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Contents
  1. Dealing with dropout
  2. DNA•VIEW Enhancements
    1. Y-haplotype capabilities
    2. Casework enhancements
    3. Kinship enhancements
    4. Graphing Kinship simulations
    5. Family case
  3. DNA•VIEW, DVI and the world
    1. Hurricane Katrina Identifications
    2. Pro-Búsqueda – reuniting families
    3. Growing family
  4. Finding Criminals
  5. PATER improvements
  6. Various worthwhile enhancements
    1. Nice user interaction features
    2. Mixture calculations
    3. Case comments
    4. Test cases
    5. Database – printout
    6. Sample switch check
    7. Worklist sizes
    8. Notation options
  7. Installation issues
    1. Free tool
    2. Installation/Technical fixes
    3. LIMS integration
  8. Travel agenda
    DNA•VIEW Latin American seminar
    European summer meetings
other newsletters

DNA·VIEW NEWSLETTER #21

March 18, 2008

  1. Dealing with dropout
  2. Allelic dropout is a common confounding factor when dealing with mixtures or in an (old) body identification by kinship. I have devised a general approach for dealing with dropout, which currently takes the form of protocols combined with various DNA•VIEW calculations (especially the Kinship dropout analysis). In the future I may enhance DNA•VIEW to incorporate the protocols and/or submit for publication papers explaining the approach. In the meanwhile I can share the approach with any subscribed users who are interested.

  3. DNA•VIEW Enhancements
    1. Y-haplotype capabilities
    2. Partly motivated by the Katrina identifications, I've enhanced and streamlined the Y-haplotype capabilities.

      I've found a very nice approach to deriving Y-haplotype matching odds, and plan to submit a paper soon.

    3. Casework enhancements
    4. The Genemapper Import wizard is nicely improved, and includes importing peak-height information, although no program uses the information as yet. Paternity/Kinship/Crime Case include a comment field and a useful comment-searching capability so that you can find and/or open cases based on the arbitrary comment.

    5. Kinship enhancements
    6. The kinship module has allowed simultaneous comparison of three or more scenarios for a while, and this has many uses when investigating the identification of two relatives (consider either or both), various combinations of odd-man-out when considering three putative siblings, and father/uncle problem among many.

      Many new menu items/features include

      Please note the "nice user interaction features" below.

      Bad bones – Kinship dropout

      Dropout [NOT] allowed is a special new feature by which, for user-specified samples ("bad bones"), homozygous genotypes may be analyzed on the assumption an allele is missing. The usefulness of this feature comes from making two kinship calculations when dealing with bad bones one with and one without dropout. The correct likelihood ratio is then somewhere in between. (Details forthcoming on request.)
      Paternity index distributions, mother tested or not. (Prof+Cof, Caucasian)

    7. Graphing Kinship Simulations
    8. The nice way to visualize a distribution of likelihood ratios is with a graph. Enhancement to the Kinship Simulation tool lets you easily do that, even compare several distributions. Export to Excel, select the data, click Scatter Plot, Finish, and switch to a logarithmic scale.

    9. Family case
    10. The new Calculate family trio option in the Paternity case menu is a convenience which tests for both paternity and maternity. It performs the usual paternity calculation and then does a maternity calculation for the mother as well. This feature is useful when dealing with livestock such as horses, where maternity is less certain than is usual with people.

  4. DNA•VIEW, DVI and the world
    1. Hurricane Katrina identifications
    2. DNA•VIEW is the worldwide standard for mass identification. In 2006 it was the principal analysis tool for the Katrina identifications, especially those involving kinship (identification with reference to relatives) of course. I was among the analysts who helped with the casework in Baton Rouge (largest surviving city near New Orleans), and also served on the scientific advisory panel convened to help sort out technical issues. Plenty of new ideas arose, supporting the maxim that every disaster is different. For example, is the prior probability of identity for an anonymous body based on the number of bodies, or the likely very inflated number of reported missing? More like the latter, but what if, as surely was the case, some bodies were never reported missing?

    3. Pro-Búsqueda – reuniting families
    4. A related application is a relatively new for me project involving reuniting adopted children with their biological families from whom they were separated (with varying degrees of violence or coercion) during the El Salvador civil war of the 1980's. The project is called Pro-Búsqueda.

      A remarkable case is that of "Juan." Raised in a military household, Juan learned when he was eight that he was adopted. As an adult he submitted a DNA sample to Pro-Búqueda. A computer search revealed a cold hit to a family who was hoping for contact with two lost daughters but not a boy. However, in a follow-up interview the family explained that the mother, who was killed in a military operation, did have a baby boy but since she was carrying the boy when she died they assumed he was dead as well. That explanation, consistent dates, and kinship matching odds of 395,000,000 are sufficient to be confident of the connection.

    5. Growing family
    6. As a follow-on to the tsunami identification project of 2005, I've enjoyed the coincidence and gratifying experience of meeting people in several different countries who learned how to use DNA•VIEW although neither directly (as is usual) nor indirectly from me. So there is developing a diaspora of DNA•VIEW users!

  5. Finding criminals
  6. Familial searching – searching against a criminal offender DNA database with the idea to find a relative of a crime scene profile when a direct match isn't there has received a lot of attention lately (see Finding Criminals Through DNA of Their Relatives, Science 2 June 2006. Email me if you would like the Supporting On-line Materials which are the scientific meat of the paper.). The Screen disaster matches module is exactly what one needs to do the searching. I've had some success finding criminals this way on pilot projects in a couple of jurisdictions.

  7. PATER improvements
  8. PATER reports can be in Spanish, if you wish.

    The nice user interaction features below apply to PATER.

  9. Various worthwhile enhancements
    1. Nice user interaction features
    2. A memory or history of prompt responses is kept so that you can recall your previous responses instead of typing them again. Use up/down arrow (or PgUp/PgDown for the multi-line Kinship scenarios) to scroll among previous answers, or ctrl-UpArrow for a menu. Note also the use of ctrl-z, as in Windows, to restore the original contents of a window. Another convenience, especially for entering kinship scenarios, is copy/paste.

    3. Mixture calculations
    4. are a bit easier thanks to the blindly calculate all loci and default unknown #'s Hp= Hd=. To help cater to dropout, Hd can be a half-integer.

    5. Case comments
    6. w help document Paternity/Kinship/Crime cases, and also can be searched to find a case.

    7. Test cases
    8. is one of several features designed to enhance testing and validation of DNA•VIEW.

    9. Database – printout
    10. is clearer and nicer looking.

    11. Sample switch check
    12. The Paternity Case program gives you a warning if a sample switch looks likely.

    13. Worklist sizes
    14. Create a report of all profiles for a worklist.

    15. Notation options
    16. The Options menu allows you to choose international decimal notation for numbers (99,8% rather than 99.8%), and standard PCR notation (allele 9.3) rather than the symbol • which sometimes exports as 9ù3.

  10. Installation issues
    1. Free tool
    2. Several important enhancements have been added to the installers for DNA•VIEW and PATER. I've made available for downloading a free installation tool. It will not alter your current version of DNA•VIEW or PATER. It just changes for the better the way the programs are started (compared to pre-summer-2006) and also supplies a few useful auxiliary capabilities. The included DNAView Report Viewer.xls is quite useful.

    3. Installation/Technical fixes
    4. No longer are DNA•VIEW and PATER "CPU hogs" (see Free Tool). This is one of several improvements that are thanks to new installation methods.

    5. LIMS integration
    6. DNA•VIEW has the ability to be harnessed as a slave process to operate invisibly under the control of your Laboratory Information Management System. There is some custom consulting involved in establishing the integration. Inquire for details.

  11. Travel agenda
  12. DNA•VIEW Latin American seminar
    Early May – schedule undecided. Guatemala. All welcome.
    European summer meetings
    I'll be at the following meetings, and in Europe in between
    May 27-30, Ancona, Italy
    June 13-14, Köln, Germany

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