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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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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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3
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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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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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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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7
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Quantification of cell-free DNA in normal and complicated pregnancies: overcoming biological and technical issues. PLoS One 2014; 9:e101500. [PMID: 24987984 PMCID: PMC4079713 DOI: 10.1371/journal.pone.0101500] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/09/2014] [Indexed: 11/23/2022] Open
Abstract
The characterization of cell-free DNA (cfDNA) originating from placental trophoblast in maternal plasma provides a powerful tool for non-invasive diagnosis of fetal and obstetrical complications. Due to its placental origin, the specific epigenetic features of this DNA (commonly known as cell-free fetal DNA) can be utilized in creating universal ‘fetal’ markers in maternal plasma, thus overcoming the limitations of gender- or rhesus-specific ones. The goal of this study was to compare the performance of relevant approaches and assays evaluating the amount of cfDNA in maternal plasma throughout gestation (7.2–39.5 weeks). Two fetal- or placental- specific duplex assays (RPP30/SRY and RASSF1A/β-Actin) were applied using two technologies, real-time quantitative PCR (qPCR) and droplet digital PCR (ddPCR). Both methods revealed similar performance parameters within the studied dynamic range. Data obtained using qPCR and ddPCR for these assays were positively correlated (total cfDNA (RPP30): R = 0.57, p = 0.001/placental cfDNA (SRY): R = 0.85, p<0.0001; placental cfDNA (RASSF1A): R = 0.75, p<0.0001). There was a significant correlation in SRY and RASSF1A results measured with qPCR (R = 0.68, p = 0.013) and ddPCR (R = 0.56, p = 0.039). Different approaches also gave comparable results with regard to the correlation of the placental cfDNA concentration with gestational age and pathological outcome. We conclude that ddPCR is a practical approach, adaptable to existing qPCR assays and well suited for analysis of cell-free DNA in plasma. However, it may need further optimization to surpass the performance of qPCR.
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9
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Clausen FB. Integration of noninvasive prenatal prediction of fetal blood group into clinical prenatal care. Prenat Diagn 2014; 34:409-15. [PMID: 24431264 DOI: 10.1002/pd.4326] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/08/2014] [Accepted: 01/12/2014] [Indexed: 12/21/2022]
Abstract
Incompatibility of red blood cell blood group antigens between a pregnant woman and her fetus can cause maternal immunization and, consequently, hemolytic disease of the fetus and newborn. Noninvasive prenatal testing of cell-free fetal DNA can be used to assess the risk of hemolytic disease of the fetus and newborn to fetuses of immunized women. Prediction of the fetal RhD type has been very successful and is now integrated into clinical practice to assist in the management of the pregnancies of RhD immunized women. In addition, noninvasive prediction of the fetal RhD type can be applied to guide targeted prenatal prophylaxis, thus avoiding unnecessary exposure to anti-D in pregnant women. The analytical aspect of noninvasive fetal RHD typing is very robust and accurate, and its routine utilization has demonstrated high sensitivities for fetal RHD detection. A high compliance with administering anti-D is essential for obtaining a clinical effect. Noninvasive fetal typing of RHC/c, RHE/e, and KEL may become more widely used in the future.
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Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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10
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Lench N, Barrett A, Fielding S, McKay F, Hill M, Jenkins L, White H, Chitty LS. The clinical implementation of non-invasive prenatal diagnosis for single-gene disorders: challenges and progress made. Prenat Diagn 2014; 33:555-62. [PMID: 23592512 DOI: 10.1002/pd.4124] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recently, we have witnessed the rapid translation into clinical practice of non-invasive prenatal testing for the common aneuploidies, most notably within the United States and China. This represents a lucrative market with testing being driven by companies developing and offering their services. These tests are currently aimed at women with high/medium-risk pregnancies identified by serum screening and/or ultrasound scanning. Uptake has been impressive, albeit limited to the commercial sector. However, non-invasive prenatal diagnosis (NIPD) for single-gene disorders has attracted less interest, no doubt because this represents a much smaller market opportunity and in the majority of cases has to be provided on a bespoke, patient or disease-specific basis. The methods and workflows are labour-intensive and not readily scalable. Nonetheless, there exists a significant need for NIPD of single-gene disorders, and the continuing advances in technology and data analysis should facilitate the expansion of the NIPD test repertoire. Here, we review the progress that has been made to date, the different methods and platform technologies, the technical challenges, and assess how new developments may be applied to extend testing to a wider range of genetic disorders.
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Affiliation(s)
- Nicholas Lench
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children, London, UK
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11
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Holmberg RC, Gindlesperger A, Stokes T, Lopez D, Hyman L, Freed M, Belgrader P, Harvey J, Li Z. Akonni TruTip(®) and Qiagen(®) methods for extraction of fetal circulating DNA--evaluation by real-time and digital PCR. PLoS One 2013; 8:e73068. [PMID: 23936545 PMCID: PMC3735556 DOI: 10.1371/journal.pone.0073068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/30/2013] [Indexed: 12/18/2022] Open
Abstract
Due to the low percentage of fetal DNA present in maternal plasma (< 10%) during early gestation, efficient extraction processes are required for successful downstream detection applications in non-invasive prenatal diagnostic testing. In this study, two extraction methods using similar chemistries but different workflows were compared for isolation efficiency and percent fetal DNA recovery. The Akonni Biosystems TruTip technology uses a binding matrix embedded in a pipette tip; the Circulating Nucleic Acids Kit from Qiagen employs a spin column approach. The TruTip method adds an extra step to decrease the recovery of DNA fragments larger than 600 bp from the sample to yield an overall higher percentage of smaller molecular weight DNA, effectively enriching for fetal DNA. In this evaluation, three separate extraction comparison studies were performed - a dilution series of fragmented DNA in plasma, a set of clinical maternal samples, and a blood collection tube time point study of maternal samples. Both extraction methods were found to efficiently extract small fragment DNA from large volumes of plasma. In the amended samples, the TruTip extraction method was ~15% less efficient with overall DNA recovery, but yielded an 87% increase in % fetal DNA relative to the Qiagen method. The average percent increase of fetal DNA of TruTip extracted samples compared to the Qiagen method was 55% for all sets of blinded clinical samples. A study comparing extraction efficiencies from whole blood samples incubated up to 48 hours prior to processing into plasma resulted in more consistent % fetal DNA recoveries using TruTip. The extracted products were tested on two detection platforms, quantitative real-time PCR and droplet digital PCR, and yielded similar results for both extraction methods.
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12
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Ordoñez E, Rueda L, Cañadas MP, Fuster C, Cirigliano V. Development and validation of multiplex real-time PCR assay for noninvasive prenatal assessment of fetal RhD status and fetal sex in maternal plasma. Fetal Diagn Ther 2013; 34:13-8. [PMID: 23548569 DOI: 10.1159/000346809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Noninvasive prenatal detection of RhD status and fetal sex is becoming part of daily practice in clinical laboratories. We evaluated a high throughput procedure for automated DNA extraction and developed a multiplex real-time PCR (rt-PCR) for the simultaneous detection of three fetal loci in a single reaction to assess fetal sex and RhD status in maternal plasma. METHODS An automated DNA extraction method was evaluated together with a new multiplex rt-PCR assay for the simultaneous detection of exons 5 and 7 of the RHD gene together with the Y chromosome marker DYS14 in maternal plasma. The test was evaluated on 60 samples of known fetal genotype obtained from RhD-negative pregnant women before being applied prospectively on 158 consecutive clinical cases. Results were compared with newborn phenotypes. RESULTS Automated DNA extraction allowed successful analysis of all samples. DYS14 was detected in 118 cases (male fetuses) and both RHD exon 5 and 7 were detected in 148 samples. In 70 samples neither RHD exon 5 nor RHD exon 7 were detected (RhD-negative fetuses). Absence of all three sequences (female RhD-negative fetuses) was assessed in 33 samples. All prenatal results were in concordance with postnatal RhD status and fetal sex without false- positive or -negative results. CONCLUSION The automated DNA extraction procedure coupled with a novel multiplex rt-PCR assay proved accurate, efficient and reliable allowing rapid and high throughput noninvasive determination of fetal sex and RhD status in clinical samples.
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Affiliation(s)
- Elena Ordoñez
- Departament de Genètica Molecular, Labco Diagnostics, Barcelona, Spain
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13
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Grande M, Ordoñez E, Cirigliano V, Cid J, Grau E, Pericot A, Teixido I, Marin JL, Borrell A. Clinical application of midtrimester non-invasive fetal RHD genotyping and identification of RHD variants in a mixed-ethnic population. Prenat Diagn 2012; 33:173-8. [PMID: 23280558 DOI: 10.1002/pd.4035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE This study aims to assess the suitability of non-invasive prenatal RHD genotyping in non-immunized midtrimester pregnant women from a mixed ethnic population, to prevent unnecessary anti-D immunoglobulin prophylaxis and to identify RHD variants METHODS Rhesus D-negative pregnant women were offered fetal RHD genotyping at 24 gestational weeks. A total of 284 samples were tested for RHD status using multiplex rt-PCR amplification of exons 5 and 7 of the RHD gene and exons 6 and 10 in selected cases. Women carrying RHD-negative fetuses were counseled about their option to avoid routine antenatal anti-D immunoglobulin administration. Diagnostic accuracy of RHD genotyping was compared with postnatal Rhesus D serotyping. RESULTS A total of 184 positives (65%), 91 negatives (32%) and 7 cases (2.5%) compatibles with RHD variants were detected by RHD genotyping. No false negative results were found, and a single false positive was observed in a twin pregnancy. Genotyping was accepted when offered by 94% of women (284/302), and anti-D immunoglobulin was avoided in 95% (90/95) of RHD-negative fetuses. CONCLUSIONS Non-invasive routine antenatal RHD genotyping at 24 weeks of pregnancy is a highly accurate method, resulting in the avoidance of 95% of unnecessary administrations of anti-D immunoglobulin, with no false negative results.
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Affiliation(s)
- M Grande
- Department of Maternal-Fetal Medicine, Institute Gynecology, Obstetrics and Neonatology, Hospital Clínic Barcelona, Catalonia, Spain
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Moise KJ, Boring NH, O'Shaughnessy R, Simpson LL, Wolfe HM, Baxter JK, Polzin W, Eddleman KA, Hassan SS, Skupski D, McLennan G, Paladino T, Oeth P, Bombard A. Circulating cell-free fetal DNA for the detection of RHD status and sex using reflex fetal identifiers. Prenat Diagn 2012; 33:95-101. [PMID: 23225162 DOI: 10.1002/pd.4018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To determine the sensitivity and specificity of circulating cell-free fetal DNA in determining the fetal RHD status and fetal sex. METHODS Maternal blood was collected in each trimester of pregnancy from RhD negative nonalloimmunized women. Whole blood was centrifuged, separated into plasma and buffy coat, and frozen at -80°C. DNA analysis was conducted via allele-specific primer extensions for exons 4, 5, and 7 of the RHD gene and for a 37-base pair insertion in exon 4 (RHD pseudogene; psi) three Y-chromosome sequences (SRY, DBY, and TTY2), and an extraction control (TGIFL-like X/Y). RhD serotyping on cord blood and gender assessment of the newborns were entered into a Web-based database. RESULTS One hundred twenty women were enrolled. The median gestational age at the first venipuncture was 12.4 (range: 10.6-13.9) weeks with 120 samples drawn; 118 samples were drawn at 17.6 (16-20.9) weeks; and 113 samples at 28.7 (27.9-33.9) weeks. Overall accuracy for RHD was 99.1%, 99.1%, and 98.1% for each trimester and was 99.1%, 99.1%, and 100% for fetal sex determination. CONCLUSIONS Fetal RHD genotyping and sex can be very accurately determined in all three trimesters using circulating cell-free fetal DNA in the maternal circulation.
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Affiliation(s)
- K J Moise
- Baylor College of Medicine, Houston, TX, USA.
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The controversy about controls for fetal blood group genotyping by cell-free fetal DNA in maternal plasma. Curr Opin Hematol 2011; 18:467-73. [DOI: 10.1097/moh.0b013e32834bab2d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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