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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

Comparison of Principal Component Analysis Excluding Different Individual GroupsColor key shows groups as defined in Figure 1.(A) All individuals with 4GP information.(B) Same individual set except exclusion of individuals of Irish descent.(C) Same individual set with exclusion of Ashkenazi Jewish individuals.
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pgen-0040004-g002: Comparison of Principal Component Analysis Excluding Different Individual GroupsColor key shows groups as defined in Figure 1.(A) All individuals with 4GP information.(B) Same individual set except exclusion of individuals of Irish descent.(C) Same individual set with exclusion of Ashkenazi Jewish individuals.

Mentions: We also explored whether the PCA was affected by either inclusion or exclusion of specific population groups or the number of individuals in different population groups. Most prominently, a major difference in the relationships among the populations for the second PC was observed when either Ashkenazi Jewish individuals or Irish individuals were excluded (Figure 2). These results suggest some caution in interpretation of specific clines and particular relationships among different European groups (see discussion).


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)

Comparison of Principal Component Analysis Excluding Different Individual GroupsColor key shows groups as defined in Figure 1.(A) All individuals with 4GP information.(B) Same individual set except exclusion of individuals of Irish descent.(C) Same individual set with exclusion of Ashkenazi Jewish individuals.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0040004-g002: Comparison of Principal Component Analysis Excluding Different Individual GroupsColor key shows groups as defined in Figure 1.(A) All individuals with 4GP information.(B) Same individual set except exclusion of individuals of Irish descent.(C) Same individual set with exclusion of Ashkenazi Jewish individuals.
Mentions: We also explored whether the PCA was affected by either inclusion or exclusion of specific population groups or the number of individuals in different population groups. Most prominently, a major difference in the relationships among the populations for the second PC was observed when either Ashkenazi Jewish individuals or Irish individuals were excluded (Figure 2). These results suggest some caution in interpretation of specific clines and particular relationships among different European groups (see discussion).

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