Preprocessing HapMap Phase 3 Genotypes

The HapMap phase 3 dataset consists of 1184 human individuals across 11 populations (ASW: African ancestry in Southwest USA; CEU: Utah residents with Northern and Western European ancestry from the CEPH collection; CHB: Han Chinese in Beijing, China; CHD: Chinese in Metropolitan Denver, Colorado; GIH: Gujarati Indians in Houston, Texas; JPT: Japanese in Tokyo, Japan; LWK: Luhya in Webuye, Kenya; MEX: Mexican ancestry in Los Angeles, California; MKK: Maasai in Kinyawa, Kenya; TSI: Toscani in Italia; YRI: Yoruba in Ibadan, Nigeria) assayed for 1,440,616 SNPs [6] (link). We performed QC on the data, including removal of SNPs with MAF , missingness , and deviation from Hardy-Weinberg equilibrium . We removed non-founders and individuals with genotyping missingness , leaving 957 individuals. Next, we removed several regions of high LD and/or known inversions (chr5∶44 Mb–51.5 Mb, chr6∶25 Mb–33.5 Mb, chr8∶8 Mb–12 Mb, chr11∶45 Mb–57 Mb) [15] (link). Finally, we used PLINK [16] (link) –indep-pairwise 1000 10 0.02 to thin the SNPs by LD ( ), leaving 14,389 SNPs.

Free full text: Click here

Abraham G, & Inouye M. (2014). Fast Principal Component Analysis of Large-Scale Genome-Wide Data. PLoS ONE, 9(4), e93766.

Publication 2014

African ancestry Chinese European Hapmap Human Inversions Japanese Populations Snps

Corresponding Organization : University of Melbourne

Top 5 similar protocols

Protocol cited in 70 other protocols

Variable analysis

independent variables

Population

dependent variables

Genotype (SNPs)

control variables

Minor Allele Frequency (MAF) > 0.01
Missingness < 0.05
Hardy-Weinberg Equilibrium p-value > 0.001
Individuals with genotyping missingness < 0.05
Regions of high LD and/or known inversions (chr5: 44 Mb–51.5 Mb, chr6: 25 Mb–33.5 Mb, chr8: 8 Mb–12 Mb, chr11: 45 Mb–57 Mb)
Thinning of SNPs by LD (r^2 < 0.02)

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!