Software including X-linked STR markers

• GenoProof
• GenoProof Mixture
• VAT
• DNA•VIEW
• Rutgers combined linkage-physical human genome map

GenoProof

GenoProof® is an analysis software for the calculation of kinship analysis and for the evaluation of population studies. The software package was especially developed for laboratories and institutes dealing with the accomplishment of paternity tests, kinship or forensic cases, and population studies.

GenoProof® calculates all important parameters like likelihood quotient, paternity index (PI), combined paternity index (CPI) and Essen-Moeller value for standard paternity tests. In addition, the software may investigate kinship relationships based on X- and Y-chromosomal STR and sibling analyses.

GenoProof® supports the analysis of all commercial multiplex PCR kits. This includes autosomal STRs, X- and Y-chromosomal STRs as well as its combined analyses. Furthermore, GenoProof® allows the analysis of in-house PCR kits.

GenoProof® provides a huge, continuously trimmed population database with over 1000 allele frequency tables including haplotype frequencies for X-chromosomal markers, which can also be extended by the user’s own population data. The calculation routine considers linkage groups, too. So all biostatistical calculations can also be carried out under inclusion of several X-markers. This way the program can be adjusted to the individual requirements of the lab.

GenoProof® facilitates the evaluation of population studies. It supports the analysis of an unrestricted number of samples and is also capable to combine autosomal and gonosomal markers in one study. The population study of the following paper, for example, was analyzed with GenoProof® [1]

GenoProof Mixture

GenoProof® Mixture is an expert system for the analysis of forensic samples and complex DNA mixtures. It covers the entire evaluation process, from raw data analysis to the biostatistical calculations according to ISFG recommendations.

The software package supports automated genotyping of data produced by using commercial multiplex PCR kits for autosomal and X- or Y-chromosomal markers as well as their combined analyses. Additionally, the user may utilize own in-house kits.

GenoProof® Mixture provides also an unique graphical user interface and a mixture sample simulator to support the analysis of complex DNA samples.
The software calculates all biostatistical values required for mixture interpretation according to ISFG recommendations. For this purpose, the program will build all possible hypotheses for a case and interpret the mixture profile using the likelihood ratio (LR) method and the probability of exclusion method (RMNE).

GenoProof® Mixture also offers several functionalities for quality control such as artifact filters, contamination checks and audit trail.

The comprehensive reference data, which allow an easy handling, include testkit, marker and size standard data and an extensive population database.
The population database comprises haplotype frequencies for X-chromosomal markers, too, as well as calculation routines for linkage groups. Therefore, all biostatistical calculations can be also carried out under inclusion of several X markers.

VAT

This is a program asisting with to the biostatistics of ancestry filiation by M. P. Baur, R. Fimmers and W. Spitz
(Rolf.Fimmers@ukb.uni-bonn.de)

DNA•VIEW

By Charles Brenner (http://www.dna-view.com/dnaview.htm)

Rutgers combined linkage-physical human genome map

Matise and her co-workers have constructed a high-resolution genetic map de novo that includes most of the polymorphic markers for which genotype data are publicly available, that combines genotype data from both the CEPH and deCODE pedigrees (for some markers), that incorporates SNPs, and that also incorporates sequence-based positional information. The position of most markers on their map is corroborated by both genomic sequence and recombination-based data. This specific combination of features maximizes marker inclusion, coverage, and resolution, making this map uniquely suited as a comprehensive resource for determining genetic map information (order and distances) for any large set of polymorphic markers.

This set of combined genotype data (exclusive of the deCODE data) and maps has been incorporated into the MAP-O-MAT web-based linkage mapping server for analysis of human linkage maps (Kong, X. and Matise T., 2005).
(http://compgen.rutgers.edu/maps/)

References

1. Becker D, Rodig H, Augustin C, Edelmann J, Götz F, Hering S, Szibor R, Brabetz W (2008) Population genetic evaluation of eight X-chromosomal short tandem repeat loci using Mentype Argus X-8 PCR amplification kit. Forensic Science International: Genetics 2:69-74