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Gao B, Jiang Y, Han M, Ji X, Zhang D, Wu L, Gao X, Huang S, Zhao C, Su Y, Yang S, Zhang X, Liu N, Han L, Wang L, Ren L, Yang J, Wu J, Yuan Y, Dai P. Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 Alleles: A Universal and Dependable Noninvasive Prenatal Diagnosis Method Applied to Autosomal Recessive Nonsyndromic Hearing Loss in At-Risk Families. J Mol Diagn 2024; 26:638-651. [PMID: 38663495 DOI: 10.1016/j.jmoldx.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/04/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. This study assessed the performance of relative haplotype dosage analysis (RHDO)-based NIPD for identifying fetal genotyping in pregnancies at risk of ARNSHL. Fifty couples carrying pathogenic variants associated with ARNSHL in either GJB2 or SLC26A4 were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of GJB2 and SLC26A4, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. Therefore, it has clinical potential as an alternative to traditional IPD for ARNSHL.
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Affiliation(s)
- Bo Gao
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Mingyu Han
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | | | - Dejun Zhang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- Department of Otolaryngology, Fujian Medical University ShengLi Clinical College, Fujian Provincial Hospital, Fuzhou, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shasha Huang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chaoyue Zhao
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yu Su
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Suyan Yang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Zhang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Na Liu
- MyGenostics Inc., Beijing, China
| | - Lu Han
- MyGenostics Inc., Beijing, China
| | | | - Lina Ren
- MyGenostics Inc., Beijing, China
| | - Jinyuan Yang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Jian Wu
- MyGenostics Inc., Beijing, China
| | - Yongyi Yuan
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
| | - Pu Dai
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
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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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Nguyen HM, Baradaran M, Daigle G, Nshimyumukiza L, Guertin JR, Reinharz D. Pregnant women's and policymakers' preferences for the expansion of noninvasive prenatal screening: A discrete choice experiment approach study. Health Sci Rep 2023; 6:e1516. [PMID: 37636285 PMCID: PMC10447874 DOI: 10.1002/hsr2.1516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/12/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Background and Aims Quantitative approaches for eliciting preferences for new interventions are mostly conducted by patients and rarely by policymakers. This study aimed to quantify the preferences of pregnant women and policymakers regarding the addition of a new test to prenatal screening programs for detecting chromosomal abnormalities. Methods A discrete choice experiment was conducted to measure the respondents' preferences for a new prenatal test. A seven-attribute instrument was built based on interviews with pregnant women and policymakers. The data were analyzed using robust conditional logistic regression and nested logit models. Results In total, 272 pregnant women and 24 policymakers completed the questionnaire (response rates of 48% and 55%, respectively). Overall, all attributes were statistically significant in the pregnant women group, whereas only three attributes (test performance, degree of test result certainty, and cost) were statistically significant in the policymakers group. Statistically significant differences in test performance and information were observed between the two groups. Conclusion Policymakers differed from pregnant women in their appraisal of attributes related to their preference for a new prenatal screening intervention. The low response rates observed in both groups suggest that further investigation of the relevance of this approach must be conducted.
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Affiliation(s)
- Hung Manh Nguyen
- Département de médecine sociale et préventiveUniversité LavalQuébecCanada
| | - Mohammad Baradaran
- Département de génie électrique et de génie informatiqueUniversité LavalQuébecCanada
| | - Gaétan Daigle
- Département de mathématiques et de statistiqueUniversité LavalQuébecCanada
| | - Leon Nshimyumukiza
- Institut national d'excellence en santé et en services sociauxQuébecCanada
- Faculté des sciences infirmièresUniversité LavalQuébecCanada
| | - Jason Robert Guertin
- Département de médecine sociale et préventiveUniversité LavalQuébecCanada
- Centre de Recherche du CHU de QuébecUniversité LavalQuébecCanada
| | - Daniel Reinharz
- Département de médecine sociale et préventiveUniversité LavalQuébecCanada
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Li Y, Jiang G, Wu W, Yang H, Jin Y, Wu M, Liu W, Yang A, Chervova O, Zhang S, Zheng L, Zhang X, Du F, Kanu N, Wu L, Yang F, Wang J, Chen K. Multi-omics integrated circulating cell-free DNA genomic signatures enhanced the diagnostic performance of early-stage lung cancer and postoperative minimal residual disease. EBioMedicine 2023; 91:104553. [PMID: 37027928 PMCID: PMC10102814 DOI: 10.1016/j.ebiom.2023.104553] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Liquid biopsy is a promising non-invasive alternative for cancer screening and minimal residual disease (MRD) detection, although there are some concerns regarding its clinical applications. We aimed to develop an accurate detection platform based on liquid biopsy for both cancer screening and MRD detection in patients with lung cancer (LC), which is also applicable to clinical use. METHODS We applied a modified whole-genome sequencing (WGS) -based High-performance Infrastructure For MultIomics (HIFI) method for LC screening and postoperative MRD detection by combining the hyper-co-methylated read approach and the circulating single-molecule amplification and resequencing technology (cSMART2.0). FINDINGS For early screening of LC, the LC score model was constructed using the support vector machine, which showed sensitivity (51.8%) at high specificity (96.3%) and achieved an AUC of 0.912 in the validation set prospectively enrolled from multiple centers. The screening model achieved detection efficiency with an AUC of 0.906 in patients with lung adenocarcinoma and outperformed other clinical models in solid nodule cohort. When applied the HIFI model to real social population, a negative predictive value (NPV) of 99.92% was achieved in Chinese population. Additionally, the MRD detection rate improved significantly by combining results from WGS and cSMART2.0, with sensitivity of 73.7% at specificity of 97.3%. INTERPRETATION In conclusion, the HIFI method is promising for diagnosis and postoperative monitoring of LC. FUNDING This study was supported by CAMS Innovation Fund for Medical Sciences, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, Beijing Natural Science Foundation and Peking University People's Hospital.
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Bi Q, Huang S, Wang H, Gao X, Ma M, Han M, Lu S, Kang D, Nourbakhsh A, Yan D, Blanton S, Liu X, Yuan Y, Yao Y, Dai P. Preimplantation genetic testing for hereditary hearing loss in Chinese population. J Assist Reprod Genet 2023:10.1007/s10815-023-02753-8. [PMID: 37017887 PMCID: PMC10352472 DOI: 10.1007/s10815-023-02753-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/13/2023] [Indexed: 04/06/2023] Open
Abstract
PURPOSE To evaluate the clinical validity of preimplantation genetic testing (PGT) to prevent hereditary hearing loss (HL) in Chinese population. METHODS A PGT procedure combining multiple annealing and looping-based amplification cycles (MALBAC) and single-nucleotide polymorphisms (SNPs) linkage analyses with a single low-depth next-generation sequencing run was implemented. Forty-three couples carried pathogenic variants in autosomal recessive non-syndromic HL genes, GJB2 and SLC26A4, and four couples carried pathogenic variants in rare HL genes: KCNQ4, PTPN11, PAX3, and USH2A were enrolled. RESULTS Fifty-four in vitro fertilization (IVF) cycles were implemented, 340 blastocysts were cultured, and 303 (89.1%) of these received a definite diagnosis of a disease-causing variant testing, linkage analysis and chromosome screening. A clinical pregnancy of 38 implanted was achieved, and 34 babies were born with normal hearing. The live birth rate was 61.1%. CONCLUSIONS AND RELEVANCE In both the HL population and in hearing individuals at risk of giving birth to offspring with HL in China, there is a practical need for PGT. The whole genome amplification combined with NGS can simplify the PGT process, and the efficiency of PGT process can be improved by establishing a universal SNP bank of common disease-causing gene in particular regions and nationalities. This PGT procedure was demonstrated to be effective and lead to satisfactory clinical outcomes.
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Affiliation(s)
- Qingling Bi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
- Departments of Otolaryngology Head & Neck Surgery, China-Japan Friendship Hospital, 2#Yinghua Road, Beijing, 100029, China
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
| | - Hui Wang
- Reproductive Center, Chinese PLA General Hospital, 28#Fuxing Road, Beijing, 100853, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088, China
| | - Minyue Ma
- Reproductive Center, Chinese PLA General Hospital, 28#Fuxing Road, Beijing, 100853, China
| | - Mingyu Han
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
| | - Sijia Lu
- Department of Clinical Research, Yikon Genomics, 1698 Wangyuan Road, Fengxian District Shanghai, 201400, China
| | - Dongyang Kang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Susan Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China.
| | - Yuanqing Yao
- Reproductive Center, Chinese PLA General Hospital, 28#Fuxing Road, Beijing, 100853, China.
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China.
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Cell-Free Fetal DNA and Non-Invasive Prenatal Diagnosis of Chromosomopathies and Pediatric Monogenic Diseases: A Critical Appraisal and Medicolegal Remarks. J Pers Med 2022; 13:jpm13010001. [PMID: 36675662 PMCID: PMC9862851 DOI: 10.3390/jpm13010001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Cell-free fetal DNA (cffDNA) analysis is a non-invasive prenatal diagnostic test with a fundamental role for the screening of chromosomic or monogenic pathologies of the fetus. Its administration is performed by fetal DNA detection in the mother's blood from the fourth week of gestation. Given the great interest regarding its validation as a diagnostic tool, the authors have set out to undertake a critical appraisal based on a wide-ranging narrative review of 45 total studies centered around such techniques. Both chromosomopathies and monogenic diseases were taken into account and systematically discussed and elucidated. Not surprisingly, cell-free fetal DNA analysis for screening purposes is already rather well-established. At the same time, considerable interest in its diagnostic value has emerged from this literature review, which recommends the elaboration of appropriate validation studies, as well as a broad discourse, involving all stakeholders, to address the legal and ethical complexities that such techniques entail.
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Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
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Wang W, Lu F, Zhang B, Zhou Q, Chen Y, Yu B. Clinical evaluation of non-invasive prenatal screening for the detection of fetal genome-wide copy number variants. Orphanet J Rare Dis 2022; 17:253. [PMID: 35804426 PMCID: PMC9264683 DOI: 10.1186/s13023-022-02406-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/26/2022] [Indexed: 12/01/2022] Open
Abstract
Objective This study explores and discusses the possible factors affecting the positive predictive value (PPV) of non-invasive prenatal screening (NIPS) for the detection of fetal copy number variants (CNVs) in pregnant women. Methods NIPS was performed for 50,972 pregnant women and 212 cases were suspected as fetal CNVs. Post additional genetic counseling for these women, 96 underwent invasive prenatal diagnosis (amniocentesis), following which they received chromosomal microarray analysis (CMA). We analyzed the PPV of NIPS for the detection of fetal CNVs and the possible interference factors that could affect the PPV. Results Among the 96 pregnant women that received prenatal diagnosis by CMA, 37 cases were confirmed to be true positive for fetal CNVs with a PPV of 38.5%. There was no significant difference between the women with different NIPS indications. Five cases were reported as the false positive and false negative of fetal CNVs and the differences were mainly reflected in the inconsistency of chromosome fragments. Depending on the sizes of the CNVs, the PPVs were 48.7% for CNVs < 3 Mb, 41.4% for CNVs falling within 3 ~ 5 Mb, 42.9% for the CNVs falling within 5 ~ 10 Mb, and 14.3% for CNVs > 10 Mb. Based on the chromosomal locations of CNVs, the PPV(4.8%) of the chromosomes of group C(including chromosomes 6 ~ 12), was lower than that of the other groups (41.2% ~ 66.7%) (p = 0.021). However, there were no significant differences in the CNV characteristics, fetal fractions, unique reads, and the Z-scores between these groups. Conclusion NIPS with a low-coverage sequencing depth has a certain effect on detection of fetal CNVs with the PPV of 38.5%. Chromosomal locations of CNVs may be the main factor that influences its effect. This study can contribute to an increased accuracy in genetic counseling and in predicting NIPS results that are positive for fetal CNVs.
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Affiliation(s)
- Wenli Wang
- Changzhou Maternal and Child Health Care Hospital, No.16 Ding Xiang Road, Changzhou, 213003, Jiangsu, China
| | - Fengying Lu
- Changzhou Maternal and Child Health Care Hospital, No.16 Ding Xiang Road, Changzhou, 213003, Jiangsu, China
| | - Bin Zhang
- Changzhou Maternal and Child Health Care Hospital, No.16 Ding Xiang Road, Changzhou, 213003, Jiangsu, China.
| | - Qin Zhou
- Changzhou Maternal and Child Health Care Hospital, No.16 Ding Xiang Road, Changzhou, 213003, Jiangsu, China
| | - Yingping Chen
- Changzhou Maternal and Child Health Care Hospital, No.16 Ding Xiang Road, Changzhou, 213003, Jiangsu, China
| | - Bin Yu
- Changzhou Maternal and Child Health Care Hospital, No.16 Ding Xiang Road, Changzhou, 213003, Jiangsu, China.
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Hanxiao D, Luming S, Songchang C, Jingmin Y, Yueping Z, Shuo Z, Hongyan C, Ning J, Daru L. Noninvasive prenatal prediction of fetal haplotype with Spearman rank correlation analysis model. Mol Genet Genomic Med 2022; 10:e1988. [PMID: 35644943 PMCID: PMC9356545 DOI: 10.1002/mgg3.1988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/29/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) has been widely used clinically to detect fetal chromosomal aneuploidy with high accuracy rates, gradually replacing traditional serological screening. However, the application of NIPT for monogenic diseases is still in an immature stage of exploration. The detection of mutations in peripheral blood of pregnant women requires precise qualitative and quantitative techniques, which limits its application. The bioinformatic strategies based on the SNP (single nucleotide polymorphism) linkage analysis are more practical, which can be divided into two types depending on whether proband information is needed. Hidden Markov Mode (HMM) and Sequential probability ratio test (SPRT) are suitable for families with probands. In contrast, methods based on databases and population demographic information are suitable for families without probands. Methods In this study, we proposed a Spearman rank correlation analysis method to infer the fetal haplotypes based on core family information. Allele frequencies of SNPs that were used to construct parental haplotypes were calculated as sets of nonparametric variables, in contrast to their theoretical values represented by a fetal fraction (FF). The effects on the calculation of the fetal concentration of two DNA enrichment methods, multiple‐PCR amplification, and targeted hybrid capture, were compared, and the heterozygosity distribution of SNPs within pedigrees was analyzed to reveal the best conditions for the model application. Results Predictions of the paternal haplotype inheritance were in line with expectations for both DNA library construction methods, while for maternal haplotype inheritance prediction, the rates were 96.55% for method multiple‐PCR amplification and 95.8% for method targeted hybrid capture. Conclusion Positive prediction rates showed that the maternal haplotype prediction was not as accurate as paternal one, due to the large amount of maternal noise in the mother's peripheral blood. Although this model is relatively immature, it provides a new perspective for noninvasive prenatal clinical tests of monogenic diseases.
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Affiliation(s)
- Du Hanxiao
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
| | - Sun Luming
- Department of Fetal Medicine & Prenatal Diagnosis CenterShanghai First Maternity and Infant Hospital, Tongji University School of MedicineShanghaiChina
| | - Chen Songchang
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Obstetrics and Gynecology Hospital, Fudan UniversityShanghaiChina
| | - Yang Jingmin
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Key Laboratory of Birth Defects and Reproductive Health of National Health and NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research InstituteChongqingChina
- Shanghai WeHealth BioMedical Technology Co., Ltd.ShanghaiChina
| | - Zhang Yueping
- Obstetrics and Gynecology Hospital, Fudan UniversityShanghaiChina
| | - Zhang Shuo
- Obstetrics and Gynecology Hospital, Fudan UniversityShanghaiChina
| | - Chen Hongyan
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
| | - Jiang Ning
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
| | - Lu Daru
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Key Laboratory of Birth Defects and Reproductive Health of National Health and NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research InstituteChongqingChina
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10
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Lv W, Liang L, Chen X, Li Z, Liang D, Zhu H, Teng Y, Wu W, Wu L, Han L. Noninvasive Prenatal Testing of Methylmalonic Acidemia cblC Type Using the cSMART Assay for MMACHC Gene Mutations. Front Genet 2022; 12:750719. [PMID: 35069678 PMCID: PMC8777107 DOI: 10.3389/fgene.2021.750719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) for monogenic disorders has been developed in recent years; however, there are still significant technical and analytical challenges for clinical use. The clinical feasibility of NIPT for methylmalonic acidemia cblC type (cblC type MMA) was investigated using our circulating single-molecule amplification and re-sequencing technology (cSMART). Trios molecular diagnosis was performed in 29 cblC type MMA-affected children and their parents by traditional Sanger sequencing. In the second pregnancy, invasive prenatal diagnosis (IPD) of the pathogenic MMACHC gene was used to determine fetal genotypes, and NIPT was performed using a novel MMACHC gene–specific cSMART assay. Maternal–fetal genotypes were deduced based on the mutation ratio in maternal plasma DNA. Concordance of fetal genotypes between IPD and NIPT, and the sensitivity and specificity of NIPT were determined. After removing two cases with a low P value or reads, the concordance ratio for NIPT and IPD was 100.00% (27/27), and the sensitivity and specificity were 100.00% (54.07–100.00%) and 100.00% (83.89–100.00%), respectively. This study demonstrates that NIPT using the cSMART assay for cblC type MMA was accurate in detecting fetal genotypes. cSMART has a potential clinical application as a prenatal diagnosis and screening tool for carrier and low-risk genotypes of cblC type MMA and other monogenic diseases.
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Affiliation(s)
- Weigang Lv
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Institute of Pediatric Research, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Zhuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Huimin Zhu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yanling Teng
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Weijuan Wu
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Lingqian Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Institute of Pediatric Research, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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11
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Gao S. Noninvasive detection of fetal genetic variations through polymorphic site sequencing of maternal plasma DNA. J Gene Med 2021; 24:e3400. [PMID: 34850495 DOI: 10.1002/jgm.3400] [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: 08/24/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) for common fetal aneuploidies has been widely adopted in clinical practice for its sensitivity and accuracy. However, detection of pathogenic copy number variations (pCNVs) or monogenic disorders (MDs) is inaccurate and not cost effective. Here we developed an assay, the noninvasive prenatal testing based on goodness-of-fit and graphical analysis of polymorphic sites (GGAP-NIPT), to simultaneously detect fetal aneuploidies, pCNVs, and MDs. METHODS Polymorphic sites were amplicon sequenced, followed by fetal fraction estimation using allelic reads counts and a robust linear regression model. The genotype of each polymorphic site or MD variant was then determined by allelic goodness-of-fit test or graphical analysis of its different alleles. Finally, aneuploidies and pCNVs were detected using collective goodness-of-fit test to select each best fit from all possible chromosomal models. RESULTS Of the simulated 1,692 chromosomes and 1,895 pCNVs, all normals and variants were correctly identified (accuracy 100%, sensitivity 100%, specificity 100%). Of the 713,320 simulated MD variants, more than 90% of the genotypes were determined correctly (accuracy: 98.3 ± 1.0%; sensitivity: 98.7 ± 1.96%; specificity: 99.7 ± 0.6%). The detection accuracies of three public MD datasets were 95.70%, 93.43%, and 96.83%. For an MD validation dataset, 75% detection accuracy was observed when a site with sample replicates was analyzed individually, and 100% accuracy was achieved when analyzed collectively. CONCLUSIONS Fetal aneuploidies, pCNVs, and MDs could be detected simultaneously and with high accuracy through amplicon sequencing of polymorphic and target sites, which showed the potential of extending NIPT to an expanded panel of genetic disorders.
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Affiliation(s)
- Song Gao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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12
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Hu CJ, Lu YC, Tsai CY, Chan YH, Lin PH, Lee YS, Yu IS, Lin SW, Liu TC, Hsu CJ, Yang TH, Cheng YF, Wu CC. Insights into phenotypic differences between humans and mice with p.T721M and other C-terminal variants of the SLC26A4 gene. Sci Rep 2021; 11:20983. [PMID: 34697379 PMCID: PMC8545921 DOI: 10.1038/s41598-021-00448-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Recessive variants of the SLC26A4 gene are an important cause of hereditary hearing impairment. Several transgenic mice with different Slc26a4 variants have been generated. However, none have recapitulated the auditory phenotypes in humans. Of the SLC26A4 variants identified thus far, the p.T721M variant is of interest, as it appears to confer a more severe pathogenicity than most of the other missense variants, but milder pathogenicity than non-sense and frameshift variants. Using a genotype-driven approach, we established a knock-in mouse model homozygous for p.T721M. To verify the pathogenicity of p.T721M, we generated mice with compound heterozygous variants by intercrossing Slc26a4+/T721M mice with Slc26a4919-2A>G/919-2A>G mice, which segregated the c.919-2A > G variant with abolished Slc26a4 function. We then performed serial audiological assessments, vestibular evaluations, and inner ear morphological studies. Surprisingly, both Slc26a4T721M/T721M and Slc26a4919-2A>G/T721M showed normal audiovestibular functions and inner ear morphology, indicating that p.T721M is non-pathogenic in mice and a single p.T721M allele is sufficient to maintain normal inner ear physiology. The evidence together with previous reports on mouse models with Slc26a4 p.C565Y and p.H723R variants, support our speculation that the absence of audiovestibular phenotypes in these mouse models could be attributed to different protein structures at the C-terminus of human and mouse pendrin.
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Affiliation(s)
- Chin-Ju Hu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ying-Chang Lu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - Yen-Hui Chan
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, 427, Taiwan
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - Yi-Shan Lee
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - I-Shing Yu
- Transgenic Mouse Models Core (TMMC), Division of Genomic Medicine, Research Center for Medical Excellence, National Taiwan University, Taipei, 100, Taiwan
| | - Shu-Wha Lin
- Transgenic Mouse Models Core (TMMC), Division of Genomic Medicine, Research Center for Medical Excellence, National Taiwan University, Taipei, 100, Taiwan
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, 427, Taiwan
| | - Ting-Hua Yang
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veteran General Hospital, 201, Sec.2, Shi-Pai Rd, Taipei, 112, Taiwan. .,Department of Otolaryngology-Head and Neck Surgery, Taipei Veteran General Hospital, Taipei, 112, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan. .,Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan. .,Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, 302, Taiwan.
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13
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Zhou L, Zhang B, Liu J, Shi Y, Wang J, Yu B. The Optimal Cutoff Value of Z-scores Enhances the Judgment Accuracy of Noninvasive Prenatal Screening. Front Genet 2021; 12:690063. [PMID: 34367249 PMCID: PMC8336938 DOI: 10.3389/fgene.2021.690063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 11/15/2022] Open
Abstract
Objective To evaluate the accuracy of Z-scores of noninvasive prenatal screening (NIPS) in predicting 21, 18 trisomy, and X chromosome aneuploidy. Methods A total of 39,310 prenatal women were recruited for NIPS from September 2015 to September 2020. Interventional prenatal diagnosis was applied to verify the diagnosis of NIPS-positive results. Logistic regression analysis was employed to relate the Z-scores to the positive predictive value (PPV) of NIPS-positive results. Using receiver operating characteristic (ROC) curves, we calculated the optimal cutoff value of Z-scores to predict fetal chromosome aneuploidy. According to the cutoff value, NIPS-positive results were divided into the medium Z-value (MZ) and high Z-value (HZ) groups, and PPV was calculated to access the accuracy of Z-scores. Results A total of 288 effective values of Z-scores were used as the final data set. The logistics regression analysis revealed that Z-scores were significantly associated with true-positive results for 21 trisomy (T21) and 18 trisomy (T18) (P < 0.05), whereas the same was not observed for X chromosome aneuploids (P > 0.05). The optimal cutoff value of the Z-score for T21, T18, XO, XXX, and XXY indicated by ROC curve analysis were 5.79, 6.05, −9.56, 5.89, and 4.47, and the area under the curve (AUC) were 0.89, 0.80, 0.48, 0.42, and 0.45, respectively. PPV in the HZ group was higher than that in the MZ group, and the application of the cutoff value reduced the false discovery rate (FDR), which was only 2.9% in the HZ group compared with 61.1% in the MZ group for T21 and T18. The difference in total PPV between the MZ and HZ groups for X chromosome aneuploids was statistically significant. Moreover, the PPV for XXX and XXY seemed to increase with Z-scores but not for XO. Conclusion The Z-score is helpful for the accurate judgment of NIPS results and for clinical prenatal counseling. Especially for T21 and T18, Z-scores have an excellent clinical association, which is superior to that seen with X chromosome aneuploids. In addition, using Z-scores to judge NIPS results offers a certain reference value for XXX and XXY but not for XO.
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Affiliation(s)
- Lingna Zhou
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Bin Zhang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Jianbing Liu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Ye Shi
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Jing Wang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
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14
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Zheng B, Liu XL, Fan R, Bai J, Wen H, Du LT, Jiang GQ, Wang CY, Fan XT, Ye YN, Qian YS, Wang YC, Liu GJ, Deng GH, Shen F, Hu HP, Wang H, Zhang QZ, Ru LL, Zhang J, Gao YH, Xia J, Yan HD, Liang MF, Yu YL, Sun FM, Gao YJ, Sun J, Zhong CX, Wang Y, Kong F, Chen JM, Zheng D, Yang Y, Wang CX, Wu L, Hou JL, Liu JF, Wang HY, Chen L. The Landscape of Cell-Free HBV Integrations and Mutations in Cirrhosis and Hepatocellular Carcinoma Patients. Clin Cancer Res 2021; 27:3772-3783. [PMID: 33947693 DOI: 10.1158/1078-0432.ccr-21-0002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/09/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Intratumoral hepatitis B virus (HBV) integrations and mutations are related to hepatocellular carcinoma (HCC) progression. Circulating cell-free DNA (cfDNA) has shown itself as a powerful noninvasive biomarker for cancer. However, the HBV integration and mutation landscape on cfDNA remains unclear. EXPERIMENTAL DESIGN A cSMART (Circulating Single-Molecule Amplification and Resequencing Technology)-based method (SIM) was developed to simultaneously investigate HBV integration and mutation landscapes on cfDNA with HBV-specific primers covering the whole HBV genome. Patients with HCC (n = 481) and liver cirrhosis (LC; n = 517) were recruited in the study. RESULTS A total of 6,861 integration breakpoints including TERT and KMT2B were discovered in HCC cfDNA, more than in LC. The concentration of circulating tumor DNA (ctDNA) was positively correlated with the detection rate of these integration hotspots and total HBV integration events in cfDNA. To track the origin of HBV integrations in cfDNA, whole-genome sequencing (WGS) was performed on their paired tumor tissues. The paired comparison of WGS data from tumor tissues and SIM data from cfDNA confirmed most recurrent integration events in cfDNA originated from tumor tissue. The mutational landscape across the whole HBV genome was first generated for both HBV genotype C and B. A region from nt1100 to nt1500 containing multiple HCC risk mutation sites (OR > 1) was identified as a potential HCC-related mutational hot zone. CONCLUSIONS Our study provides an in-depth delineation of HBV integration/mutation landscapes at cfDNA level and did a comparative analysis with their paired tissues. These findings shed light on the possibilities of noninvasive detection of virus insertion/mutation.
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Affiliation(s)
- Bo Zheng
- National Center for Liver Cancer, Shanghai, PR China.,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, PR China
| | - Xiao-Long Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, PR China
| | - Rong Fan
- Department of Infectious Diseases, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jian Bai
- Berry Oncology Corporation. Beijing, PR China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Digestive & Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, PR China
| | - Lu-Tao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, PR China.,The Clinical Research Center of Shandong Province for Clinical Laboratory, Jinan, PR China
| | - Guo-Qing Jiang
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, PR China
| | | | - Xiao-Tang Fan
- Dept of Hepatology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, PR China
| | - Yi-Nong Ye
- The Department of Infectious Disease, the First People's Hospital of Foshan, Foshan City, PR China
| | - Yun-Song Qian
- Hepatology Department, Ningbo Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, PR China
| | - Ying-Chao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, PR China
| | | | - Guo-Hong Deng
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Feng Shen
- Department of Hepatic Surgery IV, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, PR China
| | - He-Ping Hu
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, PR China
| | - Hui Wang
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, PR China
| | | | - Lan-Lan Ru
- Berry Oncology Corporation. Beijing, PR China
| | - Jing Zhang
- Berry Oncology Corporation. Beijing, PR China
| | - Yan-Hang Gao
- The First Hospital of Jilin University, Jilin, PR China
| | - Jie Xia
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Hua-Dong Yan
- Hepatology Department, Ningbo Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, PR China
| | - Min-Feng Liang
- The Department of Infectious Disease, the First People's Hospital of Foshan, Foshan City, PR China
| | - Yan-Long Yu
- Chifeng Clinical Medical School of Inner Mongolia Medical University, Chifeng, PR China
| | - Fu-Ming Sun
- Berry Oncology Corporation. Beijing, PR China
| | - Yu-Jing Gao
- Xuzhou Infectious Diseases Hospital, Xuzhou, PR China
| | - Jian Sun
- Department of Infectious Diseases, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Chun-Xiu Zhong
- Department of Infectious Diseases, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Yin Wang
- Berry Oncology Corporation. Beijing, PR China
| | - Fei Kong
- The First Hospital of Jilin University, Jilin, PR China
| | - Jin-Ming Chen
- Chifeng Clinical Medical School of Inner Mongolia Medical University, Chifeng, PR China
| | - Dan Zheng
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yuan Yang
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, PR China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, PR China
| | - Chuan-Xin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, PR China.,The Clinical Research Center of Shandong Province for Clinical Laboratory, Jinan, PR China
| | - Lin Wu
- Berry Oncology Corporation. Beijing, PR China.
| | - Jin-Lin Hou
- Department of Infectious Diseases, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, PR China.
| | - Jing-Feng Liu
- Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Jinan District, Fuzhou City, PR China.
| | - Hong-Yang Wang
- National Center for Liver Cancer, Shanghai, PR China. .,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, PR China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, PR China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, PR China
| | - Lei Chen
- National Center for Liver Cancer, Shanghai, PR China. .,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, PR China
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15
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Hu CJ, Lu YC, Yang TH, Chan YH, Tsai CY, Yu IS, Lin SW, Liu TC, Cheng YF, Wu CC, Hsu CJ. Toward the Pathogenicity of the SLC26A4 p.C565Y Variant Using a Genetically Driven Mouse Model. Int J Mol Sci 2021; 22:2789. [PMID: 33801843 PMCID: PMC8001573 DOI: 10.3390/ijms22062789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Recessive variants of the SLC26A4 gene are globally a common cause of hearing impairment. In the past, cell lines and transgenic mice were widely used to investigate the pathogenicity associated with SLC26A4 variants. However, discrepancies in pathogenicity between humans and cell lines or transgenic mice were documented for some SLC26A4 variants. For instance, the p.C565Y variant, which was reported to be pathogenic in humans, did not exhibit functional pathogenic consequences in cell lines. To address the pathogenicity of p.C565Y, we used a genotype-based approach in which we generated knock-in mice that were heterozygous (Slc26a4+/C565Y), homozygous (Slc26a4C565Y/C565Y), and compound heterozygous (Slc26a4919-2A>G/C565Y) for this variant. Subsequent phenotypic characterization revealed that mice with these genotypes demonstrated normal auditory and vestibular functions, and normal inner-ear morphology and pendrin expression. These findings indicate that the p.C565Y variant is nonpathogenic for mice, and that a single p.C565Y allele is sufficient to maintain normal inner-ear physiology in mice. Our results highlight the differences in pathogenicity associated with certain SLC26A4 variants between transgenic mice and humans, which should be considered when interpreting the results of animal studies for SLC26A4-related deafness.
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Affiliation(s)
- Chin-Ju Hu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Ying-Chang Lu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
- Department of Medical Research, Taipei Veteran General Hospital, Taipei 112, Taiwan
| | - Ting-Hua Yang
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
| | - Yen-Hui Chan
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
- Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung 427, Taiwan
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
| | - I-Shing Yu
- Transgenic Mouse Models Core (TMMC), Division of Genomic Medicine, Research Center for Medical Excellence, National Taiwan University, Taipei 100, Taiwan; (I-S.Y.); (S.-W.L.)
| | - Shu-Wha Lin
- Transgenic Mouse Models Core (TMMC), Division of Genomic Medicine, Research Center for Medical Excellence, National Taiwan University, Taipei 100, Taiwan; (I-S.Y.); (S.-W.L.)
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veteran General Hospital, Taipei 112, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veteran General Hospital, Taipei 112, Taiwan
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 100, Taiwan; (C.-J.H.); (Y.-C.L.); (T.-H.Y.); (Y.-H.C.); (C.-Y.T.); (T.-C.L.); (C.-J.H.)
- Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung 427, Taiwan
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16
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Lv W, Linpeng S, Li Z, Liang D, Jia Z, Meng D, Cram DS, Zhu H, Teng Y, Yin A, Wu L. Noninvasive prenatal diagnosis for pregnancies at risk for β-thalassaemia: a retrospective study. BJOG 2020; 128:448-457. [PMID: 32363759 DOI: 10.1111/1471-0528.16295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To evaluate the clinical feasibility of noninvasive prenatal diagnosis (NIPD) for β-thalassaemia using circulating single molecule amplification and re-sequencing technology (cSMART). DESIGN Through carrier screening, 102 pregnant Chinese couples carrying pathogenic HBB gene variants were recruited to the study. Pregnancies were managed using traditional invasive prenatal diagnosis (IPD). Retrospectively, we evaluated the archived pregnancy plasma DNA by NIPD to evaluate the performance of our cSMART assay for fetal genotyping. SETTING Chinese prenatal diagnostic centres specialising in thalassaemia testing. POPULATION Chinese carrier couples at high genetic risk for β-thalassaemia. METHODS Fetal cell sampling was performed by amniocentesis and HBB genotypes were determined by reverse dot blot. NIPD was performed by a newly designed HBB cSMART assay and fetal genotypes were called by measuring the allelic ratios in the maternal cell-free DNA. MAIN OUTCOME MEASURES Concordance of HBB fetal genotyping between IPD and NIPD and the sensitivity and specificity of NIPD. RESULTS Invasive prenatal diagnosis identified 29 affected homozygotes or compound heterozygotes, 54 heterozygotes and 19 normal homozygotes. Compared with IPD results, 99 of 102 fetuses (97%) were correctly genotyped by our NIPD assay. Two of three discordant samples were false positives and the other sample involved an incorrect call of a heterozygote carrier as a homozygote normal. Overall, the sensitivity and specificity of our NIPD assay was 100% (95% CI 88.06-100.00%) and 97.26% (95% CI 90.45-99.67%), respectively. CONCLUSIONS This study demonstrates that our cSMART-based NIPD assay for β-thalassaemia has potential clinical utility as an alternative to IPD for pregnant HBB carrier couples. TWEETABLE ABSTRACT A new noninvasive test for pregnancies at risk for β-thalassaemia.
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Affiliation(s)
- W Lv
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - S Linpeng
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Z Li
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - D Liang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Z Jia
- Prenatal Diagnosis Centre of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China
| | - D Meng
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region, China
| | - D S Cram
- Berry Genomics Corporation, Beijing, China
| | - H Zhu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Y Teng
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - A Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - L Wu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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17
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Yang J, Peng CF, Qi Y, Rao XQ, Guo F, Hou Y, He W, Wu J, Chen YY, Zhao X, Wang YN, Peng H, Wang D, Du L, Luo MY, Huang QF, Liu HL, Yin A. Noninvasive prenatal detection of hemoglobin Bart hydrops fetalis via maternal plasma dispensed with parental haplotyping using the semiconductor sequencing platform. Am J Obstet Gynecol 2020; 222:185.e1-185.e17. [PMID: 31394068 DOI: 10.1016/j.ajog.2019.07.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/03/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Thalassemia is one of the most common monogenetic diseases in the south of China and Southeast Asia. Hemoglobin Bart's hydrops fetalis syndrome was caused by a homozygous Southeast Asian deletion (-/-) in the HBA gene. Few studies have proved the potential of screen for Bart's hydrops fetalis using fetal cell-free DNA. However, the number of cases is still relatively small. Clinical trials of large samples would be needed. OBJECTIVE In this study, we aimed to develop a noninvasive method of target-captured sequencing and genotyping by the Bayesian method using cell-free fetal DNA to identify the fetal genotype in pregnant women who are at risk of having hemoglobin Bart hydrops fetalis in a large-scale study. STUDY DESIGN In total, 192,173 couples from 30 hospitals were enrolled in our study and 878 couples were recruited, among whom both the pregnant women and their husbands were detected to be carriers of Southeast Asian type (-/αα) of α-thalassemia. Prenatal diagnosis was performed by chorionic villus sampling, amniocentesis, or cordocentesis using gap-polymerase chain reaction considered as the golden standard. RESULTS As a result, we found that the sensitivity and specificity of our noninvasive method were 98.81% and 94.72%, respectively, in the training set as well as 100% and 99.31%, respectively, in the testing set. Moreover, our method could identify all of 885 maternal samples with the Southeast Asian carrier and 36 trisomy samples with 100% of sensitivity in T13, T18, and T21 and 99.89% (1 of 917) and 99.88% (1 of 888) of specificity in T18 and T21, respectively. CONCLUSION Our method opens the possibility of early screening for maternal genotyping of α-thalassemia, fetal aneuploidies in chromosomes 13/18/21, and hemoglobin Bart hydrops fetalis detection in 1 tube of maternal plasma.
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Affiliation(s)
- Jiexia Yang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Chun-Fang Peng
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Yiming Qi
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Xing-Qiang Rao
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Fangfang Guo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Wei He
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yang-Yi Chen
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Xin Zhao
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yu-Nan Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Haishan Peng
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Li Du
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Ming-Yong Luo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Quan-Fei Huang
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Hai-Liang Liu
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China.
| | - Aihua Yin
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China.
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18
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Han L, Chen C, Guo F, Ye J, Peng Z, Qiu W, Wang Y, Li W, Zhang H, Liang L, Wang Y, Wang H, Ji X, Sun J, Gu X. Noninvasive prenatal diagnosis of cobalamin C (cblC) deficiency through target region sequencing of cell-free DNA in maternal plasma. Prenat Diagn 2019; 40:324-332. [PMID: 31697851 DOI: 10.1002/pd.5601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 01/15/2023]
Abstract
OBJECTIVE This study aimed to validate the feasibility of haplotype-based noninvasive prenatal diagnosis (NIPD) of cobalamin C (cblC) deficiency. METHOD This method includes three steps: First, targeted sequencing was performed on 21 families affected by cblC deficiency (including the couples and probands). Second, parental haplotypes linked with the pathogenic variant were determined using the genotypes of trios. Then, the fetal haplotypes were inferred through a parental haplotype assisted hidden Markov model (HMM). The NIPD results were confirmed by using the invasive procedures. RESULTS Twenty-one fetal genotypes were successfully inferred by NIPD including three compound heterozygotes with cblC deficiency, nine heterozygote carriers of cblC deficiency, and nine normal fetuses. The NIPD results were confirmed using the invasive procedures with 100% concordant rate. CONCLUSION This result has shown that haplotype-based NIPD of cblC deficiency has high concordant rate and indicated potential clinical utility as a pregnancy diagnosis method for high-risk carrier couples.
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Affiliation(s)
- Lianshu Han
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Jun Ye
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wenjuan Qiu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Huiwen Zhang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Liang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanhuan Wang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Ji
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Xuefan Gu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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19
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Rechitsky S, Kuliev A, San Ramon G, Tur-Kaspa I, Wang Y, Wang W, Wu X, Wang L, Leigh D, Cram DS. Single-Molecule Sequencing: A New Approach for Preimplantation Testing and Noninvasive Prenatal Diagnosis Confirmation of Fetal Genotype. J Mol Diagn 2019; 22:220-227. [PMID: 31751677 DOI: 10.1016/j.jmoldx.2019.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/11/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022] Open
Abstract
We investigated the potential of next-generation sequencing (NGS) as an alternative method for preimplantation genetic testing of monogenic disease (PGT-M) with human leukocyte antigen (HLA) matching and for noninvasive prenatal diagnosis follow-up. The case involved parents who were carriers of the Fanconi anemia complementation group G (FANCG) 260delG mutation. After clinical PGT using conventional short tandem repeat and mutation analysis, two euploid disease-free embryos were transferred, resulting in a twin pregnancy. Using the original embryo whole genome amplification products from 10 embryos, NGS confirmed the genotypes of the eight nontransferred embryos for both mutation status and HLA combination. NGS also confirmed that the two transferred embryos, which resulted in a twin pregnancy, were euploid, Fanconi disease free, and HLA matched to their sick sibling. At 15 weeks' gestation, noninvasive prenatal diagnosis of the maternal cell-free DNA determined fetal fractions of 14% and 6.6% for twins 1 and 2, respectively. The maternal plasma FANCG 260delG mutation ratio was measured at 46.2%, consistent with the presence of a carrier fetus and a normal fetus. These findings provide proof of concept that NGS has clinical utility as a safe and effective PGT-M method for embryo genotyping as well as more complex direct HLA matching. In addition, NGS can be used to confirm the original PGT-M and HLA matching embryo results in early pregnancy without the need for invasive prenatal diagnosis.
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Affiliation(s)
| | - Anver Kuliev
- Reproductive Genetic Innovations, Chicago, Illinois
| | | | | | - Yin Wang
- Research and Development Department, Berry Genomics Corporation, Beijing, People's Republic of China
| | - Wenjie Wang
- Women Health Center of Shanxi, Children's Hospital of Shanxi, Taiyuan, People's Republic of China
| | - Xueqing Wu
- Women Health Center of Shanxi, Children's Hospital of Shanxi, Taiyuan, People's Republic of China
| | - Li Wang
- IVF Center, First Hospital of Kunming, Kunming, People's Republic of China
| | - Don Leigh
- IVF Center, First Hospital of Kunming, Kunming, People's Republic of China
| | - David S Cram
- Research and Development Department, Berry Genomics Corporation, Beijing, People's Republic of China; Women Health Center of Shanxi, Children's Hospital of Shanxi, Taiyuan, People's Republic of China; IVF Center, First Hospital of Kunming, Kunming, People's Republic of China.
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20
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Lv W, Li Z, Wei X, Zhu H, Teng Y, Zhou M, Gong Y, Cram DS, Liang D, Han L, Wu L. Noninvasive fetal genotyping in pregnancies at risk for PKU using a comprehensive quantitative cSMART assay for PAH gene mutations: a clinical feasibility study. BJOG 2019; 126:1466-1474. [PMID: 31295388 DOI: 10.1111/1471-0528.15869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To assess the diagnostic performance of a novel circulating single molecule amplification and re-sequencing technology (cSMART) method for noninvasive prenatal testing (NIPT) of Phenylketonuria (PKU). DESIGN Blinded NIPT analysis of pregnancies at high risk for PKU. SETTING Shanghai Xinhua Hospital and Hunan Jiahui Genetics Hospital, China. POPULATION Couples (n = 33) with a child diagnosed with PKU. METHODS Trio testing for pathogenic PAH mutations was performed by Sanger sequencing. In second pregnancies, invasive prenatal diagnosis (IPD) was used to determine fetal genotypes. NIPT was performed using a PAH gene-specific cSMART assay. Based on the plasma DNA mutation ratio relative to the fetal DNA fraction, fetal genotypes were assigned using a maximum-likelihood algorithm. MAIN OUTCOME MEASURES Concordance of fetal genotyping results between IPD and NIPT, and the sensitivity and specificity of the NIPT assay. RESULTS Compared with gold standard IPD results, 32 of 33 fetuses (96.97%) were accurately genotyped by NIPT. The sensitivity and specificity of the NIPT assay was 100.00% (95% CI 59.04-100.00%) and 96.15% (95% CI 80.36-99.90%), respectively. CONCLUSIONS The novel cSMART assay demonstrated high accuracy for correctly calling fetal genotypes. We propose that this test has useful clinical utility for the rapid screening of high-risk and low-risk pregnancies with a known history of PKU on one or both sides of the family. TWEETABLE ABSTRACT NIPT of couples at high risk for PKU using a full-coverage cSMART PAH gene test.
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Affiliation(s)
- W Lv
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Z Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - X Wei
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - H Zhu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Y Teng
- Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - M Zhou
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Y Gong
- Berry Genomics Corporation, Beijing, China
| | - D S Cram
- Berry Genomics Corporation, Beijing, China.,Children's Hospital of Shanxi, Women Health Center of Shanxi, Taiyuan, Shanxi, China
| | - D Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - L Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Institute of Pediatric Research, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - L Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
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21
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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22
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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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23
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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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24
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Duan H, Liu N, Zhao Z, Liu Y, Wang Y, Li Z, Xu M, Cram DS, Kong X. Non-invasive prenatal testing of pregnancies at risk for phenylketonuria. Arch Dis Child Fetal Neonatal Ed 2019; 104:F24-F29. [PMID: 29353259 DOI: 10.1136/archdischild-2017-313929] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/16/2017] [Accepted: 12/07/2017] [Indexed: 01/15/2023]
Abstract
BACKGROUND Phenylketonuria (PKU) is a common metabolic disorder caused predominately by mutations in the phenylalanine hydroxylase (PAH) gene. The aim of the study was to design and validate the performance of a non-invasive prenatal test (NIPT) for PKU using circulating single molecule amplification and resequencing technology (cSMART). METHODS A total of 18 couples at genetic risk for having a child with PKU were recruited to the study. Gold standard invasive prenatal diagnosis (IPD) was performed on amniocyte or villus cell DNA by Sanger sequencing, targeting the known parental PAH mutations. Retrospectively, NIPT was also performed on stored maternal plasma samples from the 18 pregnancies by a multiplex cSMART assay designed to target all known DNA variants in the PAH gene. RESULTS Benchmarking against IPD results, NIPT correctly genotyped all fetuses, including six compound heterozygotes with PKU, four normal non-carriers of PKU and eight heterozygote carriers of PKU comprising five cases of a maternally inherited mutation and three cases of a paternally inherited mutation. CONCLUSIONS The NIPT cSMART PKU assay was highly sensitive and specific for mutation detection and correct assignment of fetal genotypes. Based on comprehensive mutation coverage across the PAH gene, the assay may initially have clinical utility as a pregnancy screening test for high-risk carrier couples.
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Affiliation(s)
- Huikun Duan
- Genetics and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ning Liu
- Genetics and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetics and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiqian Liu
- Research and Development Department, Berry Genomics Corporation, Beijing, China
| | - Yin Wang
- Research and Development Department, Berry Genomics Corporation, Beijing, China
| | - Zhifeng Li
- Research and Development Department, Berry Genomics Corporation, Beijing, China
| | - Mengnan Xu
- Research and Development Department, Berry Genomics Corporation, Beijing, China
| | - David S Cram
- Research and Development Department, Berry Genomics Corporation, Beijing, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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25
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Wang F, Zhu L, Liu B, Zhu X, Wang N, Deng T, Kang D, Pan J, Yang W, Gao H, Guo Y. Noninvasive and Accurate Detection of Hereditary Hearing Loss Mutations with Buccal Swab Based on Droplet Digital PCR. Anal Chem 2018; 90:8919-8926. [PMID: 29987923 DOI: 10.1021/acs.analchem.8b01096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hereditary hearing loss is a common clinical neurosensory disorder in humans and has a high demand for genetic screening. Current screening techniques using peripheral blood or dried blood spots (DBSs) are invasive. Therefore, this study aims to develop a noninvasive and accurate detection method for eight hotspot deafness-associated mutations based on buccal swab and droplet digital PCR (ddPCR). First, this method was evaluated for analytic performance including specificity, detection limit, dynamic range using plasmid DNA. The specificity was 100% and the detection limit was 5 copies. The dynamic range of this ddPCR-based method was from 10 to 105 copies/μL. Next, the method was found to accurately quantify mitochondrial gene heteroplasmy rate as low as 1% for both m.1494C > T and m.1555A > G sites. Then, we demonstrated that buccal swab was a reliable sample. DNA can be extracted and accurately quantified after a buccal swab had been stored for 90 days at either room temperature or -20 °C. Finally, clinical samples (23 DBSs and 42 buccal swabs) were tested to further evaluate the accuracy and clinical applicability of this method. All clinical samples were accurately quantified and genotyped. This noninvasive and accurate method is highly promising as a genetic screening method for deafness-associated mutations due to its high sensitivity and accuracy.
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Affiliation(s)
- Fang Wang
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Lingxiang Zhu
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Baoxia Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
| | - Xiurui Zhu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
| | - Nan Wang
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Tao Deng
- Beijing CapitalBio Medical Laboratory , 88 Kechuang Six Street , Beijing 101111 , People's Republic of China
| | - Dongyang Kang
- Department of Otorhinolaryngology Head Neck Surgery , Chinese PLA General Hospital , 28 Fuxing Road , Beijing 100853 , P. R. China
| | - Junmin Pan
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
| | - Wenjun Yang
- TargetingOne Corporation , 268 Chengfu Road , Beijing 100190 , People's Republic of China
| | - Huafang Gao
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
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26
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One-step noninvasive prenatal testing (NIPT) for autosomal recessive homozygous point mutations using digital PCR. Sci Rep 2018; 8:2877. [PMID: 29440752 PMCID: PMC5811538 DOI: 10.1038/s41598-018-21236-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/16/2022] Open
Abstract
Previously, we introduced a noninvasive prenatal testing (NIPT) protocol for diagnosing compound heterozygous autosomal recessive point mutations via maternal plasma DNA and simulated control genomic DNA sampling based on fetal DNA fraction. In our present study, we have improved our NIPT protocol to make it possible to diagnose homozygous autosomal recessive point mutations without the need to acquire fetal DNA fraction. Moreover, chi-squared test and empirical statistical range based on the proportion of mutant allele reads among the total reads served as the gatekeeping method. If this method yielded inconclusive results, then the Bayesian method was performed; final conclusion was drawn from the results of both methods. This protocol was applied to three families co-segregating congenital sensorineural hearing loss with monogenic homozygous mutations in prevalent deafness genes. This protocol successfully predicted the fetal genotypes from all families without the information about fetal DNA fraction using one-step dPCR reactions at least for these three families. Furthermore, we suspect that confirmatory diagnosis under this protocol is possible, not only by using picodroplet dPCR, but also by using the more readily available chip-based dPCR, making our NIPT protocol more useful in the diagnosis of autosomal recessive point mutations in the future.
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27
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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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