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Liu Y, Sun C, Si H, Peng Z, Gu L, Guo X, Song F. Bibliometric analysis of kinship analysis from 1960 to 2023: global trends and development. Front Genet 2024; 15:1401898. [PMID: 38903754 PMCID: PMC11187311 DOI: 10.3389/fgene.2024.1401898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Kinship analysis is a crucial aspect of forensic genetics. This study analyzed 1,222 publications on kinship analysis from 1960 to 2023 using bibliometric analysis techniques, investigating the annual publication and citation patterns, most productive countries, organizations, authors and journals, most cited documents and co-occurrence of keywords. The initial publication in this field occurred in 1960. Since 2007, there has been a significant increase in publications, with over 30 published annually except for 2010. China had the most publications (n = 213, 17.43%), followed by the United States (n = 175, 14.32%) and Germany (n = 89, 7.28%). The United States also had the highest citation count. Sichuan University in China has the largest number of published articles. The University of Leipzig and the University of Cologne in Germany exhibit the highest total citation count and average citation, respectively. Budowle B was the most prolific author and Kayser M was the most cited author. In terms of publications, Forensic Science International- Genetics, Forensic Science International, and International Journal of Legal Medicine were the most prolific journals. Among them, Forensic Science International-Genetics boasted the highest h-index, citation count, and average citation rate. The most frequently cited publication was "Van Oven M, 2009, Hum Mutat", with a total of 1,361 citations. The most frequent co-occurrence keyword included "DNA", "Loci", "Paternity testing", "Population", "Markers", and "Identification", with recent interest focusing on "Kinship analysis", "SNP" and "Inference". The current research is centered around microhaplotypes, forensic genetic genealogy, and massively parallel sequencing. The field advanced with new DNA analysis methods, tools, and genetic markers. Collaborative research among nations, organizations, and authors benefits idea exchange, problem-solving efficiency, and high-quality results.
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Affiliation(s)
| | | | | | | | | | | | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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McGowan EC, O'Brien H, Sarri ME, Lopez GH, Daly JJ, Flower RL, Gardener GJ, Hyland CA. Feasibility for non-invasive prenatal fetal blood group and platelet genotyping by massively parallel sequencing: A single test system for multiple atypical red cell, platelet and quality control markers. Br J Haematol 2024; 204:694-705. [PMID: 37984869 DOI: 10.1111/bjh.19197] [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: 08/12/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Non-invasive prenatal tests (NIPT) to predict fetal red cell or platelet antigen status for alloimmunised women are provided for select antigens. This study reports on massively parallel sequencing (MPS) using a red cell and platelet probe panel targeting multiple nucleotide variants, plus individual identification single nucleotide polymorphisms (IISNPs). Maternal blood samples were provided from 33 alloimmunised cases, including seven with two red cell antibodies. Cell-free and genomic DNA was sequenced using targeted MPS and bioinformatically analysed using low-frequency variant detection. The resulting maternal genomic DNA allele frequency was subtracted from the cell-free DNA counterpart. Outcomes were matched against validated phenotyping/genotyping methods, where available. A 2.5% subtractive allele frequency threshold was set after comparing MPS predictions for K, RhC/c, RhE/e and Fya /Fyb against expected outcomes. This threshold was used for subsequent predictions, including HPA-15a, Jka /Jkb , Kpa /Kpb and Lua . MPS outcomes were 97.2% concordant with validated methods; one RhC case was discordantly negative and lacked IISNPs. IISNPs were informative for 30/33 cases as controls. NIPT MPS is feasible for fetal blood group genotyping and covers multiple blood groups and control targets in a single test. Noting caution for the Rh system, this has the potential to provide a personalised service for alloimmunised women.
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Affiliation(s)
- Eunike C McGowan
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Helen O'Brien
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- Red Cell Reference Laboratory, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Mia E Sarri
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Genghis H Lopez
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- School of Health, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - James J Daly
- Pathology Services, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Robert L Flower
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Glenn J Gardener
- Maternal Fetal Medicine, Mater Mothers' Hospital, South Brisbane, Queensland, Australia
| | - Catherine A Hyland
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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3
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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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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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Zhang R, Tan Y, Wang L, Jian H, Zhu J, Xiao Y, Tan M, Xue J, Yang F, Liang W. Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing. Front Genet 2022; 12:800598. [PMID: 35222521 PMCID: PMC8866868 DOI: 10.3389/fgene.2021.800598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022] Open
Abstract
Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting minor DNA in these mixtures is complex and challenging. We developed a new set of SNP-SNP microhaplotypes with short amplicons, and we successfully genotyped them using the new method of amplification-refractory mutation system PCR (ARMS-PCR) combined with SNaPshot technology based on a capillary electrophoresis (CE) platform. This panel reflects a high polymorphism in the Southwest Chinese Han population and thus has excellent potential for mixture studies. We evaluated the feasibility of this panel for UDM detection and noninvasive prenatal paternity testing (NIPPT). Fifteen SNP-SNPs detected minor DNA of homemade DNA mixtures, with a sensitivity of 0.025–0.05 ng and a specificity of 1:1,000. In addition, the panel successfully genotyped degraded DNA from single and mixed samples. Finally, 15 SNP-SNPs were applied to 26 trios. All samples displayed positive results with at least one marker to detect cffDNA. Besides, all fetal alleles in maternal plasma were confirmed by genotyping fetal genomic DNA from amniocentesis and paternal genomic DNA from peripheral blood. The results indicated that the SNP-SNP strategy based on the CE platform was useful for UDM detection and NIPPT.
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Affiliation(s)
- Rangran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yu Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, China
| | - Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Zhu
- Department of Forensic Science and Technology, Sichuan Police College, Luzhou, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Fan Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, China
- Department of Ultrasonography, West China Second University Hospital Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
- *Correspondence: Weibo Liang,
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Hori A, Ogata-Kawata H, Sasaki A, Takahashi K, Taniguchi K, Migita O, Kawashima A, Okamoto A, Sekizawa A, Sago H, Takada F, Nakabayashi K, Hata K. Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles. BMC Res Notes 2021; 14:380. [PMID: 34565457 PMCID: PMC8474863 DOI: 10.1186/s13104-021-05793-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022] Open
Abstract
Objective We aimed to simplify our fetal RHD genotyping protocol by changing the method to attach Illumina’s sequencing adaptors to PCR products from the ligation-based method to a PCR-based method, and to improve its reliability and robustness by introducing unique molecular indexes, which allow us to count the numbers of DNA fragments used as PCR templates and to minimize the effects of PCR and sequencing errors. Results Both of the newly established protocols reduced time and cost compared with our conventional protocol. Removal of PCR duplicates using UMIs reduced the frequencies of erroneously mapped sequences reads likely generated by PCR and sequencing errors. The modified protocols will help us facilitate implementing fetal RHD genotyping for East Asian populations into clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05793-4.
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Affiliation(s)
- Asuka Hori
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Department of Medical Genetics and Genomics, Kitasato University Graduate School of Medical Sciences, Kanagawa, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Aiko Sasaki
- Center for Maternal-Fetal, Neonatal, and Reproductive Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Ken Takahashi
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kosuke Taniguchi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Ohsuke Migita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Akihiro Kawashima
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Akihiko Sekizawa
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Haruhiko Sago
- Center for Maternal-Fetal, Neonatal, and Reproductive Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Fumio Takada
- Department of Medical Genetics and Genomics, Kitasato University Graduate School of Medical Sciences, Kanagawa, Japan
| | - Kazuhiko Nakabayashi
- Laboratory of Developmental Genomics, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.
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Calculation of Fetal Fraction for Non-Invasive Prenatal Testing. BIOTECH 2021; 10:biotech10030017. [PMID: 35822771 PMCID: PMC9245487 DOI: 10.3390/biotech10030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/05/2022] Open
Abstract
Estimating the fetal fraction of DNA in a pregnant mother’s blood is a risk-free, non-invasive way of predicting fetal aneuploidy. It is a rapidly developing field of study, offering researchers a plethora of different complementary methods. Such methods include examining the differences in methylation profiles between the fetus and the mother. Others include calculating the average allele frequency based on the difference in genotype of a number of single-nucleotide polymorphisms. Differences in the length distribution of DNA fragments between the mother and the fetus as well as measuring the proportion of DNA reads mapping to the Y chromosome also constitute fetal fraction estimation methods. The advantages and disadvantages of each of these main method types are discussed. Moreover, several well-known fetal fraction estimation methods, such as SeqFF, are described and compared with other methods. These methods are amenable to not only the estimation of fetal fraction but also paternity, cancer, and transplantation monitoring studies. NIPT is safe, and should aneuploidy be detected, this information can help parents prepare mentally and emotionally for the birth of a special needs child.
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Evaluation of a Microhaplotype-Based Noninvasive Prenatal Test in Twin Gestations: Determination of Paternity, Zygosity, and Fetal Fraction. Genes (Basel) 2020; 12:genes12010026. [PMID: 33375453 PMCID: PMC7823673 DOI: 10.3390/genes12010026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022] Open
Abstract
As a novel type of genetic marker, the microhaplotype has shown promising potential in forensic research. In the present study, we analyzed maternal plasma cell-free DNA (cfDNA) samples from twin pregnancies to validate microhaplotype-based noninvasive prenatal testing (NIPT) for paternity, zygosity, and fetal fraction (FF). Paternity was determined with the combined use of the relMix package, zygosity was evaluated by examining the presence of informative loci with two fetal genome complements, and FF was assessed through fetal allele ratios. Paternity was determined in 19 twin cases, among which 13 cases were considered dizygotic (DZ) twins based on the presence of 3~10 informative loci and the remaining 6 cases were considered monozygotic (MZ) twins because no informative locus was observed. With the fetal genomic genotypes as a reference, the accuracy of paternity and zygosity determination were confirmed by standard short tandem repeat (STR) analysis. Moreover, the lower FF, higher FF, and combined FF in each DZ plasma sample were closely related to the estimated value. This present preliminary study proposes that microhaplotype-based NIPT is applicable for paternity, zygosity, and FF determination in twin pregnancies, which are expected to be advantageous for both forensic and clinical settings.
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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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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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