Genomewide Association
razib | March 2, 2010As you know lactase persistence (LP), which confers the ability to digest lactose sugar as an adult, is an evolutionarily recent development. On the order of 1/3 of the human population exhibits LP, due to a variety of genetic mutations which seem to arise in the cultural background of the domestication of cattle. Some have asked about the possible associations between LP & height & weight before. A new paper in Human Molecular Genetics looks at just that, European lactase persistence genotype shows evidence of association with increase in body mass index:
The global prevalence of…
razib | February 11, 2010Genome-Wide Association Study in Asian Populations Identifies Variants in ETS1 and WDFY4 Associated with Systemic Lupus Erythematosus:
In this study, we first conducted a genome-wide association study in a Hong Kong Chinese population, followed by replication in three other cohorts from Mainland China and a cohort from Thailand, which totaled 3,300 Asian patients and 4,200 ethnically and geographically matched controls. We identified novel variants in ETS1 and WDFY4 associated with SLE with genome-wide significance and confirmed the association of HLA locus, STAT4, BLK, IRF5, BANK1, TNFSF,…
razib | February 1, 2010Could be the title of the paper. Anyway, Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex:
...Incidences of specific diseases are elevated in different breeds, indicating that a few genetic risk factors might have accumulated through drift or selective breeding. In this study, a GWA study with 81 affected dogs (cases) and 57 controls from the Nova Scotia duck tolling retriever breed identified five loci associated with a canine systemic lupus erythematosus (SLE)-related disease complex that includes both antinuclear antibody (ANA)-positive…
razib | January 26, 2010Update: Also see p-ter at Gene Expression Classic.
Follow up on yesterday's post on the new Dickson et al. paper from David Goldstein's lab, A New Way to Look for Diseases' Genetic Roots:
The Icelandic gene-hunting firm deCODE genetics, which emerged last week from bankruptcy, has long led in detecting SNPs associated with common disease. Dr. Kari Stefansson, the company's founder and research director, agreed that whole genome sequencing would "give us a lot of extremely exciting data." But he disputed Dr. Goldstein's view that rare variants carried most of the missing heritability. Both…
razib | January 25, 2010David Goldstein, a geneticist at Duke, has critiqued the current focus on large-scale genomwide associations before. Now he is taking to the next step, as his group has a paper out which suggests that the reason that association studies have been relatively unfruitful in terms of bang-for-buck is due to the fact that they're picking up "synthetic associations." Rare Variants Create Synthetic Genome-Wide Associations:
It has long been assumed that common genetic variants of modest effect make an important contribution to common human diseases, such as most forms of cardiovascular disease,…
razib | May 18, 2009There are several papers and letters in Nature Genetics on the relationship between menarche, menopause, etc. and genetics.
Meta-analysis of genome-wide association data identifies two loci influencing age at menarche:
We conducted a meta-analysis of genome-wide association data to detect genes influencing age at menarche in 17,510 women. The strongest signal was at 9q31.2 (P = 1.7 10-9), where the nearest genes include TMEM38B, FKTN, FSD1L, TAL2 and ZNF462. The next best signal was near the LIN28B gene (rs7759938; P = 7.0 10-9), which also influences adult height. We provide the first…
razib | April 28, 2009Dan MacArthur has a post, Genetics of complex traits in Europeans and East Asians: similarities and differences:
With those goals in mind, you can expect to see many more GWAS of non-European populations over the next couple of years, and some explicit comparisons of the differing genetic architecture of complex traits between populations. Exciting times for those of us interested in the genetic and evolutionary basis of between-population differences...
This reminds me of A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction:…
razib | April 17, 2009A much more thorough post by Dan MacArthur on the recent issue of the New England Journal of Medicine & genomics.
razib | April 16, 2009The New England Journal of Medicine has a series of articles up on the impact of new genomic techniques on medicine, specifically in the domain of pinpointing genetic markers which are correlated with increased risk of a particular disease. David Goldstein has a skeptical take up on the future returns of genomewide association studies, while Joel Hirschhorn is more hopeful. There is another review which takes a middle path, emphasizing the relatively marginal predictive power of many of the risk alleles, but suggesting that techniques and results are bound to improve.
Probably the most…