CAPS (Combined Analysis of Psychiatric Studies)

Schizophrenia New SNP Genotypes

Results are from the following paper:

Vieland VJ, Walters KA, Azaro M, Brzustowicz LM, Lehner T. The value of regenotyping older linkage data sets with denser marker panels. Hum Hered. 2014;78:9-16.

Linkage analysis can help determine regions of interest in whole genome sequence studies. However, many linkage studies rely on older microsatellite (MSAT) panels. We set out to determine whether results would change if we regenotyped families using a dense map of SNPs. Because our genotyping budget was limited, we chose a single set of families for this study, in part based on a phenotype of particular interest. Specifically, we focus on the Hispanic American SZ sample originally collected by Escamilla and colleagues in 2003 and 2005 as reported in [1, 2], and the complete subset of families (n=47) from this data set that had at least one case of strictly defined SZ as well as at least one case of schizophrenia with a strong affective component.

In the process of combining the new SNPs with the older MSAT data, we also explored alternative ways to select subsets of SNPs to include in the map in order to maximize information content while minimizing marker-to-marker LD.

  1. Escamilla, M.A., et al., A genome-wide scan for schizophrenia and psychosis susceptibility loci in families of Mexican and Central American ancestry. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 2007. 144B(2): p. 193-9.
  2. Escamilla, M., et al., A schizophrenia gene locus on chromosome 17q21 in a new set of families of Mexican and central american ancestry: evidence from the NIMH Genetics of schizophrenia in latino populations study. The American journal of psychiatry, 2009. 166(4): p. 442-9.
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