1
|
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
|
2
|
Gabriele A, Chierto E, Gino S, Inturri S, Aneli S, Robino C. Privacy and ethical challenges of the Amelogenin sex test in forensic paternity/kinship analysis: Insights from a 13-year case history. Forensic Sci Int Synerg 2023; 7:100440. [PMID: 37840559 PMCID: PMC10568343 DOI: 10.1016/j.fsisyn.2023.100440] [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: 10/28/2022] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
The Amelogenin sex test included in forensic DNA typing kits has the potential to identify congenital conditions such as differences/disorders of sex development (DSD). It can also reveal mismatches between genotypic sex and gender marker in identity documents of transgender persons who obtained legal gender recognition. In a 13-year case history of paternity/kinship tests, involving n = 962 females and n = 1001 males, two mismatches between Amelogenin sex test (male) and gender marker (female), and three cases of chromosomal DSD (Klinefelter syndrome) were observed. The concrete risk of observing Amelogenin anomalies, their potential causes, and the context in which they occur (forensic, i.e. non-medical) mean that laboratory operators are called to strike a complex balance between privacy interests and individual health rights when providing preliminary information and reporting Amelogenin incidental findings. This case history argues for the need of a more responsible approach towards the Amelogenin sex test in the forensic community.
Collapse
Affiliation(s)
- Alessandro Gabriele
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Sarah Gino
- Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100, Novara, Italy
| | - Serena Inturri
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| |
Collapse
|
3
|
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
|
4
|
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
|
5
|
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
|
6
|
Faustino M, Turchi C, Kling D, Gusmão L, Amorim A, Pinto N. Paternal half-sisters or unrelated – How can the X-chromosomal evidence be quantified when one female presents trisomy X? FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.011] [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]
|
7
|
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: 0] [Impact Index Per Article: 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
|
8
|
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
|
9
|
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
|
10
|
Aguilar-Velázquez JA, Duran-Salazar MÁ, Córdoba-Mercado MF, Coronado-Avila CE, Salas-Salas O, Martinez-Cortés G, Casals F, Calafell F, Ramos-González B, Rangel-Villalobos H. Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico). Mol Biol Rep 2022; 49:7601-7609. [PMID: 35657453 DOI: 10.1007/s11033-022-07575-y] [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: 10/26/2021] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND STR allele frequency databases from populations are necessary to take full advantage of the increased power of discrimination offered by massively parallel sequencing (MPS) platforms. MATERIAL AND METHODS For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 105 Mestizo (admixed) individuals from Monterrey City (Northeast, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit. RESULTS Most of the STR markers were in Hardy Weinberg equilibrium, with a few exceptions. We found 346 different length-based alleles for these 58 STRs; nevertheless, they became 528 alleles when the sequence was assessed. The combined power of discrimination from autosomal STRs (aSTRs) was -virtually- 100% in both length and sequence-based alleles, while the power of exclusion was 99.9999999976065 and 99.9999999999494%, respectively. Haplotypes based on X-STRs and Y-STRs showed 100% of discriminatory capacity. CONCLUSIONS These results provide -for the first time- forensic genomic population data from Mexico necessary for interpretation in kinship and criminal analyses.
Collapse
Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.,Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Miguel Ángel Duran-Salazar
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.,Programa de Doctorado en Biociencias, Centro Universitario de los Altos, Universidad de uadalajara, Tepatitlán de Morelos, Jalisco, Mexico
| | - Miranda Fabiola Córdoba-Mercado
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico
| | - Carolina Elena Coronado-Avila
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico
| | - Orlando Salas-Salas
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico
| | - Gabriela Martinez-Cortés
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico
| | - Ferrán Casals
- Servei de Genómica, Universitat Pampeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Benito Ramos-González
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico.
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico.
| |
Collapse
|
11
|
Bottinelli M, Gouy A, Utz S, Zieger M. Population genetic analysis of 12 X-chromosomal STRs in a Swiss sample. Int J Legal Med 2021; 136:561-563. [PMID: 34420081 PMCID: PMC8847170 DOI: 10.1007/s00414-021-02684-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/11/2021] [Indexed: 11/23/2022]
Abstract
X-chromosomal STRs are a powerful tool to assess a broad variety of complex kinship scenarios. We introduce herewith the first Swiss X-STR dataset based on 1198 individuals (592 female, 606 male), characterized with the Qiagen Investigator® Argus X-12 QS multiplex kit. Anomalous allele patterns, allele and haplotype frequencies, and forensic and population genetic parameters are presented. We detected linkage disequilibrium within three out of the four designated linkage groups and no apparent intra-national population substructure. We compared the dataset to a global panel of X-STR datasets and it fits well in the European context, as expected.
Collapse
Affiliation(s)
- Michel Bottinelli
- Laboratorio di Diagnostica Molecolare, Via G. Petrini 2, 6900, Lugano, Switzerland
| | - Alexandre Gouy
- Gouy Data Consulting, Sentier de Renges 4A, 1026, Denges, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular Biology Department, University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland
| | - Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular Biology Department, University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
| |
Collapse
|
12
|
Strategies for pairwise searches in forensic kinship analysis. Forensic Sci Int Genet 2021; 54:102562. [PMID: 34274795 DOI: 10.1016/j.fsigen.2021.102562] [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: 03/30/2021] [Revised: 06/29/2021] [Accepted: 07/03/2021] [Indexed: 11/20/2022]
Abstract
Testing kinship between pairs of individuals is central to a wide range of applications. We focus on cases where many tests are done jointly. Typical examples include cases where DNA profiles are available from a burial site, a plane crash or a database of convicted offenders. The task is to determine the relationships between DNA profiles or individuals. Our approach generalises previous methods and implementations in several respects. We model general, possibly inbred, pairwise relationships which is important for non-human applications and in archaeological studies of ancient inbred populations. Furthermore, we do not restrict attention to autosomal markers. Some cases, such as distinguishing between maternal and paternal half siblings, can be solved using X-chromosomal markers. When many tests are done, the risk of errors increases. We address this problem by building on the theory of multiple testing and show how optimal thresholds for tests can be determined. We point out that the likelihood ratios in a blind search may be dependent so multiple testing methods and interpretation need to account for this. In addition, we show how a Bayesian approach can be helpful. Our examples, using simulated and real data, demonstrate the practical importance of the methods and implementation is based on freely available software.
Collapse
|
13
|
Flores-Espinoza R, Paz-Cruz E, Ruiz-Pozo VA, Lopez-Carrera M, Cabrera-Andrade A, Gusmão L, Burgos G. Investigating genetic diversity in admixed populations from Ecuador. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:109-119. [PMID: 34169504 DOI: 10.1002/ajpa.24341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES According to demographic history, Ecuador has experienced shifts in its Native American populations caused by European colonization and the African slave trade. The continuous admixture events among Europeans, Native Americans, and Africans occurred differently in each region of the country, producing a stratified population. Thus, the aim of this study was to investigate the level of genetic substructure in the Ecuadorian Mestizo population. MATERIALS AND METHODS A total of 377 male and 209 female samples were genotyped for two sets of X-chromosomal markers (32 X-Indels and 12 X-STRs). Population analyses performed included Hardy-Weinberg equilibrium tests, LD analysis, PCA, pairwise FST s, and AMOVA. RESULTS Significant levels of LD were observed between markers separated by distances of less than 1 cM, as well as between markers separated by distances varying from 10.891 to 163.53 cM. Among Ecuadorian regions, Amazonia showed the highest average R2 value. DISCUSSION When X-chromosomal and autosomal differentiation values were compared, a sex-biased admixture between European men and Native American and African women was revealed, as well as between African men and Native American women. Moreover, a distinct Native American ancestry was discernible in the Amazonian population, in addition to sex-biased gene flow between Amazonia and the Andes and Pacific coast regions. Overall, these results underline the importance of integrating X chromosome information to achieve a more comprehensive view of the genetic and demographic histories of South American admixed populations.
Collapse
Affiliation(s)
- Rodrigo Flores-Espinoza
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratorios de Investigación, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Elius Paz-Cruz
- Laboratorio de ADN, Fiscalía General del Estado, Quito, Ecuador
| | | | | | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador.,Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - German Burgos
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito, Ecuador.,Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
14
|
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] [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
|
15
|
Li R, Budowle B, Sun H, Ge J. Linkage and linkage disequilibrium among the markers in the forensic MPS panels. J Forensic Sci 2021; 66:1637-1646. [PMID: 33885147 DOI: 10.1111/1556-4029.14724] [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: 02/16/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 11/28/2022]
Abstract
For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. In this study, publicly accessible genomic data from five representative populations were used to evaluate the genetic linkage and linkage disequilibrium (LD) between autosomal markers represented in six major commercial panels (in total, 362 markers). Among the 3041 syntenic marker pairs, 1524 pairs had sex-average genetic distances <50 cM, and thus, these marker pairs can be considered as genetically linked. Among the 143 marker pairs with physical distances <1 Mb, 19 LD haplotype blocks (comprising 39 SNPs in total) were detected for at least one of the tested populations. Statistical methods for interpreting linked markers and/or markers in LD were suggested for various case scenarios.
Collapse
Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| |
Collapse
|
16
|
Yuan L, Zhang J, Hao S, Liu Y. Identification of half-sisters from different mothers by autosomal and X chromosomal short tandem repeats: A case study. JOURNAL OF FORENSIC SCIENCE AND MEDICINE 2021. [DOI: 10.4103/jfsm.jfsm_30_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
17
|
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
|
18
|
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: 19] [Impact Index Per Article: 4.8] [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
|
19
|
Pereira V, Santangelo R, Børsting C, Tvedebrink T, Almeida APF, Carvalho EF, Morling N, Gusmão L. Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations. Front Genet 2020; 11:966. [PMID: 32973885 PMCID: PMC7472784 DOI: 10.3389/fgene.2020.00966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect's BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.
Collapse
Affiliation(s)
- Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roberta Santangelo
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Ana Paula F Almeida
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizeu F Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto de Investigação e Inovação em Saúde, i3S, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| |
Collapse
|
20
|
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
|
21
|
Paternal and maternal mutations in X-STRs: A GHEP-ISFG collaborative study. Forensic Sci Int Genet 2020; 46:102258. [PMID: 32066109 DOI: 10.1016/j.fsigen.2020.102258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/06/2019] [Accepted: 01/29/2020] [Indexed: 11/22/2022]
Abstract
The GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit Qiagen. A total of 16 laboratories gathered data from 1,612 father/mother/daughter trios, which were used to estimate both maternal and paternal mutation rates, when pooled together with other already published data. Data on fathers and mothers' age at the time of birth of the daughter were also available for ∼93 % of the cases. Population analyses were computed considering the genetic information of a subset of 1,327 unrelated daughters, corresponding to 2,654 haplotypes from residents in several regions of five countries: Argentina, Brazil, Ecuador, Portugal and Spain. Genetic differentiation analyses between the population samples from the same country did not reveal signs of significant stratification, although results from Hardy-Weinberg and linkage disequilibrium tests indicated the need of larger studies for Ecuador and Brazilian populations. The high genetic diversity of the markers resulted in a large number of haplotype combinations, showing the need of huge databases for reliable estimates of their frequencies. It should also be noted the high number of new alleles found, many of them not included in the allelic ladders provided with the kit, as very diverse populations were analyzed. The overall estimates for locus specific average mutation rates varied between 7.5E-04 (for DXS7423) and 1.1E-02 (for DXS10135), the latter being a troublesome figure for kinship analyses. Most of the found mutations (∼92 %) are compatible with the gain or loss of a single repeat. Paternal mutation rates showed to be 5.2 times higher than maternal ones. We also found that older fathers were more prone to transmit mutated alleles, having this trend not been observed in the case of the mothers.
Collapse
|
22
|
X-chromosome analysis in an unusual deficiency maternity case. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
23
|
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
|
24
|
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
|
25
|
Cortés-Trujillo I, Zuñiga-Chiquette F, Ramos-González B, Chávez-Briones MDL, Islas-González KL, Betancourt-Guerra DA, Peralta-Coria R, Martínez-Cortés G, Rangel-Villalobos H. Allele and haplotype frequencies of 12 X-STRs in Mexican population. Forensic Sci Int Genet 2019; 38:e11-e13. [DOI: 10.1016/j.fsigen.2018.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/20/2018] [Accepted: 10/19/2018] [Indexed: 12/12/2022]
|
26
|
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]
|
27
|
Mršić G, Ozretić P, Crnjac J, Merkaš S, Sukser V, Račić I, Rožić S, Barbarić L, Popović M, Korolija M. Expanded Croatian 12 X-STR loci database with an overview of anomalous profiles. Forensic Sci Int Genet 2018; 34:249-256. [PMID: 29573605 DOI: 10.1016/j.fsigen.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/16/2018] [Accepted: 03/02/2018] [Indexed: 02/08/2023]
Abstract
In order to implement X-chromosome short tandem repeat (X-STR) typing into routine forensic practice, reference database of a given population should be established. Therefore we extended already published data with additional 397 blood samples from unrelated Croatian citizens, and analyzed the total of 995 samples (549 male and 446 female) typed by Investigator® Argus X-12 Kit. To test genetic homogeneity of consecutively processed five historic-cultural regions covering the entire national territory, we calculated pairwise Fst genetic distances between regions based on allele and full haplotype frequencies. Since the comparison did not yield any statistically significant difference, we integrated STR profile information from all regions and used the whole data set to calculate forensic parameters. The most informative marker is DXS10135 (polymorphism information content (PIC = 0.929) and the most informative linkage group (LG) is LG1 (PIC = 0.996). We confirmed linkage disequilibrium (LD) for seven marker pairs belonging to LG2, LG3 and LG4. By including LD information, we calculated cumulative power of discrimination that amounted to 0.999999999997 in females and 0.999999005 in males. We also compared Croatia with 13 European populations based on haplotype frequencies and detected no statistically significant Fst values after Bonferroni correction in any LG. Multi-dimensional scaling plot revealed tight grouping of four Croatian regions amongst populations of southern, central and northern Europe, with the exception of northern Croatia. In this study we gave the first extensive overview of aberrant profiles encountered during Investigator® Argus X-12 typing. We found ten profiles consistent with single locus duplication followed by tetranucleotide tract length polymorphism. Locus DXS10079 is by far the most frequently affected one, presumably mutated in eight samples. We also found four profiles consistent with X-chromosome aneuploidy (three profiles with XXX pattern and one profile with XXY pattern). In conclusion, we established integral forensic Croatian X-chromosome database, proved forensic pertinence of Investigator® Argus X-12 Kit for the entire Croatian population and identified locus DXS10079 as a potential duplication hotspot.
Collapse
Affiliation(s)
- Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Petar Ozretić
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Josip Crnjac
- University Department for Forensic Sciences, University of Split, Ruđera Boškovića 31, 21000 Split, Croatia
| | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Viktorija Sukser
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Ivana Račić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Lucija Barbarić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova ulica 55, 10000 Zagreb, Croatia
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia.
| |
Collapse
|
28
|
Almarri MA, Lootah RA. Allelic and haplotype diversity of 12 X-STRs in the United Arab Emirates. Forensic Sci Int Genet 2018; 33:e4-e6. [DOI: 10.1016/j.fsigen.2017.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 11/17/2022]
|
29
|
Fukuta M, Gaballah MH, Kato H, Aoki Y. A simple method for calculating the likelihood ratio in a kinship test using X-chromosomal markers incorporating linkage, linkage disequilibrium, and mutation. Leg Med (Tokyo) 2018; 32:9-18. [PMID: 29455040 DOI: 10.1016/j.legalmed.2018.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 11/30/2022]
Abstract
X-chromosomal short tandem repeats (X-STRs) are useful for personal identification and kinship tests. However, it has not yet been fully established how to incorporate linkage and linkage disequilibrium (LD) into the calculation of the likelihood ratio (LR). In this paper, we describe a simple calculation method of LR for X-STRs that incorporated linkage, LD, and mutations. Initially, Japanese population data of 27 X-STRs (DXS6807, DXS9902, DXS6795, DXS6810, DXS10076, DXS10077, DXS10078, DXS10162, DXS10163, DXS10164, DXS7132, DXS981, DXS6800, DXS6803, DXS6809, DXS6789, DXS6799, DXS7424, DXS101, DXS7133, GATA172D05, DXS10103, HPRTB, GATA31E08, DXS8377, DXS10147, and DXS7423) were collected from 748 unrelated individuals to estimate the influence of LD. Significant LD was observed on six pairs of loci. Subsequently, using the population data, a simulation study was performed to evaluate the validity of the present calculation method for LR in cases of father-daughter, full-sisters, paternal half-sisters, maternal half-sisters, and unrelated pairs of females (FD, FS, PHS, MHS, and UR, respectively). As a result, the distribution of LR among FD was completely separated from that among UR. In the sibship test, 98.6% of FS and 98.0% of PHS surpassed the maximum value of UR in combined LR. Even in the FS versus MHS setting, 60.5% of FS had a higher LR than any MHS. We conclude that the present model is powerful in discriminating the relationship and is able to obtain a reasonable LR with fewer computations.
Collapse
Affiliation(s)
- Mamiko Fukuta
- Department of Forensic Medicine, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi Mizuho-cho Mizuho-ku, Nagoya 467-8601, Japan.
| | - Mohammed Hassan Gaballah
- Department of Forensic Medicine, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi Mizuho-cho Mizuho-ku, Nagoya 467-8601, Japan
| | - Hideaki Kato
- Department of Forensic Medicine, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi Mizuho-cho Mizuho-ku, Nagoya 467-8601, Japan
| | - Yasuhiro Aoki
- Department of Forensic Medicine, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi Mizuho-cho Mizuho-ku, Nagoya 467-8601, Japan
| |
Collapse
|
30
|
Robino C, Lacerenza D, Aneli S, Di Gaetano C, Matullo G, Robledo R, Calò C. Allele and haplotype diversity of 12 X-STRs in Sardinia. Forensic Sci Int Genet 2017; 33:e1-e3. [PMID: 29221994 DOI: 10.1016/j.fsigen.2017.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/11/2017] [Accepted: 12/02/2017] [Indexed: 11/27/2022]
Abstract
The analysis of clusters of tightly linked X-chromosome short tandem repeat (STR) markers can assist the interpretation of complex kinship cases. However, when linkage disequilibrium (LD) is present in the population of origin of tested individuals, haplotype rather than allele frequencies should be used in likelihood calculations. The diversity of twelve X-STRs arranged in four linkage groups (I: DXS10148-DXS10135-DXS8378; II: DXS7132-DXS10079-DXS10074; III: DXS10103-HPRTB-DXS10101; IV: DXS10146-DXS10134-DXS7423) was tested in a Sardinian population sample (n=516) including three open populations from the Northern, Central and Southern part of the island, and three isolates (Benetutti, Desulo, Carloforte). Evidence of LD was detected in Sardinia within each linkage group. Significant differences in haplotype and allele frequency distribution of X-STR markers was seen between isolates and open populations, which on the contrary appeared highly homogeneous. The percentage of Sardinian haplotypes previously unobserved in a similar dataset compiled for the Italian population was: 76.3% (linkage group I), 61.3% (linkage group II), 54.1% (linkage group III), 58.9% (linkage group IV). Significant pairwise genetic differences were seen between mainland Italy, the three Sardinian isolates, and the open population of Southern Sardinia. The study confirms the presence of high levels and complex patterns of LD along the X chromosome in Sardinia, and provides population-specific haplotype data for biostatistical evaluation in kinship testing.
Collapse
Affiliation(s)
- C Robino
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Italy.
| | - D Lacerenza
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Italy
| | - S Aneli
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - C Di Gaetano
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - G Matullo
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - R Robledo
- Dipartimento di Scienze Biomediche, Università di Cagliari, Italy
| | - C Calò
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Italy
| |
Collapse
|
31
|
Gomes I, Pereira PJP, Harms S, Oliveira AM, Schneider PM, Brehm A. Genetic characterization of Guinea-Bissau using a 12 X-chromosomal STR system: Inferences from a multiethnic population. Forensic Sci Int Genet 2017; 31:89-94. [PMID: 28858674 DOI: 10.1016/j.fsigen.2017.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022]
Abstract
A male West African sample from Guinea-Bissau (West-African coast) was genetically analyzed using 12 X chromosomal short tandem repeats that are grouped into four haplotype groups. Linkage disequilibrium was tested (p≤0.0008) and association was detected for the majority of markers in three out of the four studied haplotype clusters. The sample of 332 unrelated individuals analyzed in this study belonged to several recognized ethnic groups (n=18) which were used to evaluate the genetic variation of Guinea-Bissau's population. Pairwise genetic distances (FST) did not reveal significant differences among the majority of groups. An additional 110 samples from other countries also belonging to West Africa were as well compared with the sample of Guinea-Bissau. No significant differences were found between these two groups of West African individuals, supporting the genetic homogeneity of this region on the X chromosome level. The generation of over 100 DNA West African sequences provided new insights into the repeat sequence structure of some of the present X-STRs. Parameters for forensic evaluation were also calculated for each X-STR, supporting the potential application of these markers in typical kinship scenarios. Also, the high power of discrimination values for samples of female and male origin observed in this study, confirms the usefulness of the present X-STRs in identification analysis.
Collapse
Affiliation(s)
- Iva Gomes
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Plácido J P Pereira
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9020-105 Funchal, Portugal
| | - Sonja Harms
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Andréa M Oliveira
- Genetic Department, Institute of Biology, State University of Rio de Janeiro (UERJ), Brazil
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - António Brehm
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9020-105 Funchal, Portugal.
| |
Collapse
|
32
|
Curiosities of X chromosomal markers and haplotypes. Int J Legal Med 2017; 132:361-371. [DOI: 10.1007/s00414-017-1612-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/16/2017] [Indexed: 10/19/2022]
|
33
|
DNA Commission of the International Society for Forensic Genetics (ISFG): Guidelines on the use of X-STRs in kinship analysis. Forensic Sci Int Genet 2017; 29:269-275. [PMID: 28544956 DOI: 10.1016/j.fsigen.2017.05.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/21/2023]
Abstract
Forensic genetic laboratories perform an increasing amount of genetic analyses of the X chromosome, in particular to solve complex cases of kinship analysis. For some biological relationships X-chromosomal markers can be more informative than autosomal markers, and there are a large number of markers, methods and databases that have been described for forensic use. Due to their particular mode of inheritance, and their physical location on a single chromosome, some specific considerations are required when estimating the weight of evidence for X-chromosomal marker DNA data. The DNA Commission of the International Society for Forensic Genetics (ISFG) hereby presents guidelines and recommendations for the use of X-chromosomal markers in kinship analysis with a special focus on the biostatistical evaluation. Linkage and linkage disequilibrium (association of alleles) are of special importance for such evaluations and these concepts and the implications for likelihood calculations are described in more detail. Furthermore it is important to use appropriate computer software that accounts for linkage and linkage disequilibrium among loci, as well as for mutations. Even though some software exist, there is still a need for further improvement of dedicated software.
Collapse
|
34
|
Tamura T, Osawa M, Kakimoto Y, Ochiai E, Suzuki T, Nakamura T. Combined effects of multiple linked loci on pairwise sibling tests. Int J Legal Med 2016; 131:95-102. [PMID: 27878372 DOI: 10.1007/s00414-016-1491-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 11/02/2016] [Indexed: 11/24/2022]
Abstract
The advanced multiplex STR system, PowerPlex Fusion, includes four linked locus pairs. The conventional Identifiler system has one pair of linked loci. Therefore, sibling tests conducted using the advanced system might be more affected by linkage than those conducted using the conventional system. This study simulated single and combined effects of the four linked locus pairs on pairwise sibling tests. Simulated genotypes of 100,000 pairs of full siblings and nonrelatives were constructed according to allele frequencies of the Japanese population. The single linkage effect was evaluated for simulated genotype data by calculating both the likelihood ratio accounting for the linkage between two loci and the likelihood ratio ignoring the linkage. The combined effect was obtained by multiplication of the respective single effects. Furthermore, we investigated the possibility that ignoring the linkage affects subject classification by introducing a scale of the likelihood ratio into sibling tests. The single effect in the Identifiler analysis was 0.645-1.746 times if the linkage was ignored. Overestimations and underestimations were predictable from the identical-by-state status at two linked loci. The combined effect in the PowerPlex Fusion analysis was 0.217-7.390 times. Ignoring the linkage rarely caused a false conclusive or inconclusive result, even from PowerPlex Fusion analysis. Application of the advanced system improved sibling tests considerably. The additional examined loci were more beneficial than the adverse effect of the linkage derived from the four linked locus pairs.
Collapse
Affiliation(s)
- Tomonori Tamura
- Department of Forensic Medicine, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan.,Scientific Crime Laboratory, Kanagawa Prefectural Police, Yamashita-cho 155, Naka-ku, Yokohama, 231-0023, Japan
| | - Motoki Osawa
- Department of Forensic Medicine, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan.
| | - Yu Kakimoto
- Department of Forensic Medicine, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan
| | - Eriko Ochiai
- Department of Forensic Medicine, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan
| | - Takanori Suzuki
- Scientific Crime Laboratory, Kanagawa Prefectural Police, Yamashita-cho 155, Naka-ku, Yokohama, 231-0023, Japan
| | - Takashi Nakamura
- Scientific Crime Laboratory, Kanagawa Prefectural Police, Yamashita-cho 155, Naka-ku, Yokohama, 231-0023, Japan
| |
Collapse
|
35
|
Beurteilung von fraglichen Geschwister- bzw. Halbgeschwisterfällen. Rechtsmedizin (Berl) 2016. [DOI: 10.1007/s00194-016-0093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
36
|
Shyla A, Borovko SR, Tillmar AO, Kuzub NN, Kotova SA, Tsybovsky IS, Rębała K. Belarusian experience of the use of FamLinkX for solving complex kinship cases involving X-STR markers. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
37
|
Hering S, Edelmann J, Haas S, Grasern N. Paternity testing of two female siblings with Investigator Argus X-12 kit: A case with several rare mutation and recombination events. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
38
|
Mixtures with relatives and linked markers. Int J Legal Med 2015; 130:621-34. [DOI: 10.1007/s00414-015-1288-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
|