Below we provide an overview of accessing and searching SNP panels within FROG-kb. This information can also be found in Sections 3, 4, and 5 of the User Manual along with screen shots walking users through the database.
Navigating the SNP Panels
For each of the SNP panels listed there are several elements. Associated with each of the panel listings is a Detailed Overview of SNPs link into ALFRED precisely for a more detailed overview of the panel. That link opens the SNP Set page within ALFRED into a new browser window.
After clicking on the GO button to enter an AISNP, IISNP, or PISNP panel, several options are possible. Each has a link to the list of the SNPs in the panel. This can be found by selecting SNP Set button. Within the SNP Set list each rs number is an active link to the dbSNP record for that SNP. The Populations button provides the list of populations for which comparable calculations can be made. This is the set of populations for which all SNPs in the set have allele frequency data. Note, within the SNP Set in ALFRED additional populations may have data for some, but not all populations; those populations are not included in the calculations. Each population name is an active link to information on the population stored within ALFRED; that page will open in a new browser window. The Formula button gives an explanation on how the probabilities are derived in FROG-kb.
SNP Panel Example Data
Selecting the Examples button opens up a new page with option to select an individual from a population such as Hungarian, Keralite or Korean. Once a specific population is selected, a pre-entered data entry page for one individual from the population is shown. At the bottom of the pre-entered table, users can select Compute to view the results or Set All Unselected to Unknown and Compute. After selecting Compute, a table of the results and graph for the probability of genotype in each population appears for users to view. At the top of the table users can either print the results table or view the SNPs used for the calculation. We recommend trying these example individuals before experimenting by entering a new genotype profile of an unknown or a forensic case.
SNP Panel Data Entry
More important is the Data Entry button that opens the ability to specify an individual multi-site genotype and then calculate the probability of that genotype in each of the populations. Once the Data Entry button is selected users have the option to select File Upload or Selection by Radio button. More detailed information on selecting File Upload can be found in Section 4.3 of the User Manual. After selecting the Selection by Radio button, the genotype is entered by simply clicking on the radio button for the genotype at each SNP. Note, it is not necessary to click on the "NN" for missing data. Once genotypes are entered users should select the Compute button at the bottom of the table. If there are SNPs with no selection, a warning will appear and the option exists to examine which SNPs have no entry (they are highlighted) and to either enter a genotype or use the 'Set all unselected to unknown and compute' to fill those with "NN" and compute. The data is presented as described above in the SNP Set Example Data. More detailed information on Data Entry can be found in Section 4.1 of the User Manual.
Results of the Calculations
The results of the calculation are displayed as a table with three columns: the name of the population sampled with its geographic region and the sample size, the probability of the entered genotype in that population, and the likelihood ratio of the most probable population to the specified population. The probability of the entered genotype is equivalent to the probability of a random match assuming no deviation from Hardy-Weinberg ratios in the population. The populations are ordered by the probabilities of the entered genotype from highest to lowest; therefore, the likelihood ratios range from 1 to some larger number for the least likely population, representing how many times more likely the entered genotype is compared to the specific population. More detailed information on Results of the Calculations can be found in Section 4.2 of the User Manual.