Genetic Ancestry Analysis of PING Participants

Saliva samples were sent to Scripps Translational Research Institute (STRI) for analysis. Once extracted, genomic DNA was genotyped with Illumina Human660W-Quad BeadChip. Replication and quality control filters (i.e. sample call rate >99, call rates >95%, minor allele frequency >5%) were performed^{47 (link)}. To assess genetic ancestry and admixture proportions in the PING participants, a supervised clustering approach implemented in the ADMIXTURE software was used^{48 (link)}. Using this approach, a genetic ancestry factor (GAF) was developed for each participant, representing the proportion of ancestral descent for each of six major continental populations: African, Central Asian, East Asian, European, Native American and Oceanic. Implementation of ancestry and admixture proportions in the PING subjects is described in detail elsewhere^{45 (link)}. See also Akshoomoff and colleagues^{44 (link)} for a more complete description of the genetic ancestry of the PING sample.

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Noble K.G., Houston S.M., Brito N.H., Bartsch H., Kan E., Kuperman J.M., Akshoomoff N., Amaral D.G., Bloss C.S., Libiger O., Schork N.J., Murray S.S., Casey B.J., Chang L., Ernst T.M., Frazier J.A., Gruen J.R., Kennedy D.N., Zijl P.V., Mostofsky S., Kaufmann W.E., Kenet T., Dale A.M., Jernigan T.L, & Sowell E.R. (2015). Family Income, Parental Education and Brain Structure in Children and Adolescents. Nature neuroscience, 18(5), 773-778.

Publication 2015

Human660W-Quad BeadChip

African Central asian Continental populations Description East asian European Genomic Native american Replication Saliva

Corresponding Organization : Columbia University

Other organizations : University of Southern California, Robert Wood Johnson Foundation, University of California, San Diego, Institute on Aging, Children's Hospital of Los Angeles, Center for Neurologic Study, J. Craig Venter Institute

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Variable analysis

independent variables

Genetic ancestry factor (GAF) for each participant, representing the proportion of ancestral descent for each of six major continental populations: African, Central Asian, East Asian, European, Native American and Oceanic.

dependent variables

Not explicitly mentioned.

control variables

Sample call rate >99, call rates >95%, minor allele frequency >5%

controls

Positive control: Not mentioned.
Negative control: Not mentioned.

Annotations

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