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Liu D, Nong X, Lai F, Nong C, Wang T, Tang Y. Noninvasive Prenatal Diagnosis of SEA-Thalassemia by Combining 1000 Genomes Database and Relative Haplotype Dosage. Hemoglobin 2024:1-8. [PMID: 38632980 DOI: 10.1080/03630269.2024.2327830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/29/2024] [Indexed: 04/19/2024]
Abstract
To explore a noninvasive method for diagnosis of SEA-thalassemia and to investigate whether the regional factors affect the accuracy of this method. The method involved using a public database and bioinformatics software to construct parental haplotypes for proband and predicting fetal genotypes using relative haplotype dosage. We screened and downloaded sequencing data of couples who were both SEA-thalassemia carriers from the China National Genebank public data platform, and matched the sequencing data format with that of the reference panel using Ubuntu system tools. We then used Beagle software to construct parental haplotypes, predicted fetal haplotypes by relative haplotype dosage. Finally, we used Hidden Markov Model and Viterbi algorithm to determine fetal pathogenic haplotypes. All noninvasive fetal genotype diagnosis results were compared with gold standard gap-PCR electrophoresis results. Our method was successful in diagnosing 13 families with SEA-thalassemia carriers. The best diagnostic results were obtained when Southern Chinese Han was used as the reference panel, and 10 families showed full agreement between our noninvasive diagnostic results and the gap-PCR electrophoresis results. The accuracy of our method was higher when using a Chinese Han as the reference panel for haplotype construction in the Southern Chinese Han region as opposed to Beijing Chinese region. The combined use of public databases and relative haplotype dosage for diagnosing SEA-thalassemia is a feasible approach. Our method produces the best noninvasive diagnostic results when the test samples and population reference panel are closely matched in both ethnicity and geography. When constructing parental haplotypes with our method, it is important to consider the effect of region in addition to population background alone.
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Affiliation(s)
- Dewen Liu
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xuejuan Nong
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Fengming Lai
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chen Nong
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Taizhong Wang
- School of Medical Laboratory, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Yulian Tang
- School of Medical Laboratory, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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2
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Li J, Lu J, Su F, Yang J, Ju J, Lin Y, Xu J, Qi Y, Hou Y, Wu J, He W, Yang Z, Wu Y, Tang Z, Huang Y, Zhang G, Yang Y, Long Z, Cheng X, Liu P, Xia J, Zhang Y, Wang Y, Chen F, Zhang J, Zhao L, Jin X, Gao Y, Yin A. Non-Invasive Prenatal Diagnosis of Monogenic Disorders Through Bayesian- and Haplotype-Based Prediction of Fetal Genotype. Front Genet 2022; 13:911369. [PMID: 35846127 PMCID: PMC9283829 DOI: 10.3389/fgene.2022.911369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Non-invasive prenatal diagnosis (NIPD) can identify monogenic diseases early during pregnancy with negligible risk to fetus or mother, but the haplotyping methods involved sometimes cannot infer parental inheritance at heterozygous maternal or paternal loci or at loci for which haplotype or genome phasing data are missing. This study was performed to establish a method that can effectively recover the whole fetal genome using maternal plasma cell-free DNA (cfDNA) and parental genomic DNA sequencing data, and validate the method’s effectiveness in noninvasively detecting single nucleotide variations (SNVs), insertions and deletions (indels). Methods: A Bayesian model was developed to determine fetal genotypes using the plasma cfDNA and parental genomic DNA from five couples of healthy pregnancy. The Bayesian model was further integrated with a haplotype-based method to improve the inference accuracy of fetal genome and prediction outcomes of fetal genotypes. Five pregnancies with high risks of monogenic diseases were used to validate the effectiveness of this haplotype-assisted Bayesian approach for noninvasively detecting indels and pathogenic SNVs in fetus. Results: Analysis of healthy fetuses led to the following accuracies of prediction: maternal homozygous and paternal heterozygous loci, 96.2 ± 5.8%; maternal heterozygous and paternal homozygous loci, 96.2 ± 1.4%; and maternal heterozygous and paternal heterozygous loci, 87.2 ± 4.7%. The respective accuracies of predicting insertions and deletions at these types of loci were 94.6 ± 1.9%, 80.2 ± 4.3%, and 79.3 ± 3.3%. This approach detected pathogenic single nucleotide variations and deletions with an accuracy of 87.5% in five fetuses with monogenic diseases. Conclusions: This approach was more accurate than methods based only on Bayesian inference. Our method may pave the way to accurate and reliable NIPD.
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Affiliation(s)
- Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
| | - Jiaqi Lu
- Medical Genetics Centre, Guangdong Women and Children’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengxia Su
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Jia Ju
- BGI-Shenzhen, Shenzhen, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen, China
| | | | - Yiming Qi
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Wei He
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Zhengtao Yang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Yujing Wu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Zhuangyuan Tang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Yingping Huang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Guohong Zhang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Ying Yang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | | | | | | | - Jun Xia
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Jianguo Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
| | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
- College of Medical Technology, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
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3
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Zhong LPW, Chiu RWK. The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment. Annu Rev Genomics Hum Genet 2022; 23:413-425. [PMID: 35316613 DOI: 10.1146/annurev-genom-110821-113411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the widespread clinical adoption of noninvasive screening for fetal chromosomal aneuploidies based on cell-free DNA analysis from maternal plasma, more researchers are turning their attention to noninvasive prenatal assessment for single-gene disorders. The development of a spectrum of approaches to analyze cell-free DNA in maternal circulation, including relative mutation dosage, relative haplotype dosage, and size-based methods, has expanded the scope of noninvasive prenatal testing to sex-linked and autosomal recessive disorders. Cell-free fetal DNA analysis for several of the more prevalent single-gene disorders has recently been introduced into clinical service. This article reviews the analytical approaches currently available and discusses the extent of the clinical implementation of noninvasive prenatal testing for single-gene disorders. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lilian Pok Wa Zhong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; ,
| | - Rossa W K Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; ,
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4
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Chen C, Li R, Sun J, Zhu Y, Jiang L, Li J, Fu F, Wan J, Guo F, An X, Wang Y, Fan L, Sun Y, Guo X, Zhao S, Wang W, Zeng F, Yang Y, Ni P, Ding Y, Xiang B, Peng Z, Liao C. Noninvasive prenatal testing of α-thalassemia and β-thalassemia through population-based parental haplotyping. Genome Med 2021; 13:18. [PMID: 33546747 PMCID: PMC7866698 DOI: 10.1186/s13073-021-00836-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
Background Noninvasive prenatal testing (NIPT) of recessive monogenic diseases depends heavily on knowing the correct parental haplotypes. However, the currently used family-based haplotyping method requires pedigrees, and molecular haplotyping is highly challenging due to its high cost, long turnaround time, and complexity. Here, we proposed a new two-step approach, population-based haplotyping-NIPT (PBH-NIPT), using α-thalassemia and β-thalassemia as prototypes. Methods First, we deduced parental haplotypes with Beagle 4.0 with training on a large retrospective carrier screening dataset (4356 thalassemia carrier screening-positive cases). Second, we inferred fetal haplotypes using a parental haplotype-assisted hidden Markov model (HMM) and the Viterbi algorithm. Results With this approach, we enrolled 59 couples at risk of having a fetus with thalassemia and successfully inferred 94.1% (111/118) of fetal alleles. We confirmed these alleles by invasive prenatal diagnosis, with 99.1% (110/111) accuracy (95% CI, 95.1–100%). Conclusions These results demonstrate that PBH-NIPT is a sensitive, fast, and inexpensive strategy for NIPT of thalassemia. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00836-8.
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Affiliation(s)
- Chao Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaping Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lu Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jian Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Junhui Wan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Fengyu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaoying An
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaoshen Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Linlin Fan
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 490079, China
| | - Xiaosen Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sumin Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Wanyang Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fanwei Zeng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 490079, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Peixiang Ni
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yi Ding
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Bixia Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
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5
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Stevens B. Impact of Emerging Technologies in Prenatal Genetic Counseling. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036517. [PMID: 31570384 DOI: 10.1101/cshperspect.a036517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
For decades, prenatal testing has been offered to evaluate pregnancies for genetic conditions. In recent years, the number of testing options and range of testing capabilities has dramatically increased. Because of the risks associated with invasive diagnostic testing, research has focused on the detection of genetic conditions through screening technologies such as cell-free DNA. Screening for aneuploidy, copy number variants, and monogenic disorders is clinically available using a sample of maternal blood, but limited data exist on the accuracy of some of these testing options. Additional research is needed to examine the accuracy and utility of screening for increasingly rare conditions. As the breadth of prenatal genetic testing options continues to expand, patients, clinical providers, laboratories, and researchers need to find collaborative means to validate and introduce new testing technologies responsibly. Adequate validation of prenatal tests and effective integration of emerging technologies into prenatal care will become even more important once prenatal treatments for genetic conditions become available.
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Affiliation(s)
- Blair Stevens
- McGovern Medical School at UTHealth in Houston, Department of Obstetrics, Gynecology and Reproductive Sciences, Houston, Texas 77030, USA
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6
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Wang L, Kempton JB, Jiang H, Jodelka FM, Brigande AM, Dumont RA, Rigo F, Lentz JJ, Hastings ML, Brigande JV. Fetal antisense oligonucleotide therapy for congenital deafness and vestibular dysfunction. Nucleic Acids Res 2020; 48:5065-5080. [PMID: 32249312 PMCID: PMC7229850 DOI: 10.1093/nar/gkaa194] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/13/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Disabling hearing loss impacts ∼466 million individuals worldwide with 34 million children affected. Gene and pharmacotherapeutic strategies to rescue auditory function in mouse models of human deafness are most effective when administered before hearing onset, after which therapeutic efficacy is significantly diminished or lost. We hypothesize that preemptive correction of a mutation in the fetal inner ear prior to maturation of the sensory epithelium will optimally restore sensory function. We previously demonstrated that transuterine microinjection of a splice-switching antisense oligonucleotide (ASO) into the amniotic cavity immediately surrounding the embryo on embryonic day 13-13.5 (E13-13.5) corrected pre-mRNA splicing in the juvenile Usher syndrome type 1c (Ush1c) mouse mutant. Here, we show that this strategy only marginally rescues hearing and partially rescues vestibular function. To improve therapeutic outcomes, we microinjected ASO directly into the E12.5 inner ear. A single intra-otic dose of ASO corrects harmonin RNA splicing, restores harmonin protein expression in sensory hair cell bundles, prevents hair cell loss, improves hearing sensitivity, and ameliorates vestibular dysfunction. Improvements in auditory and vestibular function were sustained well into adulthood. Our results demonstrate that an ASO pharmacotherapeutic administered to a developing organ system in utero preemptively corrects pre-mRNA splicing to abrogate the disease phenotype.
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Affiliation(s)
- Lingyan Wang
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - J Beth Kempton
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Han Jiang
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Francine M Jodelka
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Alev M Brigande
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rachel A Dumont
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010 USA
| | - Jennifer J Lentz
- Department of Otorhinolaryngology, Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle L Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - John V Brigande
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR 97239, USA
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7
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Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA. Genet Med 2020; 22:962-973. [PMID: 32024963 DOI: 10.1038/s41436-019-0748-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/27/2019] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Whereas noninvasive prenatal screening for aneuploidies is widely implemented, there is an increasing need for universal approaches for noninvasive prenatal screening for monogenic diseases. Here, we present a cost-effective, generic cell-free fetal DNA (cffDNA) haplotyping approach to scan the fetal genome for the presence of inherited monogenic diseases. METHODS Families participating in the preimplantation genetic testing for monogenic disorders (PGT-M) program were recruited for this study. Two hundred fifty thousand single-nucleotide polymorphisms (SNPs) captured from maternal plasma DNA along with genomic DNA from family members were massively parallel sequenced. Parental genotypes were phased via an available genotype from a close relative, and the fetal genome-wide haplotype and copy number were determined using cffDNA haplotyping analysis based on estimation and segmentation of fetal allele presence in the maternal plasma. RESULTS In all families tested, mutational profiles from cffDNA haplotyping are consistent with embryo biopsy profiles. Genome-wide fetal haplotypes are on average 97% concordant with the newborn haplotypes and embryo haplotypes. CONCLUSION We demonstrate that genome-wide targeted capture and sequencing of polymorphic SNPs from maternal plasma cell-free DNA (cfDNA) allows haplotyping and copy-number profiling of the fetal genome during pregnancy. The method enables the accurate reconstruction of the fetal haplotypes and can be easily implemented in clinical practice.
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8
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Yang X, Zhou Q, Zhou W, Zhong M, Guo X, Wang X, Fan X, Yan S, Li L, Lai Y, Wang Y, Huang J, Ye Y, Zeng H, Chuan J, Du Y, Ma C, Li P, Song Z, Xu X. A Cell-free DNA Barcode-Enabled Single-Molecule Test for Noninvasive Prenatal Diagnosis of Monogenic Disorders: Application to β-Thalassemia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802332. [PMID: 31179213 PMCID: PMC6548944 DOI: 10.1002/advs.201802332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Indexed: 05/13/2023]
Abstract
Noninvasive prenatal testing of common aneuploidies has become routine over the past decade, but testing of monogenic disorders remains a challenge in clinical implementation. Most recent studies have inherent limitations, such as complicated procedures, a lack of versatility, and the need for prior knowledge of parental genotypes or haplotypes. To overcome these limitations, a robust and versatile next-generation sequencing-based cell-free DNA (cfDNA) allelic molecule counting system termed cfDNA barcode-enabled single-molecule test (cfBEST) is developed for the noninvasive prenatal diagnosis (NIPD) of monogenic disorders. The accuracy of cfBEST is found to be comparable to that of droplet digital polymerase chain reaction (ddPCR) in detecting low-abundance mutations in cfDNA. The analytical validity of cfBEST is evidenced by a β-thalassemia assay, in which a blind validation study of 143 at-risk pregnancies reveals a sensitivity of 99.19% and a specificity of 99.92% on allele detection. Because the validated cfBEST method can be used to detect maternal-fetal genotype combinations in cfDNA precisely and quantitatively, it holds the potential for the NIPD of human monogenic disorders.
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Affiliation(s)
- Xingkun Yang
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanGuangdong528000China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Qinghua Zhou
- The Center for Precision Medicine of First Affiliated HospitalBiomedical Translational Research InstituteSchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Wanjun Zhou
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Mei Zhong
- Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdong510515China
| | - Xiaoling Guo
- Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanGuangdong528000China
| | - Xiaofeng Wang
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Xin Fan
- Guangxi Zhuang Autonomous Region Women and Children Care HospitalNanningGuangxi530000China
| | - Shanhuo Yan
- Qinzhou Maternity & Child Healthcare HospitalQinzhouGuangxi535000China
| | - Liyan Li
- Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdong510515China
| | - Yunli Lai
- Guangxi Zhuang Autonomous Region Women and Children Care HospitalNanningGuangxi530000China
| | - Yongli Wang
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Jin Huang
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Yuhua Ye
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Huaping Zeng
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Jun Chuan
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Yuanping Du
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Chouxian Ma
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Peining Li
- Department of GeneticsYale UniversityNew HavenCT06520USA
| | - Zhuo Song
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Xiangmin Xu
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
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9
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Luo Y, Jia B, Yan K, Liu S, Song X, Chen M, Jin F, Du Y, Wang J, Hong Y, Cao S, Li D, Dong M. Pilot study of a novel multi-functional noninvasive prenatal test on fetus aneuploidy, copy number variation, and single-gene disorder screening. Mol Genet Genomic Med 2019; 7:e00597. [PMID: 30767419 PMCID: PMC6465655 DOI: 10.1002/mgg3.597] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/26/2018] [Accepted: 01/04/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The noninvasive prenatal testing (NIPT) has been successfully used in the clinical screening of fetal trisomy 13, 18, and 21 in the last few years and researches on detecting sub-chromosomal copy number variations (CNVs) and monogenic diseases are also in progress. To date, multiple tests are needed in order to complete a full set of fetus disorder screening, which is costly and time consuming. Therefore, an integrated 3-in-1 NIPT approach will be in great demand by routine clinical practice in the near future. METHODS We designed a target capture sequencing panel with an associate bioinformatics pipeline to create a novel multi-functional NIPT method and we evaluated its performance by testing 22 clinical samples containing aneuploidy, CNV, and single-gene disorder. Chromosomal aneuploidy and CNV were detected based on the Z-value approach, whereas single-gene disorder was identified by using the "pseudo-tetraploid" model to estimate the best-suited genotype for each locus. RESULTS The performance of this newly constructed 3-in-1 system was promising. We achieved a 100% detection rate for chromosomal aneuploidies (7/7), a 100% diagnosis rate for fetus CNVs larger than 20 Mb (3/3), and an 86.4% accuracy for single-gene disorder screening (19/22). CONCLUSION For the first time, we showed that it is possible to use just a single NIPT test to detect three distinct types of fetus disorder and laid a foundation for developing a cheaper, faster, and multi-functional NIPT method in the future.
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Affiliation(s)
- Yuqin Luo
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bei Jia
- The Center for Prenatal and Hereditary Disease Diagnosis, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kai Yan
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Siping Liu
- The Center for Prenatal and Hereditary Disease Diagnosis, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaojie Song
- Department of Gynecology and Obstetrics, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei, China
| | - Mingfa Chen
- Department of Prenatal Diagnosis, Nanping Maternity and Child Health Hospital, Nanping, Fujian, China
| | - Fan Jin
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yang Du
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Juan Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Yan Hong
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Sha Cao
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Dawei Li
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Minyue Dong
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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10
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Noninvasive paternal exclusion testing for cystic fibrosis in the first five to eight weeks of gestation. Sci Rep 2018; 8:15941. [PMID: 30374031 PMCID: PMC6205998 DOI: 10.1038/s41598-018-34396-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Prenatal genetic testing is not generally applicable to the very early stages of pregnancy (prior to week 8 gestation), a time period that is crucial to pregnant couples with high risk for transmission of genetic disease to their fetus. Therefore, we developed a new ultra-sensitive targeted next generation sequencing method for noninvasive haplotype-based paternal allele exclusion testing of the cystic fibrosis-associated gene, CFTR. This new method was compared to a conventional library prep and sequencing analysis method and all test results were validated by amniotic fluid testing at later stages of pregnancy. Out of 7 enrolled couples, who provided at least two blood samples (at least one week apart) for noninvasive CFTR testing, a result was obtained for 6 fetuses. Using the new hypersensitive method, all six couples (100%) received a correct diagnosis for the paternal allele as opposed to 3/6 (50%) when tested with the conventional strategy. Among 4 couples who provided just one early pregnancy blood draw for analysis, diagnosis was possible in one fetus, but only using the ultra-sensitive method. Thus, we describe a novel noninvasive CFTR screening method which demonstrates unprecedented fetal allele typing accuracy in the earliest stages of pregnancy.
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11
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Massaro G, Mattar CNZ, Wong AMS, Sirka E, Buckley SMK, Herbert BR, Karlsson S, Perocheau DP, Burke D, Heales S, Richard-Londt A, Brandner S, Huebecker M, Priestman DA, Platt FM, Mills K, Biswas A, Cooper JD, Chan JKY, Cheng SH, Waddington SN, Rahim AA. Fetal gene therapy for neurodegenerative disease of infants. Nat Med 2018; 24:1317-1323. [PMID: 30013199 PMCID: PMC6130799 DOI: 10.1038/s41591-018-0106-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 05/25/2018] [Indexed: 01/25/2023]
Abstract
For inherited genetic diseases, fetal gene therapy offers the potential of prophylaxis against early, irreversible and lethal pathological change. To explore this, we studied neuronopathic Gaucher disease (nGD), caused by mutations in GBA. In adult patients, the milder form presents with hepatomegaly, splenomegaly and occasional lung and bone disease; this is managed, symptomatically, by enzyme replacement therapy. The acute childhood lethal form of nGD is untreatable since enzyme cannot cross the blood-brain barrier. Patients with nGD exhibit signs consistent with hindbrain neurodegeneration, including neck hyperextension, strabismus and, often, fatal apnea1. We selected a mouse model of nGD carrying a loxP-flanked neomycin disruption of Gba plus Cre recombinase regulated by the keratinocyte-specific K14 promoter. Exclusive skin expression of Gba prevents fatal neonatal dehydration. Instead, mice develop fatal neurodegeneration within 15 days2. Using this model, fetal intracranial injection of adeno-associated virus (AAV) vector reconstituted neuronal glucocerebrosidase expression. Mice lived for up to at least 18 weeks, were fertile and fully mobile. Neurodegeneration was abolished and neuroinflammation ameliorated. Neonatal intervention also rescued mice but less effectively. As the next step to clinical translation, we also demonstrated the feasibility of ultrasound-guided global AAV gene transfer to fetal macaque brains.
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Affiliation(s)
- Giulia Massaro
- UCL School of Pharmacy, University College London, London, UK
| | - Citra N Z Mattar
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Andrew M S Wong
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Ernestas Sirka
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Bronwen R Herbert
- Institute for Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Stefan Karlsson
- Division of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
| | - Dany P Perocheau
- UCL Institute for Women's Health, University College London, London, UK
| | - Derek Burke
- Paediatric Laboratory Medicine, Great Ormond Street Hospital and UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Heales
- Paediatric Laboratory Medicine, Great Ormond Street Hospital and UCL Great Ormond Street Institute of Child Health, London, UK
| | - Angela Richard-Londt
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK
| | | | | | - Frances M Platt
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Kevin Mills
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Arijit Biswas
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jonathan D Cooper
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, David Geffen School of Medicine, University of California Los Angeles, Torrance, CA, USA
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Jerry K Y Chan
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | | | - Simon N Waddington
- UCL Institute for Women's Health, University College London, London, UK.
- MRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa.
| | - Ahad A Rahim
- UCL School of Pharmacy, University College London, London, UK
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12
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Targeted linked-read sequencing for direct haplotype phasing of maternal DMD alleles: a practical and reliable method for noninvasive prenatal diagnosis. Sci Rep 2018; 8:8678. [PMID: 29875376 PMCID: PMC5989205 DOI: 10.1038/s41598-018-26941-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022] Open
Abstract
For the noninvasive prenatal diagnosis (NIPD) of X-linked recessive diseases such as Duchenne muscular dystrophy (DMD), maternal haplotype phasing is a critical step for dosage analysis of the inherited allele. Until recently, the proband-based indirect haplotyping method has been preferred despite its limitations for use in clinical practice. Here, we describe a method for directly determining the maternal haplotype without requiring the proband’s DNA in DMD families. We used targeted linked-read deep sequencing (mean coverage of 692×) of gDNA from 5 mothers to resolve their haplotypes and predict the mutation status of the fetus. The haplotype of DMD alleles in the carrier mother was successfully phased through a targeted linked-read sequencing platform. Compared with the proband-based phasing method, linked-read sequencing was more accurate in differentiating whether the recombination events occurred in the proband or in the fetus. The predicted inheritance of the DMD mutation was diagnosed correctly in all 5 families in which the mutation had been confirmed using amniocentesis or chorionic villus sampling. Direct haplotyping by this targeted linked-read sequencing method could be used as a phasing method for the NIPD of DMD, especially when the genomic DNA of the proband is unavailable.
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13
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14
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Xiong L, Barrett AN, Hua R, Ho SSY, Jun L, Chan KCA, Mei Z, Choolani M. Non-invasive prenatal testing for fetal inheritance of maternal β
-thalassaemia mutations using targeted sequencing and relative mutation dosage: a feasibility study. BJOG 2018; 125:461-468. [DOI: 10.1111/1471-0528.15045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 11/26/2022]
Affiliation(s)
- L Xiong
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Department of Gynaecology & Obstetrics; Nanfang Hospital; Southern Medical University; Guangzhou China
| | - AN Barrett
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - R Hua
- Department of Gynaecology & Obstetrics; Nanfang Hospital; Southern Medical University; Guangzhou China
| | - SSY Ho
- Department of Laboratory Medicine; Molecular Diagnosis Centre; National University Hospital; Singapore
| | - L Jun
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - KCA Chan
- Centre for Research into Circulating Fetal Nucleic Acids; Li Ka Shing Institute of Health Sciences; Chinese University of Hong Kong; Shatin New Territories Hong Kong
| | - Z Mei
- Department of Gynaecology & Obstetrics; Nanfang Hospital; Southern Medical University; Guangzhou China
| | - M Choolani
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
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15
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Abstract
PURPOSE OF REVIEW Noninvasive prenatal diagnosis for single gene disorders is coming to fruition in its clinical utility. The presence of cell-free DNA in maternal plasma has been recognized for many years, and a number of applications have developed from this. Noninvasive prenatal diagnosis for single gene disorders has lagged behind due to complexities of technology development, lack of investment and the need for validation samples for rare disorders. RECENT FINDINGS Publications are emerging demonstrating a variety of technical approaches and feasibility of clinical application. Techniques for analysis of cell-free DNA including digital PCR, next-generation sequencing and relative haplotype dosage have been used most often for assay development. Analysis of circulating fetal cells in the maternal blood is still being investigated as a viable alternative and more recently transcervical trophoblast cells. Studies exploring ethical and social issues are generally positive but raise concerns around the routinization of prenatal testing. SUMMARY Further work is necessary to make testing available to all patients with a pregnancy at risk of a single gene disorder, and it remains to be seen if the development of more powerful technologies such as isolation and analysis of single cells will shift the emphasis of noninvasive prenatal diagnosis. As testing becomes possible for a wider range of conditions, more ethical questions will become relevant.
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16
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Hu P, Qiao F, Yuan Y, Sun R, Wang Y, Meng L, Lin Y, Li H, Wang Y, Han R, Liang D, Ma D, Jiang T, Jiang H, Xu Z. Noninvasive prenatal diagnosis for X-linked disease by maternal plasma sequencing in a family of Hemophilia B. Taiwan J Obstet Gynecol 2017; 56:686-690. [PMID: 29037559 DOI: 10.1016/j.tjog.2017.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE To apply a Hidden Markov Model to test Hemophilia B in a fetus by maternal plasma sequencing only employing proband and maternal haplotypes. CASE REPORT A family at risk for Hemophilia B was recruited in this study. We performed genetic diagnosis on the proband using our targeted capture system (containing F9 gene coding region, highly heterozygous SNPs and a 13-kb chromosome Y specific region), and revealed a causative F9 gene mutation (c.190T>C, p.Cys64Arg). Maternal plasma cell-free DNA obtained at 8 weeks of gestation was targeted-captured and sequenced using the customized system. The fetus inherited the F9 (c.190T>C, p.Cys64Arg) mutation according to the Hidden Markov Model. The mother continued the pregnancy. CONCLUSIONS This study is the first report of a haplotype-based approach in NIPD of Hemophilia B. With further evaluation, this method might be useful for NIPD of Hemophilia B and for other X-linked single-gene disorders.
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Affiliation(s)
- Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Fengchang Qiao
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yuan Yuan
- BGI-Shenzhen, Shenzhen, China; Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Ruihong Sun
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Lulu Meng
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | | | - Rui Han
- BGI-Shenzhen, Shenzhen, China; Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Dingyuan Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China; Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China.
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17
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Wang Y, Bao J, Zhang L, Li Y, Zhang Y, Yin L. PLAC4 mRNA SNP in non-invasive prenatal testing of Down syndrome. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:7962-7967. [PMID: 31966647 PMCID: PMC6965248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/19/2017] [Indexed: 06/10/2023]
Abstract
The purpose of this study was to explore the mRNA expression level of PLAC4 in the maternal plasma and the clinical value of its single nucleotide polymorphism (SNP) rs8130833 in non-invasive prenatal testing (NIPT) of Down syndrome. 40 pregnant women were collected in Tianjin Medical University General Hospital from January 2014 to December 2015. Amniotic puncture karyotype analysis was adapted to determine whether the fetuses with Down syndrome (DS) or not. 20 fetuses were diagnosed with Down syndrome and recorded as the DS group, and 20 fetuses were normal and recorded as the control group. Quantitative reverse transcription-PCR (qRT-PCR) was used to detect the mRNA expression level of PLAC4 both in the whole blood and plasma of pregnant women. A/G polymorphism of rs8130833 was analyzed by pyrosequencing method using the cell-free fetal RNA (cff RNA) in maternal circulation. The mRNA expression level of PLAC4 in DS group was higher than the control group, but the difference was not statistically significant (P > 0.05). A/G polymorphism of rs8130833 was about 2:1 in DS group, and it was nearly 1:1 in control group. The PLAC4 mRNA SNP (rs8130833) has a certain value of research and application in NIPT of DS.
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Affiliation(s)
- Yujie Wang
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Jianheng Bao
- Second Department of Hepatopancreatobiliary Surgery, Tianjin Nankai HospitalTianjin, People’s Republic of China
| | - Lijun Zhang
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Yongmei Li
- Institute of Basic Medicine, Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Yu Zhang
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Lirong Yin
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
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18
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Hui WWI, Jiang P, Tong YK, Lee WS, Cheng YKY, New MI, Kadir RA, Chan KCA, Leung TY, Lo YMD, Chiu RWK. Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases. Clin Chem 2017; 63:513-524. [DOI: 10.1373/clinchem.2016.268375] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/17/2016] [Indexed: 01/02/2023]
Abstract
Abstract
BACKGROUND
Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members. Recently, microfluidics-based linked-read sequencing technology has become available and allows the direct haplotype phasing of the whole genome rapidly. We explored the feasibility of applying this direct haplotyping technology in noninvasive prenatal testing.
METHODS
We first resolved the haplotypes of parental genomes with the use of linked-read sequencing technology. Then, we identified SNPs within and flanking the genes of interest in maternal plasma DNA by targeted sequencing. Finally, we applied relative haplotype dosage analysis to deduce the mutation inheritance status of the fetus.
RESULTS
Haplotype phasing and relative haplotype dosage analysis of 12 out of 13 families were successfully achieved. The mutational status of these 12 fetuses was correctly classified.
CONCLUSIONS
High-throughput linked-read sequencing followed by maternal plasma-based relative haplotype dosage analysis represents a streamlined approach for noninvasive prenatal testing of inherited single gene diseases. The approach bypasses the need for mutation-specific assays and is not dependent on the availability of DNA from other affected family members. Thus, the approach is universally applicable to pregnancies at risk for the inheritance of a single gene disease.
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Affiliation(s)
- Winnie W I Hui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peiyong Jiang
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Yu K Tong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing-Shan Lee
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yvonne K Y Cheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Maria I New
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, NY
| | - Rezan A Kadir
- Department of Obstetrics and Gynaecology, Royal Free London NHS Foundation Trust, London, UK
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
| | - K C Allen Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y M Dennis Lo
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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19
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Non-invasive prenatal diagnosis of thalassemias using maternal plasma cell free DNA. Best Pract Res Clin Obstet Gynaecol 2017; 39:63-73. [DOI: 10.1016/j.bpobgyn.2016.10.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/23/2016] [Accepted: 10/14/2016] [Indexed: 01/09/2023]
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20
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Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends. Proc Natl Acad Sci U S A 2016; 113:E8159-E8168. [PMID: 27799561 DOI: 10.1073/pnas.1615800113] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Plasma DNA obtained from a pregnant woman was sequenced to a depth of 270× haploid genome coverage. Comparing the maternal plasma DNA sequencing data with the parental genomic DNA data and using a series of bioinformatics filters, fetal de novo mutations were detected at a sensitivity of 85% and a positive predictive value of 74%. These results represent a 169-fold improvement in the positive predictive value over previous attempts. Improvements in the interpretation of the sequence information of every base position in the genome allowed us to interrogate the maternal inheritance of the fetus for 618,271 of 656,676 (94.2%) heterozygous SNPs within the maternal genome. The fetal genotype at each of these sites was deduced individually, unlike previously, where the inheritance was determined for a collection of sites within a haplotype. These results represent a 90-fold enhancement in the resolution in determining the fetus's maternal inheritance. Selected genomic locations were more likely to be found at the ends of plasma DNA molecules. We found that a subset of such preferred ends exhibited selectivity for fetal- or maternal-derived DNA in maternal plasma. The ratio of the number of maternal plasma DNA molecules with fetal preferred ends to those with maternal preferred ends showed a correlation with the fetal DNA fraction. Finally, this second generation approach for noninvasive fetal whole-genome analysis was validated in a pregnancy diagnosed with cardiofaciocutaneous syndrome with maternal plasma DNA sequenced to 195× coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis.
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21
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Massalska D, Zimowski JG, Bijok J, Kucińska-Chahwan A, Łusakowska A, Jakiel G, Roszkowski T. Prenatal diagnosis of congenital myopathies and muscular dystrophies. Clin Genet 2016; 90:199-210. [PMID: 27197572 DOI: 10.1111/cge.12801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/05/2016] [Accepted: 05/08/2016] [Indexed: 12/14/2022]
Abstract
Congenital myopathies and muscular dystrophies constitute a genetically and phenotypically heterogeneous group of rare inherited diseases characterized by muscle weakness and atrophy, motor delay and respiratory insufficiency. To date, curative care is not available for these diseases, which may severely affect both life-span and quality of life. We discuss prenatal diagnosis and genetic counseling for families at risk, as well as diagnostic possibilities in sporadic cases.
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Affiliation(s)
- D Massalska
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - J G Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - J Bijok
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - A Kucińska-Chahwan
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - A Łusakowska
- Department of Neurology, Medical University of Warsaw, Poland
| | - G Jakiel
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - T Roszkowski
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Warsaw, Poland
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