Question: Dealing With Population Stratification In Gwas
1
gravatar for Nasir
7.4 years ago by
Nasir180
United Kingdom
Nasir180 wrote:

My question is a bit 'general' and I would be very grateful for any advice. I have data from a GWAS on unrelated Western European patients with a sporadic disease. Is these a 'gold standard' way of dealing with population stratification/substructure/ancestry in the GWAS QC/analysis? If not, there a leading or widely used and accepted way of dealing with this? The way I have done this in the past is to use eigensoft/smartpca to build a principal component model using HapMap genotype data from Europe (CEU), Asia (CHB + JPT) and Africa (YRI), then clustering my samples alongside the HapMap samples and excluding outliers 'by eye'. I'm sure there will be better approaches available. Could people please suggest any approaches. If someone could direct me to an online step-by-step tutorial, if available, that would be much appreciated!

Nasir

pca • 3.8k views
ADD COMMENTlink written 7.4 years ago by Nasir180
1

You should try STRUCTURE (http://pritch.bsd.uchicago.edu/structure.html). I prefer their graphical output and you get an output file with the percentage of each ancestral population for each individual.

ADD REPLYlink written 7.4 years ago by Maxime Lamontagne2.1k
1

Yes, we used STRUCTURE for our analysis of a Puerto Rican population.

ADD REPLYlink written 7.4 years ago by Larry_Parnell16k
2
gravatar for 1234Jc4321
7.4 years ago by
1234Jc4321420
Quebec City
1234Jc4321420 wrote:

check out this post: http://www.biostars.org/post/show/16715/software-for-inferring-population-structure/#39037

ADD COMMENTlink written 7.4 years ago by 1234Jc4321420
2
gravatar for Larry_Parnell
7.4 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

I'd look at the panel of ancestry informative markers used by Seldin, particularly the last in the list here:

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels. Nassir R, Kosoy R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF. BMC Genet. 2009 Jul 24;10:39. PMID: 19630973

Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF. Hum Mutat. 2009 Jan;30(1):69-78. PMID: 18683858

A genomewide single-nucleotide-polymorphism panel for Mexican American admixture mapping. Tian C, Hinds DA, Shigeta R, Adler SG, Lee A, Pahl MV, Silva G, Belmont JW, Hanson RL, Knowler WC, Gregersen PK, Ballinger DG, Seldin MF. Am J Hum Genet. 2007 Jun;80(6):1014-23. PMID: 17557415

European population substructure: clustering of northern and southern populations. Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, Silva G, Belmont JW, Klareskog L, Gregersen PK. PLoS Genet. 2006 Sep 15;2(9):e143. Epub 2006 Jul 25. PMID: 17044734

ADD COMMENTlink written 7.4 years ago by Larry_Parnell16k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2234 users visited in the last hour