1
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Neis M, Groß T, Schneider H, Schneider PM, Courts C. Comprehensive body fluid identification and contributor assignment by combining targeted sequencing of mRNA and coding region SNPs. Forensic Sci Int Genet 2024; 73:103125. [PMID: 39182373 DOI: 10.1016/j.fsigen.2024.103125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/19/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Forensic genetic analyses aim to retrieve as much information as possible from biological trace material recovered from crime scenes. While standard short tandem repeat (STR) profiling is essential to individualize biological traces, its significance is diminished in crime scenarios where the presence of a suspect's DNA is acknowledged by all parties. In such cases, forensic (m)RNA analysis can provide crucial contextualizing information on the source level about a trace's composition, i.e., body fluids/tissues, and has therefore emerged as a powerful tool for modern forensic investigations. However, the question which of several suspects contributed a specific component (body fluid) to a mixed trace cannot be answered by RNA analysis using conventional methods. This individualizing information is stored within the sequence of the mRNA transcripts. Massively parallel sequencing (MPS) represents a promising alternative, offering not only higher multiplex capacity, but also the typing of individual coding region SNPs (cSNPs) to enable the assignment of contributors to mixture components, thereby reducing the risk of association fallacies. Herein, we describe the development of an extensive mRNA/cSNP panel for targeted sequencing on the IonTorrent S5 platform. Our panel comprises 30 markers for the detection of six body fluids/tissues (blood, saliva, semen, skin, vaginal and menstrual secretion), along with 70 linkage-controlled cSNPs for contributor assignment. It exhibited high reliable detection sensitivity with RNA inputs down to 0.75 ng and a conservatively calculated probability of identity of 0.03 - 6 % for individual body fluid-specific cSNP profiles. Limitations and areas for future work include RNA-related allele imbalances, inclusion of markers to correctly identify rectal mucosa and the optimization of specific markers. In summary, our new panel is intended to be a major step forward to interpret biological evidence at sub-source and source level based on cSNP attribution of a body fluid component to a suspect and victim, respectively.
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Affiliation(s)
- Maximilian Neis
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.
| | - Theresa Groß
- Hessian State Office of Criminal Investigation, Wiesbaden, Germany
| | - Harald Schneider
- Hessian State Office of Criminal Investigation, Wiesbaden, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
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2
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Perera N, Wijithalal R, Galhena G, Ranawaka G. Linkage, recombination and mutation rate analyses of 16 X-chromosomal STR loci in Sri Lankan Sinhalese pedigrees. Int J Legal Med 2022; 136:415-422. [PMID: 35022841 DOI: 10.1007/s00414-021-02762-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022]
Abstract
This study investigated genetic linkage, recombination fractions and mutation rates of 16 X chromosomal short tandem repeat (X-STR) markers using a recently developed multiplex PCR assay for Sinhalese population of Sri Lanka, by analyzing 81 three-generation families including 81 grandfathers with daughters and 162 grandsons. In addition, 31 two generation families involving mother father daughter trios were included for mutation analysis. The analysis of recombination fractions between marker pairs identified two linkage blocks (maximum LOD scores > 3.0) each spanning a physical distance of 44.35 Mb and 6.04 Mb respectively. Though recombination events are usually rare among closely linked markers, crossovers were observed for markers located < 1.0 Mb apart. The recombination fractions observed are not fully concordant with those reported earlier, including the second-generation Rutgers combined linkage-physical map. This suggests that linkage is not uniform among different populations. However, the overall and marker-specific mutation rates of the present study did not differ from previous reports, though it needs confirmation with a much larger sample set. The findings presented here will provide the baseline information required for biostatistical calculations conducted using X-STR markers, in complex kinship analysis of Sinhalese population.
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Affiliation(s)
- Nandika Perera
- Genetech Molecular Diagnostics, Colombo 08, Sri Lanka. .,Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka.
| | - Ruvini Wijithalal
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03, Sri Lanka
| | - Gayani Galhena
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03, Sri Lanka
| | - Gaya Ranawaka
- Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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3
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Xiao C, Yang X, Liu H, Liu C, Yu Z, Chen L, Liu C. Validation and forensic application of a new 19 X-STR loci multiplex system. Leg Med (Tokyo) 2021; 53:101957. [PMID: 34481193 DOI: 10.1016/j.legalmed.2021.101957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 07/23/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
The Microreader™ 19X Direct ID System was a newly developed multiplex PCR kit, which could detect 19 X-chromosomal STR loci (DXS6795, DXS9907, DXS6803, GATA172D05, DXS6807, GATA31E08, DXS7423, DXS6810, DXS101, DXS9902, DXS7133, DXS6800, DXS981, DXS10162, DXS6809, DXS10135, HPRTB, GATA165B12, DXS10079) and the sex determination locus of AMEL simultaneously. Different from other X-STR multiplex PCR kits, no linkage groups are included in this system, so the likelihood ratios could be calculated without the consideration of linkage groups. In this study, PCR conditions, sensitivity, species specificity, stability, DNA mixtures, concordance, stutter, sizing precision and population studies were conducted according to the SWGDAM developmental validation guidelines. The results indicated that this new X-STRs multiplex system was an efficient and reliable detection system, which could facilitate human kinship analysis and identification testing, as a powerful supplementary to autosomal STR kits.
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Affiliation(s)
- Cheng Xiao
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xingyi Yang
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, China
| | - Zhonghao Yu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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4
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Perera N, Galhena G, Ranawaka G. X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations. Sci Rep 2021; 11:12748. [PMID: 34140598 PMCID: PMC8211843 DOI: 10.1038/s41598-021-92314-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
A new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.
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Affiliation(s)
- Nandika Perera
- Genetech Molecular Diagnostics, Colombo 08, Sri Lanka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Gayani Galhena
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03, Sri Lanka.
| | - Gaya Ranawaka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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5
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Zhang Y, Yu Z, Mo X, Zhao X, Li W, Liu H, Liu C, Wu R, Sun H. Development and validation of a new 18 X-STR typing assay for forensic applications. Electrophoresis 2021; 42:766-773. [PMID: 33415769 DOI: 10.1002/elps.202000168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 11/08/2022]
Abstract
With a unique inheritance pattern compared to autosomal short tandem repeats (A-STRs), X chromosomal STRs (X-STRs) have special usage in forensic relationship testing. In this study, we designed a multiplex amplification system (named TYPER-X19 multiplex assay) consisting of 18 STR loci spreading from 7.837 to 149.460 Mb on the X chromosomes (DXS9895, DXS8378, DXS9902, DXS6810, DXS7132, DXS10079, DXS6789, DXS7424, DXS101, DXS6797, DXS7133, DXS6804, GATA165B12, DXS10103, HPRTB, GATA31E08, DXS8377, and DXS7423), and the amelogenin. PCR primers were marked with four kinds of fluorophores including FAM, HEX, TAMRA, and ROX. The multiplex system was optimized and tested for precision, concordance, reproducibility, sensitivity, stability, DNA mixture, and species specificity according to the conventional validation guidelines. The results indicated that the system was accurate, reliable, and sensitive enough, and was suitable for common forensic case-type samples. In the population genetic study, a total of 148 alleles were detected at the 18 X-STR loci in 398 Southern Han Chinese. Relatively high combined power of discrimination in male (PDm ), power of discrimination in female (PDf ), mean paternity exclusion chance in trios (MECtrio ), and mean paternity exclusion chance in duos (MECDuo ) by Desmarais were detected, and HPRTB-DXS10103 was in linkage disequilibrium. The results suggested that the TYPER-X19 multiplex assay was suitable for forensic applications.
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Affiliation(s)
- Yinming Zhang
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zhengliang Yu
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Xiaoting Mo
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Wanshui Li
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Hong Liu
- Guangzhou Forensic Institute, Guangzhou, P. R. China
| | - Chao Liu
- Guangzhou Forensic Institute, Guangzhou, P. R. China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
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6
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Perera N, Galhena G, Ranawaka G. Development of a 16 X-STR multiplex PCR system for kinship analysis and its applicability for the Sinhalese population in Sri Lanka. Int J Legal Med 2020; 135:161-166. [PMID: 33140262 DOI: 10.1007/s00414-020-02450-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
The study describes the development of a new multiplex PCR system that simultaneously amplifies 16 X chromosome short tandem repeats (X-STRs) loci in a single PCR reaction and its applicability on a sample of 200 from the Sinhalese population in Sri Lanka. 13 X-STR loci located in four clusters are selected for the assay (DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074-DXS10075, DXS6801-DXS6809-DXS6789 and DXS7424-DXS101-DXS7133). In addition, three single loci were also selected (DXS9902, HPRTB and DXS7423). Genomic DNA extracted using the Chelex-100 method was amplified with modified published primers and subjected to capillary gel electrophoresis. Complete DNA profiles were obtained with 0.20 ng 9947A DNA and the band sizes ranged between 100 and 320 bp with 10 loci having sizes below 237 bp. A total of 160 alleles were observed among the sample with 5-23 alleles for each locus. The forensic efficiency evaluation showed high values for the combined power of discrimination in males (1 in 1 × 1010) and females (1 in 1 × 1017). Combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were equally high (> 0.99999). Application of the new multiplex system to two actual kinship cases of full sibling and deficient paternity suggested that these 16 short tandem repeat loci are highly appropriate for forensic and kinship testing among the Sinhalese population.
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Affiliation(s)
- Nandika Perera
- Genetech Molecular Diagnostics, Colombo, 08, Sri Lanka. .,Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka.
| | - Gayani Galhena
- Department of Zoology and Environment Sciences, University of Colombo, Colombo, 03, Sri Lanka
| | - Gaya Ranawaka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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7
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Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population. Sci Rep 2020; 10:5652. [PMID: 32221414 PMCID: PMC7101338 DOI: 10.1038/s41598-020-62645-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022] Open
Abstract
African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East African and 40% West Eurasian genes in the Somali population, with a close relation to the Cushitic and Semitic speaking Ethiopian populations. We report the unique features of human leukocyte antigens (HLA) in the Somali population, which seem to differentiate from all other neighboring regions compared. Current study identified high prevalence of the diabetes type 1 (T1D) predisposing HLA DR-DQ haplotypes in Somalia. This finding may explain the increased T1D risk observed among Somali children. In addition, ethnic Somalis were found to host the highest frequencies observed thus far for several pharmacogenetic variants, including UGT1A4*2. In conclusion, we report that the Somali population displays genetic traits of significance to health and disease. The Somali dataset is publicly available and will add more information to the few genomic datasets available for African populations.
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8
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X-chromosome data for 12 STRs: Towards an Argentinian database of forensic haplotype frequencies. Forensic Sci Int Genet 2019; 41:e8-e13. [DOI: 10.1016/j.fsigen.2019.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/27/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022]
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9
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Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Mol Biol Evol 2017; 34:3232-3242. [DOI: 10.1093/molbev/msx256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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10
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Gomes I, Pereira PJP, Harms S, Oliveira AM, Schneider PM, Brehm A. Genetic characterization of Guinea-Bissau using a 12 X-chromosomal STR system: Inferences from a multiethnic population. Forensic Sci Int Genet 2017; 31:89-94. [PMID: 28858674 DOI: 10.1016/j.fsigen.2017.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022]
Abstract
A male West African sample from Guinea-Bissau (West-African coast) was genetically analyzed using 12 X chromosomal short tandem repeats that are grouped into four haplotype groups. Linkage disequilibrium was tested (p≤0.0008) and association was detected for the majority of markers in three out of the four studied haplotype clusters. The sample of 332 unrelated individuals analyzed in this study belonged to several recognized ethnic groups (n=18) which were used to evaluate the genetic variation of Guinea-Bissau's population. Pairwise genetic distances (FST) did not reveal significant differences among the majority of groups. An additional 110 samples from other countries also belonging to West Africa were as well compared with the sample of Guinea-Bissau. No significant differences were found between these two groups of West African individuals, supporting the genetic homogeneity of this region on the X chromosome level. The generation of over 100 DNA West African sequences provided new insights into the repeat sequence structure of some of the present X-STRs. Parameters for forensic evaluation were also calculated for each X-STR, supporting the potential application of these markers in typical kinship scenarios. Also, the high power of discrimination values for samples of female and male origin observed in this study, confirms the usefulness of the present X-STRs in identification analysis.
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Affiliation(s)
- Iva Gomes
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Plácido J P Pereira
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9020-105 Funchal, Portugal
| | - Sonja Harms
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Andréa M Oliveira
- Genetic Department, Institute of Biology, State University of Rio de Janeiro (UERJ), Brazil
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - António Brehm
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9020-105 Funchal, Portugal.
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11
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Lee JCI, Lin CY, Tsai LC, Yu YJ, Liao KH, Linacre A, Hsieh HM. Establishment of 11 linked X-STR loci within 1.1 Mb to assist with kinship testing. Int J Legal Med 2017; 132:967-973. [PMID: 28730502 DOI: 10.1007/s00414-017-1637-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/04/2017] [Indexed: 11/29/2022]
Abstract
This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci. The distance between each pair of loci ranged from 24,998 to 244,701 bp with an average of approximately 110.8 kb. The number of observed alleles ranged from 7 to 30 for these 10 loci with a polymorphic information content ranging from 0.593 to 0.930. The LOD score from a pairwise linkage study ranged from 4.40 to 23.73, indicating that these 11 loci were highly linked, as expected. In line with standard forensic practice, all 11 loci can be amplified in one multiplex reaction, and comprehensive allelic ladders for all the loci have been constructed. These newly established 11 linked STR loci on the human X chromosome were found to be highly polymorphic and have the potential to aid in kinship testing where the X chromosome loci currently plays a role.
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Affiliation(s)
- James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Chun-Yen Lin
- Institute of Forensic Medicine, Ministry of Justice, No. 123 Min'an Street., Zhonghe Dist, New Taipei City, 23552, Taiwan
| | - Li-Chin Tsai
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan
| | - Yu-Jen Yu
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Keng-Hsien Liao
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Adelaide, 5001, Australia
| | - Hsing-Mei Hsieh
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan.
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12
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Wendt FR, King JL, Novroski NM, Churchill JD, Ng J, Oldt RF, McCulloh KL, Weise JA, Smith DG, Kanthaswamy S, Budowle B. Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. Forensic Sci Int Genet 2017; 28:146-154. [DOI: 10.1016/j.fsigen.2017.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/01/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
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13
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Yang X, Zhang X, Zhu J, Chen L, Liu C, Feng X, Chen L, Wang H, Liu C. Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups. Sci Rep 2017; 7:42782. [PMID: 28211539 PMCID: PMC5314363 DOI: 10.1038/srep42782] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations. The combined powers of discrimination in males and females were calculated according to haplotype frequencies from allele distributions rather than haplotype counts in the relevant population and were high in four ethnic groups. The cumulative powers of discrimination of the tested X-STR loci were 1.000000000000000 and 0.999999999997940 in females and males, respectively. All 19 X-STR loci are highly polymorphic. The highest Reynolds genetic distances were observed for the Tibet-Uighur pairwise comparisons. This study represents an extensive report on X-STR marker variation in minor Chinese populations and a comprehensive analysis of the diversity of these 19 X STR markers in four Chinese ethnic groups.
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Affiliation(s)
- Xingyi Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Xiaofang Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Junyong Zhu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Linli Chen
- AGCU ScienTech Incorporation, Wuxi 214174, P.R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Xingling Feng
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Ling Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China
| | - Huijun Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China
| | - Chao Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
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14
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Mršić G, Ozretić P, Crnjac J, Merkaš S, Račić I, Rožić S, Sukser V, Popović M, Korolija M. Analysis of 12 X-STR loci in the population of south Croatia. Mol Biol Rep 2017; 44:183-189. [PMID: 28070706 DOI: 10.1007/s11033-017-4096-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 01/02/2017] [Indexed: 02/08/2023]
Abstract
The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator® Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org. Hardy-Weinberg equilibrium was confirmed for all X-STR markers in female samples. Biallelic patterns at DXS10079 locus were detected in four male samples. Polymorphism information content for the most (DXS10135) and the least (DXS8378) informative markers was 0.9212 and 0.6347, respectively. In both male and female samples, combined power of discrimination exceeded 0.999999999. As confirmed by linkage disequilibrium test, significant association of marker pair DXS10074-DXS10079 (P = 0.0004) within LG2 and marker pair DXS10101-DXS10103 (P = 0.0003) within LG3 was found only in male samples. Number of observed haplotypes in our sample pool amounted 3.01, 7.53, 5 and 3.25% of the number of possible haplotypes for LG1, LG2, LG3 and LG4, respectively. According to haplotype diversity value of 0.9981, LG1 was the most informative. In comparison of south Croatia with 26 world populations, pair-wise [Formula: see text] values increase in parallel with geographical distance. Overall statistical assessment confirmed suitability of Investigator® Argus X-12 kit for forensic casework in both identification and familial testing in the population of south Croatia.
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Affiliation(s)
- Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | | | - Josip Crnjac
- University Department for Forensic Sciences, University of Split, Split, Croatia
| | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Ivana Račić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Viktorija Sukser
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia.
- Forensic Science Office, University of Zagreb, Zagreb, Croatia.
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15
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Crnjac J, Ozretić P, Merkaš S, Ratko M, Lozančić M, Korolija M, Popović M, Mršić G. Investigator Argus X-12 study on the population of northern Croatia. Genet Mol Biol 2017; 40:80-83. [PMID: 27768154 PMCID: PMC5409765 DOI: 10.1590/1678-4685-gmb-2015-0261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/03/2016] [Indexed: 02/08/2023] Open
Abstract
X chromosome STR typing has emerged recently as a powerful tool, complementary to autosomal STR typing, in solving complex forensic and missing person cases. Investigator® Argus X-12 is a commercial product that allows co-amplification of 12 X chromosomal markers belonging to four linkage groups (LGs). In this study, we analyzed by capillary electrophoresis blood samples from 100 females and 102 males from a population of northern Croatia. Statistical analysis included calculation of allele and haplotype frequencies, as well as forensic parameters. The most informative marker for the northern Croatia population was DXS10135 with PIC=0.9211 and a total of 27 alleles. The least polymorphic marker was DXS8378 with 6 alleles. The proportion of observed haplotypes from the number of possible haplotypes varied from 2.74-8.57% across all LGs, with LG1 being the most informative. Of the 11 tested world populations compared to the population of northern Croatia, significant differences in genetic distance (FST) were found for Greenlandic and all non-European populations. We found that all tested markers are in HWE and can thus be used for match probability calculation. Because of high combined power of discrimination in both men and women, Investigator® Argus X-12 is applicable for the northern Croatia population in routine forensic casework.
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Affiliation(s)
- Josip Crnjac
- University Department for Forensic Sciences, University of Split, Split, Croatia
| | | | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
| | - Martina Ratko
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
| | | | | | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
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16
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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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17
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Beurteilung von fraglichen Geschwister- bzw. Halbgeschwisterfällen. Rechtsmedizin (Berl) 2016. [DOI: 10.1007/s00194-016-0093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Mixtures with relatives and linked markers. Int J Legal Med 2015; 130:621-34. [DOI: 10.1007/s00414-015-1288-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
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19
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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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20
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Kling D, Dell’Amico B, Tillmar AO. FamLinkX – implementation of a general model for likelihood computations for X-chromosomal marker data. Forensic Sci Int Genet 2015; 17:1-7. [DOI: 10.1016/j.fsigen.2015.02.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/16/2015] [Accepted: 02/20/2015] [Indexed: 11/26/2022]
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21
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Siegert S, Roewer L, Nothnagel M. Shannon's equivocation for forensic Y-STR marker selection. Forensic Sci Int Genet 2015; 16:216-225. [PMID: 25682312 DOI: 10.1016/j.fsigen.2015.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/08/2015] [Accepted: 02/07/2015] [Indexed: 11/29/2022]
Abstract
Short tandem repeat (STR) markers are widely and continuously used in forensic applications. However, past research has demonstrated substantial allelic association between STR markers on both autosomes and the X chromosome, leading to partially redundant information that these markers can provide. Here, we quantify the allelic association between Y-chromosomal STR markers that are part of established forensic panels, separately for three different continental groups. We further propose a sequential marker selection procedure that is based on Shannon's equivocation and that accounts for allelic association between STR markers, leading to a maximal gain in independent information. In application to three real-world data sets, we demonstrate the procedure's superior performance when compared to single-locus diversity selection strategies, resulting in the optimal marker set for a given data set in the majority of marker subsets. Noting the inferior performance of the established Y-STR marker panels in a retrospective investigation, we suggest that future forensic marker selection should be guided, besides by other technical selection criteria, by an equivocation-based approach to obtain maximally discriminatory marker sets at minimal cost.
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Affiliation(s)
- Sabine Siegert
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Cologne, Germany.
| | - Lutz Roewer
- Dept. Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Cologne, Germany.
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22
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Liu QL, Li ZD, Li CT, Zhao H, Wu YD, Li Q, Lu DJ. X chromosomal recombination--a family study analyzing 26 X-STR Loci in Chinese Han three-generation pedigrees. Electrophoresis 2013; 34:3016-22. [PMID: 24002797 DOI: 10.1002/elps.201300204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 11/06/2022]
Abstract
The aim of this study is to investigate genetic linkage and recombination fractions of 26 X chromosomal (X-STR) loci with two multiplex PCR systems (MX15-STR and MX12-STR). MX15-STR (including DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079) and MX12-STR (including DXS6854, DXS9902, DXS6800, GATA172D05, DXS7423, HPRTB, DXS6807, DXS6803, DXS6804, DXS6799, DXS8378, and DXS8377) were successful analyzed on 206 two-generation families with two or more children and 33 three-generation families with 72 grandsons. Segregation analysis and calculation of recombination fractions between pairs of markers were performed. Linkage analysis of pairs of markers showed that there existed significant linkage (maximum LOD scores >2.0) within the physical distance of 48.5 Mb. Recombination events could be observed within the clusters of closed linked makers spanning <1.0 Mb. These results indicate that close cluster X-STRs used and recombination fractions of the selected loci will be very useful for biostatistical calculations in complex kinship analysis.
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Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China; Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
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23
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Nothnagel M, Szibor R, Vollrath O, Augustin C, Edelmann J, Geppert M, Alves C, Gusmão L, Vennemann M, Hou Y, Immel UD, Inturri S, Luo H, Lutz-Bonengel S, Robino C, Roewer L, Rolf B, Sanft J, Shin KJ, Sim JE, Wiegand P, Winkler C, Krawczak M, Hering S. Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome. Forensic Sci Int Genet 2012; 6:778-84. [DOI: 10.1016/j.fsigen.2012.02.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/01/2012] [Accepted: 02/29/2012] [Indexed: 10/28/2022]
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24
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The publication of population genetic data in the International Journal of Legal Medicine: guidelines. Int J Legal Med 2012. [DOI: 10.1007/s00414-012-0700-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Pamjav H, Kugler R, Zalán A, Völgyi A, Straky Z, Endrédy P, Kozma Z. X chromosomal recombination study in three-generation families in Hungary. Forensic Sci Int Genet 2012; 6:e95-6. [DOI: 10.1016/j.fsigen.2011.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/10/2011] [Accepted: 08/23/2011] [Indexed: 11/27/2022]
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26
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Capillary electrophoresis of an X-chromosome STR decaplex for kinship deficiency cases. Methods Mol Biol 2012; 830:57-71. [PMID: 22139653 DOI: 10.1007/978-1-61779-461-2_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
During the two last decades, STR markers located on the autosomes have been gaining relevance and have nearly replaced the use of other type of markers in most cases of genetic identification, paternity testing, as well as in other situations of kinship analysis. Nevertheless, in some complex cases, independently of the number of polymorphisms being typed, autosomal markers convey very little information. Depending on the parentage constellation available for analysis, as well as the gender of the subjects, this problem can sometimes be solved by using markers that have different modes of transmission. Therefore, most forensic laboratories are nowadays prepared to analyse lineage markers (Y chromosome and mtDNA) and many have recently set up methods for the analysis of X-STRs. In the present chapter, a method is described for the typing of ten X chromosome-specific markers in a single PCR amplification reaction, followed by capillary electrophoresis separation and fluorescent detection in an ABI Genetic Analyser apparatus. This typing strategy was developed and optimized for the simultaneous amplification of ten X-linked specific STRs well distributed along the chromosome: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 and DXS7423.
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27
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Oki T, Hayashi T, Ota M, Asamura H. Development of multiplex assay with 16 SNPs on X chromosome for degraded samples. Leg Med (Tokyo) 2011; 14:11-6. [PMID: 22177906 DOI: 10.1016/j.legalmed.2011.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/28/2011] [Accepted: 10/07/2011] [Indexed: 10/14/2022]
Abstract
We selected 16 new X chromosomal SNPs (rs4827155, rs471205, rs7884160, rs16982419, rs985251, rs3813932, rs6630351, rs4132871, rs5966270, rs7471388, rs6641116, rs6521038, rs5990560, rs5959408, rs414960, and rs3006142) and developed the two X chromosomal SNPs Octaplex systems using multiplex single base extension reactions. To make the systems more useful for analyzing degraded DNA samples, we designed primers to render amplicons of 100 bp or shorter (shorter PCR products). Statistical analyses of the 16 SNPs indicated a high usefulness for the Japanese forensic practice. In addition, results of tests on degraded DNA confirm the usefulness of this technique in such samples.
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Affiliation(s)
- Takahito Oki
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
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28
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Yoo SY, Cho NS, Park SW, Hwang JH, Kim JN, Chung KW, Han MS. Genetic polymorphisms of eight X-STR loci of Mentype Argus X-8 kit in Koreans. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Castañeda M, Mijares V, Riancho JA, Zarrabeitia MT. Haplotypic blocks of X-linked STRs for forensic cases: study of recombination and mutation rates. J Forensic Sci 2011; 57:192-5. [PMID: 21923782 DOI: 10.1111/j.1556-4029.2011.01916.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In complex kinship cases, markers situated in haplotypic blocks may provide additional clues to other unlinked markers. We have established a protocol to amplify six X-chromosome microsatellites, located in two haplotype blocks, using PCR with fluorochrome-labeled primers and capillary electrophoresis. The segregation stability was explored in 92 unrelated families with individuals from three generations. Sixty-one different haplotypes were found in the DXS10079-DXS10074-DXS10075 block in the grandfathers and 96 in the mothers, with estimated haplotype diversities of 0.9828 and 0.9842, respectively. Fifty and 73 different haplotypes were found in the DXS6801-DXS6809-DXS6789 block in the grandfathers and the mothers, with estimated haplotype diversities of 0.9711 and 0.9742, respectively. We observed 10 between-cluster and one within-cluster recombinations in 99 female meioses. The overall per-locus mutation rate was 0.0034. This protocol allows for the characterization of the alleles of two sets of linked markers of the X-chromosome that can be useful in complex forensic cases.
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Affiliation(s)
- María Castañeda
- Unit of Legal Medicine, University of Cantabria-IFIMAV, Santander, Spain
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30
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Phillips C, Ballard D, Gill P, Court DS, Carracedo A, Lareu MV. The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data. Forensic Sci Int Genet 2011; 6:354-65. [PMID: 21871851 DOI: 10.1016/j.fsigen.2011.07.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 07/09/2011] [Accepted: 07/24/2011] [Indexed: 11/30/2022]
Abstract
Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses.
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Affiliation(s)
- C Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
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31
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Tillmar AO. Population genetic analysis of 12 X-STRs in Swedish population. Forensic Sci Int Genet 2011; 6:e80-1. [PMID: 21813348 DOI: 10.1016/j.fsigen.2011.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 07/05/2011] [Indexed: 11/25/2022]
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32
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Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast. Int J Legal Med 2011; 125:749-52. [DOI: 10.1007/s00414-011-0591-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
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33
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Łuczak S, Rogalla U, Malyarchuk BA, Grzybowski T. Diversity of 15 human X chromosome microsatellite loci in Polish population. Forensic Sci Int Genet 2011; 5:e71-7. [DOI: 10.1016/j.fsigen.2010.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 12/20/2010] [Accepted: 12/24/2010] [Indexed: 11/25/2022]
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34
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Inturri S, Menegon S, Amoroso A, Torre C, Robino C. Linkage and linkage disequilibrium analysis of X-STRs in Italian families. Forensic Sci Int Genet 2011; 5:152-4. [DOI: 10.1016/j.fsigen.2010.10.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Tillmar AO, Egeland T, Lindblom B, Holmlund G, Mostad P. Using X-chromosomal markers in relationship testing: calculation of likelihood ratios taking both linkage and linkage disequilibrium into account. Forensic Sci Int Genet 2010; 5:506-11. [PMID: 21167800 DOI: 10.1016/j.fsigen.2010.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 11/11/2010] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
Abstract
X-chromosomal markers in forensic genetics have become more widely used during recent years, particularly for relationship testing. Linkage and linkage disequilibrium (LD) must typically be accounted for when using close X-chromosomal markers. Thus, when producing the weight-of-evidence, given by a DNA-analysis with markers that are linked, the normally used product rule is invalid. Here we present an implementation of an efficient model for calculating likelihood ratios (LRs) with markers on the X-chromosome which are linked and in LD. Furthermore, the model was applied on several cases based on data from the eight X-chromosomal loci included in the Mentype(®) Argus X-8 (Biotype). Using a simulation approach we showed that the use of X-chromosome data can offer valuable information for choosing between the alternatives in each of the cases we studied, and that the LR can be high in several cases. We demonstrated that when linkage and LD were disregarded, as opposed to taken into account, the difference in calculated LRs could be considerable. When these differences were large, the estimated haplotype frequencies often had a strong impact and we present a method to estimate haplotype frequencies. Our conclusion is that linkage and LD should be accounted for when using the tested set of markers, and the used model is an efficient way of doing so.
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Affiliation(s)
- Andreas O Tillmar
- National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology, Artillerigatan 12, SE-58758, Linköping, Sweden.
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36
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Medina-Acosta E, Machado FB. Eyes wide open: the (mis)use of combined power of discrimination for X-linked short tandem repeats. Mol Biol Rep 2010; 38:4003-6. [PMID: 21110111 DOI: 10.1007/s11033-010-0518-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/13/2010] [Indexed: 01/15/2023]
Affiliation(s)
- Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego 2000, Parque Califórnia, Campos dos Goytacazes, RJ, CEP 28013-602, Brazil.
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37
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Gebrauch X-chromosomaler Marker in der forensischen Genetik. Rechtsmedizin (Berl) 2010. [DOI: 10.1007/s00194-010-0662-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Potentials and limits of pairwise kinship analysis using autosomal short tandem repeat loci. Int J Legal Med 2010; 124:205-15. [DOI: 10.1007/s00414-009-0413-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 12/18/2009] [Indexed: 10/19/2022]
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Evidence of partial and weak gametic disequilibrium across clusters of pericentromeric short tandem repeats loci on human X chromosome: proceed with caution in forensic genetics. Forensic Sci Int Genet 2010; 5:545-7. [PMID: 20457061 DOI: 10.1016/j.fsigen.2009.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 12/10/2009] [Indexed: 11/22/2022]
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Medina-Acosta E. Interlocus non-random association of multiallelic polymorphisms spanning the coagulation factor VIII gene on human chromosome distalmost Xq28. Haemophilia 2010; 16:525-37. [PMID: 20050928 DOI: 10.1111/j.1365-2516.2009.02161.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The most common severe hereditary bleeding disorder phenotype in humans, the coagulation factor VIII (F8) deficiency haemophilia A (HEMA), maps on Xq28 band, a region that comprises 11.7% of genes and 14.2% of phenotypes on X chromosome. Information about the distribution and extent of gametic disequilibrium (GD) covering the F8 gene is scarce, despite its relevance for linkage and association studies. The aim of this study was to determine the patterns, by frequency and strength, of non-random multiallelic interallelic associations between two-locus combinations of seven microsatellite loci (REN90833, F8Int25.2, F8Int22, F8Int13.2, HEMA154311.3, TMLHEInt5 and HEMA154507.3, in that physical order) spanning 0.813 Mb on distalmost Xq28. We measured sign-based interallelic D' coefficients in 106 men and in 100 women drawn from a single unrelated Brazilian population. Significance and patterns of GD using haploid and phased diploid sample probabilities were close to conformity. Only 9.18% of the variance of D' could be accounted for by changes in length, indicating that GD is not a monotonically decreasing function of length. We defined two regions of overlapping long-range GD extending 698 735 base pairs (bp) (REN90833/TMLHEInt5 block) and 689 900 bp (F8Int13.2/HEMA154507.3 block) The extent of GD overlap is 575 637 bp (F8Int13.2/TMLHEInt5 interstice). Extended haplotype homozygosity analysis centred at the F8 intronic loci revealed that the most frequent core haplotypes decay the least in the flanking GD. The F8 intronic loci attend distinct non-random association forces; F8Int13.2 serves at maintenance of the long-range overlapping pattern of GD, whereas F8Int25.2 and F8Int22 serve at lessening it in force or effect.
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Affiliation(s)
- E Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil.
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Bekada A, Benhamamouch S, Boudjema A, Fodil M, Menegon S, Torre C, Robino C. Analysis of 21 X-chromosomal STRs in an Algerian population sample. Int J Legal Med 2009; 124:287-94. [DOI: 10.1007/s00414-009-0397-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 11/18/2009] [Indexed: 11/29/2022]
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X chromosomal recombination—a family study analysing 39 STR markers in German three-generation pedigrees. Int J Legal Med 2009; 124:483-91. [DOI: 10.1007/s00414-009-0387-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 10/21/2009] [Indexed: 10/20/2022]
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Luo HB, Ye Y, Wang YY, Liang WB, Yun LB, Liao M, Yan J, Wu J, Li YB, Hou YP. Characteristics of eight X-STR loci for forensic purposes in the Chinese population. Int J Legal Med 2009; 125:127-31. [DOI: 10.1007/s00414-009-0386-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 10/23/2009] [Indexed: 10/20/2022]
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Sim JE, Lee HY, Yang WI, Shin KJ. Population genetic study of four closely-linked X-STR trios in Koreans. Mol Biol Rep 2009; 37:333-7. [DOI: 10.1007/s11033-009-9733-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 08/04/2009] [Indexed: 11/29/2022]
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