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SCAMP: a spreadsheet to collate autozygosity mapping projects
  1. T Forshew,
  2. C A Johnson
  1. Section of Medical and Molecular Genetics, Department of Paediatrics and Child Health, University of Birmingham Medical School, Birmingham B15 2TT, UK
  1. Correspondence to:
 Colin A Johnson
 Section of Medical and Molecular Genetics, Department of Paediatrics and Child Health, University of Birmingham Medical School, Birmingham, B15 2TT, UK;

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Autosomal recessive disorders are an important cause of childhood morbidity and mortality, and may reach significant frequencies in specific ethnic groups.1 The affected progeny of consanguineous parents provide an opportunity to undertake gene mapping and positional-candidate gene analysis,2 since it is highly likely that the disease locus is identical-by-descent from a common ancestor. The strategy of searching for regions of homozygosity in affected individuals from consanguineous families, using the methodology of autozygosity mapping, has proven to be highly effective for mapping loci and identifying autosomal recessive genes.3 The identification of recessive disease genes enables diagnostic and carrier testing and can provide critical insights into the pathogenesis of the disease.

Most researchers who perform autozygosity mapping currently use panels of approximately 400 highly polymorphic microsatellite markers in an initial genome-wide linkage screen, to give a marker spacing of between 10 and 12 cM throughout the autosomal genome. The accurate and reliable genotyping of genetic markers is, of course, essential for the success of such mapping projects. However, we have found the subsequent collation of the large datasets generated in mapping projects to be both time consuming and prone to error if performed manually (by using, for example, “cut and paste” into a spreadsheet). We have therefore designed a simple but versatile Microsoft Excel spreadsheet which automatically collates and analyses genotyping data, and enables shared regions of homozygosity to be identified quickly following visual inspection of the collated data. The expected average length of autozygous regions, that are identical-by-descent around a disease locus, have been calculated by Génin et al to be 28 cM for affected individuals from a first cousin mating, and 22 cM from a second cousin mating.4 In our experience, these values are good approximations …

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  • Conflict of interest: none declared.