1
|
Calò L, Gentile F, Baio E, Raschellà C, Capelli C, Marino A. Variability and forensic efficiency of 12 X-STR markers in Namibian populations. Int J Legal Med 2024:10.1007/s00414-024-03299-9. [PMID: 39105780 DOI: 10.1007/s00414-024-03299-9] [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: 03/29/2024] [Accepted: 07/16/2024] [Indexed: 08/07/2024]
Abstract
STR loci localized on the X chromosome provide information additional to the autosomal markers routinely analyzed in forensic genetics, integrating genetic systems as Y-STRs and mitochondrial DNA in the investigation of complex kinship scenarios and mass disaster cases.In this study we genotyped 12 X-STR loci in 251 male samples from four populations of Namibia in southern Africa using the Investigator Argus X-12 kit (Qiagen, Hilden, Germany). Forensic efficiency parameters indicated high power of discrimination in the considered populations. As part of our investigation, we highlighted partial linkage associations between loci within known linkage groups (LGs) and identified several occurrences of previously unreported out-of-ladder (OL) alleles.Genetic distances between the Namibian populations here investigated and other African (Eritrea, Ethiopia, Somalia, Guinea, Cape Verde) and non-African (Germany, China, Philippines) populations using loci grouped in LGs mirrored their biogeographical distribution differently for each linkage group. Haplotype sharing within each LG revealed a high degree of population-specific types, hinting to the potential of these markers for ancestry applications.These results highlight the importance to produce specific and freely available population databases especially for multi-ethnic countries. This novel dataset is expected to be of interest for population studies that need an accessible reference dataset of African regions not currently well represented, as well as possible relevance for forensic applications focusing on the biogeographic origin of samples.
Collapse
Affiliation(s)
- Luca Calò
- Reparto Carabinieri Investigazioni Scientifiche di Parma - Sezione Biologia, Parma, Italy
| | - Fabiano Gentile
- Reparto Carabinieri Investigazioni Scientifiche di Parma - Sezione Biologia, Parma, Italy
| | - Elisa Baio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Alberto Marino
- Reparto Carabinieri Investigazioni Scientifiche di Parma - Sezione Biologia, Parma, Italy.
| |
Collapse
|
2
|
M. Albarzinji B, Hadi S, Ismael B, Barqee A, Hadi A, Lazim H. An X-STRs analysis of the Iraqi Sorani Kurds. PLoS One 2023; 18:e0294973. [PMID: 38011210 PMCID: PMC10681225 DOI: 10.1371/journal.pone.0294973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023] Open
Abstract
A database for the Iraqi Sorani Kurds, specifically focused on the 12 X-short tandem repeat (STR) loci, has been developed to fascilitate forensic and population genetics investigations. The present study involved genotyping 117 unrelated individuals from the Sorani Kurds ethnic group using the Investigator Argus X-12 QS kit. The analysis revealed that the DXS10135 locus exhibited the highest degree of polymorphism, as indicated by a polymorphism information content (PIC) value of 0.94565 and a gene diversity (GD) value of 0.95623. Conversely, the DXS8378 locus displayed the lowest level of polymorphism, with a PIC value of 0.61026 and a GD value of 0.68170. Notably, two individuals were found to possess a rare allele (allele = 6) at the DXS8378 locus, which was not included in the allelic ladder of the kit. Furthermore, a significant linkage disequilibrium (LD) (p < 0.05/117) was observed between the DXS10103 and DXS10101 loci on linkage group 3 (LG3). The ancestral composition of the five primary geographic regions, namely Africa, Middle East, East Asia, Europe, and South America, was determined through the utilization of the [Formula: see text] ratio. The findings of this analysis revealed that the Middle Eastern populations exhibited the lowest [Formula: see text] ratio, measuring at 0.23243, indicating a relatively lower ancestral diversity. Conversely, the European populations showcased the highest [Formula: see text] ratio, measuring at 0.27122, indicative of a greater ancestral diversity within this region. Additionally, the allelic richness indicators, namely distinctive and private alleles, indicated that Africa and the Middle East displayed the highest levels, while Far East Asia exhibited the lowest. This analysis supports the hypothesis of repeated founder effects during outward migrations, as evidenced by both the ancestry variability and the allelic richness. Consequently, the findings of this study have important implications for forensic genetics and population genetics research, particularly in relation to the consideration of genetic predispositions within specific ethnic groups.
Collapse
Affiliation(s)
- Balnd M. Albarzinji
- Kurdistan Institution for Strategic Studies and Scientific Research (KISSR), Sulaymaniyah, Iraq
| | - Shams Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Bahez Ismael
- Kurdistan Institution for Strategic Studies and Scientific Research (KISSR), Sulaymaniyah, Iraq
| | - Ahmed Barqee
- Kurdistan Institution for Strategic Studies and Scientific Research (KISSR), Sulaymaniyah, Iraq
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Hayder Lazim
- Faculty of Health, Social Care and Medicine (FHSCM), School of Medicine, Edge Hill University, Ormskirk, United Kingdom
| |
Collapse
|
3
|
Yang C, He M, Liu C, Liu X, Lun M, Su Q, Han X, Liu H, Wang M, Chen L, Liu C. Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application. Electrophoresis 2023; 44:1704-1713. [PMID: 37622566 DOI: 10.1002/elps.202300044] [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: 02/27/2023] [Revised: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresis platform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25 ng. All genotypes were obtained in the presence of 80 ng/µL humic acid, 2000 µmol/L calcium, 3000 µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951 × 10-32 and 1-4.2956 × 10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.
Collapse
Affiliation(s)
- Chengliang Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Meiyun He
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Miaoqiang Lun
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Qin Su
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xiaolong Han
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, P. R. China
| |
Collapse
|
4
|
Alwi AR, Mahat NA, Mohd Salleh F, Ishar SM, Kamaluddin MR, Rashid MRA. Internal validation of reduced PCR reaction volume of the Qiagen Investigator® Argus X-12 QS Kit from blood samples on FTA cards. J Forensic Sci 2023; 68:2103-2115. [PMID: 37646344 DOI: 10.1111/1556-4029.15370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
The onus of proof in criminal cases is beyond any reasonable doubt, and the issue on the lack of complete internal validation data can be manipulated when it comes to justifying the validity and reliability of the X-chromosomal short tandem repeats analysis for court representation. Therefore, this research evaluated the efficiency of the optimized 60% reduced volumes for polymerase chain reaction (PCR) amplification using the Qiagen Investigator® Argus X-12 QS Kit, as well as the capillary electrophoresis (CE) sample preparation for blood samples on Flinder's Technology Associates (FTA) cards. Good-quality DNA profile (3000-12,000 RFU) from the purified blood sample on FTA card (1.2 mm) were obtained using the optimized PCR (10.0 μL of PCR reaction volume and 21 cycles) and CE (9.0 μL Hi-Di™ Formamide and 0.3 μL DNA Size Standard 550 [BTO] and 27 s injection time) conditions. The analytical and stochastic thresholds were 100 and 200 RFU, respectively. Hence, the internal validation data supported the use of the optimized 60% reduced PCR amplification reaction volume of the Qiagen Investigator® Argus X-12 QS Kit as well as the CE sample preparation for producing reliable DNA profiles that comply with the quality assurance standards for forensic DNA testing laboratories, while optimizing the analytical cost.
Collapse
Affiliation(s)
- Aedrianee Reeza Alwi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia
- Department of Chemistry Malaysia Johor State, Johor Bahru, Malaysia
| | - Naji Arafat Mahat
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia
- Centre for Sustainable Nanomaterials, Ibnu Sina Institute for Scientific and Industrial Research, Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia
| | - Seri Mirianti Ishar
- Forensic Science Program, Faculty of Health Sciences, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Mohammad Rahim Kamaluddin
- Psychology and Human Well Being Research Centre, Faculty of Social Sciences and Humanities, Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Mohd Radzniwan A Rashid
- Family Medicine Unit, Faculty of Medicine and Health Science, Universiti Sains Islam Malaysia (USIM), Nilai, Malaysia
| |
Collapse
|
5
|
Xiao C, Yang X, Yu Z, Wu W, Wang Y, Xu Q, Chen L. Genetic polymorphism and variability in the Guangdong Hakka, Teochew, and Cantonese groups: A comprehensive analysis of 19 X-STRs. Ann Hum Genet 2023; 87:232-240. [PMID: 37337755 DOI: 10.1111/ahg.12518] [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: 09/27/2022] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND X chromosomeshort tandem repeat (X-STR) loci are playing an increasingly important role inforensic work, identifying female traces in male contamination and explainingcomplex kinship analyses. METHODS In this study, we analyzed thegenetic polymorphism of 19 X-STR loci in the Guangdong Hakka, Teochew and Cantonese groups, respectively, aswell as in the Guangdong Hakka, Teochew andCantonese pooled Han. The genetic diversity and forensic characteristics of the19 X-STRs and 7 linkage groups were investigated, respectively. RESULTS The experiments showed that the genetic diversity (GD) and polymorphism information content (PIC) in the pooledGuangdong Han ranged from 0.5320 to 0.9234 and 0.4369 to 0.9171, respectively, and the cumulative power of discrimination for males (PDM), power of discrimination for females (PDF) and mean paternity exclusion chance (MEC) were higher than 0.9999999, indicating that the 19 X-STRs had high geneticpolymorphism and discriminatory power. Genetic differences among Chinese Hansubgroups and among different Chinese populations were investigated byphylogenetic reconstruction and principal component analysis (PCA), respectively. Genetic analyses based on neighbor-joining (NJ) tree and principal component analysis plot showed that Cantonese, Teochew and Hakka were closely genetically related, and different populations with closer linguistic components had more genetic affinity. CONCLUSIONS This study adds to the forensic X-STR database and demonstrates the forensic efficiency of 19 X-STRs for the Hakka, Teochewand Cantonese populations in Guangdong, and the pooled Han of Hakka, Teochewand Cantonese people in Guangdong.
Collapse
Affiliation(s)
- Cheng Xiao
- Guangzhou Red Cross Hospital, Guangzhou, China
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xingyi Yang
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Zhonghao Yu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Weibin Wu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Yuan Wang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Quyi Xu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| |
Collapse
|
6
|
Aneli S, Fariselli P, Chierto E, Bini C, Robino C, Birolo G. Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics. PLoS Comput Biol 2023; 19:e1011474. [PMID: 37721960 PMCID: PMC10538763 DOI: 10.1371/journal.pcbi.1011474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/28/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns we developed Recombulator-X, a new open-source Python tool. The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm. Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. In conclusion, Recombulator-X makes the estimation process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices.
Collapse
Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Carla Bini
- Department of Medical and Surgical Sciences, Section of Legal Medicine, University of Bologna, Bologna, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
- S.C. Medicina Legale, AOU Città della Salute e della Scienza, Turin, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
| |
Collapse
|
7
|
Long F, Fang H, Zhang C, Chen S, Huang D, Xiao C. Genetic polymorphisms of 19 X-STRs in populations of Hubei Han and Guangxi Zhuang and their comparisons with 13 other Chinese populations. Ann Hum Biol 2023; 50:8-14. [PMID: 36636011 DOI: 10.1080/03014460.2023.2166990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND A prerequisite for applying short tandem repeat (STR) kits is obtaining population allele and/or haplotype frequencies and forensic parameters. AIM Firstly, we aimed to investigate the population data of 19 X-chromosomal STRs (X-STRs) included in the AGCU X19 STR kit in the Han people residing in Hubei Province, Central China, and the Zhuang people residing in the Guangxi Zhuang Autonomous Region of South China. Furthermore, we compared these population data with those for other Chinese populations. SUBJECTS AND METHODS In total, 509 unrelated Han males and 266 unrelated Zhuang males were genotyped using the AGCU X19 STR kit. Allele frequencies, haplotype frequencies, and forensic parameters were computed, and genetic differences among 15 Chinese populations were analysed. RESULTS The 19 X-STRs showed a high power of discrimination and high mean chance of exclusion, whether calculated using allele or haplotype frequencies. Major differences were found between Han and Oroqen, Uyghur, Mongolian, Tibetan, Li, and Yi populations. Aberrant biallelic patterns at DXS10159, DXS10134, and DXS10079 and allelic dropouts at DXS10164 were observed. CONCLUSION The 19 X-STRs were highly polymorphic in the Hubei Han and Guangxi Zhuang populations, and the AGCU X19 STR kit was shown to be suitable for forensic casework.
Collapse
Affiliation(s)
- Fei Long
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Fang
- Department of Criminal Investigation, Wuhan Public Security Bureau, Wuhan, China
| | - Chunmei Zhang
- Department of Criminal Investigation, Wuhan Public Security Bureau, Wuhan, China
| | - Shengjie Chen
- Nanning Public Security Bureau Qingxiu Branch, Nanning, China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
8
|
Kakkar S, Sarma P, Panigrahi I, Mandal SP, Shrivastava P, Kumawat RK. Development of a new screening method for faster kinship analyses in mass disasters: a proof of concept study. Sci Rep 2022; 12:20372. [PMID: 36437267 PMCID: PMC9701697 DOI: 10.1038/s41598-022-22805-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Kinship analysis in forensics is based on the calculation of the respective kinship indices. However, this calculation is only possible when the subject under identification has been associated with a particular population, whose allele frequency data is available for the particular set of STR markers used in the forensic practices. In the case of mass disasters, where a large number of individuals are to be identified, gathering the population frequency data and calculating the kinship indices can be an intricate process which requires a lot of time and huge resources. The new method of allele matching cut off score (AMCOS) developed in this study is based on the allele sharing approach. This approach simply refers to the number of shared alleles (1 or 2) between the two individuals; also known as identical by state (IBS) alleles which might have been inherited from a recent common ancestor in which the alleles are identical by descendent (IBD). In case of mass disasters, this method can be used to narrow down the number of pairs (dead and alive) to be matched for kinship without using the allele frequency data. The results obtained from this method could further be confirmed by LR based method, which uses the allele frequency data of the respective population of the pairs being tested for kinship. AMCOS method has been tested for its sensitivity, specificity and various other statistical parameters and has shown promising values for the same in various types of kinship analyses. This ascertains the authenticity and potential use of this method in forensic practice but only after its validation in a larger sample size. AMCOS method has been tested on siblings and grandparent-grandchildren by using autosomal and X-STR markers both, as the reference samples from the parents cannot always be available for the identification. The present study also compared the results shown by the autosomal and X-STR markers in siblings and grandparent-grandchildren identification, thereby suggesting the use of better set of markers on the basis of obtained values of various statistical parameters.
Collapse
Affiliation(s)
- Sonia Kakkar
- grid.415131.30000 0004 1767 2903Department of Forensic Medicine, PGIMER, Chandigarh, 160012 India
| | - Phulen Sarma
- Department of Pharmacology, AIIMS, Guwahati, 781101 India
| | - Inusha Panigrahi
- grid.415131.30000 0004 1767 2903Advanced Pediatrics Centre, PGIMER, Chandigarh, 160012 India
| | - S. P. Mandal
- grid.415131.30000 0004 1767 2903Department of Forensic Medicine, PGIMER, Chandigarh, 160012 India
| | - Pankaj Shrivastava
- Biology and Serology Division, Department of Home (Police), Govt. of MP, Regional Forensic Science Laboratory, Bhopal, 462003 India
| | - R. K. Kumawat
- grid.513284.9DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan 302016 India
| |
Collapse
|
9
|
Jin X, Ren Z, Zhang H, Wang Q, Liu Y, Ji J, Yang M, Zhang H, Hu W, Wang N, Wang Y, Huang J. Development and forensic efficiency evaluations of a novel multiplex amplification panel of 17 Multi-InDel loci on the X chromosome. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.985933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multi-InDel, as the novel genetic markers, showed great potential in forensic research. Whereas, most scholars mainly focused on autosomal Multi-InDels, which might provide limited genetic information in some complex kinship cases. In this study, we selected 17 Multi-InDels on the X chromosome and developed a multiplex amplification panel based on the next-generation sequencing (NGS) technology. Genetic distributions of these 17 loci in Beijing Han, Chinese Southern Han, and the studied Guizhou Han populations revealed that most loci showed relatively high forensic application values in these Han populations. In addition, more allelic variations of some loci were observed in the Guizhou Han than those in Beijing Han and Southern Han populations. Pairwise FST values, multi-dimensional analysis, and phylogenetic tree of different continental populations showed that selected 17 loci generally could differentiate African, European, East Asian, and South Asian populations. To sum up, the developed panel in this study is not only viewed as the high-efficient supplementary tool for forensic individual identification and paternity analysis, but it is also beneficial for inferring biogeographical origins of different continental populations.
Collapse
|
10
|
Forensic Applications of Markers Present on the X Chromosome. Genes (Basel) 2022; 13:genes13091597. [PMID: 36140765 PMCID: PMC9498577 DOI: 10.3390/genes13091597] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.
Collapse
|
11
|
Song F, Wei X, Zhou C, Wang S, Deng C, Liao M, Luo H. Resolving the recombination pattern of 38 X-STRs from Chinese Han three-generation pedigrees. Leg Med (Tokyo) 2022; 59:102135. [PMID: 36029693 DOI: 10.1016/j.legalmed.2022.102135] [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: 06/29/2022] [Revised: 07/26/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
X-chromosomal markers have been proved as a useful tool for solving complex kinship cases due to its sex-linked inheriting feature. Among these markers, tightly linked X-STR clusters forming haplotypes are highly informative. The analysis of the haplotypes requires determination of linkage disequilibrium. In this study, genetic linkage, recombination fractions and mutation rates of 38 X-STR loci in 177 three-generation pedigrees were investigated. Genetic linkage analysis and calculation of recombination fractions were performed within each pair of markers and clusters. Then mutation rates were calculated. The results showed that, a) 22 recombination events happened within the tightly linked X-STR clusters, which span<1.0 Mb; b) significantly linked marker pairs were observed with the LOD (logarithm of the odds) scores > 2.0 (2.0104 to 54.8316); c) the average mutation rate of the 38 X-STR loci was 1.32 × 10-3 per meiosis in the Chinese Han population, with DXS10135 and DXS8377 presenting notably high mutation rate (6.5 × 10-3). Our results confirmed that meiotic recombination was not a simple function of physical distance, so that whether recombination occurred at the closely clustered X-STRs or not should be assumed cautiously considering the stability of haplotypes in inheritance process for kinship analysis. This study supplemented the existing database and laid an experimental foundation for the future study on genetic characteristics, recombination, and mutation of the X-STRs.
Collapse
Affiliation(s)
- Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chengye Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chuncao Deng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
12
|
Extended population genetic analysis of 12 X-STRs - Exemplified using a Norwegian population sample. Forensic Sci Int Genet 2022; 60:102745. [PMID: 35870434 DOI: 10.1016/j.fsigen.2022.102745] [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: 10/21/2021] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022]
Abstract
The use of X-chromosomal markers to resolve questions of relatedness has experienced a significant increase during the last years in forensic genetics. Perhaps primarily due to the emergence of commercial kits, but equally important due to an increased awareness of the utility of those markers. The X-chromosomal inheritance pattern entails that some cases, for instance paternal half-sisters, can potentially be resolved using a few X-chromosomal markers alone. For the statistical assessment in kinship cases it is of importance to have relevant population frequency data. In the present study 631 unrelated males from a Norwegian population sample are analyzed. The resulting haplotypes are compared to previously studied population samples and a deeper analysis of the linkage disequilibrium (LD) structure is conducted. We demonstrate that the power to detect LD will be low when few males, say below 300, are analyzed. We use entropy to describe the degree of LD between multiallelic loci and describe how this measure varies between different studied populations. Large population frequency databases have been recommended when using X-chromosomal markers, and we show that by combining reference databases from genetically similar populations, more precise haplotype frequency estimates can be obtained for rare haplotypes which improves the statistical assessment of the weight of evidence. In addition, we promote the use of simulations to assess the utility of STR markers in contrast to standard forensic parameters. Specifically we perform extensive simulations on cases where X-chromosomal markers are important and illustrate how the results can be used to infer the information gained from these markers.
Collapse
|
13
|
Curtis R, Ward D, Taylor D, Henry J. Investigation of X-STR haplotype diversity in the Australian Aboriginal population. AUST J FORENSIC SCI 2022. [DOI: 10.1080/00450618.2022.2048690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rhianna Curtis
- Division of Biology, Forensic Science SA, Adelaide, South Australia
| | - Denise Ward
- Division of Biology, Forensic Science SA, Adelaide, South Australia
| | - Duncan Taylor
- Division of Biology, Forensic Science SA, Adelaide, South Australia
- College of Science and Engineering, Flinders University of South Australia, Adelaide, South Australia
| | - Julianne Henry
- Division of Biology, Forensic Science SA, Adelaide, South Australia
- College of Science and Engineering, Flinders University of South Australia, Adelaide, South Australia
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Yang Q, Qian J, Shao C, Yao Y, Zhou Z, Xu H, Tang Q, Qian X, Xie J. Identification and Characterization of Nine Novel X-Chromosomal Short Tandem Repeats on Xp21.1, Xq21.31, and Xq23 Regions. Front Genet 2021; 12:784605. [PMID: 34868274 PMCID: PMC8635773 DOI: 10.3389/fgene.2021.784605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The application of X-chromosomal short tandem repeats (X-STRs) has been recognized as a powerful tool in complex kinship testing. To support further development of X-STR analysis in forensic use, we identified nine novel X-STRs, which could be clustered into three linkage groups on Xp21.1, Xq21.31, and Xq23. A multiplex PCR system was built based on the electrophoresis. A total of 198 unrelated Shanghai Han samples along with 168 samples from 43 families was collected to investigate the genetic polymorphism and forensic parameters of the nine loci. Allele numbers ranged from 5 to 12, and amplicon sizes ranged from 146 to 477 bp. The multiplex showed high values for the combined power of discrimination (0.99997977 in males and 0.99999999 in females) and combined mean exclusion chances (0.99997918 and 0.99997821 in trios, 0.99984939 in duos, and 0.99984200 in deficiency cases). The linkage between all pairs of loci was estimated via Kosambi mapping function and linkage disequilibrium test, and further investigated through the family study. The data from 43 families strongly demonstrated an independent transmission between LGs and a tight linkage among loci within the same LG. All these results support that the newly described X-STRs and the multiplex system are highly promising for further forensic use.
Collapse
Affiliation(s)
- Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jinglei Qian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaoqin Qian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
16
|
Semikhodskii A, Krassotkin Y, Makarova T, Zavarin V, Ilina V, Sutyagina D. Genetic diversity and forensic parameters of 12 X-STR included in Argus X-12® marker panel in the population of the Russian Federation. Ann Hum Biol 2021; 48:430-436. [PMID: 34514921 DOI: 10.1080/03014460.2021.1980104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND X-chromosome specific short tandem repeats (X-STR) are indispensable for parentage analysis, kinship determination and forensic casework. AIM To determine allelic frequencies and forensic parameters of the 12 X-STR markers from the Investigator® Argus X-12® kit panel for the population of the Russian Federation. SUBJECTS AND METHODS We analysed 803 unrelated individuals from 58 localities across the Russian Federation. Intra-population genetic diversity was evaluated and comparison of the Russian population with 19 geographically distant populations performed. RESULTS Heterozygosity values across all the loci ranged from 0.685 for DXS7423 to 0.939 for DXS10135. Deviations from the Hardy-Weinberg equilibrium were observed for DXS10074 (p < 0.05) and DXS10146 (p < 0.01). The value for power of discrimination across all the loci in males was 0.9999999996, while in females it equalled 0.9999999999. Combined mean exclusion chances MECKruger, MECKishida, MECD-trio, and MECD-duo were 0.9999988168, 0.9999999983, 0.9999999983, and 0.9999995797, respectively. Phylogenetic analysis indicated small genetic differences between the Russian population and the populations of neighbouring Lithuania, Belarus and the Slavic-speaking countries (Czech Republic, Serbia and Croatia). CONCLUSIONS This paper is the first report of forensically important parameters and allele frequencies for the 12 X-STR loci included in Argus X-12® marker system in the population of the Russian Federation.
Collapse
Affiliation(s)
| | | | | | | | - Viktoria Ilina
- Scientific Department, Medical Genomics LLC, Russian Federation
| | - Daria Sutyagina
- Scientific Department, Medical Genomics LLC, Russian Federation
| |
Collapse
|
17
|
Polymorphism and haplotype analysis of three novel short tandem repeat loci in the p11.4 region of human X chromosome. Int J Legal Med 2021; 136:513-518. [PMID: 34741211 DOI: 10.1007/s00414-021-02739-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
X-chromosomal short tandem repeats (X-STRs) are useful for the identification of absent single parents and complex blood relations. In the present study, we aimed to identify novel STR loci for use as DNA markers by conducting polymorphism and haplotype analyses. We detected three novel STR loci (LC552061, LC552062, and LC552063, with repetitive structures of (GGAA)n(GGGA)m, (CCTT)n(CCCT)m, and (ATTT)n, respectively) in the p11.4 region of the X chromosome. For these X-STRs, the polymorphism information content values ranged from 0.5766 to 0.6377 and the power of discrimination in males and females ranged from 0.6269 to 0.6844 and from 0.8105 to 0.8537, respectively. The linkage disequilibrium analysis revealed p values of < 0.0001, < 0.0001, and 0.00909 between LC552061 and LC552062, LC552061 and LC552063, and LC552062 and LC552063, respectively. Additional linkage disequilibrium analysis including seven previously analyzed loci (LC149476, LC149479, LC149480, LC149484, LC317283, LC317284, and LC317285) revealed a p value of < 0.001 among each of the five loci (LC149476, LC149479, LC149480, LC149484, and LC317283) and between LC317284 and LC317285, indicating that they were a linked group. These results indicate that, in addition to the seven previously detected loci, the three novel X-STR loci identified in the present study might be useful DNA markers for complex kinship analysis and might support the Investigator® Argus X-12 kit.
Collapse
|
18
|
Liu L, Yuan J, Miao L, Huang R, Zhang X, Nie S, Hu L. Genetic polymorphisms of 16 X-STR loci analyzed in the Han population of Yunnan Province, Southwest China. Leg Med (Tokyo) 2021; 54:101974. [PMID: 34736140 DOI: 10.1016/j.legalmed.2021.101974] [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: 08/04/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
To investigate the genetic diversity and forensic identification efficiency of X-chromosomal short tandem repeats (X-STRs) in the Yunnan Han population, 16 X-STRs in 415 Yunnan Han individuals (247 males and 168 females) were studied. A total of 137 alleles were detected, and all loci in the Yunnan Han population were highly polymorphic. The combined discrimination of males (PDm) and females (PDf) was 0.9999997769115 and 0.999999999999999999996, respectively. Interpopulation comparisons between the Yunnan Han population and 21 other populations showed that the evolutionary relationships between different groups with the same ethnic group or nearby geographic origins were closer. This study provides the first data on X-STR genetic polymorphisms in the Yunnan Han population and enriches the X-STR database for the Chinese Han population.
Collapse
Affiliation(s)
- Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Jiahui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Lei Miao
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Renwu Huang
- Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| |
Collapse
|
19
|
Liu Y, Ye Y, Yi XQ, Zhang JH, Fan GY, Hao DY. Phylogenetic analyses of the 19 STR loci in X chromosome revealed discriminant forensic characteristics for Chinese Daur and Oroqen minorities. Int J Legal Med 2021; 136:551-553. [PMID: 34510269 DOI: 10.1007/s00414-021-02697-7] [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: 07/26/2021] [Accepted: 08/27/2021] [Indexed: 10/20/2022]
Abstract
In respect of forensic genetics, X-STRs are widely applied for deficiency paternity cases. Given the popularization of AGCU-X19 STR Kit in China, there has been investigation conducted into the genetic data and forensic parameters of 19 X-STR loci in many of the Chinese ethnic groups, which makes it possible to perform nationwide phylogenetic comparation. To evaluate the allele and haplotype diversity of 19 X-STR loci and to explore their forensic efficiency in the Daur and Oroqen minorities, unrelated healthy Daur (n = 86) and Oroqen (n = 165) individuals were recruited from Heilongjiang province, so as to reveal the phylogenetic relationship between the two minorities and other Chinese ethnic groups. Of the Daur and Oroqen minorities, 172 and 183 alleles at the 19 X-STR loci were observed, respectively. Haplotype diversity exceeded 0.9 among all the linkage clusters. High cumulative value was observed for the power of discrimination, the probability of exclusion, and the mean exclusion chance for deficiency cases (normal trios and duo cases). As revealed by this study, the panel of 19 X-STR loci is an effective supplementary tool for the kinship test of the studied nationalities.
Collapse
Affiliation(s)
- Yang Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China.,Forensic Center, College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, Zhejiang, China
| | - Yi Ye
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiao-Qin Yi
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jia-Hui Zhang
- College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, Zhejiang, China
| | - Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, Zhejiang, China.
| | - Dong-Yun Hao
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China.
| |
Collapse
|
20
|
Chen L, Pan X, Wang Y, Du W, Wu W, Tang Z, Xiao C, Han X, Liu C, Liu C. Development and Validation of a Forensic Multiplex System With 38 X-InDel Loci. Front Genet 2021; 12:670482. [PMID: 34484288 PMCID: PMC8416044 DOI: 10.3389/fgene.2021.670482] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
In the present study, a novel multiplex system, AGCU X-InDel 38 kit, was designed to amplify 38 X-InDel markers and amelogenin in a single Polymerase Chain Reaction (PCR). To demonstrate the suitability and efficiency for forensic applications, a series of validation experiments were conducted, including sensitivity, species specificity, reproducibility, stability, case samples, balance of peak height, size precision, as well as allele frequency and forensic parameter analysis. The results showed that AGCU X-InDel 38 kit was capable to get full profiles even with 62.5 pg of template DNA, and full profiles can be obtained when hematin concentration ≤25 μmol/L, or hemoglobin concentration ≤50 μmol/L, showing good tolerance to six common inhibitors. Moreover, the analyzed case samples indicated that AGCU X-InDel 38 kit had better performance for degraded and trace DNA samples. The 200 unrelated males from Guangdong Han population showed that the combined PDMale and PDFemale were both more than 0.999999999, and the combined MECKrüger, MECKishida, and MECDesmarais Duo were 0.999369481, 0.999999917, and 0.999941556, respectively. Robust discrimination capability of this novel multiplex system could be demonstrated through the high values of forensic parameters. In conclusion, AGCU X-InDel 38 kit is sensitive, precise, reproducible, and highly informative and could be used as a complementary tool for complex and challenging kinship cases.
Collapse
Affiliation(s)
- Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiyong Pan
- School of Forensic Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuan Wang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Weian Du
- Guangdong Homy Genetics Incorporation, Foshan, China.,AGCU ScienTech Incorporation, Wuxi, China
| | - Weibin Wu
- Guangdong Homy Genetics Incorporation, Foshan, China.,AGCU ScienTech Incorporation, Wuxi, China
| | - Zhenya Tang
- Guangdong Provincial Forensic Science Center, Guangzhou, China
| | - Cheng Xiao
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Xiaolong Han
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangzhou Forensic Science Institute, Guangzhou, China
| | - Changhui Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangzhou Forensic Science Institute, Guangzhou, China
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Messaoudi SA, Babu SR, Alsaleh AB, Albujja M, Al-Snan NR, Chaudhary AR, Kassab AC, Assidi M. Population genetic data for 12 X-STR loci in the Central Saudi region using investigator Argus X-12 amplification kit. Ann Hum Biol 2021; 48:321-326. [PMID: 34340612 DOI: 10.1080/03014460.2021.1957147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND X-chromosome short tandem repeat (X-STR) markers are important in forensic identity investigations and kinship analysis. SUBJECT AND METHODS In the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of Saudi Arabia in order to develop an allelic frequency database for the markers included in the kit. RESULTS DXS10146 locus was the most informative with 21 alleles, while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci, either as individual markers or as linkage groups, provide genetic information with high discrimination that is appropriate for forensic purposes with polymorphism information content (PIC), power of exclusion (PE), and paternity index (PI) varying from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically closer to the Egyptian and Emirati populations and distant to the Turkish population. CONCLUSION The current study revealed that Investigator® Argus 12 X-STR kit would support the forensic application, kinship testing involving female offspring, and human identification in the Saudi population.
Collapse
Affiliation(s)
- Safia A Messaoudi
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Saranya R Babu
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Abrar B Alsaleh
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Albujja
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Noora R Al-Snan
- Forensic Science Laboratory, Directorate of Forensic Science, General Directorate of Criminal Investigation and Forensic Science, Ministry of Interior, Manama, Kingdom of Bahrain
| | - Abdul Rauf Chaudhary
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Ahmed Ch Kassab
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research (CEGMR), Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Liu L, Yao J, Huang Y, Gao L, Dai J, Yuan X, Zhang X, Nie S, Hu L. Genetic polymorphisms of 16 X-STR loci in the Hani population from Southwest China. Forensic Sci Res 2021; 7:196-201. [PMID: 35784423 PMCID: PMC9246014 DOI: 10.1080/20961790.2021.1877389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Jinyong Yao
- Honghe Public Security Bureau, Honghe, China
| | | | - Lei Gao
- Honghe Public Security Bureau, Honghe, China
| | - Jiameng Dai
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | | | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| |
Collapse
|
25
|
Jia J, Liu X, Fan Q, Fang C, Wang M, Zhang J, Li W, Shi L, Zhang X, Chen C, Yu Z, Li C, Yun K, Yan J. Development and validation of a multiplex 19 X-chromosomal short tandem repeats typing system for forensic purposes. Sci Rep 2021; 11:609. [PMID: 33436869 PMCID: PMC7803774 DOI: 10.1038/s41598-020-80414-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/15/2020] [Indexed: 11/20/2022] Open
Abstract
X-chromosome short tandem repeat (X-STR) markers are a powerful complementary system used for paternity and forensic casework. This study presents the development and validation of a new highly efficient multiplex-fluorescent-labeled 19 X-STR typing system, including DXS10079, DXS101, DXS10135, DXS10162, DXS6795, DXS6800, DXS6803, DXS6807, DXS6809, DXS6810, DXS7133, DXS7423, DXS981, DXS9902, DXS9907, GATA165B12, GATA172D05, GATA31E08 and HPRTB along with sex-typing locus, amelogenin. The system was validated according to guidelines issued by the Scientific Working Group on DNA Analysis Methods. Allele frequency and forensic parameters were investigated from 1085 (494 males and 591 females) unrelated Beijing Han individuals, the combined power of discrimination by the 19 X-STR loci in females and males, as well as the combined mean exclusion chance in trios and duos, were 0.999999999999999995, 0.99999999995, 0.9999999995, and 0.9999996, respectively. The results demonstrate that this multiplex system is robust and reliable, and considered to be a powerful tool for forensic application.
Collapse
Affiliation(s)
- Juan Jia
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Xu Liu
- Beijing Center for Physical and Chemical Analysis, Beijing, 10089, China
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing, 100089, China
| | - Qingwei Fan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Chen Fang
- Beijing Center for Physical and Chemical Analysis, Beijing, 10089, China
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing, 100089, China
| | - Mengchun Wang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Jiarong Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Linyu Shi
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Chuguang Chen
- Beijing Microread Genetics Co., Ltd, Beijing, 100044, China
| | - Zailiang Yu
- Beijing Microread Genetics Co., Ltd, Beijing, 100044, China
| | - Chen Li
- Beijing Microread Genetics Co., Ltd, Beijing, 100044, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China.
| |
Collapse
|
26
|
Khacha-Ananda S, Mahawong P. Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population. MEDICINE, SCIENCE, AND THE LAW 2021; 61:34-43. [PMID: 33045921 DOI: 10.1177/0025802420965000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Short tandem repeats (STRs) are widely used as DNA markers in paternity testing and criminal investigations because of their high genetic polymorphism among individuals in population. However, many factors influence genetic variations of STRs. Therefore, understanding STR information within individual populations could provide database and scientifically reliable STR genotyping for forensic genetic purposes. We aimed to examine allele frequencies of X-STRs, including some forensic parameters, in a northern Thai population. A retrospective descriptive study was conducted by collecting X-STR data from unrelated individuals living in a northern region of Thailand. The allele frequency and forensic parameters - for example polymorphism information content (PIC), power of discrimination in females and males (PDf and PDm), mean exclusion chance (MEC) and haplotype frequency - were calculated. The Hardy-Weinberg equilibrium was analysed. A total of 132 alleles were observed, with corresponding allele frequency ranging from 0.0064 to 0.4904. The PIC of all loci was >0.6, representing high genetic polymorphism, except DXS8378 and DXS7423. Notably, DXS10135 was the most diverse loci with the highest PD and MEC, while DXS7423 was the least polymorphic marker with the lowest PD and MEC. The highest haplotype diversity in male data was on linkage group III (DXS10101-DXS10103-HPRTB) by 0.9895. The genetic distance analysis demonstrated that the northern Thai population had a close relationship with Taiwanese (DA = 0.023). There are no significant deviations among the Hardy-Weinberg equilibrium except DXS10148. This study has established a northern Thai X-STRs reference database to be used as a tool for forensic genetic purposes.
Collapse
Affiliation(s)
- Supakit Khacha-Ananda
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Thailand
| | - Phatcharin Mahawong
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Thailand
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Luo L, Gao H, Yao L, Long F, Zhang H, Zhang L, Liu Y, Yu J, Yu L, Chen P. Genetic diversity, forensic feature, and phylogenetic analysis of Guizhou Tujia population via 19 X-STRs. Mol Genet Genomic Med 2020; 8:e1473. [PMID: 32881358 PMCID: PMC7667307 DOI: 10.1002/mgg3.1473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 08/04/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND X-chromosome short tandem repeats (X-STRs) with unique sex-linkage inheritance models play a complementary role in forensic science. Guizhou is a multiethnic province located in southwest China and some genetic evidence focusing on X-STRs for various minorities was reported. However, population data of Guizhou Tujia are scarce. METHODS A total of 507 Guizhou Tujia individuals were profiled using the AGCU X-19 STR kit. Allele frequencies and forensic parameters were calculated. Additionally, population genetic relationships between Guizhou Tujia and other 19 populations were explored. RESULTS A total of 257 alleles with the allele frequencies ranged from 0.0013 to 0.6098 were found. The combined power of discrimination in males and females and mean exclusion chances in all case scenarios were all greater than 0.99999. Population comparisons showed Guizhou Tujia had a homogeneity with all Han populations from different administrative regions, and other ethnic populations residing in Guizhou, while had obviously genetic heterogeneity with the Altaic family populations except Xibe. CONCLUSION Nineteen X-STRs can afford a reliable and informative database of Guizhou Tujia population for human identification and paternity testing, especially in complex biological relations. The genetic relationships of Chinese are significantly influenced by the geographic position and ethnolinguistic origin.
Collapse
Affiliation(s)
- Li Luo
- Key Laboratory of Cell Engineering in Guizhou ProvinceAffiliated Hospital of Zunyi Medical UniversityZunyiChina
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic ScienceShanghaiChina
| | - Hongyan Gao
- Key Laboratory of Cell Engineering in Guizhou ProvinceAffiliated Hospital of Zunyi Medical UniversityZunyiChina
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou ProvinceAffiliated Hospital of Zunyi Medical UniversityZunyiChina
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Fei Long
- Department of Forensic Biology EvidenceZunyi City Public Security BureauZunyiGuizhouChina
| | - Hao Zhang
- Key Laboratory of Cell Engineering in Guizhou ProvinceAffiliated Hospital of Zunyi Medical UniversityZunyiChina
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Lushun Zhang
- Department of Pathology and PathophysiologyChengdu Medical CollegeChengduChina
| | - Yong Liu
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Jian Yu
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Limei Yu
- Key Laboratory of Cell Engineering in Guizhou ProvinceAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou ProvinceAffiliated Hospital of Zunyi Medical UniversityZunyiChina
- Center of Forensic ExpertiseAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| |
Collapse
|
29
|
Katja K, Inga V, Ramona L, Almuth C, Maria MN. Mucopolysaccharidosis type I due to maternal uniparental disomy of chromosome 4 with partial isodisomy of 4p16.3p15.2. Mol Genet Metab Rep 2020; 25:100660. [PMID: 33117653 PMCID: PMC7582098 DOI: 10.1016/j.ymgmr.2020.100660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/27/2022] Open
Abstract
Mucopolysaccharidosis type I (MPS I) is a rare lysosomal storage disease caused by biallelic mutations in IDUA, the gene coding for the lysosomal enzyme alpha L-iduronidase. Clinically MPS I is a chronic progressive multisystem disease typically presenting with coarse facial features, skeletal deformities, joint contractures, and multi-organ involvement. Hurler syndrome (MPS IH) represents the severe end of the spectrum of mucopolysaccharidosis type I and is characterized by central nervous system involvement leading to childhood dementia. Here we report on a severe affected MPS IH patient who is homozygous for a splice site mutation (c.158 + 1G > A) in the IDUA gene. Further analyses revealed maternal uniparental disomy of chromosome 4 with partial isodisomy of the telomeric end of chromosome 4 (4.p16.3p15.2), representing an extraordinary mode of inheritance with a much lower re-occurrence risk for MPS I in the family.
Collapse
Affiliation(s)
- Kloth Katja
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vater Inga
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Lindschau Ramona
- International Center for Lysosomal Disorders (ICLD), Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Caliebe Almuth
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Muschol Nicole Maria
- International Center for Lysosomal Disorders (ICLD), Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
30
|
Khubrani YM, Jobling MA, Wetton JH. Massively parallel sequencing of sex-chromosomal STRs in Saudi Arabia reveals patrilineage-associated sequence variants. Forensic Sci Int Genet 2020; 49:102402. [PMID: 33035796 DOI: 10.1016/j.fsigen.2020.102402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/18/2020] [Accepted: 09/27/2020] [Indexed: 11/27/2022]
Abstract
Massively parallel sequencing (MPS) of forensic STRs has the potential to reveal additional allele diversity compared to conventional capillary electrophoresis (CE) typing strategies, but population studies are currently relatively few in number. The Verogen ForenSeq™ DNA Signature Prep Kit includes both Y-STRs and X-STRs among its targeted loci, and here we report the sequences of these loci, analysed using Verogen's ForenSeq™ Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0, in a representative sample of 89 Saudi Arabian males. We identified 56 length variants (equivalent to CE alleles) and 75 repeat sequence sub-variants across the six X-STRs analysed; equivalent figures for the set of 24 Y-STRs were 147 and 192 respectively. We also observed two flanking sequence variants for the X-, and six for the Y-STRs. Recovery of sequence data and concordance with CE data (where available) across the tested loci was good, though rare flanking variation affected interpretation and allele calling at DYF387S1 and DXS7132. Examination of flanking sequences of the Y-STRs revealed five SNPs (L255, M4790, BY7692, Z16708 and S17543) previously shown to define specific haplogroups by Y-chromosome sequencing. These define Y-haplogroups in 62 % of our sample, a proportion that increases to 91 % when haplogroup-associated repeat-sequence motifs are also considered. A population-level comparison of the Saudi Arabian X-STRs with a global sample showed our dataset to be part of a large cluster of populations of West Eurasian and Middle Eastern origin.
Collapse
Affiliation(s)
- Yahya M Khubrani
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK; Forensic Genetics Laboratory, General Administration of Criminal Evidence, Public Security, Ministry of Interior, Saudi Arabia
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| |
Collapse
|
31
|
Gomes I, Pinto N, Antão-Sousa S, Gomes V, Gusmão L, Amorim A. Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics. Front Genet 2020; 11:926. [PMID: 33093840 PMCID: PMC7527635 DOI: 10.3389/fgene.2020.00926] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmission characteristics, besides the obvious clinical impact (sex chromosome aneuploidies are extremely frequent), make the X chromosome an irreplaceable genetic tool for population genetic-based studies as well as for kinship and forensic investigations. In the early 2000s, the number of publications using X-chromosomal polymorphisms in forensic and population genetic applications increased steadily. However, nearly 20 years later, we observe a conspicuous decrease in the rate of these publications. In light of this observation, the main aim of this article is to provide a comprehensive review of the advances and applications of X-chromosomal markers in population and forensic genetics over the last two decades. The foremost relevant topics are addressed as: (i) developments concerning the number and types of markers available, with special emphasis on short tandem repeat (STR) polymorphisms (STR nomenclatures and practical concerns); (ii) overview of worldwide population (frequency) data; (iii) the use of X-chromosomal markers in (complex) kinship testing and the forensic statistical evaluation of evidence; (iv) segregation and mutation studies; and (v) current weaknesses and future prospects.
Collapse
Affiliation(s)
- Iva Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Nádia Pinto
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Center of Mathematics, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sofia Antão-Sousa
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Verónica Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - António Amorim
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
32
|
Albujja MH, Messaoudi SA, Vasudevan R, Al Ghamdi S, Chong PP, Ghani KA, Ranneh Y, Alaidarous M, Ismail P. Identification of Potential Genes for Benign Prostatic Hyperplasia and Prostate Cancer Susceptibility in Four X-chromosome Regions with High Frequency of Microvariant Alleles. Asian Pac J Cancer Prev 2020; 21:2271-2280. [PMID: 32856855 PMCID: PMC7771924 DOI: 10.31557/apjcp.2020.21.8.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/06/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The X-chromosome has been suggested to play a role in prostate cancer (PrCa) since epidemiological studies have provided evidence for an X-linked mode of inheritance for PrCa based on the higher relative risk among men who report an affected brother(s) as compared to those reporting an affected father. The aim of this study was to examine the potential association between the forensic STR markers located at four regions Xp22.31, Xq11.2-12, Xq26.2, and Xq28 and the risk of BPH and PrCa to confirm the impact of ChrX in the PrCa incidence. This may be helpful in the incorporation of STRs genetic variation in the early detection of men population at risk of developing PrCa. METHODS DNA samples from 92 patients and 156 healthy controls collected from two medical centers in Riyadh, Saudi Arabia were analyzed for four regions located at X-chromosome using the Investigator® Argus X-12 QS Kit. RESULTS The results demonstrated that microvariant alleles of (DXS7132, DXS10146, HPRTB, DXS10134, and DXS10135) are overrepresented in the BPH group (p < 0.00001). Allele 28 of DXS10135 and allele 15 of DXS7423 could have a protective effect, OR 0.229 (95%CI, 0.066-0.79); and OR 0.439 (95%CI, 0.208-0.925). On the other hand, patients carrying allele 23 of DXS10079 and allele 26 of DXS10148 presented an increased risk to PrCa OR 4.714 (95%CI, 3.604-6.166). CONCLUSION The results are in concordance with the involvement of the X chromosome in PrCa and BPH development. STR allele studies may add further information from the definition of a genetic profile of PrCa resistance or susceptibility. As TBL1, AR, LDOC1, and RPL10 genes are located at regions Xp22.31, Xq11.2-12, Xq26.2, and Xq28, respectively, these genes could play an essential role in PrCa or BPH.
Collapse
Affiliation(s)
- Mohammed H Albujja
- Department ofForensic Sciences, Faculty of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
| | - Safia A Messaoudi
- Department ofForensic Sciences, Faculty of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Ramachandran Vasudevan
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
| | - Saleh Al Ghamdi
- Research Center, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia.
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor University, Subang Jaya, Selangor, Malaysia.
| | - Khairul Asri Ghani
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor Malaysia.
| | - Yazan Ranneh
- Department of Technology and Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Parit Raja, Batu Pahat Johor, Malaysia.
| | - Mohammed Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Riyadh, Saudi Arabia.
| | - Patimah Ismail
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
| |
Collapse
|
33
|
Hering S, Klimova A, Edelmann J. German population data for 18 X-STRs: a hexaplex PCR adding two clusters of X-STRs to the Argus X-12 set and expanding the German haplotype databases. Int J Legal Med 2020; 134:2061-2062. [PMID: 32367330 DOI: 10.1007/s00414-020-02306-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/20/2020] [Indexed: 11/28/2022]
Abstract
In kinship analysis, large data sets with estimated haplotype frequencies for marker clusters are very important for the likelihood calculation. Practical use of the X-STRs demonstrated that in some complex kinship cases, the marker set of the Investigator Argus X-12 kit can be insufficient. This study aimed to extend the German data base of the Argus X-12 kit (1037 haplotypes) and for a cluster in Xq21 (806 haplotypes) with additional 700 male haplotypes and to include a further cluster in Xp22.3 to complete the X-STR marker set for complex kinship cases.
Collapse
Affiliation(s)
- Sandra Hering
- Institute of Legal Medicine, University of Dresden, Dresden, Germany
| | - Anna Klimova
- Institute for Medical Informatics and Biometry, University of Dresden, Dresden, Germany
| | - Jeanett Edelmann
- Institute of Legal Medicine, University of Leipzig, Leipzig, Germany.
| |
Collapse
|
34
|
Nishi T, Fukui K, Iwadate K. Genetic polymorphism analyses of three novel X chromosomal short tandem repeat loci in the Xp22.3 region. Leg Med (Tokyo) 2020; 45:101709. [PMID: 32371301 DOI: 10.1016/j.legalmed.2020.101709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/13/2020] [Accepted: 04/17/2020] [Indexed: 11/18/2022]
Abstract
X chromosomal short tandem repeats (X-STRs) can be useful for haplotype analysis in DNA testing, particularly for complex kinship testing or when one parent is absent. We searched downstream of four previously detected loci in the Xp22.3 region (LC149476, LC149479, LC149480, and LC149484) and detected and analyzed three novel short tandem repeats (STRs), LC317283, LC317284, and LC317285, with the repeat sequences TATAA, TTTA, and TATC, respectively. The forensic statistical values in Japanese subjects were confirmed to be noninferior to existing loci, with values for polymorphism information content, the power of discrimination in males (PDm), and the power of discrimination in females (PDf) of 0.5606-0.7448, 0.6078-0.7774, and 0.7990-0.9178, respectively. Haplotype analysis also revealed linkage disequilibrium between LC317283 and the four known loci (LC149476, LC149479, LC149480, and LC149484) and between two other novel loci (LC317284 and LC317285). Analysis of three family samples suggested that these STRs could be useful in complex kinship testing, so we developed an X-STR multiplex polymerase chain reaction (PCR) system for the seven loci and confirmed its ability to provide favorable amplification. We anticipate that the identified loci and developed multiplex PCR system will be beneficial to the field of forensic medicine.
Collapse
Affiliation(s)
- Takeki Nishi
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan.
| | - Kenji Fukui
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan
| | - Kimiharu Iwadate
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan
| |
Collapse
|
35
|
Tao R, Zhang J, Xia R, Yang Z, Wang S, Zhang X, Yang Q, Zhang S, Li C. Genetic investigation and phylogenetic analysis of three Chinese ethnic groups using 16 X chromosome STR loci. Ann Hum Biol 2020; 47:59-64. [PMID: 32064953 DOI: 10.1080/03014460.2019.1704871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background: The value of using X-chromosomal short tandem repeats (X-STRs) as genetic markers in human genetics has been widely recognised. However, the 16 X-STRs in the Goldeneye® DNA ID System 17X kit have not been thoroughly applied.Aim: To investigate the genetic polymorphisms of 16 X-STRs in three main ethnic minorities (Tibetan, Mongolian and Kazakh) in China and to reveal the phylogenetic relationships of different populations.Subjects and methods: A total of 245 Tibetan, 168 Mongolian and 105 Kazakh individuals were genotyped using this 17X kit. The allelic frequencies and other parameters were calculated. An additional eight Chinese populations and nine global populations were included in genetic comparisons based on 16 or 8 overlapped X-STRs.Results: A total of 147 alleles were observed from 16 X-STRs with allelic frequencies ranging from 0.0024 to 0.7952 in the three studied groups. Based on 16 X-STRs, Tibetans, Kazakhs and Mongolians showed more similarity to each other and were genetically distinct from the Shanghai Han group; based on 8 X-STRs, only the genetic relationships between different nations could be clarified.Conclusions: Our study presents an extensive report on a novel X-STR assay in three Chinese ethnic groups and a comprehensive genetic comparison between different populations based on these X-STRs.
Collapse
Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, P.R. China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, P.R. China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, P.R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P.R. China
| |
Collapse
|
36
|
Gomes C, Quintero-Brito JD, Martínez-Gómez J, Pereira R, Baeza-Richer C, Aler Gay M, Díez-Juárez L, Palomo-Díez S, López-Parra AM, Labajo-González E, Esteban-Ramos VJ, Perea-Pérez B, Arroyo-Pardo E. Spanish allele and haplotype database for 32 X-chromosome Insertion-Deletion polymorphisms. Forensic Sci Int Genet 2020; 46:102262. [PMID: 32088644 DOI: 10.1016/j.fsigen.2020.102262] [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: 06/18/2019] [Revised: 01/27/2020] [Accepted: 02/08/2020] [Indexed: 01/21/2023]
Abstract
X-chromosome markers have been proved to be decisive both complementing and solving kinship analysis, particularly when autosomal markers are not able to produce adequate likelihood ratios between different hypothesis. On the other hand, Pereira et al., (2012) have demonstrated that 32 Insertion/Deletion (InDel) markers located on the X-Chromosome have a very important power of discrimination in human populations, being a novel tool in the forensic and population fields. So, the aim of the present work was testing the forensic and population genetic efficiency of the 32 X-InDel polymorphisms in the Spanish population, and subsequently build an allele/haplotype frequencies database. To accomplish this objective, a total of 555 samples comprising male individuals from 13 Spanish regions were analysed for the above mentioned 32 X-InDels in two independent laboratories. A pairwise FST analysis was performed in order to understand if the studied Spanish sub-populations present significant differences among them, detecting possible population substructure. Also, linkage disequilibrium analyses were computed to investigate the presence of association between markers in the Spanish population. After Bonferroni correction, the absence of significant differences among the studied regions supports a global Spanish population database. Concerning LD, besides previously reported linked markers MID356-MID357 and MID3690-MID3719-MID2089, we also detected significant association between MID3703-MID3774, even after Bonferroni correction. Finally, after computing allele and haplotype frequencies, forensic efficiency parameters were calculated (PDmales = 99.999976 %; PDfemales = 99.99999999998 %). Mean exclusion chance values for duos were 0.999 and trios 0.99999. These results reinforce the suitability of the 32 X-InDels marker set both in identification and kinship studies.
Collapse
Affiliation(s)
- Cláudia Gomes
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain.
| | | | - Jesús Martínez-Gómez
- Laboratory of the Biology Department, Criminalistics Service, Civil Guard, Madrid, Spain
| | - Rui Pereira
- Instituto de Investigação e Inovação em Saúde da Universidade do Porto (i3S), Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Carlos Baeza-Richer
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Mercedes Aler Gay
- Sección de Genética y Criminalística, Servicio de Laboratorio, Instituto de Medicina Legal y Ciencias Forenses de Valencia, Spain
| | - Laura Díez-Juárez
- Laboratory of the Biology Department, Criminalistics Service, Civil Guard, Madrid, Spain
| | - Sara Palomo-Díez
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Ana María López-Parra
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Elena Labajo-González
- Legal Medicine School, Complutense University of Madrid, Pza Ramón y Cajal s/n, 28040 Madrid, Spain
| | | | - Bernardo Perea-Pérez
- Legal Medicine School, Complutense University of Madrid, Pza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Eduardo Arroyo-Pardo
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| |
Collapse
|
37
|
Lin L, Li J, Hu Y, Wang H, Marah FA, Moseray M, Kureshi A, Wang C, Zeye MMJ, Zha L. Genetic characterization of 19 X-STRs in Sierra Leone population from Freetown. Int J Legal Med 2020; 134:1659-1661. [PMID: 31897669 DOI: 10.1007/s00414-019-02243-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/19/2019] [Indexed: 11/26/2022]
Abstract
A total of 550 individuals (265 males and 285 females) from Sierra Leone, a west-African coastal country, were genotyped using the Microreader™ 19X ID System kit. No significant deviations from the Hardy-Weinberg equilibrium were observed. A total of 250 alleles were identified with corresponding allele frequencies spanning from 0.0012 to 0.6762. PIC of the loci ranged from 0.4615 to 0.9481. The CPE, CPDF, and CPDM were 0.9999997856, 0.999999999999999999995774, and 0.999999999998997, respectively. The highly combined MECKruger, MECKishida, MECDesmarais, and MECDesmarais Duo were achieved as 0.99999992508, 0.999999999990802, 0.999999999990836, and 0.99999998412, respectively. Genetic comparisons revealed that genetic homogeneity existed in similar ethno origin or geographic origin populations. This is a pioneering genetic investigation using the Microreader™ 19X ID System kit in the population of Sierra Leone.
Collapse
Affiliation(s)
- Lin Lin
- Xiangya Hospital, Central South University, No87. Xiangya Road, Changsha, Hunan, People's Republic of China
- Reproductive Medicine Center, Fujian Provincial Maternity and Children's Hospital, No18. Daoshan Road, Fuzhou, Fujian, People's Republic of China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Yize Hu
- Wuxi Municipal Public Security Bureau, Wuxi, Jiangsu, People's Republic of China
| | - Han Wang
- Department of Clinical Diagnostic Centre, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, People's Republic of China
| | - Foday Ambrose Marah
- The GREY Bush Community Health Center, Grey Bush, Ascension-town, Sierra Leone
| | - Moses Moseray
- Joint Medical Unit, Freetown, Sierra Leone
- Clinical Laboratory, 34 Military hospital, Freetown, Sierra Leone
| | - Aliye Kureshi
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, 01 BP 364, Ouagadougou 01, Burkina Faso
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China.
- China-Africa Research Center of Infectious Deseases, Central South University, Changsha, People's Republic of China.
| |
Collapse
|
38
|
Zambrano AK, Vaca-Pólit M, Boada L, Vela M, Rodríguez-Pólit C, Fiallos G, Gruezo C, Paz-y-Miño C, Gaviria A. X-STR decaplex study in the population of Imbabura-Ecuador. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
39
|
X-InDels efficacy evaluation in a critical samples paternity case: A Spanish Civil War case from the memorial of the camposines (Tarragona, Spain). FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
40
|
Kalaoglu E, Ay M, Ulubay A, Canan H, Serin A, Alper B. Population data of 12 X-STRs in Turkey. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
41
|
Gao H, Wang C, Zhang R, Wu H, Sun S, Xiao D, Wang Y, Zhang M. Application of CPI cutoff value based on parentage testing of duos and trios typed by four autosomal kits. PLoS One 2019; 14:e0225174. [PMID: 31721797 PMCID: PMC6853303 DOI: 10.1371/journal.pone.0225174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/29/2019] [Indexed: 11/24/2022] Open
Abstract
In this study, we analyzed the application of four autosomal kits and the sensitivity of the combined paternity index (CPI) cutoff value (CPI≥10000) in parentage testing. First, 1442 real trios and 803 real duos were tested using the Goldeneye 25A kit. The Goldeneye 25A kit covers the autosomal short tandem repeat (STR) loci of the other three kits, so we calculated the CPI value of every case for the four kits. Second, three complex close relative kinship cases were also analyzed to evaluate the application of the CPI cutoff value. The CPI values of all trio cases were higher than 10000 using the four kits; the CPI values of all duo cases were higher than 10000 using the Goldeneye 25A kit; and the CPI values of a portion of the duo cases were lower than 10000 using the other three kits. In the three complex close relative cases, the alleged father or mother was not excluded using 40 autosomal STRs. Adding X chromosome short tandem repeats (X-STR) and samples of biological fathers or mothers, the conclusions were confirmed. The four kits were adequate to draw conclusions in the trio cases; the Goldeneye 25A Kit was adequate to draw conclusions in the duo cases; and the other three kits were not sufficient for a portion of the duo cases. The CPI cutoff value was sensitive for real trio and duo cases. In complex close relative kinship cases, high CPI values may result in false conclusions.
Collapse
Affiliation(s)
- Hongmei Gao
- Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Jinan Di’en Forensic Institute of Jinan Central Hospital, Jinan, Shandong, China
| | - Chang Wang
- Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Jinan Di’en Forensic Institute of Jinan Central Hospital, Jinan, Shandong, China
| | - Ruxia Zhang
- Department of Nursing, Shandong Medical College, Jinan, Shandong, China
| | - Hanyang Wu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shanhui Sun
- Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Jinan Di’en Forensic Institute of Jinan Central Hospital, Jinan, Shandong, China
| | - Dongjie Xiao
- Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Jinan Di’en Forensic Institute of Jinan Central Hospital, Jinan, Shandong, China
| | - Yunshan Wang
- Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Jinan Di’en Forensic Institute of Jinan Central Hospital, Jinan, Shandong, China
| | - Maoxiu Zhang
- Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Jinan Di’en Forensic Institute of Jinan Central Hospital, Jinan, Shandong, China
- * E-mail:
| |
Collapse
|
42
|
Yang X, Chen Y, Zeng X, Chen L, Liu C, Liu H, Xu Q, Budowle B, Liu C. Linkage, recombination, and mutation rate analyses of 19 X-chromosomal STR loci in Chinese Southern Han pedigrees. Int J Legal Med 2019; 133:1691-1698. [PMID: 31317316 DOI: 10.1007/s00414-019-02121-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
From Southern Han Chinese samples, we analyzed 19 X-STR markers for linkage, linkage disequilibrium (LD), and mutation rate. The data were collected from two- and three-generation Southern Han Chinese families. These data suggested that both linkage and linkage disequilibrium should be considered while calculating likelihood ratios with X-STR markers in relationship tests. The linkage disequilibrium of these 19 X-STR markers was calculated in our previous research study that was conducted on Southern Han Chinese population. In this study, the recombination fractions between pairs of markers and those obtained from the second-generation Rutgers combined linkage-physical map of the human genome were compared. The observed differences indicated that recombination was not homogeneous along the X chromosome. Therefore, we evaluated the effect on likelihood calculations by referring to haplotype frequencies obtained from allele distributions rather than haplotype counts of Southern Han Chinese population.
Collapse
Affiliation(s)
- Xingyi Yang
- Guangzhou Forensic Science Institute, 1708 Baiyun Avenue, Guangzhou, 510030, China
| | - Yutian Chen
- Forensic Science Center of Yuexiu District Branch of Guangzhou Public, Security Bureau in Guangdong Province, Guangzhou, 510080, China
| | - Xiangpei Zeng
- Center for Human Identification, University of North Texas Health Science Center, Ft Worth, TX, USA
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, 1708 Baiyun Avenue, Guangzhou, 510030, China
| | - Hong Liu
- Guangzhou Forensic Science Institute, 1708 Baiyun Avenue, Guangzhou, 510030, China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, 1708 Baiyun Avenue, Guangzhou, 510030, China
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Ft Worth, TX, USA.
| | - Chao Liu
- Guangzhou Forensic Science Institute, 1708 Baiyun Avenue, Guangzhou, 510030, China. .,School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
43
|
Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
|
44
|
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]
|
45
|
Chen M, Ren H, Liu Z, Zhao J, Chen C, Shi Y, Jia L, Cheng F, Chen T, Fan Q, Yang Y, Liu Y, Zhang G, Yan J. Genetic polymorphisms and mutation rates of 16 X-STRs in a Han Chinese population of Beijing and application examples in second-degree kinship cases. Int J Legal Med 2019; 134:163-168. [PMID: 30937593 DOI: 10.1007/s00414-019-02047-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
Abstract
As a supplementary tool in forensic cases, X chromosomal short tandem repeats (X-STRs) might bridge large pedigree gaps and bring inspiration to forensic practices for the special mode of inheritance. To standardize the application of X-STRs, the DNA Commission of the International Society for Forensic Genetics (ISFG) presented recommendations concentrating on biostatistical evaluations. Following this guideline, in this study, 1247 (655 females and 592 males) unrelated individuals and 770 families originating from a Han Chinese population of Beijing were investigated with 16 X-STRs. The combined PDF and PDM were 0.999999999999994 and 0.999999997, respectively. The combined MECKrüger, MECKishida, MECDesmarais, and MECDesmarais duo were 0.999972736708864, 0.999999975670766, 0.999999975720931, and 0.999993489709197, respectively. In addition, a population comparison demonstrated that genetic heterogeneity widely exists between the Han population of Beijing and other populations, especially southern Han Chinese, European, and West African populations. Additionally, the overall mutation rates of the paternal and maternal germlines of the 16 X-STRs were 0.0021 and 0.0003, respectively. Among them, HPRTB showed the highest paternal mutation rate of 0.0094. Finally, based on these forensic parameters, the likelihood ratios of four second-degree kinship cases were evaluated. Comparing with autosomal STR, X-STR showed significant advantages for hypothesis exclusion. Our study indicated that the 16 X-STR loci are highly polymorphic in the Han population of Beijing and could be a satisfactory complimentary tool for forensic applications.
Collapse
Affiliation(s)
- Man Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - He Ren
- Beijing Police College, Beijing, 102202, People's Republic of China
| | - Zhiyong Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Chong Chen
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, 100192, People's Republic of China
| | - Yan Shi
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, 100192, People's Republic of China
| | - Li Jia
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, 100192, People's Republic of China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030009, People's Republic of China
| | - Tong Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qingwei Fan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030009, People's Republic of China
| | - Yaran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, 100192, People's Republic of China
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030009, People's Republic of China.
| | - Jiangwei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China. .,School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030009, People's Republic of China.
| |
Collapse
|
46
|
Population genetic analysis of Chinese Zhuang and Mulao minorities using AGCU-X19 STR kit. Int J Legal Med 2019; 134:501-503. [PMID: 30675640 DOI: 10.1007/s00414-019-02004-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/16/2019] [Indexed: 10/27/2022]
Abstract
To investigate the genetic variation and forensic efficiency of 19 X-STR loci in the Zhuang and Mulao minorities, we calculated allele frequencies, forensic parameters, and haplotype frequencies of 405 Zhuang and 234 Mulao unrelated healthy individuals from Guangxi Zhuang Autonomous Region of China. Furthermore, we analyzed the population genetic differentiations between the two minorities and other reported Chinese populations.
Collapse
|
47
|
Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil). Int J Legal Med 2019; 133:1385-1388. [DOI: 10.1007/s00414-018-01988-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
|
48
|
Sun S, Yang Z, Wen D, Lan L, Xie P, Xiao J, Li G, Zhu W, Zha L. Genetic polymorphism investigation of 16 X-STR loci in a Han population in Central South China. Forensic Sci Int Genet 2018; 39:e21-e23. [PMID: 30538076 DOI: 10.1016/j.fsigen.2018.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/07/2018] [Accepted: 11/25/2018] [Indexed: 11/19/2022]
Affiliation(s)
- Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Lingmei Lan
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Pingli Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Junxin Xiao
- Center of Forensic Services of Xiangya of Hunan Province, Changsha, 410013, Hunan, PR China
| | - Guanlin Li
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, PR China
| | - Wenbing Zhu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medicine, Central South University, Changsha, 410013, Hunan, PR China.
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China.
| |
Collapse
|
49
|
Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers. Sci Rep 2018; 8:14585. [PMID: 30275508 PMCID: PMC6167355 DOI: 10.1038/s41598-018-32945-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/19/2018] [Indexed: 01/10/2023] Open
Abstract
X-chromosome short tandem repeat markers (X-STRs), due to their special inheritance models, physical location on a single chromosome and the absence of recombination in male meiosis, play an important role in forensic and population genetics. While a series of genetic analyses focusing on the genetic diversity and forensic characteristics of X-STRs are well studied for ethnically/linguistically diverse and demographically large Chinese populations, genetic evidence from Gelao ethnicity is still sparse. Here, we genotyped the first batch of 19 X-STRs in 513 Chinese Gelao individuals (265 females and 248 males), and reported genetic polymorphisms, forensic characteristics based on the single locus and seven linkage groups. DXS10135 with the highest PIC (0.9106) and LG1 (DXS10148-DXS10135-DXS8378) with the largest HD (0.9970) are polymorphic and informative. The CPDs in Gelao males and females are respectively larger than 0.999999999997095 and 0.99999999999999999999918, and the combined MECs are larger than 0.999999975715109. Subsequently, we investigated the population relationships among 14 Chinese populations based on 19 X-STRs and among 23 populations based on 11 overlapped X-STRs. Our results revealed genetic differentiations among Tibeto-Burman, Altaic and other Chinese homogenous populations, and demonstrated that Guizhou Gelao has the genetically closer relationships with Han Chinese and geographically close Guizhou Miao.
Collapse
|
50
|
Salvador JM, Apaga DLT, Delfin FC, Calacal GC, Dennis SE, De Ungria MCA. Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Sci Int Genet 2018; 36:e8-e12. [DOI: 10.1016/j.fsigen.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 01/11/2023]
|