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Bae S, Won S, Kim H. Selection and evaluation of bi-allelic autosomal SNP markers for paternity testing in Koreans. Int J Legal Med 2021; 135:1369-1374. [PMID: 33907870 PMCID: PMC8205914 DOI: 10.1007/s00414-020-02495-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Abstract
Due to the advantages of single-nucleotide polymorphisms (SNPs) in forensic science, many forensic SNP panels have been developed. However, the existing SNP panels have a problem that they do not reflect allele frequencies in Koreans or the number of markers is not sufficient to perform paternity testing. Here, we filtered candidate SNPs from the Ansan-Ansung cohort data and selected 200 SNPs with high allele frequencies. To reduce the risk of false inclusion and false exclusion, we calculated likelihood ratios of alleged father-child pairs from simulated families when the alleged father is the true father, the close relative of the true father, and the random man. As a result, we estimated that 160 SNPs were needed to perform paternity testing. Furthermore, we performed validation using Twin-Family cohort data. When 160 selected SNPs were used to calculate the likelihood ratio, paternity and non-paternity were accurately distinguished. Our set of 160 SNPs could be useful for paternity testing in Koreans.
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Affiliation(s)
- Soyeon Bae
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sohyoung Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea. .,eGnome, Inc., Seoul, Republic of Korea.
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Weymaere J, Vander Plaetsen AS, Tilleman L, Tytgat O, Rubben K, Geeraert S, Deforce D, Van Nieuwerburgh F. Kinship analysis on single cells after whole genome amplification. Sci Rep 2020; 10:14647. [PMID: 32887915 PMCID: PMC7474072 DOI: 10.1038/s41598-020-71562-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Short Tandem Repeat (STR-) and Single Nucleotide Polymorphism (SNP-) genotyping have been extensively studied within forensic kinship analysis. Nevertheless, no results have been reported on kinship analysis after whole genome amplification (WGA) of single cells. This WGA step is a necessary procedure in several applications, such as cell-based non-invasive prenatal testing (cbNIPT) and pre-implantation genetic diagnosis (PGD). In cbNIPT, all putative fetal cells must be discriminated from maternal cells after enrichment from whole blood. This study investigates the efficacy and evidential value of STR- and SNP-genotyping methods for the discrimination of 24 single cells after WGA, within three families. Formaldehyde-fixed and unfixed cells are assessed in offspring-parent duos and offspring-mother-father trios. Results demonstrate that both genotyping methods can be used in all tested conditions and scenarios with 100% sensitivity and 100% specificity, with a similar evidential value for fixed and unfixed cells. Moreover, sequence-based SNP-genotyping results in a higher evidential value than length-based STR-genotyping after WGA, which is not observed using high-quality offspring bulk DNA samples. Finally, it is also demonstrated that the availability of the DNA genotypes of both parents strongly increases the evidential value of the results.
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Affiliation(s)
- Jana Weymaere
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium.,Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Kaat Rubben
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Sofie Geeraert
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium.
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Larsen B, Gardner K, Pedersen C, Ørgaard M, Migicovsky Z, Myles S, Toldam-Andersen TB. Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing. PLoS One 2018; 13:e0201889. [PMID: 30110387 PMCID: PMC6093671 DOI: 10.1371/journal.pone.0201889] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a putative clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Using the GBS approach allowed us to estimate ploidy levels, which were in accordance with flow cytometry results. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allows detection of a much more detailed population structure and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purpose of identifying clones and pedigree relations in a diverse apple gene bank and discuss the advantages and constraints of the two approaches.
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Affiliation(s)
- Bjarne Larsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
| | - Kyle Gardner
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Faculty of Agriculture, Agricultural Campus, Truro, NS, Canada
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Faculty of Agriculture, Agricultural Campus, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Faculty of Agriculture, Agricultural Campus, Truro, NS, Canada
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Mo SK, Liu YC, Wang SQ, Bo XC, Li Z, Chen Y, Ni M. Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms. Forensic Sci Int Genet 2016; 22:161-168. [PMID: 26952733 DOI: 10.1016/j.fsigen.2016.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 11/17/2022]
Abstract
Short tandem repeats (STRs) are conventional genetic markers typically used for paternity and kinship testing. As supplementary markers of STRs, single nucleotide polymorphisms (SNPs) have less discrimination power but broader applicability to degraded samples. The rapid improvement of next-generation sequencing (NGS) and multiplex amplification technologies also make it possible now to simultaneously identify dozens or even hundreds of SNP loci in a single pool. However, few studies have been endeavored to kinship testing based on SNP loci. In this study, we genotyped 90 autosomal human identity SNP loci with NGS, and investigated their testing efficacies based on the likelihood ratio model in eight pedigree scenarios involving paternity, half/full-sibling, uncle/nephew, and first-cousin relationships. We found that these SNPs might be sufficient to discriminate paternity and full-sibling, but impractical for more distant relatives such as uncle and cousin. Furthermore, we conducted an in silico study to obtain the theoretical tendency of how testing efficacy varied with increasing number of SNP loci. For each testing battery in a given pedigree scenario, we obtained distributions of logarithmic likelihood ratio for both simulated relatives and unrelated controls. The proportion of the overlapping area between the two distributions was defined as a false testing level (FTL) to evaluate the testing efficacy. We estimated that 85, 127, 491, and 1,858 putative SNP loci were required to discriminate paternity, full-sibling, half-sibling/uncle-nephew, and first-cousin (FTL, 0.1%), respectively. To test a half-sibling or nephew, an additional uncle relative could be included to decrease the required number of putative SNP loci to ∼320 (FTL, 0.1%). As a systematic computation of paternity and kinship testing based only on SNPs, our results could be informative for further studies and applications on paternity and kinship testing using SNP loci.
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Affiliation(s)
- Shao-Kang Mo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Ya-Cheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, 23 Yongtai Middle Road, Beijing 100192, People's Republic of China.
| | - Sheng-Qi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Xiao-Chen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Ying Chen
- Department of Radiation Toxicology & Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, People's Republic of China.
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
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Canturk KM, Emre R, Kınoglu K, Başpınar B, Sahin F, Ozen M. Current status of the use of single-nucleotide polymorphisms in forensic practices. Genet Test Mol Biomarkers 2014; 18:455-60. [PMID: 24754266 DOI: 10.1089/gtmb.2013.0466] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Forensic geneticists often use short tandem repeats (STRs) to solve cases. However, STRs can be insufficient when DNA samples are degraded due to environmental exposure and mass disasters, alleged and real relatives are genetically related in paternity or kinship analyses, or a suspect is lacking. In such cases, single-nucleotide polymorphisms (SNPs) can provide valuable information and thus should be seriously considered as a tool to help resolve challenging cases. In this review, the current status of SNP analyses in forensic applications and the comparative advantages and disadvantages of SNPs with other biomarkers are discussed.
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Neuvonen AM, Palo JU, Hedman M, Sajantila A. Discrimination power of Investigator DIPplex loci in Finnish and Somali populations. Forensic Sci Int Genet 2012; 6:e99-102. [DOI: 10.1016/j.fsigen.2011.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 10/16/2022]
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Pimenta J, Pena S. Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms. GENETICS AND MOLECULAR RESEARCH 2010; 9:601-7. [DOI: 10.4238/vol9-1gmr838] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Børsting C, Rockenbauer E, Morling N. Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard. Forensic Sci Int Genet 2009; 4:34-42. [DOI: 10.1016/j.fsigen.2009.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 04/03/2009] [Accepted: 04/09/2009] [Indexed: 11/25/2022]
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Negrini R, Nicoloso L, Crepaldi P, Milanesi E, Colli L, Chegdani F, Pariset L, Dunner S, Leveziel H, Williams JL, Ajmone Marsan P. Assessing SNP markers for assigning individuals to cattle populations. Anim Genet 2009; 40:18-26. [PMID: 19016674 DOI: 10.1111/j.1365-2052.2008.01800.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- R Negrini
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy.
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Asari M, Watanabe S, Matsubara K, Shiono H, Shimizu K. Single nucleotide polymorphism genotyping by mini-primer allele-specific amplification with universal reporter primers for identification of degraded DNA. Anal Biochem 2008; 386:85-90. [PMID: 19070585 DOI: 10.1016/j.ab.2008.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 11/12/2008] [Accepted: 11/14/2008] [Indexed: 11/28/2022]
Abstract
Single nucleotide polymorphism (SNP) is informative for human identification, and much shorter regions are targeted in analysis of biallelic SNP compared with highly polymorphic short tandem repeat (STR). Therefore, SNP genotyping is expected to be more sensitive than STR genotyping of degraded human DNA. To achieve simple, economical, and sensitive SNP genotyping for identification of degraded human DNA, we developed 18 loci for a SNP genotyping technique based on the mini-primer allele-specific amplification (ASA) combined with universal reporter primers (URP). The URP/ASA-based genotyping consisted of two amplifications followed by detection using capillary electrophoresis. The sizes of the target genome fragments ranged from 40 to 67bp in length. In the Japanese population, the frequencies of minor alleles of 18 SNPs ranged from 0.36 to 0.50, and these SNPs are informative for identification. The success rate of SNP genotyping was much higher than that of STR genotyping of artificially degraded DNA. Moreover, we applied this genotyping method to case samples and showed successful SNP genotyping of severely degraded DNA from a 4-year buffered formalin-fixed tissue sample for human identification.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical College, Japan.
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Performance of the SNPforID 52 SNP-plex assay in paternity testing. Forensic Sci Int Genet 2008; 2:292-300. [DOI: 10.1016/j.fsigen.2008.03.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 03/25/2008] [Accepted: 03/27/2008] [Indexed: 11/20/2022]
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“False positive” or true paternity: Investigating one or two STR mismatches by detailed SNP analyses. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Weir BS, Anderson AD, Hepler AB. Genetic relatedness analysis: modern data and new challenges. Nat Rev Genet 2006; 7:771-80. [PMID: 16983373 DOI: 10.1038/nrg1960] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Individuals who belong to the same family or the same population are related because of their shared ancestry. Population and quantitative genetics theory is built with parameters that describe relatedness, and the estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science. The large number of multiallelic microsatellite loci and biallelic SNPs that are now available have markedly increased the precision with which relationships can be estimated, although they have also revealed unexpected levels of genomic heterogeneity of relationship measures.
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Affiliation(s)
- Bruce S Weir
- Department of Biostatistics, University of Washington, BOX 357232, Seattle, Washington 98195-7232, USA.
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