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Paternal and maternal mutations in X-STRs: A GHEP-ISFG collaborative study. Forensic Sci Int Genet 2020; 46:102258. [PMID: 32066109 DOI: 10.1016/j.fsigen.2020.102258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/06/2019] [Accepted: 01/29/2020] [Indexed: 11/22/2022]
Abstract
The GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit Qiagen. A total of 16 laboratories gathered data from 1,612 father/mother/daughter trios, which were used to estimate both maternal and paternal mutation rates, when pooled together with other already published data. Data on fathers and mothers' age at the time of birth of the daughter were also available for ∼93 % of the cases. Population analyses were computed considering the genetic information of a subset of 1,327 unrelated daughters, corresponding to 2,654 haplotypes from residents in several regions of five countries: Argentina, Brazil, Ecuador, Portugal and Spain. Genetic differentiation analyses between the population samples from the same country did not reveal signs of significant stratification, although results from Hardy-Weinberg and linkage disequilibrium tests indicated the need of larger studies for Ecuador and Brazilian populations. The high genetic diversity of the markers resulted in a large number of haplotype combinations, showing the need of huge databases for reliable estimates of their frequencies. It should also be noted the high number of new alleles found, many of them not included in the allelic ladders provided with the kit, as very diverse populations were analyzed. The overall estimates for locus specific average mutation rates varied between 7.5E-04 (for DXS7423) and 1.1E-02 (for DXS10135), the latter being a troublesome figure for kinship analyses. Most of the found mutations (∼92 %) are compatible with the gain or loss of a single repeat. Paternal mutation rates showed to be 5.2 times higher than maternal ones. We also found that older fathers were more prone to transmit mutated alleles, having this trend not been observed in the case of the mothers.
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Diegoli TM, Rohde H, Borowski S, Krawczak M, Coble MD, Nothnagel M. Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization. Forensic Sci Int Genet 2016; 25:39-44. [PMID: 27497644 DOI: 10.1016/j.fsigen.2016.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/27/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations. To meet the computational requirements of this family-based type of analysis, we modified a previous implementation so as to allow multi-core parallelization on a high-performance computing system. While we obtained recombination rate estimates larger than zero for all but one pair of adjacent markers within the four previously proposed linkage groups, none of the three X STR pairs defining the junctions of these groups yielded a recombination rate estimate of 0.50. Corroborating previous studies, our results therefore argue against a simple model of independent X chromosomal linkage groups. Moreover, the refined recombination fraction estimates obtained in our study will facilitate the appropriate joint consideration of all 15 investigated markers in forensic analysis.
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Affiliation(s)
- Toni Marie Diegoli
- Office of the Chief Scientist, Defense Forensic Science Center, Ft. Gillem, GA, USA; Analytical Services, Inc., Arlington, VA, USA
| | - Heinrich Rohde
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Stefan Borowski
- Regional Computing Centre, University of Cologne, Cologne, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Michael D Coble
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
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Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 2015; 18:140-51. [DOI: 10.1016/j.fsigen.2015.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
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Mutation rates of 15 X chromosomal short tandem repeat markers. Int J Legal Med 2014; 128:579-87. [DOI: 10.1007/s00414-014-1016-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/30/2014] [Indexed: 11/25/2022]
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Diegoli TM, Coble MD. Development and characterization of two mini-X chromosomal short tandem repeat multiplexes. Forensic Sci Int Genet 2010; 5:415-21. [PMID: 20943451 DOI: 10.1016/j.fsigen.2010.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/27/2010] [Accepted: 08/30/2010] [Indexed: 10/19/2022]
Abstract
This study presents the development and characterization of two X chromosomal short tandem repeat (STR) multiplexes utilizing reduced-size amplicons (less than 200 base pairs) for identity and kinship testing with degraded DNA. Approximately 1360 samples across 4 U.S. population groups were typed for 15 X chromosomal STR markers: DXS6789, DXS7130, DXS9902, GATA31E08, DXS7424, GATA165B12, DXS101, DXS6795, GATA172D05, DXS10147, DXS8378, DXS7132, DXS6803, HPRTB, and DXS7423. A high degree of polymorphism was observed for each marker and both multiplexes were sensitive down to 200pg of pristine DNA. The two proposed multiplexes are suitable for forensic use, and show potential for improved analysis of compromised bone samples.
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Affiliation(s)
- Toni M Diegoli
- Armed Forces DNA Identification Laboratory, Research Section, 1413 Research Blvd., Suite 101, Rockville, MD 20850, USA.
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Hwa HL, Chang YY, Lee JCI, Yin HY, Chen YH, Tseng LH, Su YN, Ko TM. Thirteen X-chromosomal short tandem repeat loci multiplex data from Taiwanese. Int J Legal Med 2009; 123:263-9. [DOI: 10.1007/s00414-008-0310-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 11/24/2008] [Indexed: 10/21/2022]
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Ribeiro Rodrigues EM, Leite FPDN, Hutz MH, Palha TDJBF, Ribeiro dos Santos ÂKC, dos Santos SEB. A multiplex PCR for 11 X chromosome STR markers and population data from a Brazilian Amazon Region. Forensic Sci Int Genet 2008; 2:154-8. [DOI: 10.1016/j.fsigen.2007.10.179] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 09/25/2007] [Accepted: 10/16/2007] [Indexed: 11/29/2022]
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Gomes I, Prinz M, Pereira R, Meyers C, Mikulasovich RS, Amorim A, Carracedo A, Gusmão L. Genetic analysis of three US population groups using an X-chromosomal STR decaplex. Int J Legal Med 2007; 121:198-203. [PMID: 17237948 DOI: 10.1007/s00414-006-0146-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 11/27/2006] [Indexed: 11/29/2022]
Abstract
An X-chromosomal multiplex amplifying ten short tandem repeats (STRs) in one single PCR reaction was developed and optimized in this work. The X-STRs included were DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101, and DXS6789. Decaplex performance was tested on 377 male samples from three United States population groups, namely, 130 African Americans, 104 Asians, and 143 Hispanics. DXS8377 was the most polymorphic locus across all three populations, whereas DXS7423 was the least informative marker. Genetic distance analysis (R (ST) and F (ST)) performed for the three populations residing in New York showed significant genetic distances between population groups for most pairwise comparisons, except for HPRTB, DXS6809, and DXS7132. When testing linkage disequilibrium for all pairs of loci in the three groups, no significant association was found between any pair of the loci studied, after applying Bonferroni correction. The high values for the average probability of excluding a random man obtained in all three populations when both mother and daughter are tested or when father/daughter relationships are evaluated support the potential of this decaplex system in kinship analysis. Also, the overall high power of discrimination values for samples of female and male origin, confirms the usefulness of this decaplex system in identification analysis. As expected, results also support the use of independent databases comprising these ten X-linked loci for the three US populations evaluated.
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Affiliation(s)
- Iva Gomes
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
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Liu QL, Lü DJ, Zhu JZ, Lu HL, Luo YM, Fang Q. Fluorescent Multiplex Amplification of Three X-STR Loci. ACTA ACUST UNITED AC 2006; 33:1053-9. [PMID: 17185164 DOI: 10.1016/s0379-4172(06)60142-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 06/12/2006] [Indexed: 10/23/2022]
Abstract
This study was carried out to evaluate the value of three X-STR loci (DXS6803, DXS981and DXS6809) in forensic application and thereby investigate their polymorphism. The primer for each locus was labeled with fluorochrome 6-FAM. A fluorescent multiplex PCR for simultaneously amplifying three X-STR loci was set up. The PCR products that were obtained were analyzed using capillary electrophoresis and ABI PRISM 3100 Genetic Analyzer, with GENESCAN Analysis Software. When 340 male and 195 female individuals of Han population in China were tested, 13, 12, and 11 alleles were observed for DXS6803, DXS981 and DXS6809, respectively. One hundred and eighty three haplotypes were detected in the male individuals. The haplotype diversity reached 0.9926. The results show that the three loci of the multiplex system provide significant information on polymorphism for forensic identification and paternity testing, particularly for complicated paternity deficient cases.
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Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510089, China
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Hering S, Augstin C, Edelmann J, Heidel M, Dreßler J, Szibor R. A cluster of six closely linked STR-markers: Recombination analysis in a 3.6-Mb region at Xq12-13.1. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gomes I, Carracedo A, Amorim A, Gusmão L. A multiplex PCR design for simultaneous genotyping of X chromosome short tandem repeat markers. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.09.124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Zarrabeitia MT, Amigo T, Sañudo C, Zarrabeitia A, González-Lamuño D, Riancho JA. A new pentaplex system to study short tandem repeat markers of forensic interest on X chromosome. Forensic Sci Int 2002; 129:85-9. [PMID: 12243875 DOI: 10.1016/s0379-0738(02)00228-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A new method has been optimised to amplify five X chromosome short tandem repeat (STR) markers of interest in forensic medicine: human phosphoribosyl transferase (HPRTB), DXS101, androgen receptor (ARA), DXS7423 and DXS8377. Markers were conveniently amplified in a single PCR reaction with fluorochrome-labelled primers, which allowed the analysis of fragment sizes after injection into a capillary electrophoresis system. The most common alleles of each locus were sequenced and used in a control ladder to type unknown samples.
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Affiliation(s)
- María T Zarrabeitia
- Unit of Legal Medicine, Faculty of Medicine, University of Cantabria, Av. Herrera Oria, s/n 30911 Santander, Spain.
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