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He W, Xu L, Wang J, Yue Z, Jing Y, Tai S, Yang J, Fang X. VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs. BMC Bioinformatics 2024; 25:173. [PMID: 38693489 PMCID: PMC11064410 DOI: 10.1186/s12859-024-05770-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 05/03/2024] Open
Abstract
Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals usually generate tens of millions of SNPs, making it challenging for PCA analysis and interpretation. Here we present VCF2PCACluster, a simple, fast and memory-efficient tool for Kinship estimation, PCA and clustering analysis, and visualization based on VCF formatted SNPs. We implemented five Kinship estimation methods and three clustering methods for its users to choose from. Moreover, unlike other PCA tools, VCF2PCACluster possesses a clustering function based on PCA result, which enabling users to automatically and clearly know about population structure. We demonstrated the same accuracy but a higher performance of this tool in performing PCA analysis on tens of millions of SNPs compared to another popular PLINK2 software, especially in peak memory usage that is independent of the number of SNPs in VCF2PCACluster.
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Affiliation(s)
- Weiming He
- BGI Research, Sanya, 572025, People's Republic of China
| | - Lian Xu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 226001, People's Republic of China
| | - JingXian Wang
- BGI Research, Sanya, 572025, People's Republic of China
| | - Zhen Yue
- BGI Research, Sanya, 572025, People's Republic of China
| | - Yi Jing
- BGI Research, Sanya, 572025, People's Republic of China
| | | | - Jian Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 226001, People's Republic of China.
| | - Xiaodong Fang
- BGI Research, Sanya, 572025, People's Republic of China.
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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.
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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
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Tao R, Xu Q, Wang S, Xia R, Yang Q, Chen A, Qu Y, Lv Y, Zhang S, Li C. Pairwise kinship analysis of 17 pedigrees using massively parallel sequencing. Forensic Sci Int Genet 2021; 57:102647. [PMID: 34902810 DOI: 10.1016/j.fsigen.2021.102647] [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: 07/12/2021] [Revised: 11/18/2021] [Accepted: 11/28/2021] [Indexed: 01/23/2023]
Abstract
With the tremendous development of massively parallel sequencing (MPS) in the last decade, it has been widely applied in basic science, clinical diagnostics, microbial genomics, as well as forensic genetics. MPS has lots of advantages that may facilitate the kinship analysis. In this study, 243 Chinese Han individuals from 17 families were involved and sequenced using the ForenSeq™ DNA Signature Prep Kit (Verogen, Inc., San Diego, USA), which provided the sequence information of 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative SNPs (iSNPs). A total of 275 pairs of parent-child, 123 pairs of full siblings, 1 pair of twins, 1 pair of half siblings, 158 pairs of grandparent-grandchild, 222 pairs of uncle/aunt-nephew/niece and 121 pairs of first cousins, as well as 701 pairs of unrelated individuals were identified. Using both likelihood ratio (LR) and identical by state (IBS) methods, the kinship analysis was conducted among these relative and non-relative pairs based on the A-STRs and SNPs. As a result, the ForenSeq Signature Kit could solve the analysis of parent-child (t1 = -4, t2 = 4), full siblings (t1 = -2, t2 = 2) and most second-degree kinships (t1 = -1, t2 = 1) using the LR method. When the IBS method was applied, 123 full sibling pairs had a higher average IBS value than other kinship groups in this study. And the IBS method could play a role in the testing of parent-child and full siblings.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Shouyu Wang
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Yehui Lv
- Shanghai University of Medicine & Health Sciences, Shanghai 200237, PR China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China.
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Zhang G, Liu J, Wang J, Zhang X, Wang X, Shen J, Chen D. Evaluation of the Full-sibling Kinship Regarding Attendance of Multiple Full-siblings. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2017.1311078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Xiaojia Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Xudong Wang
- Institute of Criminal Investigation, Southwest University of Political Science and Law, Chongqing 401 120, China
| | - Junyi Shen
- Department of Science and Technology, Public Security Bureau of Shanxi Province, Taiyuan, Shanxi 030001, China
| | - Deqing Chen
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
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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.
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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
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Sibling assessment based on likelihood ratio and total number of shared alleles using 21 short tandem repeat loci included in the GlobalFiler™ kit. Leg Med (Tokyo) 2016; 19:122-6. [DOI: 10.1016/j.legalmed.2015.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/05/2015] [Accepted: 07/20/2015] [Indexed: 11/23/2022]
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Effects of using the GlobalFiler™ multiplex system on parent–child analyses of cases with single locus inconsistency. Leg Med (Tokyo) 2016; 18:72-4. [DOI: 10.1016/j.legalmed.2015.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 11/25/2015] [Accepted: 12/25/2015] [Indexed: 11/20/2022]
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Allelic Imbalance of mRNA Associated with α2-HS Glycoprotein (Fetuin-A) Polymorphism. DISEASE MARKERS 2015; 2015:865053. [PMID: 26549924 PMCID: PMC4624919 DOI: 10.1155/2015/865053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/20/2015] [Indexed: 12/29/2022]
Abstract
Alpha 2-HS glycoprotein (AHSG), also designated as fetuin-A, exhibits polymorphism in population genetics consisting of two major alleles of AHSG∗1 and AHSG∗2. The serum level in the AHSG∗1 homozygote is significantly higher than that of the AHSG∗2 homozygote. This study examined the molecular mechanism for the cis-regulatory expression. To quantitate allele-specific mRNA in intra-assays of the heterozygote, RT-PCR method employing primers that were incorporated to the two closely located SNPs was developed. The respective magnitudes of AHSG∗1 to AHSG∗2 in the liver tissues and hepatic culture cells of PLC/PRF/5 were determined quantitatively as 2.5-fold and 6.2-fold. The mRNA expressional difference of two major alleles was observed, which is consistent with that in the serum level. The culture cells carried heterozygous genotypes in rs4917 and rs4918, but homozygous one in rs2248690. It was unlikely that the imbalance was derived from the SNP located in the promotor site. Furthermore, to investigate the effect of mRNA degradation, RNA synthesis in the cell culture was inhibited potently by the addition of actinomycin-D. No marked change was apparent between the two alleles. The results indicated that the cis-regulatory expressional difference is expected to occur at the level of transcription or splicing of mRNA.
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Tamura T, Osawa M, Ochiai E, Suzuki T, Nakamura T. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis. Leg Med (Tokyo) 2015; 17:320-5. [DOI: 10.1016/j.legalmed.2015.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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