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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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2
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Laufer BI, Hasegawa Y, Zhang Z, Hogrefe CE, Del Rosso LA, Haapanen L, Hwang H, Bauman MD, Van de Water J, Taha AY, Slupsky CM, Golub MS, Capitanio JP, VandeVoort CA, Walker CK, LaSalle JM. Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models. Nat Commun 2022; 13:5538. [PMID: 36130949 PMCID: PMC9492781 DOI: 10.1038/s41467-022-33162-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. We conclude that in this model, maternal obesity was associated with changes in the infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Yu Hasegawa
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Casey E Hogrefe
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Laura A Del Rosso
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Lori Haapanen
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Melissa D Bauman
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
| | - Judy Van de Water
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Internal Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Ameer Y Taha
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Nutrition, University of California Davis, Davis, CA, 95616, USA
| | - Mari S Golub
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - John P Capitanio
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychology, University of California Davis, Davis, CA, 95616, USA
| | - Catherine A VandeVoort
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Cheryl K Walker
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA.
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA.
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3
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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Shen X, Li R, Li H, Gao Y, Chen H, Qu N, Peng D, Wu R, Sun H. Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing. Genes (Basel) 2021; 12:genes12030454. [PMID: 33810139 PMCID: PMC8004970 DOI: 10.3390/genes12030454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/05/2021] [Accepted: 03/20/2021] [Indexed: 01/04/2023] Open
Abstract
Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology.
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Affiliation(s)
- Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yu Gao
- Department of Obstetrics, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China;
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ning Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
| | - Riga Wu
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, China
- Correspondence: (R.W.); (H.S.)
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; (X.S.); (R.L.); (H.L.); (H.C.); (N.Q.); (D.P.)
- Correspondence: (R.W.); (H.S.)
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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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6
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Jacobsen D, Krog GR, Clausen FB. Early and Accurate Sex Determination by qPCR of Y Chromosome Repetitive Sequence (YRS) In Cell-Free Fetal DNA from Maternal Plasma. J Appl Lab Med 2019; 3:346-356. [PMID: 33636925 DOI: 10.1373/jalm.2018.026799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/17/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Circulating cell-free fetal DNA (cffDNA) provides the opportunity for noninvasive prenatal diagnosis. Early knowledge of the fetal sex is essential in cases with a risk of a sex-linked genetic disease. A reliable and highly sensitive sex determination test is required for first trimester testing because of the low amounts of cffDNA. METHODS First trimester blood samples from 326 pregnant women were analyzed by real-time quantitative polymerase chain reaction (qPCR) for the presence of Y chromosome repetitive sequence (YRS). Blood samples were collected from gestational weeks 4-12. Fetal sex was predicted on the basis of results from the YRS assay of cffDNA extracted from maternal plasma. The predicted sex was compared with the phenotypic sex of the newborn baby (n = 294). RESULTS There was high concordance between the test results from the YRS assay and the actual sex at birth. There were no false-positive results, indicating agreement between male YRS results and male sex at birth. Two results were false negative (from gestational weeks 4 and 6) predicting female fetuses, when the actual sex at birth was male. Overall, the sensitivity of the YRS assay was 98.6% (95% CI, 95.1%-99.8%), specificity was 100% (95% CI, 97.5%-100%), and accuracy was 99.3% (95% CI, 97.5%-99.9%). From 7 weeks of gestation, sensitivity, specificity, and accuracy were 100%. CONCLUSIONS This study shows that qPCR can be used to detect and quantify repetitive DNA sequences from 0.3 genome equivalents per milliliter of plasma. Prenatal sex determination by qPCR of YRS in cffDNA from maternal plasma was reliable and robust with cffDNA extracted from 1 mL of nonhemolyzed plasma, with a plasma equivalent per PCR of 167 μL. The YRS assay can be used for early noninvasive prenatal sex determination from a gestational age of 7 weeks.
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Affiliation(s)
- Ditte Jacobsen
- Faculty of Health and Technology, University College Copenhagen, Denmark
| | - Grethe Risum Krog
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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7
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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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8
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Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
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Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
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9
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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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10
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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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11
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Burgener JM, Rostami A, De Carvalho DD, Bratman SV. Cell-free DNA as a post-treatment surveillance strategy: current status. Semin Oncol 2017; 44:330-346. [DOI: 10.1053/j.seminoncol.2018.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/18/2018] [Accepted: 01/31/2018] [Indexed: 02/06/2023]
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12
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McGrath JA. The Molecular Revolution in Cutaneous Biology: Era of Molecular Diagnostics for Inherited Skin Diseases. J Invest Dermatol 2017; 137:e83-e86. [DOI: 10.1016/j.jid.2016.02.819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 10/19/2022]
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13
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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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14
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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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15
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Pisarska MD, Akhlaghpour M, Lee B, Barlow GM, Xu N, Wang ET, Mackey AJ, Farber CR, Rich SS, Rotter JI, Chen YDI, Goodarzi MO, Guller S, Williams J. Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling. Prenat Diagn 2016; 36:1061-1070. [PMID: 27718505 DOI: 10.1002/pd.4936] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/02/2016] [Accepted: 10/05/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Multiple testing to understand global changes in gene expression based on genetic and epigenetic modifications is evolving. Chorionic villi, obtained for prenatal testing, is limited, but can be used to understand ongoing human pregnancies. However, optimal storage, processing and utilization of CVS for multiple platform testing have not been established. RESULTS Leftover CVS samples were flash-frozen or preserved in RNAlater. Modifications to standard isolation kits were performed to isolate quality DNA and RNA from samples as small as 2-5 mg. RNAlater samples had significantly higher RNA yields and quality and were successfully used in microarray and RNA-sequencing (RNA-seq). RNA-seq libraries generated using 200 versus 800-ng RNA showed similar biological coefficients of variation. RNAlater samples had lower DNA yields and quality, which improved by heating the elution buffer to 70 °C. Purification of DNA was not necessary for bisulfite-conversion and genome-wide methylation profiling. CVS cells were propagated and continue to express genes found in freshly isolated chorionic villi. CONCLUSIONS CVS samples preserved in RNAlater are superior. Our optimized techniques provide specimens for genetic, epigenetic and gene expression studies from a single small sample which can be used to develop diagnostics and treatments using a systems biology approach in the prenatal period. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Margareta D Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marzieh Akhlaghpour
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bora Lee
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gillian M Barlow
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ning Xu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Erica T Wang
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Aaron J Mackey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, LABiomed/Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-der I Chen
- Institute for Translational Genomics and Population Sciences, LABiomed/Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Seth Guller
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - John Williams
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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16
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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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17
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Rumbajan JM, Yamaguchi Y, Nakabayashi K, Higashimoto K, Yatsuki H, Nishioka K, Matsuoka K, Aoki S, Toda S, Takeda S, Seki H, Hatada I, Hata K, Soejima H, Joh K. The HUS1B promoter is hypomethylated in the placentas of low-birth-weight infants. Gene 2016; 583:141-146. [DOI: 10.1016/j.gene.2016.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/16/2016] [Accepted: 02/10/2016] [Indexed: 11/25/2022]
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18
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Bianco-Miotto T, Mayne BT, Buckberry S, Breen J, Rodriguez Lopez CM, Roberts CT. Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction 2016; 152:R23-30. [PMID: 27026712 PMCID: PMC5064761 DOI: 10.1530/rep-16-0014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/29/2016] [Indexed: 12/20/2022]
Abstract
Epigenetic modifications, and particularly DNA methylation, have been studied in many tissues, both healthy and diseased, and across numerous developmental stages. The placenta is the only organ that has a transient life of 9 months and undergoes rapid growth and dynamic structural and functional changes across gestation. Additionally, the placenta is unique because although developing within the mother, its genome is identical to that of the foetus. Given these distinctive characteristics, it is not surprising that the epigenetic landscape affecting placental gene expression may be different to that in other healthy tissues. However, the role of epigenetic modifications, and particularly DNA methylation, in placental development remains largely unknown. Of particular interest is the fact that the placenta is the most hypomethylated human tissue and is characterized by the presence of large partially methylated domains (PMDs) containing silenced genes. Moreover, how and why the placenta is hypomethylated and what role DNA methylation plays in regulating placental gene expression across gestation are poorly understood. We review genome-wide DNA methylation studies in the human placenta and highlight that the different cell types that make up the placenta have very different DNA methylation profiles. Summarizing studies on DNA methylation in the placenta and its relationship with pregnancy complications are difficult due to the limited number of studies available for comparison. To understand the key steps in placental development and hence what may be perturbed in pregnancy complications requires large-scale genome-wide DNA methylation studies coupled with transcriptome analyses.
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Affiliation(s)
- Tina Bianco-Miotto
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin T Mayne
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical ResearchThe University of Western Australia, Crawley, Western Australia, Australia Plant Energy BiologyARC Centre of Excellence, The University of Western Australia, Crawley, Western Australia, Australia
| | - James Breen
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia Bioinformatics HubUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Carlos M Rodriguez Lopez
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Claire T Roberts
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
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19
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Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci U S A 2015; 112:E5503-12. [PMID: 26392541 DOI: 10.1073/pnas.1508736112] [Citation(s) in RCA: 473] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma.
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20
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Hatt L, Aagaard MM, Graakjaer J, Bach C, Sommer S, Agerholm IE, Kølvraa S, Bojesen A. Microarray-Based Analysis of Methylation Status of CpGs in Placental DNA and Maternal Blood DNA--Potential New Epigenetic Biomarkers for Cell Free Fetal DNA-Based Diagnosis. PLoS One 2015; 10:e0128918. [PMID: 26230497 PMCID: PMC4521692 DOI: 10.1371/journal.pone.0128918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 05/03/2015] [Indexed: 11/18/2022] Open
Abstract
Epigenetic markers for cell free fetal DNA in the maternal blood circulation are highly interesting in the field of non-invasive prenatal testing since such markers will offer a possibility to quantify the amount of fetal DNA derived from different chromosomes in a maternal blood sample. The aim of the present study was to define new fetal specific epigenetic markers present in placental DNA that can be utilized in non-invasive prenatal diagnosis. We have conducted a high-resolution methylation specific beadchip microarray study assessing more than 450.000 CpG sites. We have analyzed the DNA methylation profiles of 10 maternal blood samples and compared them to 12 1st trimesters chorionic samples from normal placentas, identifying a number of CpG sites that are differentially methylated in maternal blood cells compared to chorionic tissue. To strengthen the utility of these differentially methylated CpG sites to be used with methyl-sensitive restriction enzymes (MSRE) in PCR-based NIPD, we furthermore refined the list of selected sites, containing a restriction sites for one of 16 different methylation-sensitive restriction enzymes. We present a list of markers on chromosomes 13, 18 and 21 with a potential for aneuploidy testing as well as a list of markers for regions harboring sub-microscopic deletion- or duplication syndromes.
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Affiliation(s)
- Lotte Hatt
- Department of Clinical Genetics, Vejle Hospital, 7100, Vejle, Denmark
- Department of Gynecology and Obstetrics, Horsens Hospital, 8700, Horsens, Denmark
- Institute of Regional Health research, University of Southern Denmark, 5000, Odense, Denmark
- * E-mail:
| | - Mads M. Aagaard
- Department of Clinical Genetics, Vejle Hospital, 7100, Vejle, Denmark
| | - Jesper Graakjaer
- Department of Clinical Genetics, Vejle Hospital, 7100, Vejle, Denmark
| | - Cathrine Bach
- Department of Gynecology and Obstetrics, Horsens Hospital, 8700, Horsens, Denmark
| | - Steffen Sommer
- Department of Gynecology and Obstetrics, Horsens Hospital, 8700, Horsens, Denmark
| | - Inge E. Agerholm
- Department of Gynecology and Obstetrics, Horsens Hospital, 8700, Horsens, Denmark
| | - Steen Kølvraa
- Department of Clinical Genetics, Vejle Hospital, 7100, Vejle, Denmark
- Institute of Regional Health research, University of Southern Denmark, 5000, Odense, Denmark
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, 7100, Vejle, Denmark
- Institute of Regional Health research, University of Southern Denmark, 5000, Odense, Denmark
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