Characterisation of X Chromosomal Short Tandem Repeat Markers for Forensic Use

Author: Toni Marie Diegoli

Diegoli, Toni Marie, 2014 Characterisation of X Chromosomal Short Tandem Repeat Markers for Forensic Use, Flinders University, School of Biological Sciences

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Abstract

The use of X chromosomal short tandem repeat (STR) markers has been greatly increasing in the forensic setting. The marker system offers the potential to provide information in addition to that which is obtained from autosomal STR systems currently employed at forensic and paternity laboratories and in the courtroom. In certain scenarios, markers on the X chromosome may be the only means of obtaining the required information. Any investigated relationship situation where at least one female is involved will benefit from the use of X STRs, which can be applied to cases of missing persons, criminal incest, immigration, deficiency paternity or other questioned relationships. In-depth characterisation of the marker system is the first step in maximizing the power of this additional tool in the forensic arsenal. Using guidelines set forth within the 1991 report of the International Society for Forensic Genetics (ISFG) relating to the use of DNA polymorphisms, all aspects of the feasibility of routine X STR use were evaluated. Two mini-X chromosomal STR multiplexes capable of amplifying 15 total markers (DXS6795, DXS9902, DXS8378, DXS7132, DXS6803, DXS6789, DXS7424, DXS101, GATA172D05, DXS7130, GATA165B12, HPRTB, GATA31E08, DXS10147, and DXS7423) were developed and optimised for use in the investigation and characterisation of allele nomenclature, allele/genotype frequencies, mutation rates, and linkage between markers. To simplify the transition into routine use, the assays utilised techniques and instrumentation already present in most forensic laboratories as well as analyses familiar to forensic scientists. Several large sample sets from four U.S. populations (African Americans, U.S. Asians, U.S. Caucasians, and U.S. Hispanics) were studied to address the lack of relevant data available for the United States, where the use of X STRs remains limited. Much of the knowledge gained, however, is universally applicable. Though commercial kits are available that probe a wide variety of genetic markers on both the Y chromosome and the autosomes, there is only one commercial kit currently manufactured assaying markers on the X chromosome, the Investigator Argus X-12 kit (QIAGEN, Hilden, Germany). Due to patent and intellectual property issues between the United States and European STR kit manufacturers, the kit cannot be sold or marketed in the U.S. at this time. Nonetheless, four markers overlapping with those present in the Argus X-12 kit were included in the optimised multiplexes and were the subject of an extensive concordance study. With greater than 99% concordance across 975 alleles, comparability of the data was established for these four markers while the utility of the kit with U.S. populations was evaluated for the first time. This extensive developmental validation study investigated each aspect of the X STR marker system that would require consideration before implementation by a forensic laboratory. The optimised assays were found to be robust and the markers discriminating, while the mutation rate was estimated with high accuracy and the extent of linkage between the 15 markers was thoroughly evaluated. The combination of the results obtained as part of this study form the foundation upon which the introduction and routine use of X STRs may be built.

Keywords: short tandem repeats,forensic genetics,United States,population database,X chromosome
Subject: Biological Sciences thesis

Thesis type: Doctor of Philosophy
Completed: 2014
School: School of Biological Sciences
Supervisor: Dr. Adrian Linacre