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Analysis and application of European genetic substructure using 300 K SNP information.

Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, Selmi C, Klareskog L, Pulver AE, Qi L, Gregersen PK, Seldin MF - PLoS Genet. (2008)

Bottom Line: A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations.In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information.The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.

View Article: PubMed Central - PubMed

Affiliation: Rowe Program in Human Genetics, University of California Davis, Davis, California, United States of America.

ABSTRACT
European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.

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Related in: MedlinePlus

Graphic Display of Principal Components 3 and 4 after Deletion of Chromosome 8 InversionResults of individuals with 4GP information are shown.
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Related In: Results  -  Collection


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pgen-0040004-g006: Graphic Display of Principal Components 3 and 4 after Deletion of Chromosome 8 InversionResults of individuals with 4GP information are shown.

Mentions: To further explore European substructure we examined additional PCs in the initial all European participant set after excluding the SNPs within the Chromosome 8 inversion. The distribution of individuals in the first two vectors in the entire group did not change. However, the third vector now showed clusters corresponding to population affiliation (Figure 6). However, this PC accounts for only very small amount of the population variation within our different sample sets (see Table 1). Although PC4 showed marginal evidence for clustering by the ANOVA test there was little apparent correlation with self-identified ancestry. Additional PCs did not show evidence for substructure by ANOVA, or a significant split half reliability test.


Analysis and application of European genetic substructure using 300 K SNP information.

Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, Selmi C, Klareskog L, Pulver AE, Qi L, Gregersen PK, Seldin MF - PLoS Genet. (2008)

Graphic Display of Principal Components 3 and 4 after Deletion of Chromosome 8 InversionResults of individuals with 4GP information are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2211544&req=5

pgen-0040004-g006: Graphic Display of Principal Components 3 and 4 after Deletion of Chromosome 8 InversionResults of individuals with 4GP information are shown.
Mentions: To further explore European substructure we examined additional PCs in the initial all European participant set after excluding the SNPs within the Chromosome 8 inversion. The distribution of individuals in the first two vectors in the entire group did not change. However, the third vector now showed clusters corresponding to population affiliation (Figure 6). However, this PC accounts for only very small amount of the population variation within our different sample sets (see Table 1). Although PC4 showed marginal evidence for clustering by the ANOVA test there was little apparent correlation with self-identified ancestry. Additional PCs did not show evidence for substructure by ANOVA, or a significant split half reliability test.

Bottom Line: A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations.In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information.The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.

View Article: PubMed Central - PubMed

Affiliation: Rowe Program in Human Genetics, University of California Davis, Davis, California, United States of America.

ABSTRACT
European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.

Show MeSH
Related in: MedlinePlus