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Genome Scan Meta-Analysis

GSMA is a rank-based method to perform meta-analysis of genome-wide linkage studies. The genome is divided into equal length bins (eg 30cM). For each study, the maximum evidence for linkage within each bin is assessed, and then the bins ranked according to this information for linkage. For each bin, the ranks across studies are summed, and this summed rank forms the statistic to test for evidence of linkage within the bin. Significance is assessed using a distribution function (Wise et al, 1999), or by simulation (Levinson et al, 2003).

GSMA can be used to:

  • confirm linkage for a region which arises in most scans
  • identify novel linked regions, which are not significant in any single scan, but show some evidence of linkage in many scans
  • prioritise regions of linkage for further study

Software for performing GSMA is now available.
(Pardi F, Levinson DF, Lewis CM: GSMA: software implementation of the genome search meta-analysis method. /Bioinformatics/ 2005; *21:* 4430-4431.)

Executables are available for Sun, Windows and OSX and may be downloaded from the link in the menu.

Further information

Please contact Prof. Cathryn Lewis, Department of Medical and Molecular Genetics.


If you use GSMA, please cite:
Levinson DF, Levinson MD, Segurado R, Lewis CM (2003) Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part I: Methods and Power Analysis. American Journal of Human Genetics 73: 17-33.
Wise LH, Lanchbury JS, Lewis CM (1999) Meta-Anlysis of Genome Searches. Annals of Human Genetics 63: 263-272.

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