SCAMP: a spreadsheet to collate autozygosity mapping projects.

A utosomal recessive disorders are an important cause of childhood morbidity and mortality, and may reach significant frequencies in specific ethnic groups. The affected progeny of consanguineous parents provide an opportunity to undertake gene mapping and positionalcandidate gene analysis, 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. 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. In our experience, these values are good approximations to the length of homozygous regions found in real genome-wide linkage screens (fig 1), and, therefore, a marker spacing of 10 cM is adequate for a cohort of affected individuals from a first cousin mating. We have called our spreadsheet ‘‘SCAMP’’ for spreadsheet to collate autozygosity mapping projects. The spreadsheet is available as a freeware download from the Medical and Molecular Genetics website at http://www.rch.bham.ac.uk/ MMG/SCAMP.htm in the form of a Microsoft Excel workbook compressed as a .zip file or can be obtained from http:// jmg.bmjjournals.com/supplemental/ as either a .zip or an .xls file. We have successfully used SCAMP in several autozygosity mapping projects for which it provided a simple and practical solution for the analysis of genotyping data and facilitated the subsequent identification of disease loci and genes. The key features of SCAMP are described in the following paragraphs. I. SCAMP is based on the popular ABI PRISM Linkage Mapping Set v2.5, and contains the details of all 811 markers in panels 1–28 for the ‘‘MD10’’ configuration (coverage at 10 cM resolution) and the markers in panels 29–86 for the ‘‘HD5’’ configuration (,5 cM resolution). Marker details are collated in the ‘‘ABI mapping panels v2.5’’ spreadsheet and include panel number, chromosome number, locus and primer identifiers, dye colour, and heterozygosity value. In addition, each marker is annotated with sex-average genetic distances, based on the Marshfield and deCODE genetic maps, 9 and the physical distance from the deCODE genetic map. The order of the markers has been sorted by using the Excel ‘‘data sort’’ command, on the basis of chromosome number, followed by the Marshfield genetic distance. The values of genetic distance and physical location are linked to the separate spreadsheets ‘‘Marshfield markers’’ and ‘‘deCODE markers’’ using the data lookup function VLOOKUP. If required, other marker sets could be included in additional spreadsheets, although the data range for the VLOOKUP functions must be changed. The syntax for data lookup functions is easily accessible using the help files in Microsoft Excel. II. The ‘‘genotypes’’ spreadsheet contains only the 400 ABI PRISM ‘‘MD10’’ markers which would be usual for a general genome-wide linkage screen. The markers are sorted on the basis of chromosome number and genetic distance, and the values for their genetic distances and physical locations are linked to the ‘‘ABI mapping panels v2.5’’ spreadsheet by VLOOKUP, although other spreadsheets containing marker details could be used. Figure 1 shows a small section of the ‘‘genotypes’’ spreadsheet that covers the genotyping data for chromosome 1 markers for samples 1–6. III. Genotyping data is entered into the ‘‘raw data’’ spreadsheet. This is most easily done by saving the output from, for example, ABI PRISM ‘‘Genotyper’’ software as a Key points