FROG-kb FAQ

What is FROG-kb?: The primary objective of FROG-kb is to provide a web interface that, from a forensic perspective, is useful for teaching and research and can serve as a tool facilitating forensic practice. The R in FROG-kb stands for both Resource and Reference. The Resource is the ability to identify many different panels of SNPs used for forensics and to calculate random match probabilities and ancestry likelihoods for an individual typed for the SNPs in one of the panels. The Reference is the ability to search through the data in ALFRED for molecular, anthropological, and other information on the various SNPs as well as the sources of the allele frequency data.
What are the sources of data in FROG-kb?: The SNP panels in FROG-kb are from the published literature. The underlying data utilized for the calculations of likelihood in FROG-kb are housed in the ALlele FREquency Database, ALFRED, described in Rajeevan et al., Nucleic Acids Research 2012 Jan;40(Database issue):D1010-1015. ALFRED is a publicly available resource for gene frequency data on human populations; extracted, curated, and organized from various sources including published literature, collaborators, and public high throughput data sources such as the HGDP-CEPH website and Human Genome Diversity Project at Stanford University. Some unpublished data from the host laboratory are also being made available through ALFRED.
How is FROG-kb different from ALFRED?: FROG-kb is a web-based resource and reference tool that primarily is intended to serve the forensic community. It's abilities include a web interface to select a SNP panel, input genotype information for a selected set of SNPs, run calculations employing the underling data, and display in a user-friendly interface the match probabilities and ancestry likelihoods. While, ALFRED is a compilation of gene frequency data on human populations, provided through a web application in an organized, searchable, user-friendly manner. In the system architecture framework of FROG-kb, ALFRED provides the 'reference' module.
Can ALFRED be used to search data within FROG-kb?: Yes, all the SNPs in FROG-kb are provided with links to navigate to ALFRED for additional information on the SNPs and populations typed. In addition, all the SNP panels in FROG-kb are also provided in ALFRED. While interface for entering genotype data and calculating likelihoods is not available from ALFRED, users can explore the allele frequency tables and graphs on additional population samples for these SNPs.
What are the browser requirements for viewing and searching FROG-kb?: It is recommended to use latest versions of Mozilla Firefox, Internet Explorer, Safari, or Google Chrome on PC and MAC since some browsing capabilities provided by HTML5 might not be available on older versions.
What types of SNP panels are included in FROG-kb?: Individual Identification (IISNP), Ancestry Inference (AISNP), and Phenotype Informative (PISNP) SNP panels are included in FROG-kb.
What is an IISNP panel?: IISNP stands for Individual Identification SNPs. This implementation provides examples and the ability to calculate random match probabilities for user-specified genotypes. The IISNP panels have less information on actual ancestry than the AISNP panels, but there is some information. It is up to the user to decide whether the relevant breadth of global coverage is sufficient to use the highest probability for the entered genotype as a forensically relevant maximum probability for a random match.
What is an AISNP panel?: AISNP stands for Ancestry Inference SNP. This implementation provides examples and ability to calculate relative likelihoods of ancestry from different populations for user-specified genotypes. Seven published AISNP panels are implemented and more will be added. No AISNP panel has data on all of the roughly 7000 different human populations. The user must decide which set of SNPs to test and use based on how well each panel covers the biogeographic region of relevance to the specific forensic issue.
What is a PISNP panel?: PISNP stands for Phenotype Informative SNPs. This implementation provides ability to predict eye color for user-specified genotypes. One published PISNP panel can currently be used to test the eye color prediction functionality which is based on a published formula (Liu et al. & Walsh et al.). We will be implementing other SNP panels associated with various phenotypes whenever there is a formula to use genotypes at associated loci to predict from those genotypes the actual phenotype.
How should I cite FROG-kb?: Use http://frog.med.yale.edu/FrogKB/ to cite the Website. For publications relating to FROG-kb use: Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. “Introducing the forensic research/reference on genetics knowledge base, FROG-kb” Investigative Genetics 3(18). (2012)
How often is FROG-kb updated?: New SNP panels with the calculations and the reference populations are added to FROG-kb after all the SNPs in the panel, reference populations and allele frequency tables are in ALFRED. A new population or populations are added to an existing panel when allele frequencies for all the SNPs on that population are in ALFRED. SNPs, population samples and allele frequency tables in ALFRED are updated on a daily basis.
Do I need to have data for all the SNPs in a panel?: No, the calculations are based only on the SNPs with a genotype entered.
What is the effect of data missing for some SNPs in the panel?: In general, the results will be less discriminating but still valid. How much less differentiation among populations will depend on the individual and the specific SNPs with missing data. The statistical consequences will be taken into account in the likelihoods and their ratios. The likelihoods will all be somewhat larger and the ratios smaller. The number of populations that have similar likelihoods will generally be larger.
What is ALFRED?: ALFRED, the ALlele FREquency Database, contains the documentation of the alleles and their frequencies in different populations. The data are highly curated and links exist to molecular and anthropologic databases as well as to the published literature. The ALFRED web interface has extensive search and display functions. ALFRED has over 37 million tables of the frequency of a specific SNP in a specific population sample.
How do I interpret the resulting list of populations, probabilities, and likelihood ratios?: The user must determine whether sufficient biogeographic regions of the world are represented as possible origins of the sample. For example, for the SNPforID 34-plex AISNP panel there is no Korean population typed for all SNPs and hence capable of being used for the calculations. In the input examples, the Korean individual has data on only 24 of the SNPs. In the results table the top eight populations are not significantly different and these eight and the next four all come from East Asia. Therefore, while one cannot with these data specify the population, one can safely conclude that the sample was an individual from an East Asian population. For more information go to “Functionality”.

FROG-kb FAQ

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