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From: steven perkins <>
Subject: [DNA] Article: DNA identification by pedigree likelihood ratioaccommodating population substructure and mutations
Date: Sun, 28 Nov 2010 17:54:44 -0500


Interesting article on genetic identification.
====================================

Open Access Research
Investigative Genetics 2010, 1:8 doi:10.1186/2041-2223-1-8
http://www.investigativegenetics.com/content/1/1/8

DNA identification by pedigree likelihood ratio accommodating
population substructure and mutations

Jianye Ge*, Bruce Budowle and Ranajit Chakraborty

* Corresponding author: Jianye Ge

Author Affiliations

Department of Forensic and Investigative Genetics, University of North
Texas Health Science Center, Ft Worth, Texas 76107, USA

Institute of Investigative Genetics, University of North Texas Health
Science Center, Ft Worth, Texas 76107, USA

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Investigative Genetics 2010, 1:8 doi:10.1186/2041-2223-1-8

The electronic version of this article is the complete one and can be
found online at: http://www.investigativegenetics.com/content/1/1/8

Received:29 September 2009
Accepted:4 October 2010
Published:4 October 2010

© 2010 Ge et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the
Creative Commons Attribution License
(http://creativecommons.org/licenses/by/2.0), which permits
unrestricted use, distribution, and reproduction in any medium,
provided the original work is properly cited.
Abstract

DNA typing is an important tool in missing-person identification,
especially in mass-fatality disasters. Identification methods
comparing a DNA profile from unidentified human remains with that of a
direct (from the person) or indirect (for example, from a biological
relative) reference sample and ranking the pairwise likelihood ratios
(LR) is straightforward and well defined. However, for indirect
comparison cases in which several members from a family can serve as
reference samples, the full power of kinship analysis is not entirely
exploited. Because biologically related family members are not
genetically independent, more information and thus greater power can
be attained by simultaneous use of all pedigree members in most cases,
although distant relationships may reduce the power.

In this study, an improvement was made on the method for
missing-person identification for autosomal and lineage-based markers,
by considering jointly the DNA profile data of all available family
reference samples. The missing person is evaluated by a pedigree LR of
the probability of DNA evidence under alternative hypotheses (for
example, the missing person is unrelated or if they belong to this
pedigree with a specified biological relationship) and can be ranked
for all pedigrees within a database. Pedigree LRs are adjusted for
population substructure according to the recommendations of the second
National Research Council (NRCII) Report. A realistic mutation model
was also incorporated to accommodate the possibility of false
exclusion.

The results show that the effect of mutation on the pedigree LR is
moderate, but LRs can be significantly decreased by the effect of
population substructure. Finally, Y chromosome and mitochondrial DNA
were integrated into the analysis to increase the power of
identification. A program titled MPKin was developed, combining the
aforementioned features to facilitate genetic analysis for identifying
missing persons. The computational complexity of the algorithms is
explained, and several ways to reduce the complexity are introduced.


--
Steven C. Perkins      
http://stevencperkins.com/
Online Journal of Genetics and Genealogy
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