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Damour G, Baumer K, Legardeur H, Hall D. Early noninvasive prenatal paternity testing by targeted fetal DNA analysis. Sci Rep 2023; 13:12139. [PMID: 37495669 PMCID: PMC10372148 DOI: 10.1038/s41598-023-39367-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Today the challenge in paternity testing is to provide an accurate noninvasive assay that can be performed early during pregnancy. This requires the use of novel analytical methods capable of detecting the low fraction of circulating fetal DNA in maternal blood. We previously showed that forensic compound markers such as deletion/insertion polymorphisms-short tandem repeats (DIP-STR) can efficiently resolve complex mixed biological evidence including the target analysis of paternally inherited fetal alleles. In this study, we describe for the first time the validation of this type of markers in the first trimester of pregnancies, in addition to defining the statistical framework to evaluate paternity. To do so, we studied 47 DIP-STRs in 87 cases, with blood samples collected throughout gestation starting from the seven weeks of amenorrhea. Fetal DNA detection in the first trimester shows a false negative rate as low as 6%. The combined paternity index (CPI) results indicate that seven markers with fully informative genotypes are sufficient to determine the paternity. This study demonstrates that DIP-STR markers can be used from early pregnancy and that a small set of markers (about 40) is sufficient to address the question of paternity. The novel method offers substantial improvements over similar approaches in terms of reduced number of markers, lower costs and increased accuracy.
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Affiliation(s)
- Géraldine Damour
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000, Lausanne, Switzerland
| | - Karine Baumer
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000, Lausanne, Switzerland
| | - Hélène Legardeur
- Woman-Mother-Child Department, Lausanne University Hospital, Lausanne, Switzerland
| | - Diana Hall
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000, Lausanne, Switzerland.
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Gao S, Li B, Mao L, Wang W, Zou D, Zheng J, Zhou M, Yu S, Zheng F, Yin Y, Liu SQ, Yang H, Wang H. A theoretical base for non-invasive prenatal paternity testing. Forensic Sci Int 2023; 346:111649. [PMID: 36996580 DOI: 10.1016/j.forsciint.2023.111649] [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: 01/29/2023] [Revised: 03/12/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023]
Abstract
There is an increasing demand for prenatal paternity testing in the forensic applications, which identify biological fathers before the birth of children. Currently, one of the most effective and safe Non-Invasive Prenatal Paternity Testing (NIPPT) methods is high-throughput Next-Generation Sequencing (NGS)-based SNP genotyping of cell-free DNA in maternal peripheral blood. To the best of our knowledge, nearly all methods being used in such applications are based on traditional postnatal paternity tests and/or statistical models of conventional polymorphism sites. These methods have shown unsatisfactory performance due to the uncertainty of fetal genotype. In this study, we propose a cutting-edge methodology called the Prenatal paternity Test Analysis System (PTAS) for cell-free fetal DNA-based NIPPT using NGS-based SNP genotyping. With the implementation of our proposed PTAS methodology, 63 out of 64 early-pregnancy (i.e., less than seven weeks) samples can be precisely identified to determine paternity, except for one sample that does not meet quality control requirements. Although the fetal fraction of the non-identified sample is extremely low (0.51%), its paternity can still be detected by our proposed PTAS methodology through unique molecular identifier tagging. Paternity of the total 313 samples for mid-to-late pregnancy (i.e., more than seven weeks) can be accurately identified. Extensive experiments indicate that our methodology makes a significant breakthrough in the NIPPT theory and will bring substantial benefits to forensic applications.
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Affiliation(s)
- Shengjie Gao
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China; The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China.
| | - Bowen Li
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China
| | - Likai Mao
- MGI, BGI Australia, L6, CBCRC Building, QIMR, 300 Herston Rd, Herston, QLD 4006, Australia
| | - Wenfeng Wang
- CHINA Electronics Standardization Institute (CESI), Beijing 100007, China
| | - Dan Zou
- College of Meteorology and Oceanography, National University of Defense Technology, Changsha 410073, China
| | - Jianchao Zheng
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China
| | - Mi Zhou
- Wuhu Public Security Bureau, Wuhu 241000, China
| | - Simin Yu
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China
| | - Feixue Zheng
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China
| | - Ye Yin
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China
| | - Shi Qiang Liu
- School of Economics and Management, Fuzhou University, Fuzhou 350108, China
| | - Huanming Yang
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China.
| | - Hongqi Wang
- BGI Forensic Technology (Shenzhen) Co., Ltd., Shenzhen 518083, China.
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Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing. PLoS One 2022; 17:e0266332. [PMID: 35363835 PMCID: PMC8974964 DOI: 10.1371/journal.pone.0266332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/19/2022] [Indexed: 11/23/2022] Open
Abstract
Objectives To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) haplotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. Subsequentlly, the paternity testing parameters were attributed to each case quantitatively. Results The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699–99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.
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Zhou Y, Wang Y, Addai FP, Li X, Zhang X, Liu H, Yang G, Zeng F, Jiang T, Liu J. Analysis of cell-free fetal DNA in 16,843 pregnant women from a single center in China using targeted sequencing approach. Placenta 2022; 122:18-22. [DOI: 10.1016/j.placenta.2022.03.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022]
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Tan Y, Zhang L, Bai P, Li Z, Zhang R, Yang F, Wang L, Liang W. Detection of cell-free fetal DNA in maternal plasma using two types of compound markers. Electrophoresis 2021; 42:1158-1167. [PMID: 33570191 DOI: 10.1002/elps.202000318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/04/2021] [Accepted: 01/19/2021] [Indexed: 11/11/2022]
Abstract
With the discovery of circulating cell-free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing became possible. However, analysis of low-level cffDNA against high background maternal DNA remains complicated and challenging. To circumvent this limitation, selective amplification of cffDNA was used in this study. Two kinds of compound markers (namely DIP-STR and SNP-STR), both based on selective amplification, were used here for targeting fetal DNA. By designing two allele-specific forward primers for DIP-STR and SNP-STR, DNA fragments with different DIP/SNP alleles can be selectively amplified. When analyzing maternal plasma DNA, these markers can selectively target paternally inherited fetal alleles whose DIP/SNP allele was not shared with the mother. In this study, 21 families were studied with six DIP-STRs and 11 SNP-STRs. Fetal DNA was successfully detected across plasma samples for at least one marker. Detection rate varied between DIP-STR and SNP-STR markers, and DIP-STR outperforms SNP-STR. Fetal alleles obtained from maternal plasma were double confirmed by genotyping paternal genomic DNA and fetal genomic DNA from amniocentesis. This study demonstrated that selective amplification strategy can be used to target cffDNA in maternal plasma, which will be a promising method for noninvasive prenatal paternity testing.
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Affiliation(s)
- Yu Tan
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sichuan, P. R. China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, P. R. China.,Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan, P. R. China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, P. R. China
| | - Zhilong Li
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan, P. R. China
| | - RanRan Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, P. R. China
| | - Fan Yang
- Department of Ultrasonography, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sichuan, P. R. China
| | - Li Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, P. R. China
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Wang JYT, Whittle MR, Puga RD, Yambartsev A, Fujita A, Nakaya HI. Noninvasive prenatal paternity determination using microhaplotypes: a pilot study. BMC Med Genomics 2020; 13:157. [PMID: 33097049 PMCID: PMC7584091 DOI: 10.1186/s12920-020-00806-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022] Open
Abstract
Background The use of noninvasive techniques to determine paternity prenatally is increasing because it reduces the risks associated with invasive procedures. Current methods, based on SNPs, use the analysis of at least 148 markers, on average.
Methods To reduce the number of regions, we used microhaplotypes, which are chromosomal segments smaller than 200 bp containing two or more SNPs. Our method employs massively parallel sequencing and analysis of microhaplotypes as genetic markers. We tested 20 microhaplotypes and ascertained that 19 obey Hardy–Weinberg equilibrium and are independent, and data from the 1000 Genomes Project were used for population frequency and simulations. Results We performed simulations of true and false paternity, using the 1000 Genomes Project data, to confirm if the microhaplotypes could be used as genetic markers. We observed that at least 13 microhaplotypes should be used to decrease the chances of false positives. Then, we applied the method in 31 trios, and it was able to correctly assign the fatherhood in cases where the alleged father was the real father, excluding the inconclusive results. We also cross evaluated the mother-plasma duos with the alleged fathers for false inclusions within our data, and we observed that the use of at least 15 microhaplotypes in real data also decreases the false inclusions. Conclusions In this work, we demonstrated that microhaplotypes can be used to determine prenatal paternity by using only 15 regions and with admixtures of DNA.
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Affiliation(s)
- Jaqueline Yu Ting Wang
- Department of Clinical Toxicological Analyzes, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | - Anatoly Yambartsev
- Statistics Department, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - André Fujita
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Helder I Nakaya
- Department of Clinical Toxicological Analyzes, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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Ou X, Qu N. Noninvasive prenatal paternity testing by target sequencing microhaps. Forensic Sci Int Genet 2020; 48:102338. [PMID: 32593163 DOI: 10.1016/j.fsigen.2020.102338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/21/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023]
Abstract
Microhaplotypes (i.e.,microhaps or MHs) are emerging multi-allelic markers with at least two single nucleotide polymorphisms (SNPs) within ∼ 200 bp that have alleles of the same length and do not generate stutter products. Based on massively parallel sequencing (MPS) technology, microhaps have proven applicability in forensics for different application purposes. Here we evaluate the feasibility of non-invasive prenatal paternity testing (NIPPT) with a panel of polymorphic microhap markers, using cell-free DNA (cfDNA) in the maternal circulation. A custom MPS-based assay targeting 60 microhaps was developed in our previous study. Herein, we applied the developed assay to cfDNA samples in 15 NIPPT cases in the first trimester of pregnancy (6∼13 weeks). The R package relMix was employed for data interpretation, with a regression dropout estimating model. As a result, the targeted sequencing wherein target enrichment is by hybridization capture can be effectively employed for microhap sequencing with cfDNA samples. With the combined use of relMix, the paternity of the biological fathers in 15 cases was correctly determined, with the combined paternity index (CPI) value > 1012. Moreover, the specificity of this approach was validated by the successful paternity exclusion of 3 close relatives (father, full sibling and uncle) of the biological father in one case, and further by the significant separation in CPI distribution between the biological father and 112 unrelated males in each cases. Our results indicate that this MPS-based microhap sequencing strategy could be utilized in NIPPT. This method may contribute to developments in NIPPT and to the resolution of issues related to DNA mixtures of close relatives for specific purposes.
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Affiliation(s)
- Xueling Ou
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, PR China.
| | - Ning Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, PR China
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8
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Xie Y, Qu N, Lin S, Jiang H, Zhang Y, Zhang X, Liang H, Chen F, Ou X. Noninvasive prenatal paternity testing by maternal plasma DNA sequencing in twin pregnancies. Electrophoresis 2020; 41:1095-1102. [PMID: 32249439 DOI: 10.1002/elps.202000036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/26/2020] [Indexed: 11/10/2022]
Abstract
SNPs, combined with massively parallel sequencing technology, have proven applicability in noninvasive prenatal paternity testing (NIPPT) for singleton pregnancies in our previous research, using circulating cell-free DNA in maternal plasma. However, the feasibility of NIPPT in twin pregnancies has remained uncertain. As a pilot study, we developed a practical method to noninvasively determine the paternity of twin pregnancies by maternal plasma DNA sequencing based on a massively parallel sequencing platform. Blood samples were collected from 15 pregnant women (twin pregnancies at 9-18 weeks of gestation). Parental DNA and maternal plasma cell-free DNA were analyzed with custom-designed probes covering 5226 polymorphic SNP loci. A mathematical model for data interpretation was established, including the zygosity determination and paternity index calculations. Each plasma sample was independently tested against the alleged father and 90 unrelated males. As a result, the zygosity in each twin case was correctly determined, prior to paternity analysis. Further, the correct biological father was successfully identified, and the paternity of all 90 unrelated males was excluded in each case. Our study demonstrates that NIPPT can be performed for twin pregnancies. This finding may contribute to development in NIPPT and diagnosis of certain genetic diseases.
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Affiliation(s)
- Yifan Xie
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, P. R. China.,MGI Tech Co., Ltd., Shenzhen, P. R. China
| | - Ning Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, P. R. China
| | - Shaobin Lin
- Department of Obstetrics and Gynecology, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. China
| | | | | | | | - Hao Liang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, P. R. China
| | - Fang Chen
- MGI Tech Co., Ltd., Shenzhen, P. R. China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xueling Ou
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, P. R. China
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Tam JCW, Chan YM, Tsang SY, Yau CI, Yeung SY, Au KK, Chow CK. Noninvasive prenatal paternity testing by means of SNP-based targeted sequencing. Prenat Diagn 2020; 40:497-506. [PMID: 31674029 PMCID: PMC7154534 DOI: 10.1002/pd.5595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022]
Abstract
Objective To develop a method for noninvasive prenatal paternity testing based on targeted sequencing of single nucleotide polymorphisms (SNPs). Method SNPs were selected based on population genetics data. Target‐SNPs in cell‐free DNA extracted from maternal blood (maternal cfDNA) were analyzed by targeted sequencing wherein target enrichment was based on multiplex amplification using QIAseq Targeted DNA Panels with Unique Molecular Identifiers. Fetal SNP genotypes were called using a novel bioinformatics algorithm, and the combined paternity indices (CPIs) and resultant paternity probabilities were calculated. Results Fetal SNP genotypes obtained from targeted sequencing of maternal cfDNA were 100% concordant with those from amniotic fluid‐derived fetal genomic DNA. From an initial panel of 356 target‐SNPs, an average of 148 were included in paternity calculations in 15 family trio cases, generating paternity probabilities of greater than 99.9999%. All paternity results were confirmed by short‐tandem‐repeat analysis. The high specificity of the methodology was validated by successful paternity discrimination between biological fathers and their siblings and by large separations between the CPIs calculated for the biological fathers and those for 60 unrelated men. Conclusion The novel method is highly effective, with substantial improvements over similar approaches in terms of reduced number of target‐SNPs, increased accuracy, and reduced costs.
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Affiliation(s)
| | - Yee Man Chan
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shui Ying Tsang
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chung In Yau
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shuk Ying Yeung
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Ka Ki Au
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chun Kin Chow
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
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Chang L, Yu H, Miao X, Zhang J, Li S. Development and comprehensive evaluation of a noninvasive prenatal paternity testing method through a scaled trial. Forensic Sci Int Genet 2019; 43:102158. [PMID: 31479931 DOI: 10.1016/j.fsigen.2019.102158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 08/23/2019] [Accepted: 08/28/2019] [Indexed: 11/24/2022]
Abstract
PURPOSE To eliminate the miscarriage risks caused by traditional invasive sampling methods, we develop a noninvasive prenatal paternity testing (NIPPT) method and evaluate its efficiency, reliability and sensitivity based on a scaled trial. METHODS We use maternal cell-free DNA and massive parallel sequencing to obtain NIPPT genotypes for parents and fetuses based on quality-controlled genome-wide single nucleotide polymorphisms (SNPs). In a preliminary testing, data from 14 pregnant women and 7 negative controls are used for setting threshold of fetal genotyping in reference to postpartum children. After that, those from 349 cases with pregnancies of 6-35 gestational weeks (GW) and 9 negative controls from non-pregnant women who have fertility experience previously are in-depth evaluated. RESULTS In all cases, the biological fathers have been successfully identified from unrelated with a combined paternity index (CPI) of 3.58 × 1018 - 1.46 × 10165 for the cases versus 1.52 × 10-22 - 2.30 × 10-839 for the controls. For negative controls, fetal SNPs originating from previous pregnancies could not be detected. Our NIPPT results completely aligned with the invasive prenatal test results using PCR-CE STR methods. CONCLUSION NIPPT can be applied to determine paternity accurately from 6 weeks after conception until birth and may serve as an alternative prenatal paternity test advantageous to the currently-used methods.
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Affiliation(s)
- Liao Chang
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Huiyun Yu
- BGI-shenzhen, Shenzhen, 518083, China
| | - Xinyao Miao
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jianbo Zhang
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China; BGI-shenzhen, Shenzhen, 518083, China.
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Non-invasive prenatal paternity testing using a standard forensic genetic massively parallel sequencing assay for amplification of human identification SNPs. Int J Legal Med 2019; 133:1361-1368. [PMID: 31243529 DOI: 10.1007/s00414-019-02106-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023]
Abstract
Prenatal paternity testing often relies on invasive procedures that cause risk to both the mother and the foetus. Non-invasive, prenatal paternity testing by investigating paternally inherited single nucleotide polymorphisms (SNPs) in cell-free foetal DNA (cffDNA) in maternal plasma was performed at consecutive time points during early gestation. Plasma from 15 pregnant women was investigated at consecutive time points from gestational weeks (GWs) 4-20. The Precision ID Identity Panel and an Ion S5 Sequencer was used to analyse the cffDNA. Paternally inherited foetal SNP alleles were detected from GW7. The median foetal fractions were 0%, 3.9%, 5.1%, 5.2%, and 4.7% at GWs 4, 7, 12, 16, and 20, respectively. The corresponding median numbers of detected paternally inherited foetal autosomal SNP alleles were 0, 3, 9, 10, and 12, respectively. The typical (i.e. geometric mean) paternity indices at GW12 and GW20 were 24 (range 0.0035-8389) and 199 (range 5.1-30,137), respectively. The method is very promising. However, the method can be improved by shortening the lengths of the PCR amplicons and increasing the number of SNPs. To our knowledge, this is the first study to successfully identify paternally inherited foetal SNP alleles at consecutive time points in early gestation independently of the foetal gender.
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Sosiawan A, Raharjo D, Nuraini I, Kartikasari N, Nugraha AP, Ari MDA. Detection of short tandem repeats at 5 loci and amelogenin with cell-free fetal DNA as a specimen in the development of prenatal paternity diagnostic tests. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0047-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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NGS-based likelihood ratio for identifying contributors in two- and three-person DNA mixtures. Comput Biol Chem 2018; 74:428-433. [DOI: 10.1016/j.compbiolchem.2018.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 01/26/2023]
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Zhang S, Han S, Zhang M, Wang Y. Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies. Leg Med (Tokyo) 2018; 32:98-103. [PMID: 29626747 DOI: 10.1016/j.legalmed.2018.03.009] [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: 04/04/2017] [Revised: 03/01/2018] [Accepted: 03/31/2018] [Indexed: 12/13/2022]
Abstract
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.
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Affiliation(s)
- Shanshan Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Shuyi Han
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
| | - Maoxiu Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
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Qu N, Xie Y, Li H, Liang H, Lin S, Huang E, Gao J, Chen F, Shi Y, Ou X. Noninvasive prenatal paternity testing using targeted massively parallel sequencing. Transfusion 2018. [PMID: 29536546 DOI: 10.1111/trf.14577] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Recent advances in massively parallel sequencing (MPS) technology have provided efficient methods for noninvasive prenatal paternity testing (NIPAT). However, a well-accepted protocol has not been established. The present study developed an MPS-based approach for NIPAT and compared the performance of two recently reported methods for MPS data interpretation. STUDY DESIGN AND METHODS We selected 1795 unlinked polymorphic single-nucleotide polymorphisms (SNPs) and performed paternity analysis in 34 real parentage test cases with maternal plasma samples using the Illumina HiSeq platform. Sequencing data were interpreted by the straightforward counting method for the identification of paternal alleles and mathematical algorithms for paternity index (PI) calculation, respectively. RESULTS Based on the sequencing data from each family case, both of the two statistical approaches produced a significant separation between the biological father and 90 unrelated males (p < 0.0001) when sufficient effective loci were attained. Nevertheless, up to 30.82% of real paternal alleles were filtered by a predefined cutoff and resulted in insufficient effective loci, especially in plasma samples with low fetal fraction (approx. 90.60% were filtered). In contrast, the PI calculation model utilized all maternal homozygous SNPs as effective loci (approx. 40% of total SNPs) and successfully identified the correct biological father, with the log-transformed combined PI (Lg(CPI)) value varying from 68.23 to 158.01 in each family case. CONCLUSION Our study illustrates that the Bayesian approach represents the better choice in NIPAT data interpretation. Further, the adoption of more informative markers (e.g., tri-allelic SNPs, tetra-allelic SNPs, and micro-haplotypes) or deeper sequencing is recommended for the improvement of the testing efficiency.
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Affiliation(s)
- Ning- Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Beijing, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510089, P.R. China
| | - Yifan Xie
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, P.R. China.,BGI-Shenzhen, Shenzhen, P.R. China
| | - Haiyan Li
- The Center of Criminal Technology of Guangdong Province, Guangzhou, 510050, P.R. China
| | - Hao- Liang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Beijing, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510089, P.R. China
| | - Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510050, P.R. China
| | - Erwen Huang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Beijing, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510089, P.R. China
| | - Jun- Gao
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P.R. China
| | - Fang- Chen
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yanwei Shi
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Beijing, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510089, P.R. China
| | - Xueling Ou
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Beijing, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510089, P.R. China
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Garcia-Rosa S, de Amorim MG, Valieris R, Marques VD, Lorenzi JCC, Toller VB, do Olival GS, da Silva Júnior WA, da Silva IT, Barreira AA, Nunes DN, Dias-Neto E. Exome sequencing of multiple-sclerosis patients and their unaffected first-degree relatives. BMC Res Notes 2017; 10:735. [PMID: 29233175 PMCID: PMC5727932 DOI: 10.1186/s13104-017-3072-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 12/06/2017] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The understanding of complex multifactorial diseases requires the availability of a variety of data for a large-number of affected individuals. In this data note here we provide whole exome sequencing data from a set of non-familiar multiple-sclerosis (MS) patients as well as their unaffected first-degree relatives. This data might help the identification of genomic alterations, including single nucleotide polymorphisms, de novo variations and structural genomic variations, such as copy-number alterations that may impact this disease. DATA DESCRIPTION This dataset comprises the full exome of 28 Brazilian subjects grouped in eight distinct families, consisting of four complete trios (mother-patient-father) plus another four complete trios with one added unaffected sibling. In total, we present the full exome data of eight patients diagnosed with recurrent remittent multiple sclerosis. Diagnoses were made by experienced neurologists and all enrolled patients had at least 5 years of follow up and specific MS treatment. Exomes were sequenced from leukocyte-derived DNA, after the capture of exons using biotinylated probes, in the Ion Proton platform. For each exome we generated an average of 66.1 million good quality mapped reads with an average length of ~ 160nt. On average, for 90% of the exome a vertical coverage above 20× was reached.
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Affiliation(s)
- Sheila Garcia-Rosa
- Lab. of Medical Genomics, International Research Center, A.C.Camargo Cancer Center, Rua Taguá 440, 1st Floor, São Paulo, SP 01508-010 Brazil
| | - Maria Galli de Amorim
- Lab. of Medical Genomics, International Research Center, A.C.Camargo Cancer Center, Rua Taguá 440, 1st Floor, São Paulo, SP 01508-010 Brazil
| | - Renan Valieris
- Laboratory of Computational Biology and Bioinformatics, International Research Center, A.C.Camargo Cancer Center, Rua Taguá 440, 1st Floor, São Paulo, SP 01508-010 Brazil
| | - Vanessa Daccach Marques
- Department of Neurosciences, Clinical Neuroimmunology Division, Medical School and Hospital das Clínicas of Ribeirão Preto, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
- Center for Medical Genomics, HCFMRP/USP, Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Julio Cesar Cetrulo Lorenzi
- Center for Medical Genomics, HCFMRP/USP, Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Vania Balardin Toller
- Neurosciences Research Group, Faculdade de Ciências Médicas da Santa Casa de São Paulo, Rua Doutor Cesário Motta Júnior, 61 - Vila Buarque, São Paulo, SP 01221-020 Brazil
| | - Guilherme Sciascia do Olival
- Neurosciences Research Group, Faculdade de Ciências Médicas da Santa Casa de São Paulo, Rua Doutor Cesário Motta Júnior, 61 - Vila Buarque, São Paulo, SP 01221-020 Brazil
| | - Wilson Araújo da Silva Júnior
- Center for Medical Genomics, HCFMRP/USP, Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Israel Tojal da Silva
- Laboratory of Computational Biology and Bioinformatics, International Research Center, A.C.Camargo Cancer Center, Rua Taguá 440, 1st Floor, São Paulo, SP 01508-010 Brazil
| | - Amilton Antunes Barreira
- Department of Neurosciences, Clinical Neuroimmunology Division, Medical School and Hospital das Clínicas of Ribeirão Preto, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
- Center for Medical Genomics, HCFMRP/USP, Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Diana Noronha Nunes
- Lab. of Medical Genomics, International Research Center, A.C.Camargo Cancer Center, Rua Taguá 440, 1st Floor, São Paulo, SP 01508-010 Brazil
| | - Emmanuel Dias-Neto
- Lab. of Medical Genomics, International Research Center, A.C.Camargo Cancer Center, Rua Taguá 440, 1st Floor, São Paulo, SP 01508-010 Brazil
- Lab. of Neurosciences (LIM-27), Institute of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP Brazil
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17
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Routine implementation of noninvasive prenatal paternity testing with STRs. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Yang D, Liang H, Lin S, Li Q, Ma X, Gao J, Sun H, Chen Q, Wu J, Ou X. An SNP panel for the analysis of paternally inherited alleles in maternal plasma using ion Torrent PGM. Int J Legal Med 2017; 132:343-352. [DOI: 10.1007/s00414-017-1594-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/11/2017] [Indexed: 11/29/2022]
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19
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Yang D, Liang H, Gao Y, Lin S, He Z, Gao J, Sun H, Li Q, Ma X, Ou X. Noninvasive fetal genotyping of paternally inherited alleles using targeted massively parallel sequencing in parentage testing cases. Transfusion 2017; 57:1505-1514. [PMID: 28295384 DOI: 10.1111/trf.14077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/21/2017] [Accepted: 01/27/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Researchers have sought to develop a noninvasive protocol for paternity analysis that uses fetal cell-free DNA (cfDNA) in maternal plasma. Massively parallel sequencing (MPS) is expected to overcome this challenge because it enables the analysis of millions of DNA molecules at a single-base resolution. STUDY DESIGN AND METHODS Seven women were involved in prenatal paternity testing cases. Before conventional invasive procedures, cfDNA was isolated from maternal plasma. Fetal tissues were then collected, as were blood samples from the alleged fathers. A custom array was designed that targeted 1497 regions containing single-nucleotide polymorphisms. These regions were massively parallel sequenced. RESULTS In these seven cases, the mean nonmaternal allele fractions in maternal plasma ranged from 3.22% to 6.17%. Setting the allele fraction cutoff of 2.5%, 300 to 491 loci were considered informative for paternal origin and no genetic incompatibilities with the alleged fathers were found. These results were concordant with those of conventional short tandem repeat genotyping. Validation results performed using fetal samples showed that sequencing noise was completely filtered out, and 78.35% to 99.19% of the paternal alleles were accurately genotyped. The fetal cfDNA concentrations ranged from 7.12% to 13.81%, and the overall sequencing error rates ranged from 0.40% to 0.93%. CONCLUSION In our study, we evaluate a straightforward method that can be used to identify paternal alleles based on analyses of paternal alleles and sequencing errors in maternal plasma. Our results support the notion that an MPS-based method could be utilized in noninvasive fetal genotyping and prenatal paternity analyses.
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Affiliation(s)
- Donggui Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University
| | - Hao Liang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University
| | - Yu Gao
- Department of Obstetrics, The Sixth Affiliated Hospital of Sun Yat-sen University
| | - Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology
| | - Zhiming He
- Fetal Medicine Center, Department of Obstetrics and Gynecology
| | - Jun Gao
- Reproductive Medicine Center, The First Affiliated Hospital of Sun Yat-sen University
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University
| | - Qing Li
- Forensic Identification Institute of The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P.R. China
| | - Xiaoyan Ma
- Forensic Identification Institute of The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P.R. China
| | - Xueling Ou
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University
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Jiang H, Xie Y, Li X, Ge H, Deng Y, Mu H, Feng X, Yin L, Du Z, Chen F, He N. Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study. PLoS One 2016; 11:e0159385. [PMID: 27631491 PMCID: PMC5025199 DOI: 10.1371/journal.pone.0159385] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 07/03/2016] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels in order to verify the performance in clinical cases. Combining targeted deep sequencing of selective SNP and informative bioinformatics pipeline, we calculated the combined paternity index (CPI) of 17 cases to determine paternity. Sequencing-based NIPAT results fully agreed with invasive prenatal paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future.
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Affiliation(s)
- Haojun Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- BGI-Shenzhen, Shenzhen, 518000, China
| | - Yifan Xie
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518000, China
| | - Xuchao Li
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huijuan Ge
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqiang Deng
- Department of stomatology, The Second People’s Hospital of Shenzhen, Shenzhen, 518000, China
| | - Haofang Mu
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China
- Center of Forensic Sciences, Beijing Genomics Institute, Beijing, 100049, China
| | - Xiaoli Feng
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China
- Center of Forensic Sciences, Beijing Genomics Institute, Beijing, 100049, China
| | - Lu Yin
- Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China
- Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China
| | - Zhou Du
- Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China
- Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China
| | - Fang Chen
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China
- Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China
- Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China
- Shenzhen Municipal Key Laboratory of Birth Defects Screening and Engineering, BGI-Shenzhen, Shenzhen, 518000, China
- Guangdong Provincial Key Laboratory of human diseases genome, BGI-Shenzhen, Shenzhen, 518000, China
- Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1165 København K, Denmark
- * E-mail: (FC); (NH)
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- * E-mail: (FC); (NH)
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Riley KE, Salvemini H, Haan E, Fitzgerald L, Stallard K, Borrie S, Pontikinas E, Baxendale A. Is there a Role for Genetic Counselors in Prenatal Paternity Testing? - an Assessment Based on Audit of 13 years of Clinical Experience in South Australia. J Genet Couns 2016; 26:159-172. [PMID: 27443149 DOI: 10.1007/s10897-016-9994-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
The role of genetic counselors in prenatal paternity testing has not been widely studied in the genetic counseling literature. In South Australia, the genetic counselors of the State's public sector clinical genetics service are the primary contact point for women seeking information and testing, also coordinating the testing process. This has provided the opportunity to review all prenatal paternity testing performed in the State over a 13 year period and to consider the role played by the genetic counselor. We explored the reasons why women requested prenatal paternity testing and whether the genetic counselor was an appropriate health professional to facilitate this testing for women. The study had two parts, an audit of the clinical genetics files of 160 women who requested prenatal paternity testing between March 2001 and March 2014, and qualitative interviews of genetic counselors, clinical geneticists, obstetricians and social workers with involvement in this area. The audit determined that in 69.9 % of cases the long-term partner was the father of the pregnancy, for 23.7 % the short-term or other partner was the father and for 6.4 % the paternity results were not known by the genetic counselor. For 45.5 % of women whose long-term partner was excluded as the father, the women chose to have a termination of pregnancy. The results of the qualitative interviews yielded five major themes: accessibility of testing, role of the genetic counselor, social and relationship issues, decision making in pregnancy and emotional issues. We conclude that the genetic counselor is an appropriate health professional to facilitate prenatal paternity testing. Genetic counselors did not view their role as significantly different from a request for prenatal testing for another indication.
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Affiliation(s)
- Kate E Riley
- Monash Ultrasound for Women, The Epworth Centre, Suite 2.5, Level 2, 32 Erin Street, Richmond, VIC, 3121, Australia.
| | - Hayley Salvemini
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), 72 King William Road, North Adelaide, SA, 5006, Australia
| | - Eric Haan
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), 72 King William Road, North Adelaide, SA, 5006, Australia.,School of Medicine, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Lara Fitzgerald
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), 72 King William Road, North Adelaide, SA, 5006, Australia
| | - Kirsty Stallard
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), 72 King William Road, North Adelaide, SA, 5006, Australia
| | - Sarah Borrie
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), 72 King William Road, North Adelaide, SA, 5006, Australia
| | - Electra Pontikinas
- SA Pathology Parentage Laboratory, Frome Road, Adelaide, SA, 5000, Australia
| | - Anne Baxendale
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), 72 King William Road, North Adelaide, SA, 5006, Australia
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Gysi M, Arora N, Sulzer A, Voegeli P, Kratzer A. Non-invasive prenatal paternity testing with STRs: A pilot study. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Barra GB, Santa Rita TH, Chianca CF, Velasco LFR, de Sousa CF, Nery LFA, Costa SSS. Fetal male lineage determination by analysis of Y-chromosome STR haplotype in maternal plasma. Forensic Sci Int Genet 2014; 15:105-10. [PMID: 25434746 DOI: 10.1016/j.fsigen.2014.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 01/26/2023]
Abstract
The aim of this study is to determine the fetus Y-STR haplotype in maternal plasma during pregnancy and estimate, non-invasively, if the alleged father and fetus belong to the same male lineage. The study enrolled couples with singleton pregnancies and known paternity. All participants signed informed consent and the local ethics committee approved the study. Peripheral blood was collected in EDTA tubes (mother) and in FTA paper (father). Maternal plasma DNA was extracted by using NucliSens EasyMAG. Fetal gender was determined by qPCR targeting DYS-14 in maternal plasma and it was also confirmed after the delivery. From all included volunteers, the first consecutive 20 mothers bearing male fetuses and 10 mothers bearing female fetuses were selected for the Y-STR analysis. The median gestational age was 12 weeks (range 12-36). All DNA samples were subjected to PCR amplification by PowerPlex Y23, ampFLSTR Yfiler, and two in-house multiplexes, which together accounts for 27 different Y-STR. The PCR products were detected with 3500 Genetic Analyzer and they were analyzed using GeneMapper-IDX. Fetuses' haplotypes (Yfiler format) were compared to other 5328 Brazilian haplotypes available on Y-chromosome haplotypes reference database (YHRD). As a result, between 22 and 27 loci were successfully amplified from maternal plasma in all 20 cases of male fetuses. None of the women bearing female fetuses had a falsely amplified Y-STR haplotype. The haplotype detected in maternal plasma completely matched the alleged father haplotype in 16 out of the 20 cases. Four cases showed single mismatches and they did not configure exclusions; 1 case showed a mutation in the DYS 458 locus due to the loss of one repeat unit and 3 cases showed one DYS 385I/II locus dropout. All mismatches were confirmed after the delivery. Seventeen fetuses' haplotypes were not found in YHRD and one of them had a mutation, which corresponded to the paternity probability of 99.9812% and 95.7028%, respectively. Three fetuses' haplotypes occurred twice in YHRD, which corresponded to paternity probability of 99.9437%. In conclusion, high discriminatory fetal Y-STR haplotype could be determined from maternal plasma during pregnancy starting at 12 weeks of gestation. All male fetuses could be attributed to the alleged father male lineage early in pregnancy. The high probability of paternity associated with each case suggests that the relationship is not random and this strategy can be use as an alternative for male fetal kinship analysis.
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Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil.
| | - Ticiane Henriques Santa Rita
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil
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Drábek J, Cereda G. Interpreting noninvasive prenatal paternity tests. Genet Med 2014; 16:793-4. [DOI: 10.1038/gim.2014.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/26/2014] [Indexed: 11/10/2022] Open
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Ou X, Wang H, Qu D, Chen Y, Gao J, Sun H. Epigenome-wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single-nucleotide polymorphism genotyping in maternal plasma. Transfusion 2014; 54:2523-33. [PMID: 24749853 DOI: 10.1111/trf.12659] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/14/2014] [Accepted: 02/19/2014] [Indexed: 01/03/2023]
Abstract
BACKGROUND The use of DNA methylation difference between maternal blood cell and fetal (placental) DNA is one of the main areas of interest for the development of fetal epigenetics markers in maternal plasma. STUDY DESIGN AND METHODS We employed a methylation array (HumanMethylation450 array, Illumina, Inc.) to identify novel biomarkers that are specially hypermethylated in placental DNA versus maternal blood cells in a genome-wide basis. Validation by bisulfite genomic sequencing was performed and the priority was given to potential targets that harbor differential methylated CpG sites overlapped with at least two methylation-sensitive restriction enzyme (MSRE) recognizing sites, as well as one polymorphic single-nucleotide polymorphism (SNP), within a short DNA stretch. Three candidate regions of PSMB8, SKI, and CHST11 gene were selected for developing a preliminary polymerase chain reaction assay with MSRE digestion of maternal plasma DNA. SNP genotypes were confirmed by direct sequencing. RESULTS We identified 2944 and 5218 fetal-specific hypermethylated CpG sites in the first- and third-trimester placenta, respectively, of which 2613 were overlapped, suggesting a consistency of differential methylation during the whole pregnancy. The array results were confirmed by bisulfite genomic sequencing. The preliminary tests in maternal plasma showed that postdigestion hypermathylated versions of these candidate molecules were detectable only in pregnant women. We further revealed that methylated targets in maternal plasma possessed the fetal SNP genotypes. CONCLUSION The present studies systematically identified hypermethylated sites in fetal tissues and preliminarily demonstrated that some of the fetal epigenetic markers that contain informative SNPs have great potential for noninvasive fetal genetic diagnosis.
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Affiliation(s)
- Xueling Ou
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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