down be sure to check out Variable Genome where Larry Parnell is summarizing what's going on at the talks he's been to. Also see the commentary on Genetic Inference by Luke Jostins. The 1000 Genomes tutorial from Wednesday night will be made available on genome.gov soon, and the presidential address, plenary sessions, and distinguished speaker symposium talks were recorded and will also soon be online.

Seminar announcement for Vanderbilt folks: Vanderbilt-Ingram Cancer Center Quantitative Sciences Seminar Series Presents Reproducible Research in the Omics Era: A Presentation and Panel Discussion Kevin R. Coombes, PhD Deputy Chair, Bioinformatics, and Professor of Bioinformatics and Computational BiologyM.D. Anderson Cancer Center and Keith Baggerly, PhD Associate Professor, Dept.

Pacific Biosciences is hosting a reception and dinner, and is screening their film The New Biology at this year's ASHG meeting.

While writing my thesis I came across this nice review by Rita Cantor, Kenneth Lange, and Janet Sinsheimer at UCLA, "Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application." Skip the introduction unless you're new to GWAS, in which case you'll probably want to start with this more recent review by Teri Manolio.

There will be a (free) tutorial on the 1000 genomes project at this year's ASHG meeting on Wednesday, November 3, 7:00 – 9:30pm. You can register online at the link below.

I know I've been MIA for a while. My defense date is December 3, and I've still got a thesis to write! I'll try to post more soon, but in the meantime follow me on Twitter for things that won't make it into a full blog post. For those at Vanderbilt and the surrounding environs: I saw this announcement for the next cancer biostatistics workshop that looked interesting.

About a year ago I reiterated a point made nicely in a Nature Reviews Genetics article, that there is no such thing as a common disorder - only extremes of quantitative traits. Such is the theme of this year's Annual Vanderbilt Genetics Symposium, "Beyond Disease Dichotomy - Quantitative Traits and Intermediate Phenotypes." This is a day-long event held at the Vanderbilt Student Life Center on Wednesday October 13, 8am-4pm.