Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb

Abstract

Background: Online 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.

Methods: The 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.

Results: We 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.

Conclusion: The 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.

Figure 1

Additional tables added to ALFRED for FROG-kb. The full relational schema of ALFRED is described in [26]; these tables and their interconnections illustrate the additions needed for the functionality of FROG-kb.

Figure 2

Snapshot of functionalities on FROG-kb. Portions of relevant screens seen in FROG-kb. ( a) The basic navigation panel seen on the left side of all screens. ( b) An example of one of the specific sets of SNPs, in this case an IISNP panel, with the [Go] button to enter the page with options for that set. Also, on the right is the link to ALFRED to view details on all the SNPs in this specific panel. ( c) The upper row of buttons for options for a specific panel. Other panels may have a slightly different set and a second row of buttons usually has additional options. However, the list of the SNPs, the list of the populations, the data entry, clearing the data entry fields, and at least one example dataset are common buttons to all panels. ( d) The top portion of the data entry page showing the radio buttons to be used to enter the genotype for each SNP. ( e) The buttons at the bottom of the data entry screen allowing the option of autofilling for missing data and printing of the input data plus the [Compile] button to initiate calculation.

Figure 3

Graph of log₁₀ (Probability of Genotype). An example of the plot of results for one individual input genotype with the populations ordered by the log10 probabilities from largest to smallest. This is part of the results display common to all IISNP and AISNP panel calculations. One can mouse over the graph to see the specific population and its value, as illustrated for Portuguese in this example. Not shown here is the list of those populations with the values also displayed on the same page. The option exists to print the list.