DNA•VIEW Immigration Module


First released September 1998. Development and refinement is ongoing.
Links
Immigration example
Kinship in DNA•VIEW
Other information about DNA•VIEW
Forensic mathematics home page
For further details inquire to Charles Brenner, Ph.D.

Immigration and Kinship

Overview of the program

The Immigration suboption of Paternity Case is a link to the Symbolic Kinship Program that runs the Kinship program automatically, without user intervention, through the various loci for which there is data.

Compared to the stand-alone version of the Kinship program, Immigration requires that any DNA typing data for the parties to the inquiry must already have been fed into DNA•VIEW.note Once this has been done, Immigration automatically iterates through the Kinship program locus-by-locus, augmenting the user-supplied pedigree definitions with the appropriate symbolic genotype patterns for each locus, evaluating the resultant symbolic likelihood ratio formulas with automatically-computed allele frequencies, and compiling the per-locus results into a brief summary report that includes the cumulative likelihood ratio across all loci.

Evaluation of scenarios is therefore very rapid and simple, and it is practical to experiment with multiple combinations of possible ways that the people in a case may be related.

Note: Size data can be introduced in various ways including typing in the alleles or sizes, digitizing tablet (i.e. measurement on a gel), or importing Genotyper, Bioimage, Hitachi StarCall, and other file formats.

Initiation

First select a case. To create an immigration case, put all the people of interest into the case, without regard to role (child, mother, etc.) For the race list ("edit race list"), choose the main race to use for calculation.

Then Immigration becomes an available sub-menu option. Select it and the program collects all genotype data for the people in question.

Genotypes and genotype frequencies

Now the program proceeds to prepare tables of relevant genotypes and genotype frequencies. If it comes to a locus for which there is no appropriately specified database, it will prompt you to select one. (And, optionally, you may specify the selected database to be selected automatically in the future.)

If you refuse to select a database (hit ENTER with no selection), then you will subsequently be prompted to supply frequencies. So this is a viable option.

Menu of Immigration options

Operation

(a) Type in (or edit) scenario 1 (a), or (p) create a pedigree definition for evaluation.

In (a), an editing screen is opened. On the top is a summary of the genotypic patterns of the people. The bottom is space for you to type in a Kinship-type pedigree/locus definition. Do not include genotype information; that will be provided automatically, and locus-by-locus for all loci.

Type ctrl-e when finished entering the pedigree/locus.

(b) Display the raw sizes (for eyeball check) displays the raw data on the screen so you can proof-read it
(c) Find formulas and evaluate for all loci Calculations are performed automatically across all loci. The summary (d) is then displayed.
(d) Show summary of calculation Show the summary – on the screen, a 1-line-per locus, plus overall likelihood ratio, for the last scenario computed.

The summary is NOT appended to the final report unless you specifically choose to have it be:

(e) Add summary of calculation to report Add summary for this scenario to the report.
(f) Add scenario to/ modify the pick list Pick list maintenance – see (p).

The pick list is permanently saved on the hard drive, and gives you a way to save and re-use frequent pedigree definitions.

The "Add" command is really general maintenance, which permits

  • adding the new scenario
  • deleting items from the pick list
  • re-ordering the pick list by following the on-screen instructions.
(g) Silent alleles: not allowed toggle to specify whether null alleles (or primer mismatch) is considered in the computation
(h) Parsing & hints are: not shown toggle to specify whether extra analysis and progress information is shown on the screen
(i) Reconstruction report: Don't include in output Select this option (turn it to "Do") if you want the tables of genotype symbolic assignments, and frequencies, included in the printed report. You do need to include it if you want to see for certain what allele corresponds to each allele letter.
(j) quit from Immigration quit from Immigration to the next-higher menu (Paternity case)
(p) ; missing child C : M/? + F/? (p) are examples from the user-created "pick list" of favorite pedigres.

The (a) and (p) create a scenario but do not cause computation. Choose next option (c) for computation.

; trio C : M + F/?
(r) Race is: Caucasian choose the race for computation
(s) Don't "restrict" the data toggle for advanced option; manual control over which data is included
(t) Automatic frequencies toggle for advance option; allow user to edit (modify) the allele frequencies as each locus is computed
Repeat (a or p), (c), (e) – and perhaps (f) – for as many scenarios as desired – i.e. sibling vs. parent+child, child of both parents vs. neither, etc.