1
|
Lee DG, Kim SJ, Cho WC, Cho Y, Park JH, Lee J, Jung JY. Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs. Forensic Sci Int Genet 2023; 65:102875. [PMID: 37084624 DOI: 10.1016/j.fsigen.2023.102875] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father-son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10-3 per generation, with an average mutation rate of 2.17 × 10-3 (95% CI, 1.5-3.1 × 10-3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10-3 (95% CI, 2.3-3.7 × 10-3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.
Collapse
Affiliation(s)
- Dong Gyu Lee
- Forensic DNA Division, National Forensic Service, Wonju, South Korea; Department of forensics Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Su Jin Kim
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Woo-Cheol Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Yoonjung Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Jinmyung Lee
- DNA Analysis Division, National Forensic Service Busan Institute, Busan, South Korea
| | - Ju Yeon Jung
- Forensic DNA Section, National Forensic Service Jeju Branch, Jeju, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
| |
Collapse
|
2
|
Fan G, Zhao Q, Wuo NA, Li Q, Mao Z. Developmental validation of a complementary Y-STR system for the amplification of forensic samples. Forensic Sci Int 2023; 346:111667. [PMID: 37003122 DOI: 10.1016/j.forsciint.2023.111667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023]
Abstract
In this study, a new complementary Y-STR system that includes 31 loci was developed (DYS522, DYS388, DYF387S1a/b, DYS510, DYS587, DYS645, DYS531, DYS593, DYS617, GATA_A10, DYS622, DYS552, DYS508, DYS447, DYS527a/b, DYS446, DYS459a/b, DYS444, DYS557, DYS443, DYS626, DYS630, DYS526a, DYF404S1a/b, DYS520, DYS518, and DYS526b). This 31-plex Y-STR system, SureID® Y-comp, is designed for biological samples from forensic casework and reference samples from forensic DNA database. To validate the suitability of this novel kit, many developmental works including size precision testing, sensitivity, male specificity testing, species specificity, PCR inhibitors, stutter precision, reproducibility, suitability for use on DNA mixture and parallel testing of different capillary electrophoresis devices were performed. Mutation rates were investigated using 295 DNA-confirmed father-son pairs. The results demonstrate that the SureID® Y-comp Kit is time-efficient, accurate, and reliable for various case-type samples. It possessed a higher discrimination power and can be a stand-alone kit for male identification. Moreover, the simply acquired additional Y-STR loci will be conductive to construct a robust database. Even if various commercial Y-STR kits are used in distinct forensic laboratories, a wider trans-database retrieval will become feasible with the effort of the SureID® Y-comp Kit.
Collapse
Affiliation(s)
- Guangyao Fan
- Forensic Center, School of Medicine, Shaoxing University, Shaoxing 312000, China.
| | - Qian Zhao
- Shanghai Xuhui District Dahua Hospital, Shanghai 200031, China
| | - Nixon Austin Wuo
- College of Life Sciences, Shaoxing University, Shaoxing 312000, China
| | - Qinghao Li
- Tongshan District Branch of Xuzhou Public Security Bureau, Xuzhou 221100, China
| | - Zemin Mao
- Ningbo Health Gene Technologies Co. Ltd., Ningbo 315040, China
| |
Collapse
|
3
|
Grosjean F, Favre M, Castella V. Comparison between MACSprep™ forensic sperm microbead kit and Erase Sperm Isolation kit for the enrichment of sperm fractions recovered from sexual assault samples. Int J Legal Med 2023; 137:267-278. [PMID: 35773355 PMCID: PMC9816209 DOI: 10.1007/s00414-022-02861-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Sexual assault samples often contain mixtures of cells coming from at least two donors. Ideally, one would need to separate the cells into two cellular fractions: one consisting of the alleged aggressor's spermatozoa (the sperm fraction) and the other containing the victim's epithelial cells (the non-sperm fraction). This separation increases the probability of obtaining the alleged offender's autosomal DNA profile. However, spermatozoa are often collected along with an excess of biological material originating from the victim, and with unfavorable male:female biological material ratios, the absence of separation could result in the PCR amplification of the victim's DNA profile only. Several approaches are available to enrich/purify the spermatozoa present on sexual assault samples. In this paper, we compare a new method, the MACSprep™ Forensic Sperm MicroBead Kit (MACSprep, based on microbeads conjugated with antibodies bound to spermatozoa and their retention within a magnetic column) with the Erase Sperm Isolation Kit (Erase, a standard differential lysis separation procedure combined with a specific removal of free DNA) routinely used in our lab. The performance of both kits was tested using sets of vaginal and buccal swabs loaded with different dilutions of sperm, or azoospermic semen, representing a total of 120 independent samples. For the samples containing undiluted sperm, an average recovery of 58% was observed for the MACSprep's sperm fractions and 43% for Erase's. Significantly better recovery of azoospermic semen was observed in MACSprep's non-sperm fractions (~ 85%) compared to Erase (~ 28%). Erase performed significantly better than MACSprep in terms of recovery for diluted sperm samples (1:10 to 1:800 sperm dilutions) in the presence of vaginal cells, while the purities of the achieved sperm fractions were in favor of MACSprep for the highest sperm dilutions tested. Similar trends were observed with buccal swabs loaded with 1:200 sperm dilutions. Increased sperm dilutions on vaginal swabs resulted in higher variability in the male material recovered, whatever the separation method used. Both methods were easy to perform and resulted in male DNA extracts ready to use in less than 2 h. Both kits showed their specificities in terms of recovery efficiency and purity of the sperm fractions. Ideally, additional experiments should be performed in different laboratories, using workflow and chemistries different than ours, to better define the peculiarities observed with MACSprep for high dilutions. Improving the recovery of MACSprep for diluted samples, in addition to its better purity observed in the experiments performed, could make it a method of choice for laboratory workflow, despite MACSprep's current price per sample being about twice the price of Erase's.
Collapse
Affiliation(s)
- Frederic Grosjean
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Marylou Favre
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Vincent Castella
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| |
Collapse
|
4
|
Albastaki A, Naji M, Lootah R, Almheiri R, Almulla H, Alreyami A, Almarri I, Yu Z, Zhang Y, Shu C, Alghafri R. Design and development of novel single multiplex system incorporating 26 rapidly mutating Y-STRs; 26 RM Yplex. Electrophoresis 2022; 43:1911-1919. [PMID: 35899438 DOI: 10.1002/elps.202200099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023]
Abstract
This article details the development of a single multiplex system amplifying 26 rapidly mutating Y-STR markers. A sequenced allelic ladder, constructed for calling alleles of all loci, is introduced. The multiplex system shows the ability to address the limitations of Y-STRs commercial kits in differentiating closely related males. The multiplex performed well in the prevalidation tests and showed great potential to be used in forensic casework.
Collapse
Affiliation(s)
- Abdulla Albastaki
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Mohammed Naji
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Lootah
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Almheiri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Hanan Almulla
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Afra Alreyami
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Iman Almarri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Zailiang Yu
- Suzhou Microread Genetics Co., Ltd, Suzhou, P. R. China
| | - Yueke Zhang
- Suzhou Microread Genetics Co., Ltd, Suzhou, P. R. China
| | - Chang Shu
- Beijing Microread Genetics Co., Ltd, Beijing, P. R. China
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| |
Collapse
|
5
|
Nazir S, Adnan A, Rehman RA, Al-Qahtani WS, Alsaleh AB, Al-Harthi HS, Safhi FA, Almheiri R, Lootah R, Alreyami A, Almarri I, Wang CC, Rakha A, Hadi S. Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan. Genes (Basel) 2022; 13:genes13081403. [PMID: 36011314 PMCID: PMC9407599 DOI: 10.3390/genes13081403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1−20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father−son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.
Collapse
Affiliation(s)
- Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Abrar B. Alsaleh
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Hussam S. Al-Harthi
- Prince Sultan Military Medical City, Makkah Al Mukarramah Road, Al-Sulimaniyah, Riyadh 12233, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Reem Almheiri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Reem Lootah
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Afra Alreyami
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Imran Almarri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| |
Collapse
|
6
|
Della Rocca C, Trombetta B, Barni F, D’Atanasio E, Hajiesmaeil M, Berti A, Hadi S, Cruciani F. Improving discrimination capacity through rapidly mutating Y-STRs in structured populations from the African continent. Forensic Sci Int Genet 2022; 61:102755. [DOI: 10.1016/j.fsigen.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/21/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
|
7
|
Jin X, Zhang H, Ren Z, Wang Q, Liu Y, Ji J, Zhang H, Yang M, Zhou Y, Huang J. Developmental Validation of a Rapidly Mutating Y-STR Panel Labeled by Six Fluoresceins for Forensic Research. Front Genet 2022; 13:777440. [PMID: 35309136 PMCID: PMC8927084 DOI: 10.3389/fgene.2022.777440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 11/23/2022] Open
Abstract
The male-specific region of the human Y chromosome is a useful genetic marker for genealogical searching, male inheritance testing, and male DNA mixture deconvolution in forensic studies. However, the Y chromosomal short tandem repeats (Y-STRs) are difficult to distinguish among related males due to their low/medium mutation rate. In contrast, rapidly mutating (RM) Y-STRs exhibit unusually high mutation rates and possess great potential for differentiating male lineages. In this study, we developed a novel Y-STRs multiplex amplification assay of 32 RM Y-STRs by fragment analysis using six dye-labeled technologies (FAM, HEX, TAMRA, ROX, VIG, and SIZ). The development and the validation of the kit were carried out in accordance with the Scientific Working Group guidelines on DNA Analysis Methods. Identical allelic profiles of the 32 RM Y-STRs using a DNA 9948 sample as the positive control could be observed at different concentrations of PCR reagents. Further, the RM Y-STRs did not show cross-reactions with other common animal species, and the developed assay could tolerate interferences from common PCR inhibitors and mixed DNA samples. More importantly, the kit showed relatively high sensitivity and could detect trace DNA samples. Genetic distributions of 32 RM Y-STRs in the Guizhou Han population revealed that these RM Y-STRs showed relatively high genetic diversities. In conclusion, the RM Y-STR assay developed here showed good species specificity, high sensitivity, tolerance to inhibitors, and sample compatibility, which can be viewed as a highly efficient tool with high discrimination capacity for forensic male differentiation.
Collapse
Affiliation(s)
- Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yongsong Zhou
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
- *Correspondence: Jiang Huang,
| |
Collapse
|
8
|
Moon MH, Hong SR, Shin KJ. Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. J Korean Med Sci 2022; 37:e40. [PMID: 35166077 PMCID: PMC8845103 DOI: 10.3346/jkms.2022.37.e40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS. METHODS We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85-274 bp. Barcoded libraries from 220 unrelated males from four populations-African Americans, Caucasians, Hispanics, and Koreans-were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated. RESULTS In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold. CONCLUSION The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases.
Collapse
Affiliation(s)
- Mi Hyeon Moon
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea
| | - Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea.
| |
Collapse
|
9
|
Lin YC, Tsai LC, Liu KL, Huang NE, Yang LJ, Su CW, Lee JCI, Linacre A, Hsieh HM. A novel co-amplification system for simultaneous amplification of 23 Y-STR and identification of spermatozoa. Int J Legal Med 2021; 136:73-84. [PMID: 34713334 DOI: 10.1007/s00414-021-02723-8] [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: 07/30/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
In alleged sexual assault cases, identification of the presence of spermatozoa at the crime scene, or on items of eventual significance, or associated with the body of the victim, is integral to the forensic investigation to support or refute the proposition that sexual act has occurred. A 3-plex MSRE-PCR (methylation-sensitive restriction enzyme-PCR) system has been developed previously to identify spermatozoa based on the presence or absence of DNA methylation. This assay showed that 0.1 ng of DNA from a semen extract was sufficient to identify the presence of spermatozoa even when there was excessively more DNA isolated from vaginal fluid than DNA from a semen extract (80 ng/0.1 ng) or a mix of the menstrual blood/semen DNA (5 ng/0.1 ng). In this study, we combine spermatozoa detection with co-amplification of 23 Y-STR loci. We perform standard validation steps to present a novel test that saves time and uses the same sample for both DNA typing and spermatozoa detection in the same reaction. The combined assay can identify Y-STR and spermatozoa simultaneously using just 0.1 ng semen DNA, even in the presence of 5 ng of DNA from a female (male/female:1/50). No other body fluid tested, such as saliva, gave a result for the presence of spermatozoa. A total of 9 non-probative forensic samples from 7 sexual assault cases were tested by this co-amplification system. In all cases, the same sperm-positive data were obtained, concordant with our previous study analyzed by only 3-plex MSRE-PCR, and the Y-STR results were also consistent with that analyzed by only PowerPlex® Y23 kit. The co-amplification will be beneficial for the limited samples in many criminal cases.
Collapse
Affiliation(s)
- Yu-Chih Lin
- Taichung City Government Police Department, No.500 Fengxing Road Section 1, Tanzi District, Taichung City, 427003, Taiwan, Republic of China
| | - Li-Chin Tsai
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan, Republic of China
| | - Kuo-Lan Liu
- Forensic Examination Division, Criminal Investigation Bureau, National Police Agency, No.5 Lane 553, Chung Hsiao East Road Section 4, Xinyi District, Taipei, 11072, Taiwan, Republic of China
| | - Nu-En Huang
- Forensic Biology Division, Criminal Investigation Bureau, National Police Agency, No.5 Lane 553, Chung Hsiao East Road Section 4, Xinyi District, Taipei, 11072, Taiwan, Republic of China
| | - Lih-Jing Yang
- International Criminal Affairs Division, Criminal Investigation Bureau, National Police Agency, No.5 Lane 553, Chung Hsiao East Road Section 4, Xinyi District, Taipei, 11072, Taiwan, Republic of China
| | - Chih-Wen Su
- Forensic Biology Division, Criminal Investigation Bureau, National Police Agency, No.5 Lane 553, Chung Hsiao East Road Section 4, Xinyi District, Taipei, 11072, Taiwan, Republic of China
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, Republic of China
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, 5001, Australia
| | - Hsing-Mei Hsieh
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan, Republic of China.
| |
Collapse
|
10
|
Ralf A, Zandstra D, Weiler N, van Ijcken WFJ, Sijen T, Kayser M. RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates. Forensic Sci Int Genet 2021; 55:102595. [PMID: 34543845 DOI: 10.1016/j.fsigen.2021.102595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) with high mutation rates are recognized as valuable genetic markers for differentiating paternally related men, who typically cannot be separated with standard Y-STRs, and were shown to provide paternal lineage differentiation on a higher resolution level than standard Y-STRs. Both features make Y-STRs with high mutation rates relevant in criminal casework, particularly in sexual assault cases involving highly unbalanced male-female DNA mixtures that often fail autosomal forensic STR profiling for the male donor. Previously, the number of known Y-STRs with mutation rates higher than 10-2 per locus per generation termed rapidly mutating Y-STRs (RM Y-STRs) was limited to 13, which has recently been overcome by the discovery and characterization of 12 additional RM Y-STRs. Here, we present the development and validation of RMplex, an efficient genotyping system for analyzing 30 Y-STRs with high mutation rates, including all currently known RM Y-STRs, using multiplex PCR with capillary electrophoresis (CE) or massively parallel sequencing (MPS), overall targeting a total of 44 male-specific loci. If previously unavailable, repeat number assignations were provided based on newly generated MPS data. Validation tests based on the CE method demonstrated that the results were both repeatable and reproducible, full profiles were achieved with minimal input DNA of 250 pg for RMplex 1 and 100 pg for RMplex 2, and in the presence of inhibitors, or with a surplus of female DNA, the assays performed reasonably well. Application of RMplex to differentiate between paternally related men was exemplified in 32 males belonging to five different paternal pedigrees. Given further successful forensic validation testing, we envision the future application of RMplex in criminal cases where it is suspected, or cannot be excluded, that the crime scene trace originated from a male relatives of the suspect who is highlighted with standard Y-STR matching. Other applications of RMplex are in criminal cases without known suspects to differentiate between male relatives highlighted in familial searching based on standard Y-STR matching.
Collapse
Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dion Zandstra
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Natalie Weiler
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| |
Collapse
|
11
|
Zhou Y, Song F, Dai H, Wang S, Zhang K, Wei X, Wang X, Luo H. Developmental validation of the Microreader™ RM-Y ID System: a new rapidly mutating Y-STR 17-plex system for forensic application. Int J Legal Med 2021; 136:501-512. [PMID: 34302216 DOI: 10.1007/s00414-021-02632-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 10/20/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely applied to evolutionary, genealogical, and kinship analyses of male linages in forensic studies, but these low to midrange mutated Y-STRs typically fail to separate related males from the same paternal lineage. Recently, rapidly mutating Y-STRs (RM Y-STRs) have been demonstrated to improve the differentiation of male relatives and individuals. The Microreader™ RM-Y ID System is a new RM Y-STR kit that is capable of simultaneously amplifying 17 RM Y-STRs. Herein, to verify the efficiency and accuracy of the Microreader™ RM-Y ID System, developmental validation was conducted, including PCR-based studies, sensitivity, stability, species specificity, mixture, stutter percentage, and precision studies. Full profiles could be obtained when the hematin concentration was 250 μM, humic acid concentration was 1500 ng/μl, and tannic acid concentration was 200 ng/μl. Full profiles of the mixture of males/males could be detected up to a ratio of 19:1, and full profiles of females/males could always be detected even at ratios up to 24,000:1. Moreover, the forensic characteristics of 250 DNA-confirmed father-son pairs were analysed. The results showed that these 17 RM Y-STRs had high power for forensic discrimination (HD = 1) in the Chinese Han population, and the mutation rates were in the range of 4 × 10-3 (95% CI 1.00 × 10-4 to 2.21 × 10-2, DYS464) to 8.8 × 10-2 (95% CI 5.60 × 10-2 to 1.30 × 10-1, DYF399S1), indicating that the kit was effective for RM Y-STR studies and absolute individualisation of interrelated male individuals.
Collapse
Affiliation(s)
- Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Hao Dai
- Department of Forensic Pathology, 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, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Ke Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China.
| |
Collapse
|
12
|
Bredemeyer S, Roewer L, Willuweit S. Next generation sequencing of Y-STRs in father-son pairs and comparison with traditional capillary electrophoresis. Forensic Sci Res 2021; 7:484-489. [PMID: 36353309 PMCID: PMC9639519 DOI: 10.1080/20961790.2021.1898078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To evaluate the promising advantages of massively parallel sequencing (MPS) in our casework, we analysed a total of 33 Y-chromosomal short tandem repeats (Y-STRs) with traditional capillary electrophoresis (CE) and 25 Y-STRs using the newer MPS technology. We studied the outcome of both technologies in 64 father-son pairs using stock and custom-designed kits. Current MPS technology confirmed the 13 mutational events observed with CE and improved our understanding of the complex nature of STR mutations. By detecting isometric sequence variants between unrelated males, we show that sequencing Y-STRs using MPS can boost discrimination power.
Collapse
Affiliation(s)
- Steffi Bredemeyer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
13
|
STRNaming: Generating simple, informative names for sequenced STR alleles in a standardised and automated manner. Forensic Sci Int Genet 2021; 52:102473. [PMID: 33607395 DOI: 10.1016/j.fsigen.2021.102473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 11/20/2022]
Abstract
The introduction of Massively Parallel Sequencing in the forensic domain has exposed the need for comprehensive nomenclature of sequenced Short Tandem Repeat (STR) alleles. In general, three strategies are at hand: 1) the full sequence mapped to the human genome reference sequence, which ensures exact data exchange; 2) shortened, human-readable formats for forensic reporting and data presentation and 3) very short codes that enable compact figures and tables but do not convey any sequence information. Here, we describe an algorithm of the second type: STRNaming, which generates human-readable names for sequenced STR alleles. STRNaming is guided by a reference sequence at each locus and then functions independently to automatically assign a unique, sequence-descriptive name that also includes the capillary electrophoresis allele number. STRNaming settings were established based on preferences that were surveyed internationally in the forensic community. These settings ensure that a small change in the sequence corresponds to a small change in the allele name, which is helpful for recognising for instance stutter products. Sequence variants outside of the repeat units are indicated as simple variant calls. Since the STR name is sequence-descriptive, the sequence can be traced back from the allele name. Because STRNaming is fully guided by an assignable reference sequence, no central coordination or configuration is required and the method will work for any STR locus, be it autosomal, Y-, X-chromosomal in current or future use. The algorithm is publicly available online and offline.
Collapse
|
14
|
Zeyad T, Adam A, Alghafri R, Iratni R. Study of 27 Y-STR markers in United Arab Emirates population. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
15
|
Ye Y, An Y, Yang Y, Wu H, Zheng Y, Liao L. Assessment of the forensic application of 50 Y-STR markers in a large pedigree. Forensic Sci Res 2020; 7:207-210. [PMID: 35784420 PMCID: PMC9246022 DOI: 10.1080/20961790.2020.1802827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Short tandem repeats on the Y chromosome (Y-STRs), characterized by paternal inheritance, are valuable in forensic practice. Notably, the potential application of Y-STRs in pedigrees should be drawn upon, especially in China’s surname-concentrated natural villages. The study focused on 50 Y-STRs, including 13 rapidly mutating (RM) Y-STRs that largely constitute the current Y-STR commercial kits, and determined the differences in these Y-STRs between branches in a large pedigree and the discriminatory power of these haplotypes in different units for male relatives. As indicated in the results, 14 inconsistencies were observed at 9 Y-STRs between 10 father-son pairs. In addition, these 50 Y-STR haplotypes discriminated 10 out of 47 father-son pairs, 106 of 148 cousin pairs, 70 of 119 uncle-nephew pairs, 17 of 39 brother pairs, and 14 out of 33 grandfather-grandson pairs in a large pedigree. The RM Y-STR set is able to differentiate close male relatives in a large pedigree.
Collapse
Affiliation(s)
- Yi Ye
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yuran An
- Criminal Technology Department, Liupanshui Public Security Bureau, Guizhou, China
| | - Yiwen Yang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Hao Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yuzi Zheng
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Linchuan Liao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
16
|
Fu J, Cheng J, Wei C, Khan MA, Jin Z, Fu J. Assessing 23 Y-STR loci mutation rates in Chinese Han father-son pairs from southwestern China. Mol Biol Rep 2020; 47:7755-7760. [PMID: 32989501 DOI: 10.1007/s11033-020-05851-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022]
Abstract
In this study, we have analyzed 23 Y-chromosomal short tandem repeats (Y-STRs) (DYS576, DYS389I, DYS389II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS460, DYS385ab, DYS456 and Y-GATA-H4) in 175 father-son sample pairs using a Microreader™ 24Y Direct ID system. Sixteen repeat mutations of father-son pairs at 10 loci, including three mutations at DYS570, 2 mutations at DYS549, DYS460, DYS458, and DYS576, and 1 mutation at other five loci, were revealed. Furthermore, all of the observed repeat mutations were single repeat changes with 5 (31.25%) repeat insertions and 11 (68.75%) repeat deletions. The deletion rate is more than two fold higher than of insertions (11:5 = 2.2-fold). Locus-specific mutation rates estimated varied between 5.71 × 10-3 (CI from 0.1 × 10-3 to 31.4 × 10-3) and 1.71 × 10-2 (CI from 3.6 × 10-3 to 49.3 × 10-3) for the 23 Y-STRs. An average mutation rate across all 23 Y-STR markers was estimated as 3.97 × 10-3 (CI 2.3 × 10-3 to 6.4 × 10-3). Thus, locus-specific mutation rates in DYS460, DYS458, and DYS438, estimated are much higher than previously published comprehensive data, but an average mutation rate across all 23 Y-STR markers is similar to previous reports (3.97 × 10-3 vs 4.34 × 10-3). These results by characterizing Y-STR mutations will not only provided new information for Y-STR mutations but also might be important for paternal lineage identification, kinship analysis, and family relationship reconstruction in our forensic Y-STR analysis.
Collapse
Affiliation(s)
- Jiewen Fu
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jingliang Cheng
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Chunli Wei
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Md Asaduzzaman Khan
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Zeming Jin
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Junjiang Fu
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| |
Collapse
|
17
|
Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples. Int J Legal Med 2020; 135:409-419. [PMID: 32524192 DOI: 10.1007/s00414-020-02326-9] [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: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
The SureID® PathFinder Plus is a new 6-dye, 41-plex Y-STR system that includes the 17 loci from the Yfiler® kit (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4) plus 14 rapidly mutating Y-STR loci (DYS449, DYS481, DYS518, DYS527a/b, DYS533, DYS549, DYS570, DYS576, DYS627, DYF387S1a/b, and DYF404S1), and 10 low-medium mutation loci (DYS388, DYS444, DYS447, DYS460, DYS522, DYS557, DYS593, DYS596, DYS643, and DYS645). The inclusion of the 14 rapidly mutating Y-STR loci improves the discrimination of related individuals. Conversely, the 10 low-medium mutation loci are suitable not only for familial searching but also for providing a higher refinement in the construction of Y chromosome phylogenetic relationships among lineages. The 41-plex Y-STR system is designed for direct amplification of reference samples, such as blood samples on an FTA® Card, gauze, tissue, or cotton substrates as well as hair root or buccal samples on swabs. We performed developmental validation work including accuracy, stability, stutter precision, species specificity, sensitivity, PCR inhibitors, reproducibility, parallel testing of the system, and suitability for use on DNA mixtures. In addition, mutations of the loci were analyzed by 754 DNA-confirmed father-son pairs. The results demonstrate that this kit, developed in-house, is time-efficient, accurate, reliable, and highly informative for forensic database, familial searching, and distinguishing related males.
Collapse
|
18
|
Roewer L, Andersen MM, Ballantyne J, Butler JM, Caliebe A, Corach D, D'Amato ME, Gusmão L, Hou Y, de Knijff P, Parson W, Prinz M, Schneider PM, Taylor D, Vennemann M, Willuweit S. DNA commission of the International Society of Forensic Genetics (ISFG): Recommendations on the interpretation of Y-STR results in forensic analysis. Forensic Sci Int Genet 2020; 48:102308. [PMID: 32622324 DOI: 10.1016/j.fsigen.2020.102308] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Forensic genetic laboratories perform a large amount of STR analyses of the Y chromosome, in particular to analyze the male part of complex DNA mixtures. However, the statistical interpretation of evidence retrieved from Y-STR haplotypes is challenging. Due to the uni-parental inheritance mode, Y-STR loci are connected to each other and thus haplotypes show patterns of relationship on the familial and population level. This precludes the treatment of Y-STR loci as independently inherited variables and the application of the product rule. Instead, the dependency structure of Y-STRs needs to be included in the haplotype frequency estimation process affecting also the current paradigm of a random match probability that is in the autosomal case approximated by the population frequency assuming unrelatedness of sampled individuals. Information on the degree of paternal relatedness in the suspect population as well as on the familial network is however needed to interpret Y-chromosomal results in the best possible way. The previous recommendations of the DNA commission of the ISFG on the use of Y-STRs in forensic analysis published more than a decade ago [1] cover the interpretation issue only marginally. The current recommendations address a number of topics (frequency estimators, databases, metapopulations, LR formulation, triage, rapidly mutating Y-STRs) with relevance for the Y-STR statistics and recommend a decision-based procedure, which takes into account legal requirements as well as availability of population data and statistical methods.
Collapse
Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Dept. Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany.
| | - Mikkel Meyer Andersen
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark; Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, USA
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, USA
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Immunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina; National Research Council, CONICET, Buenos Aires, Argentina
| | - Maria Eugenia D'Amato
- University of the Western Cape, Department of Biotechnology, Forensic DNA Lab, Cape Town, South Africa
| | - Leonor Gusmão
- State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, China
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Mechthild Prinz
- John Jay College of Criminal Justice, Dept. of Sciences, New York, USA
| | - Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Duncan Taylor
- Forensic Science South Australia, Adelaide, Australia; Flinders University, Adelaide, Australia
| | | | - Sascha Willuweit
- Institute of Legal Medicine and Forensic Sciences, Dept. Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany
| |
Collapse
|
19
|
Liu Y, Guo Y, Jin X, Mei S, Xie T, Lan Q, Fang Y, Zhu B. Developmental validation study of a 24-plex Y-STR direct amplification system for forensic application. Int J Legal Med 2019; 134:945-951. [PMID: 31853674 DOI: 10.1007/s00414-019-02220-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022]
Abstract
In the present study, validation data for 24 Y-STR loci from the Microreader™ 24Y Direct ID System was presented. Eight Y-STR loci have PCR product sizes with less than 220 bp in this multiplex amplification system, which can better detect degraded DNA samples from a crime scene. Developmental validation studies were conducted following the SWGDAM guidelines and consisted of PCR-based studies, sensitivity testing, species specificity, stability studies, accuracy and reproducibility evaluation, mixture studies, and case-type samples. The genetic diversities and forensic parameters of the 24 Y-STR loci were also investigated in Jiangsu Han population. Results demonstrated that this kit had the characteristics of high detection accuracy, strong species specificity, favorable anti-inhibition effect, and high sensitivity, and the minimum detection amount was 125 pg. When the mixed female template amount was below 3.2 times that of the male, or the male-male mixed ratio did not exceed 1:9, the typing results produced by 24Y Direct System still exhibited a higher discriminating ability for the mixture. The system was compatible with some typical biological samples such as bloodstain, hair, buccal swab, rib cartilage, and nail. The haplotype diversity (HD) and discrimination capacity (DC) of the 24 Y-STR loci were 0.9952 and 0.8500, respectively. The results revealed that the 24 Y-STR loci were highly polymorphic in Jiangsu Han population and could be useful for forensic cases and population genetic studies.
Collapse
Affiliation(s)
- Yanfang Liu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Shuyan Mei
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Lan
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China. .,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China. .,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China. .,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China.
| |
Collapse
|
20
|
Evaluation of 13 rapidly mutating Y-STRs on a Dravidian pedigree. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Ay M, Serin A, Canan H, Cekin N. Haplotype data for the 12 RM Y-STR loci in a Syrian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
22
|
Investigation on rapidly mutating Y-STRs multiplex in Indian population: A pilot study. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Farhatullah M, Absar M, Rauf S, Tracy M, Almulla H, Almheiri R, Adam A, Alghafri R, Khan MR. Evaluation of rapidly mutating Y-STRs in Pakistani population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
24
|
A comprehensive mutation study in wide deep-rooted R1b Serbian pedigree: mutation rates and male relative differentiation capacity of 36 Y-STR markers. Forensic Sci Int Genet 2019; 41:137-144. [DOI: 10.1016/j.fsigen.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/05/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022]
|
25
|
Jung L, Hogan ME, Sun Y, Liang BM, Hayward JA. Rapid authentication of pharmaceuticals via DNA tagging and field detection. PLoS One 2019; 14:e0218314. [PMID: 31194827 PMCID: PMC6564018 DOI: 10.1371/journal.pone.0218314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/26/2019] [Indexed: 11/23/2022] Open
Abstract
A small PCR-generated DNA fragment was introduced into a pharmaceutical grade ink as a molecular taggant, and the DNA tagged ink was delivered onto the surface of capsules by standard high-speed offset printing. The amount of DNA in the ink on each capsule is roughly 10−12 fold lower than that allowed as safe by the United States Food and Drug Administration (FDA) and the WHO with regards to acceptable limits of residual DNA. The printed ink on the capsule surface was sampled by swabbing, followed by direct analysis of the DNA-swab complex, without subsequent DNA purification. It was shown that DNA recovered from the ink by swabbing was suitable for PCR-CE analysis—a widely used method in forensic science and was also suitable for qPCR and isothermal DNA amplification, when coupled with portable devices similar to those used for environmental sampling and food safety testing. The data set a precedent: A small DNA fragment could be introduced as an excipient into a pharmaceutical application, and thereafter tracked through the pharmaceutical supply chain via forensic DNA authentication.
Collapse
Affiliation(s)
- Lawrence Jung
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
- * E-mail: (MEH); (LJ)
| | - Michael E. Hogan
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
- * E-mail: (MEH); (LJ)
| | - Yuhua Sun
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
| | | | - James A. Hayward
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
| |
Collapse
|
26
|
Roewer L. Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1336] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin and Berlin Institute of Health, Charité‐Universitätsmedizin Berlin 13353 Berlin Germany
| |
Collapse
|
27
|
The validation study of a novel assay with 30 slow and moderate mutation Y-STR markers for criminal investigation and database applications. Int J Legal Med 2019; 134:491-499. [DOI: 10.1007/s00414-019-02037-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/01/2019] [Indexed: 11/26/2022]
|
28
|
Serin A, Ay M, Sevay H, Gurkan C, Canan H. Genetic characterisation of 13 rapidly mutating Y-STR loci in 100 father and son pairs from South and East Turkey. Ann Hum Biol 2019; 45:506-515. [DOI: 10.1080/03014460.2018.1559353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ayse Serin
- Department of Forensic Medicine, Faculty of Medicine, University of Cukurova, Adana, Turkey
| | - Mustafa Ay
- Department of Forensic Medicine, Institute of Health Science, University of Cukurova, Adana, Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
- Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta (North Cyprus), Turkey
| | - Husniye Canan
- Department of Forensic Medicine, Faculty of Medicine, University of Cukurova, Adana, Turkey
| |
Collapse
|
29
|
McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| |
Collapse
|
30
|
Mutation analysis of 13 RM Y-STR loci in Han population from Beijing of China. Int J Legal Med 2018; 133:59-63. [DOI: 10.1007/s00414-018-1949-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/10/2018] [Indexed: 11/26/2022]
|
31
|
Wang Q, Jin B, An G, Zhong Q, Chen M, Luo X, Li Z, Jiang Y, Liang W, Zhang L. Rapidly mutating Y-STRs study in Chinese Yi population. Int J Legal Med 2018; 133:45-50. [PMID: 30062654 DOI: 10.1007/s00414-018-1894-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/17/2018] [Indexed: 12/01/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic analysis and population genetics. With low to moderate mutation rates, conventional Y-STR panels, including commercially available Y-STR kits, enable the identification of male pedigrees but typically fail to differentiate related male individuals. The introduction of rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) with higher mutation rates (μ > 10-2) has been demonstrated to increase the discrimination capacity of unrelated men and the differentiation rate of related men compared with standard Y-STRs. To date, several studies have been performed worldwide. Here, 260 father-son pairs from Chinese Yi population were investigated, and 18.8% of them were differentiated with the 13 RM Y-STR markers, which was close to the theoretical estimate of 19.5% based on the mutation rates of these markers. Among the 57 mutations observed, repeat gains were more common than repeat losses (1.48:1), and one-step mutations were more common than two-step mutations (27.5:1). Locus-specific mutation rates ranged from < 3.85 × 10-3 (95% CI 0.00-1.41 × 10-2) to 3.85 × 10-2 (95% CI 1.86 × 10-2-6.96 × 10-2), with an average mutation rate of 1.46 × 10-2 (95% CI 1.11 × 10-2-1.89 × 10-2). Furthermore, we combined the father-son pair data from the present study with the data from the previous studies, generating an overall mutation rate of 1.70 × 10-2. The high differentiation rate obtained in the present study indicates the suitability of RM Y-STRs to distinguish paternal lineages in Chinese Yi population.
Collapse
Affiliation(s)
- Qian Wang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Bo Jin
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.,Department of Forensic Medicine, North Sichuan Medical College, Nanchong, 637000, Sichuan, China.,Forensic Science Service Center, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Gang An
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Qian Zhong
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Meijun Chen
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Xiaoying Luo
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Zhilong Li
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Youjing Jiang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
32
|
Javed F, Sumbal S, Shafique M, Shahid AA, Shahzadi A, Rani N, Javid H, Javed M, Gillani N, Husnain T. Male individualization using 12 rapidly mutating Y-STRs in Araein ethnic group and shared paternal lineage of Pakistani population. Int J Legal Med 2018; 132:1621-1624. [PMID: 29797282 DOI: 10.1007/s00414-018-1851-3] [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: 08/28/2017] [Accepted: 05/11/2018] [Indexed: 10/16/2022]
Abstract
A multiplex assay has been developed with newly designed primer sets comprising high mutation rate 12 RM Y-STR markers (DYS570, DYF399S1, DYS547, DYS612, DYF387S1, DYS449, DYS576, DYS5626, DYF403S1 (a + b), DYS627, DYS526, and DYF404S1). Rapidly mutating Y-STRs were evaluated in 167 male individuals among 97 were unrelated from Araein ethnic group and 70 belonged to shared paternal lineage including 20 pairs of father-son and 15 pairs of brother-brother relationship collected from Punjabi population of Pakistan. Forensic competency parameters were implemented for each marker and exceptionally significant results found wherein polymorphism information content (PIC) was in range of 0.7494 (DYS576) to 0.8994 (DYS627). Samples were also analyzed with Y-filer kit for comparison and marked differentiations observed. Haplotype discrimination capacity was 100% as no haplotype shared among all the unrelated individuals of same ethnic group as compared to 17 Y-filer loci (78%). While in closely related males, discrimination capacity was 96.4% with haplotype diversity value of 0.98. Resulted high mutation rate 1 × 10-2 to 7.14 × 10-2 as compared to Y-filer (1 × 10-4 to 1 × 10-3) manifested the power of RM Y-STRs for considering absolute individualization of interrelated and unrelated male individuals. However, multiplex assay would be useful for male discrimination in mixed DNA specimen, azoospermic males, and multiple male DNA contributors in sexual assault cases and mass disasters victim's identification as well as anthropological studies.
Collapse
Affiliation(s)
- Faqeeha Javed
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Sumbal Sumbal
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Muhammad Shafique
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.
| | - Ahmad Ali Shahid
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Abida Shahzadi
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Noshaba Rani
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Hira Javid
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Madeeha Javed
- De'montmorency College of Dentistry, Lahore, Pakistan
| | - Noman Gillani
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Tayyab Husnain
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| |
Collapse
|
33
|
|
34
|
Zgonjanin D, Alghafri R, Antov M, Toljić D, Almheiri R, Petković S, Stojiljković G, Vuković R. Rapidly mutating Y-STRs population data in the population of Serbia and haplotype probability assessment for forensic purposes. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
35
|
Zgonjanin D, Alghafri R, Almheiri R, Antov M, Toljic D, Vukovic R, Petkovic S. Mutation rate at 13 rapidly mutating Y-STR loci in the population of Serbia. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
36
|
Lang M, Ye Y, Li J, Zhang Y, Yuan T, Hou Y. Comprehensive mutation analysis of 53 Y-STR markers in father-son pairs. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
37
|
Oldoni F, Castella V, Hall D. Application of DIP-STRs to sexual/physical assault investigations: Eight case reports. Forensic Sci Int Genet 2017; 30:106-113. [DOI: 10.1016/j.fsigen.2017.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/12/2017] [Accepted: 06/27/2017] [Indexed: 11/16/2022]
|
38
|
Alghafri R, Zupanič Pajnič I, Zupanc T, Balažic J, Shrivastava P. Rapidly mutating Y-STR analyses of compromised forensic samples. Int J Legal Med 2017; 132:397-403. [PMID: 28466124 DOI: 10.1007/s00414-017-1600-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/24/2017] [Indexed: 11/25/2022]
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were identified to improve differentiation of unrelated males and also to enable separating closely and distantly related males in human identity testing in forensic and other applications. RM-Yplex assay was developed as a single multiplex that is capable of simultaneously amplifying all currently known RM Y-STRs, and reproducibility and sensitivity testing were performed on reference samples. Additional analyses are necessary to test its suitability for analysing compromised forensic samples. For this purpose, we applied the RM-Yplex assay to approximately 70-year-old skeletons that were used as a model for poorly preserved, challenging forensic samples. We analysed 57 male skeletal remains (bones and teeth) from 55 skeletons excavated from the Second World War (WWII) mass graves in Slovenia. The RM-Yplex typing was successful in all 57 samples; there were 56% full profiles obtained, and in partial profiles, up to 7 locus drop-outs were observed and they appeared correlated with low DNA quantities and degradation of DNA obtained from WWII bone and tooth samples. The longest loci, DYS403S1b, DYS547, DYS627 and DYS526b, were the most often dropped-out RM Y-STRs. In spite of high frequency of drop-out events, the RM-Yplex typing was successful in all WWII samples, showing the possibility of successful amplification of at least half of the RM Y-STRs even from the most compromised samples analysed.
Collapse
Affiliation(s)
- Rashed Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Al Tawar 1, Dubai, United Arab Emirates
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Jože Balažic
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Govt. of Madhya Pradesh, Sagar, 470001, India
| |
Collapse
|
39
|
Oldoni F, Castella V, Grosjean F, Hall D. Sensitive DIP-STR markers for the analysis of unbalanced mixtures from “touch” DNA samples. Forensic Sci Int Genet 2017; 28:111-117. [DOI: 10.1016/j.fsigen.2017.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/27/2017] [Accepted: 02/09/2017] [Indexed: 01/31/2023]
|
40
|
Kayser M. Forensic use of Y-chromosome DNA: a general overview. Hum Genet 2017; 136:621-635. [PMID: 28315050 PMCID: PMC5418305 DOI: 10.1007/s00439-017-1776-9] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022]
Abstract
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.
Collapse
Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| |
Collapse
|
41
|
Lee EY, Lee HY, Kwon SY, Oh YN, Yang WI, Shin KJ. A multiplex PCR system for 13 RM Y-STRs with separate amplification of two different repeat motif structures in DYF403S1a. Forensic Sci Int Genet 2017; 26:85-90. [DOI: 10.1016/j.fsigen.2016.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/28/2016] [Accepted: 10/26/2016] [Indexed: 12/09/2022]
|
42
|
Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples. Anal Bioanal Chem 2016; 409:939-947. [PMID: 27900418 DOI: 10.1007/s00216-016-9950-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/18/2016] [Accepted: 09/14/2016] [Indexed: 10/20/2022]
Abstract
In this paper, we demonstrate a rapid analysis procedure for use with a small set of rapidly mutating Y chromosomal short tandem repeat (Y-STR) loci that combines both rapid polymerase chain reaction (PCR) and microfluidic separation elements. The procedure involves a high-speed polymerase and a rapid cycling protocol to permit PCR amplification in 16 min. The resultant amplified sample is next analysed using a short 1.8-cm microfluidic electrophoresis system that permits a four-locus Y-STR genotype to be produced in 80 s. The entire procedure takes less than 25 min from sample collection to result. This paper describes the rapid amplification protocol as well as studies of the reproducibility and sensitivity of the procedure and its optimisation. The amplification process utilises a small high-speed thermocycler, microfluidic device and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The four loci used for the multiplex were selected due to their rapid mutation rates and should proved useful in preliminary screening of samples and suspects. Overall, this technique provides a method for rapid sample screening of suspect and crime scene samples in forensic casework. Graphical abstract ᅟ.
Collapse
|
43
|
Cloete KW, Ristow PG, Kasu M, D'Amato ME. Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis. Electrophoresis 2016; 38:617-623. [PMID: 27859383 DOI: 10.1002/elps.201600257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
CE equipment detects and deconvolutes mixtures containing up to six fluorescently labeled DNA fragments. This deconvolution is done by the collection software that requires a spectral calibration file. The calibration file is used to adjust for the overlap that occurs between the emission spectra of fluorescence dyes. All commercial genotyping and sequencing kits require the installation of a corresponding matrix standard to generate a calibration file. Due to the differences in emission spectrum overlap between fluorescent dyes, the application of existing commercial matrix standards to the electrophoretic separation of DNA labeled with other fluorescent dyes can yield undesirable results. Currently, the number of fluorescent dyes available for oligonucleotide labeling surpasses the availability of commercial matrix standards. Therefore, in this study we developed and evaluated a customized matrix standard using ATTO 633, ATTO 565, ATTO 550, ATTO Rho6G, and 6-FAM dyes for which no commercial matrix standard is available. We highlighted the potential genotyping errors of using an incorrect matrix standard by evaluating the relative performance of our custom dye set using six matrix standards. The specific performance of two genotyping kits (UniQTyper™ Y-10 version 1.0 and PowerPlex® Y23 System) was also evaluated using their specific matrix standards. The procedure we followed for the construction of our custom dye matrix standard can be extended to other fluorescent dyes.
Collapse
Affiliation(s)
- Kevin Wesley Cloete
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Peter Gustav Ristow
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Mohaimin Kasu
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| |
Collapse
|
44
|
Multiplex assay development and mutation rate analysis for 13 RM Y-STRs in Chinese Han population. Int J Legal Med 2016; 131:345-350. [DOI: 10.1007/s00414-016-1489-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022]
|
45
|
Forensic genetic study of 29 Y-STRs in Korean population. Leg Med (Tokyo) 2016; 23:17-20. [DOI: 10.1016/j.legalmed.2016.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/10/2016] [Accepted: 09/01/2016] [Indexed: 11/21/2022]
|
46
|
Abuidrees AS, Alghafri RH, Hadi S. Rapid amplification of the RM-Yplex assay. Electrophoresis 2016; 37:2817-2821. [PMID: 26970423 DOI: 10.1002/elps.201500549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/23/2016] [Accepted: 03/07/2016] [Indexed: 11/07/2022]
Abstract
A multiplex PCR assay consisting of 13 Rapidly Mutating Y STR loci called RM-Yplex was previously developed. Platinum® Taq DNA polymerase was used to amplify the 13 Y STR loci in a single reaction at an amplification time of approximately 2.5 h. In order to shorten the process with reliable results, two DNA polymerases were tested with the multiplex. Phusion® Flash High Fidelity, TAKARA Z-taqTM , and Platinum® Taq DNA polymerases were investigated for conducting RM-Yplex assay at various PCR cycling conditions. Rapid, robust, and efficient amplification of all the markers within the multiplex were achieved. The amplification time was reduced from 2.5 h to less than 28 min with Phusion® Flash High Fidelity DNA polymerase using Veriti® PCR thermal cycler.
Collapse
Affiliation(s)
- Aqeela S Abuidrees
- Directorate of Forensic Science Evidence, Public Prosecution, Manama, Bahrain. ,
| | - Rashed H Alghafri
- Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Dubai, United Arab Emirates
| | - Sibte Hadi
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK
| |
Collapse
|
47
|
Jung JY, Kim KS, Park SW, Lim SK, Lee DS, Lee YH. Sensitivity study of the Yfiler ® PLUS PCR Amplification Kit in forensic casework samples. ANALYTICAL SCIENCE AND TECHNOLOGY 2016. [DOI: 10.5806/ast.2016.29.1.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
48
|
Abstract
Rapidly mutating (RM) Y-STRs were recently identified and can help to differentiate between paternally related males in paternity and forensic casework. Normal Y-STRs are often used in casework due to their paternal inheritance, which can help to resolve kinship cases, and identify male components in male/female mixtures; however, more discriminating profiles are obtained if rapidly mutating Y-STRs are used. Previously two or three multiplex PCRs have been used to amplify 13 RM Y-STRs; here, an assay amplifying these 13 markers in a single multiplex PCR is described. Commercially available male control DNA samples have been genotyped during the validation of this assay, thus providing a tool for calibrating genotyping results. It is expected that the assay will provide a niche tool for genotyping casework samples.
Collapse
Affiliation(s)
- Sibte Hadi
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK.
| |
Collapse
|
49
|
Development and validation of an allelic frequency database for Qatari population using 13 rapidly mutating Y-STRs multiplex assay. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|