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Zhuang X, Zhu Y, Hsing IM. Rationally Designed Universal Melting Probes (Uni-Melt) for Multiplex Genotyping. Anal Chem 2024; 96:19312-19320. [PMID: 39600140 DOI: 10.1021/acs.analchem.4c03050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Polymerase chain reaction (PCR) with probe-based melting curve techniques has been widely used in multiplex genotyping for early diagnosis of genetic diseases and common cancers. However, traditional designs face limitations due to the high modification cost of sensing probes and complex background fluorescence signals. Herein, we introduce the Universal Melting Probes (Uni-Melt) system, a closed-tube PCR assay for multiplex genotyping that incorporates barcoded PCR amplification and universal hybridization probes for melting curve analysis. Uni-Melt can detect multiple genotypes using a single set of universal fluorophore-modified probes and unmodified target-specific mediator strands, which was verified by detecting five different human papillomavirus (HPV) genotypes utilizing two fluorescent channels with the lowest detectable concentration at 102 copies/μL. In addition, Uni-Melt can differentiate multiple mutation sites including single nucleotide polymorphisms (SNPs), as demonstrated in the SLC25A13 gene. Overall, Uni-Melt is a closed-tube, sensitive, and specific system for multiplexed genotyping compatible with commonly employed quantitative polymerase chain reaction (qPCR) thermocyclers. Compared to the traditional probe-based melting curve analysis, Uni-Melt can reduce the assay cost associated with multiple probe modifications and decrease the complexity of the reaction without sacrificing sensitivity and specificity, which makes it a practically useful tool for clinical screening.
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Affiliation(s)
- Xinyu Zhuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Yuxuan Zhu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
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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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Rogers R, Mardy A. Chorionic Villous Testing Versus Amniocentesis After Abnormal Noninvasive Prenatal Testing. Clin Obstet Gynecol 2023; 66:595-606. [PMID: 37650670 DOI: 10.1097/grf.0000000000000801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In the setting of a normal first-trimester ultrasound, an amniocentesis may be a better option than chorionic villous sampling for invasive diagnostic testing after a cell-free DNA high risk for trisomy 13, given the high rates of confined placental mosaicism. In unaffected fetuses, other evaluations should be considered depending on the cell-free DNA results, including maternal karyotyping for monosomy X, uniparental disomy testing for chromosomes with imprinted genes, serial growth scans for trisomy 16, and a workup for maternal malignancy for multiple aneuploidies or autosomal monosomy.
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Affiliation(s)
- Rosemary Rogers
- Department of Women's Health, Dell Medical School-UT Health Austin, Austin, Texas
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Hanson B, Paternoster B, Povarnitsyn N, Scotchman E, Chitty L, Chandler N. Non-invasive prenatal diagnosis (NIPD): current and emerging technologies. EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2023; 4:3-26. [PMID: 39698301 PMCID: PMC11648410 DOI: 10.20517/evcna.2022.44] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 12/20/2024]
Abstract
Prenatal testing is important for the early detection and diagnosis of rare genetic conditions with life-changing implications for the patient and their family. Gaining access to the fetal genotype can be achieved using gold-standard invasive sampling methods, such as amniocentesis and chorionic villus sampling, but these carry a small risk of miscarriage. Non-invasive prenatal diagnosis (NIPD) for select rare monogenic conditions has been in clinical service in England since 2012 and has revolutionised the field of prenatal diagnostics by reducing the number of women undergoing invasive sampling procedures. Fetal-derived genomic material is present in a highly fragmented form amongst the maternal cell-free DNA (cfDNA) in circulation, with sequence coverage across the entire fetal genome. Cell-free fetal DNA (cffDNA) is the foundation for NIPD, and several technologies have been clinically implemented for the detection of paternally inherited and de novo pathogenic variants. Conversely, a low abundance of cffDNA within a high background of maternal cfDNA makes assigning maternally inherited variants to the fetal fraction a significantly more challenging task. Research is ongoing to expand available tests for maternal inheritance to include a broader range of monogenic conditions, as well as to uncover novel diagnostic avenues. This review covers the scope of technologies currently clinically available for NIPD of monogenic conditions and those still in the research pipeline towards implementation in the future.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London WC1N 3BH, UK
| | - Ben Paternoster
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London WC1N 3BH, UK
| | - Nikita Povarnitsyn
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London WC1N 3BH, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London WC1N 3BH, UK
| | - Lyn Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London WC1N 3BH, UK
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London WC1N 3BH, UK
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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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Zhong LPW, Chiu RWK. The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment. Annu Rev Genomics Hum Genet 2022; 23:413-425. [PMID: 35316613 DOI: 10.1146/annurev-genom-110821-113411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the widespread clinical adoption of noninvasive screening for fetal chromosomal aneuploidies based on cell-free DNA analysis from maternal plasma, more researchers are turning their attention to noninvasive prenatal assessment for single-gene disorders. The development of a spectrum of approaches to analyze cell-free DNA in maternal circulation, including relative mutation dosage, relative haplotype dosage, and size-based methods, has expanded the scope of noninvasive prenatal testing to sex-linked and autosomal recessive disorders. Cell-free fetal DNA analysis for several of the more prevalent single-gene disorders has recently been introduced into clinical service. This article reviews the analytical approaches currently available and discusses the extent of the clinical implementation of noninvasive prenatal testing for single-gene disorders. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lilian Pok Wa Zhong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; ,
| | - Rossa W K Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; ,
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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: 5] [Impact Index Per Article: 1.7] [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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Characterization of phenylalanine hydroxylase gene variants and analysis of genotype-phenotype correlation in patients with phenylalanine hydroxylase deficiency from Fujian Province, Southeastern China. Mol Biol Rep 2022; 49:10409-10419. [PMID: 36104584 PMCID: PMC9618490 DOI: 10.1007/s11033-022-07579-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Phenylalanine hydroxylase deficiency (PAHD) is the most prevalent inherited disorder of amino acid metabolism in China. Its complex phenotype includes many variants and genotypes among different populations. METHODS AND RESULTS In this study, we analyzed the phenylalanine hydroxylase gene (PAH) variants in a cohort of 93 PAHD patients from Fujian Province. We also assessed genotype and phenotype correlation in patients with PAHD. A total of 44 different pathogenic variants were identified, including five novel variants. The three most prevalent variants among all patents were c.158G > A, p.(Arg53His) (18.03%), c.721C > T, p.(Arg241Cys) (14.75%), and c.728G > A, p.(Arg243Gln) (7.65%). The frequency of the c.158G > A, p.(Arg53His) variant was highest in patients with mild hyperphenylalaninemia, whereas the frequency of the c.1197A > T, p.(Val399 =) and c.331C > T, p.(Arg111Ter) variants was highest in patients with classic phenylketonuria. The most abundant genotypes observed in PAHD patients were c.[158G > A];[728G > A], c.[158G > A];[442-1G > A], and c.[158G > A];[721C > T]. Comparing allelic phenotype to genotypic phenotype values yielded fairly accurate predictions of phenotype, with an overall consistency rate was 85.71% for PAHD patients. CONCLUSIONS Our study identified a PAH variant spectrum in PAHD patients from Fujian Province, Southeastern China. Quantitative correlation analysis between genotype and phenotype severity is helpful for genetic counseling and management.
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Peng D, Ganye Z, Gege S, Yanjie X, Ning L, Xiangdong K. Clinical application of non-invasive prenatal diagnosis of phenylketonuria based on haplotypes via paired-end molecular tags and weighting algorithm. BMC Med Genomics 2021; 14:294. [PMID: 34920737 PMCID: PMC8684071 DOI: 10.1186/s12920-021-01141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/01/2021] [Indexed: 11/11/2022] Open
Abstract
Background Phenylketonuria (PKU) is a metabolic disease that can cause severe and irreversible brain damage without treatment. Methods Here we developed a non-invasive prenatal diagnosis (NIPD) technique based on haplotypes via paired-end molecular tags and weighting algorithm and applied it to the NIPD of PKU to evaluate its accuracy and feasibility in the early pregnancy. A custom-designed hybridization probes containing regions in phenylalanine hydroxylase (PAH) gene and its 1 Mb flanking region were used for target sequencing on genomic and maternal plasma DNA (7–13 weeks of gestation) to construct the parental haplotypes and the proband’s haplotype. Fetal haplotype was then inferred combined with the parental haplotypes and the proband’s haplotype. The presence of haplotypes linked to both the maternal and paternal mutant alleles indicated affected fetuses. The fetal genotypes were further validated by invasive prenatal diagnosis in a blinded fashion. Results This technique has been successfully applied in twenty-one cases. Six fetuses were diagnosed as patients carrying both of the mutated haplotypes inherited from their parents. Eleven fetuses were carriers of one heterozygous PAH variants, six of which were paternal and five of which were maternal. Four fetuses were absence of pathogenic alleles. All results were consistent with the prenatal diagnosis through amniotic fluid. Conclusions The results showed that our new technique applied to the genotyping of fetuses with high risk for PKU achieves an accurate detection at an early stage of pregnancy with low fetal fraction in cell free DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01141-4.
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Affiliation(s)
- Dai Peng
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhao Ganye
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Sun Gege
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xia Yanjie
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Liu Ning
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Kong Xiangdong
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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10
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Mardy AH, Norton ME. Diagnostic testing after positive results on cell free DNA screening: CVS or Amnio? Prenat Diagn 2021; 41:1249-1254. [PMID: 34386984 DOI: 10.1002/pd.6021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/03/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVE The positive predictive values of cell free DNA (cfDNA) and rates of confined placental mosaicism (CPM), imprinting and other factors vary by chromosome. METHODS We sought to review the literature for each of these features for each chromosome and provide recommendations on chorionic villus sampling (CVS) versus amniocentesis after an abnormal cfDNA result. RESULTS For chromosomes with high rates of CPM (trisomy 13, monosomy X and rare autosomal trisomies [RATs]), an amniocentesis should be considered if the first trimester ultrasound is normal. For monosomy X on cfDNA with an unaffected fetus, maternal karyotyping should be considered after normal fetal diagnostic testing. In cfDNA cases with a trisomy involving a chromosome with imprinted genes (6, 7, 11, 14, 15 and 20), CVS should be considered, followed by amniocentesis if abnormal. If the fetus is unaffected, methylation studies should be considered given the risk of uniparental disomy. A third trimester growth ultrasound should be considered for patients with a positive cfDNA screen for a RAT and an unaffected fetus, especially in the case of trisomy 16. For patients with multiple aneuploidy results on cfDNA, a work-up for maternal malignancy should be considered. CONCLUSIONS Clinicians should consider rates of CPM, imprinting, ultrasound findings and maternal factors when considering whether to recommend amniocentesis or CVS after an abnormal cfDNA result.
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Affiliation(s)
- Anne H Mardy
- Division of Maternal Fetal Medicine, University of California, San Francisco, California, USA
| | - Mary E Norton
- Division of Maternal Fetal Medicine, University of California, San Francisco, California, USA
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11
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Cognitive analysis of metabolomics data for systems biology. Nat Protoc 2021; 16:1376-1418. [PMID: 33483720 DOI: 10.1038/s41596-020-00455-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/27/2020] [Indexed: 01/30/2023]
Abstract
Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. The four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1-4 h or more to complete, depending on the processing time of the various software used.
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12
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Chen C, Li R, Sun J, Zhu Y, Jiang L, Li J, Fu F, Wan J, Guo F, An X, Wang Y, Fan L, Sun Y, Guo X, Zhao S, Wang W, Zeng F, Yang Y, Ni P, Ding Y, Xiang B, Peng Z, Liao C. Noninvasive prenatal testing of α-thalassemia and β-thalassemia through population-based parental haplotyping. Genome Med 2021; 13:18. [PMID: 33546747 PMCID: PMC7866698 DOI: 10.1186/s13073-021-00836-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
Background Noninvasive prenatal testing (NIPT) of recessive monogenic diseases depends heavily on knowing the correct parental haplotypes. However, the currently used family-based haplotyping method requires pedigrees, and molecular haplotyping is highly challenging due to its high cost, long turnaround time, and complexity. Here, we proposed a new two-step approach, population-based haplotyping-NIPT (PBH-NIPT), using α-thalassemia and β-thalassemia as prototypes. Methods First, we deduced parental haplotypes with Beagle 4.0 with training on a large retrospective carrier screening dataset (4356 thalassemia carrier screening-positive cases). Second, we inferred fetal haplotypes using a parental haplotype-assisted hidden Markov model (HMM) and the Viterbi algorithm. Results With this approach, we enrolled 59 couples at risk of having a fetus with thalassemia and successfully inferred 94.1% (111/118) of fetal alleles. We confirmed these alleles by invasive prenatal diagnosis, with 99.1% (110/111) accuracy (95% CI, 95.1–100%). Conclusions These results demonstrate that PBH-NIPT is a sensitive, fast, and inexpensive strategy for NIPT of thalassemia. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00836-8.
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Affiliation(s)
- Chao Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaping Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lu Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jian Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Junhui Wan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Fengyu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaoying An
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaoshen Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Linlin Fan
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 490079, China
| | - Xiaosen Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sumin Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Wanyang Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fanwei Zeng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 490079, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Peixiang Ni
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yi Ding
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Bixia Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
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Zhuang X, Lee Yu HL, Hsing IM. Toehold probe-based interrogation for haplotype phasing of long nucleic acid strands. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4185-4190. [PMID: 32785301 DOI: 10.1039/d0ay00946f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The arrangement of multiple single nucleotide polymorphisms (SNPs) in a gene, called a haplotype phase, is increasingly recognized as critical for accurate determination of disease risk and severity. However, conventional toehold-mediated strand displacement reactions are only able to interrogate SNPs, but not phase them since it is not known whether two SNPs in the same copy of the gene (cis) or in different copies of the same gene (trans) will give the same readout. While the rational introduction of an enzyme enables haplotype phasing, the complicated and stable secondary structure of long, single-stranded DNA sequences at room temperature limits its use. Complex nucleic acid structures make the hybridization of the probes difficult. Thus, we designed a molecular method to reveal the relative positions of SNPs located 1.4 kb apart in two copies of a gene by employing a competitive toehold probes and sink strategy at an elevated temperature. As such, we have successfully differentiated 20 nM of the 10 possible diplotypes in a long DNA target with two SNP sites located 1.4 kb apart within an hour without any additional amplification step. This offers a promising technology for accurate and fast haplotype phasing of SNPs that are over multiple kilobases away from each other.
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Affiliation(s)
- Xinyu Zhuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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Management of Women With Phenylalanine Hydroxylase Deficiency (Phenylketonuria): ACOG Committee Opinion, Number 802. Obstet Gynecol 2020; 135:e167-e170. [PMID: 32217978 DOI: 10.1097/aog.0000000000003768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Phenylalanine hydroxylase (PAH) deficiency is an autosomal recessive disorder of phenylalanine metabolism that is characterized by insufficient activity of PAH, a hepatic enzyme. Throughout this document, PAH deficiency is used instead of the older nomenclature of phenylketonuria, in order to reflect the spectrum of PAH deficiency and in accordance with the terminology established by the American College of Medical Genetics and Genomics. Aspects of PAH deficiency management that are particularly relevant to obstetrician-gynecologists or other obstetric care providers include the prevention of embryopathy associated with maternal hyperphenylalaninemia and PAH deficiency and the risk of genetic transmission of PAH deficiency. Family planning and prepregnancy counseling are recommended for all reproductive-aged women with PAH deficiency. The fetal brain and heart are particularly vulnerable to high maternal concentrations of phenylalanine. The crucial role played by maternal dietary restriction before and during pregnancy should be stressed in counseling patients with PAH deficiency; the goal should be to normalize blood phenylalanine levels (less than 6 mg/dL) for at least 3 months before becoming pregnant and to maintain at 2-6 mg/dL during pregnancy, in order to optimize developmental outcomes for the fetus. Although phenylalanine levels are increased in the breast milk of patients with PAH deficiency, breastfed infants who do not have PAH deficiency have normal enzyme levels and no dietary restriction. Breastfeeding is safe for infants born to women who have PAH deficiency provided the infants do not have PAH deficiency. Coordinated medical and nutritional care, as well as follow-up with the patient's metabolic geneticist or specialist, are important in the postpartum period. Because newborns with PAH deficiency appear normal at birth and early detection can improve developmental outcomes for children, newborn screening for PAH deficiency is mandated in all states. This Committee Opinion has been revised to include updates on advances in the understanding and management of women with PAH deficiency and recommendations on prepregnancy counseling, serial fetal growth assessments, and fetal echocardiography.
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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: 0.3] [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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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: 1.3] [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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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: 0.7] [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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Chen M, Chen C, Li Y, Yuan Y, Lai Z, Guo F, Wang Y, Huang X, Li S, Wu R, Peng Z, Sun J, Chen D. Haplotype-Based noninvasive prenatal diagnosis for duchenne muscular dystrophy: A pilot study in South China. Eur J Obstet Gynecol Reprod Biol 2019; 240:15-22. [PMID: 31207536 DOI: 10.1016/j.ejogrb.2019.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To explore the accuracy and feasibility of noninvasive prenatal diagnosis (NIPD) for Duchenne Muscular Dystrophy (DMD) based on the haplotype approach. METHODS We recruited singleton pregnancies at-risk of DMD at 12-25 weeks of gestation from 17 families who all had a proband child affected by DMD. We have identified the pathogenic mutations in probands and their mothers by multiplex ligation-dependent probe amplification (MLPA). To construct parental haplotypes, we performed captured sequencing on genomic DNA from parents and probands. The integration analysis of parental haplotypes and targeted sequencing results of maternal plasma DNA were used to infer the fetal haplotype and genotypes in the DMD gene. Fetal DMD genotypes were further confirmed by invasive prenatal diagnosis. RESULT We have successfully performed the haplotype-based NIPD in all recruited families. Ten fetuses were identified as normal, including four female and six male fetuses. Four female fetuses were carriers, and the other three male fetuses were affected by DMD with exons 49-52 deletion, exons 8-37 deletion and c.628 G > T mutation, respectively. The results of NIPD were consistent with those of invasive diagnosis. CONCLUSION Haplotype-based NIPD for DMD by targeted sequencing is promising and has the potential for clinical application.
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Affiliation(s)
- Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | - Yingting Li
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | - Zhengfei Lai
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | | | - Shiquan Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China; BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Renhua Wu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China.
| | - Dunjin Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, China.
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19
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Guimarães MF, Rabelo FA, Figueiredo I. Knowledge about Neonatal Screening among Postpartum Women and Complexity Level of Birthing Facilities. Int J Neonatal Screen 2019; 5:8. [PMID: 33072968 PMCID: PMC7510197 DOI: 10.3390/ijns5010008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/20/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND To ascertain the degree of knowledge of postpartum women about important aspects related to the neonatal screening process and whether differences of opinion exist between those who deliver in low-complexity versus high-complexity health facilities (low-risk versus high-risk pregnancies, respectively). METHODS This was a prospective, cross-sectional, questionnaire-based study. The sample consisted of postpartum women recruited from 2013 to 2015 at public maternity hospitals in the city of Niterói, Brazil. Participants were divided into two groups and completed a questionnaire consisting of Likert-scored items. Continuous variables were analyzed with the Mann-Whitney test, and categorical variables, with Fisher's test. A confirmatory factor analysis of participants' answers was performed. RESULTS Of 188 women enrolled, 54 (28.7%) had incomplete elementary education; 119 (62.2%) had attended more than six antenatal care visits. The mean age was 25.57 years. Nearly all women (n = 179, 95.2%) were roomed-in with their infants. Knowledge of neonatal screening was very similar in the high-complexity and low-complexity groups. Divergences were limited to items regarding the risks of neonatal screening. CONCLUSIONS The degree of knowledge among postpartum women was similar among high- and low-complexity facilities. Those who attended high-complexity facilities had longer hospital stays and greater adherence to ethical issues regarding neonatal screening.
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Affiliation(s)
- Mariana F. Guimarães
- Departamento Materno-Infantil, Faculdade de Medicina, Hospital Universitário Antonio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brasil
| | | | - Israel Figueiredo
- Departamento Materno-Infantil, Faculdade de Medicina, Hospital Universitário Antonio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brasil
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20
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Horton RH, Wellesley DG. Extending non-invasive prenatal testing to non-invasive prenatal diagnosis. Arch Dis Child Fetal Neonatal Ed 2019; 104:F6-F7. [PMID: 29954879 DOI: 10.1136/archdischild-2018-314845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/10/2018] [Accepted: 06/12/2018] [Indexed: 11/03/2022]
Affiliation(s)
- Rachel Helen Horton
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Southampton, UK
| | - Diana Gay Wellesley
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Southampton, UK
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