Abstract
BackgroundOnline tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. The Fst value of each CODIS marker tends to be low across the populations of the world and most populations typically have all the common STRP alleles present diminishing the ability of these systems to discriminate ethnicity. Recently, considerable research is being conducted on single nucleotide polymorphisms (SNPs) to be considered for human identification and description. However, online tools and databases that can be used for forensic research and investigation are limited.MethodsThe back end DBMS (Database Management System) for FROG-kb is Oracle version 10. The front end is implemented with specific code using technologies such as Java, Java Servlet, JSP, JQuery, and GoogleCharts.ResultsWe present an open access web application, FROG-kb (Forensic Research/Reference on Genetics-knowledge base, http://frog.med.yale.edu), that is useful for teaching and research relevant to forensics and can serve as a tool facilitating forensic practice. The underlying data for FROG-kb are provided by the already extensively used and referenced ALlele FREquency Database, ALFRED (http://alfred.med.yale.edu). In addition to displaying data in an organized manner, computational tools that use the underlying allele frequencies with user-provided data are implemented in FROG-kb. These tools are organized by the different published SNP/marker panels available. This web tool currently has implemented general functions possible for two types of SNP panels, individual identification and ancestry inference, and a prediction function specific to a phenotype informative panel for eye color.ConclusionThe current online version of FROG-kb already provides new and useful functionality. We expect FROG-kb to grow and expand in capabilities and welcome input from the forensic community in identifying datasets and functionalities that will be most helpful and useful. Thus, the structure and functionality of FROG-kb will be revised in an ongoing process of improvement. This paper describes the state as of early June 2012.
Highlights
Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations
The large numbers of alleles and high heterozygosity relate to the high mutation rates of these loci; this means that matching of Short tandem repeat polymorphism (STRP) alleles is matching by state and not of alleles that are identical by descent
While all allele frequency data required for running the computations in FROG-kb were already in the ALFRED database, the new tables provide the framework for displaying information related to the different forensically relevant single nucleotide polymorphisms (SNPs) sets in an efficient and user-friendly manner
Summary
Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. Online tools and databases that can be used for forensic research and investigation are limited It is considerably more than a decade since the forensic community settled on a set of short tandem repeat (STR) polymorphisms ( STRP) for human identity testing [1]. These markers are multi-allelic and are excellent for individual matching of suspect and crime scene DNA. The extensive allele frequency data that have been accumulated over the years in large public databases allow populationspecific estimates of the probability of a random match of two unrelated individuals It is exactly the high level of polymorphism in almost all populations that limits the ability of these markers to determine ancestry of an individual. The large numbers of alleles and high heterozygosity relate to the high mutation rates of these loci; this means that matching of STRP alleles is matching by state and not of alleles that are identical by descent
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