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Ngo LT, Chaudhari P, Wang WK, Tseng YT, Kuo PL, Huang CJ, Chiang CY, Chau LK, Huang TT. Noninvasive Prenatal Genetic Screening of Cell-Free Fetal DNA for Early Prediction of β-Thalassemia Using Fiber Optic Nanogold-Linked Sorbent Assay. ACS Sens 2024; 9:4207-4215. [PMID: 39088458 DOI: 10.1021/acssensors.4c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
β-Thalassemia is a prevalent type of severe inherited chronic anemia, primarily identified in developing countries. The identification of single nucleotide polymorphisms (SNPs) plays a vital role in the early diagnosis of genetic diseases. Here, we reported the development of an amplification-free fiber optic nanogold-linked sorbent assay method using a fiber optic particle plasmon resonance (FOPPR) biosensor for rapid and ultrasensitive detection of SNPs. Herein, MutS protein was selected as the biorecognition capture probe and immobilized on the sensing region to capture the target mutant DNA, which was hybridized with a single-base mismatched single-stranded DNA labeled by a gold nanoparticle (AuNP). The AuNP acts as a signaling agent to be detected by the FOPPR biosensor when it is bound on the fiber core surface. The method effectively differentiates mismatched double-stranded DNA by MutS protein from perfectly matched/complementary dsDNA. It exhibits an impressively low detection limit for the detection of SNPs at approximately 10-16 M using low-cost sensor chips and devices. By determination of the ratio of mutant DNA to normal DNA in cell-free genomic DNA from blood samples, this method is promising for diagnosing β-thalassemia in fetuses without invasive testing techniques.
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Affiliation(s)
- Loan Thi Ngo
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pallavi Chaudhari
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Wei-Kai Wang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
| | - Yen-Ta Tseng
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics Gynecology, College of Medicine, National Cheng Kung University Hospital, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Obstetrics & Gynecology, E-Da Hospital, 1 Yida Rd., Yanchao District, Kaohsiung City 82445, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, National Central University, 300 Zhongda Rd., Zhongli District, Taoyuan City 320, Taiwan
- R&D Center for Membrane Technology, Chung Yuan Christian University, 200 Chung Pei Rd., Chung-Li City 32023, Taiwan
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
- Center for Nano Bio-Detection, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Tze-Ta Huang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Stomatology, College of Medicine and Hospital, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
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Erlich HA, Ko L, Lee J, Eaton K, Calloway CD, Lal A, Das R, Jamwal M, Lopez-Pena C, Mack SJ. Non-invasive prenatal testing of beta-hemoglobinopathies using next generation sequencing, in-silico sequence size selection, and haplotyping. Croat Med J 2024; 65:180-188. [PMID: 38868964 PMCID: PMC11157249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
AIM To develop a non-invasive prenatal test for beta-hemoglobinopathies based on analyzing maternal plasma by using next generation sequencing. METHODS We applied next generation sequencing (NGS) of maternal plasma to the non-invasive prenatal testing (NIPT) of autosomal recessive diseases, sickle cell disease and beta-thalassemia. Using the Illumina MiSeq, we sequenced plasma libraries obtained via a Twist Bioscience probe capture panel covering 4 Kb of chromosome 11, including the beta-globin (HBB) gene and >450 genomic single-nucleotide polymorphisms (SNPs) used to estimate the fetal fraction (FF). The FF is estimated by counting paternally transmitted allelic sequence reads present in the plasma but absent in the mother. We inferred fetal beta-globin genotypes by comparing the observed mutation (Mut) and reference (Ref) read ratios to those expected for the three possible fetal genotypes (Mut/Mut; Mut/Ref; Ref/Ref), based on the FF. RESULTS We bioinformatically enriched the FF by excluding reads over a specified length via in-silico size selection (ISS), favoring the shorter fetal reads, which increased fetal genotype prediction accuracy. Finally, we determined the parental HBB haplotypes, which allowed us to use the read ratios observed at linked SNPs to help predict the fetal genotype at the mutation site(s). We determined HBB haplotypes via Oxford Nanopore MinION sequencing of a 2.2 kb amplicon and aligned these sequences using Soft Genetics' NextGENe LR software. CONCLUSION The combined use of ISS and HBB haplotypes enabled us to correctly predict fetal genotypes in cases where the prediction based on variant read ratios alone was incorrect.
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Affiliation(s)
- Henry A Erlich
- Henry A. Erlich, UCSF Benioff Children's Hospital Oakland Research Institute, 747 52nd St, Oakland, CA 94609, USA,
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Sebire E, Rodrigo CH, Bhattacharya S, Black M, Wood R, Vieira R. The implementation and impact of non-invasive prenatal testing (NIPT) for Down's syndrome into antenatal screening programmes: A systematic review and meta-analysis. PLoS One 2024; 19:e0298643. [PMID: 38753891 PMCID: PMC11098470 DOI: 10.1371/journal.pone.0298643] [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: 10/11/2023] [Accepted: 01/25/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) is a widely adopted maternal blood test that analyses foetal originating DNA to screen for foetal chromosomal conditions, including Down's syndrome (DS). The introduction of this test, which may have implications for important decisions made during pregnancy, requires continual monitoring and evaluation. This systematic review aims to assess the extent of NIPT introduction into national screening programmes for DS worldwide, its uptake, and impact on pregnancy outcomes. METHODS AND FINDINGS The study protocol was published in PROSPERO (CRD42022306167). We systematically searched MEDLINE, CINAHL, Scopus, and Embase for population-based studies, government guidelines, and Public Health documents from 2010 onwards. Results summarised the national policies for NIPT implementation into screening programmes geographically, along with population uptake. Meta-analyses estimated the pooled proportions of women choosing invasive prenatal diagnosis (IPD) following a high chance biochemical screening result, before and after NIPT was introduced. Additionally, we meta-analysed outcomes (termination of pregnancy and live births) amongst high chance pregnancies identified by NIPT. Results demonstrated NIPT implementation in at least 27 countries. Uptake of second line NIPT varied, from 20.4% to 93.2% (n = 6). Following NIPT implementation, the proportion of women choosing IPD after high chance biochemical screening decreased from 75% (95% CI 53%, 88%, n = 5) to 43% (95%CI 31%, 56%, n = 5), an absolute risk reduction of 38%. A pooled estimate of 69% (95% CI 52%, 82%, n = 7) of high chance pregnancies after NIPT resulted in termination, whilst 8% (95% CI 3%, 21%, n = 7) had live births of babies with DS. CONCLUSIONS NIPT has rapidly gained global acceptance, but population uptake is influenced by healthcare structures, historical screening practices, and cultural factors. Our findings indicate a reduction in IPD tests following NIPT implementation, but limited pre-NIPT data hinder comprehensive impact assessment. Transparent, comparable data reporting is vital for monitoring NIPT's potential consequences.
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Affiliation(s)
- Elinor Sebire
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, The University of Aberdeen, Aberdeen, Scotland
| | - Chithramali Hasanthika Rodrigo
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, The University of Aberdeen, Aberdeen, Scotland
| | - Sohinee Bhattacharya
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, The University of Aberdeen, Aberdeen, Scotland
| | - Mairead Black
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, The University of Aberdeen, Aberdeen, Scotland
| | - Rachael Wood
- Department of Covid-19 Health Protection Response, Public Health Scotland, Edinburgh, Scotland
| | - Rute Vieira
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, The University of Aberdeen, Aberdeen, Scotland
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Gambari R, Waziri AD, Goonasekera H, Peprah E. Pharmacogenomics of Drugs Used in β-Thalassemia and Sickle-Cell Disease: From Basic Research to Clinical Applications. Int J Mol Sci 2024; 25:4263. [PMID: 38673849 PMCID: PMC11050010 DOI: 10.3390/ijms25084263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In this short review we have presented and discussed studies on pharmacogenomics (also termed pharmacogenetics) of the drugs employed in the treatment of β-thalassemia or Sickle-cell disease (SCD). This field of investigation is relevant, since it is expected to help clinicians select the appropriate drug and the correct dosage for each patient. We first discussed the search for DNA polymorphisms associated with a high expression of γ-globin genes and identified this using GWAS studies and CRISPR-based gene editing approaches. We then presented validated DNA polymorphisms associated with a high HbF production (including, but not limited to the HBG2 XmnI polymorphism and those related to the BCL11A, MYB, KLF-1, and LYAR genes). The expression of microRNAs involved in the regulation of γ-globin genes was also presented in the context of pharmacomiRNomics. Then, the pharmacogenomics of validated fetal hemoglobin inducers (hydroxyurea, butyrate and butyrate analogues, thalidomide, and sirolimus), of iron chelators, and of analgesics in the pain management of SCD patients were considered. Finally, we discuss current clinical trials, as well as international research networks focusing on clinical issues related to pharmacogenomics in hematological diseases.
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Affiliation(s)
- Roberto Gambari
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, Department of Life Sciences and Biotechnology, Ferrara University, 40124 Ferrara, Italy
| | - Aliyu Dahiru Waziri
- Department of Hematology and Blood Transfusion, Ahmadu Bello University Teaching Hospital Zaria, Kaduna 810001, Nigeria;
| | - Hemali Goonasekera
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo P.O. Box 271, Sri Lanka;
| | - Emmanuel Peprah
- Implementing Sustainable Evidence-Based Interventions through Engagement (ISEE) Lab, Department of Global and Environmental Health, School of Global Public Health, New York University, New York, NY 10003, USA;
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Messmore M, Kassab AJ, Prather RO, Arceo DAC, DeCampli W. Cilia and Nodal Flow in Asymmetry: An Engineering Perspective. Crit Rev Biomed Eng 2024; 52:63-82. [PMID: 38523441 DOI: 10.1615/critrevbiomedeng.2024051678] [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: 03/26/2024]
Abstract
Over the past several years, cilia in the primitive node have become recognized more and more for their contribution to development, and more specifically, for their role in axis determination. Although many of the mechanisms behind their influence remain undocumented, it is known that their presence and motion in the primitive node of developing embryos is the determinant of the left-right axis. Studies on cilial mechanics and nodal fluid dynamics have provided clues as to how this asymmetry mechanism works, and more importantly, have shown that direct manipulation of the flow field in the node can directly influence physiology. Although relatively uncommon, cilial disorders have been shown to have a variety of impacts on individuals from chronic respiratory infections to infertility, as well as situs inversus which is linked to congenital heart disease. After first providing background information pertinent to understanding nodal flow and information on why this discussion is important, this paper aims to give a review of the history of nodal cilia investigations, an overview of cilia mechanics and nodal flow dynamics, as well as a review of research studies current and past that sought to understand the mechanisms behind nodal cilia's involvement in symmetry-breaking pathways through a biomedical engineering perspective. This discussion has the additional intention to compile interdisciplinary knowledge on asymmetry and development such that it may encourage more collaborative efforts between the sciences on this topic, as well as provide insight on potential paths forward in the field.
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Affiliation(s)
| | - Alain J Kassab
- Department of Mechanical and Aerospace Engineering, University of Central Florida, 4000 Central Florida Blvd, Orlando, Florida, USA
| | - Ray O Prather
- Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA; University of Central Florida, Orlando, FL 32816, USA; The Heart Center at Orlando Health Arnold Palmer Hospital for Children, Orlando, FL 32806, USA
| | - David A Castillo Arceo
- College of Engineering and Computer Science (CECS), University of Central Florida, Orlando, FL, USA
| | - William DeCampli
- University of Central Florida, Orlando, FL, 32816, USA; The Heart Center, Arnold Palmer Hospital for Children, Orlando, FL, 32806, USA
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Abedalthagafi M, Bawazeer S, Fawaz RI, Heritage AM, Alajaji NM, Faqeih E. Non-invasive prenatal testing: a revolutionary journey in prenatal testing. Front Med (Lausanne) 2023; 10:1265090. [PMID: 38020177 PMCID: PMC10666054 DOI: 10.3389/fmed.2023.1265090] [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: 07/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) is a pioneering technique that has consistently advanced the field of prenatal testing to detect genetic abnormalities and conditions with the aim of decreasing the incidence and prevalence of inherited conditions. NIPT remains a method of choice for common autosomal aneuploidies, mostly trisomy 21, and several monogenic disorders. The advancements in gene sequencing techniques have expanded the panel of conditions where NIPT could be offered. However, basic research on the impact of several genetic conditions lags behind the methods of detection of these sequence aberrations, and the impact of the expansion of NIPT should be carefully considered based on its utility. With interest from commercial diagnostics and a lack of regulatory oversight, there remains a need for careful validation of the predictive values of different tests offered. NIPT comes with many challenges, including ethical and economic issues. The scientific evidence, technical feasibility, and clinical benefit of NIPT need to be carefully investigated before new tests and developments are translated into clinical practice. Moreover, the implementation of panel expansion of NIPT should accompany expert genetic counseling pre- and post-testing.
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Affiliation(s)
- Malak Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, GA, United States
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Shahad Bawazeer
- Department of Medical Genetics, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | - Nouf M. Alajaji
- Department of Maternal Fetal Medicine, Women's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Medical Genetics, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
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Wang M, Cai J, Chen J, Liu J, Geng X, Yu X, Yang J. PCR Techniques and Their Clinical Applications. POLYMERASE CHAIN REACTION [WORKING TITLE] 2023. [DOI: 10.5772/intechopen.110220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Kary B. Mullis developed a revolutionary method name polymerase chain reaction (PCR) in 1983, which can synthesize new strand of DNA complementary to the template strand of DNA and produce billions of copies of a DNA fragment only in few hours. Denaturation, annealing, and extension are the three primary steps involved in the PCR process, which generally requires thermocyclers, DNA template, a pair of primers, Taq polymerase, nucleotides, buffers, etc. With the development of PCR, from traditional PCR, quantitative PCR, to next digital PCR, PCR has become a powerful tool in life sciences and medicine. Applications of PCR techniques for infectious diseases include specific or broad-spectrum pathogen detection, assessment and surveillance of emerging infections, early detection of biological threat agents, and antimicrobial resistance analysis. Applications of PCR techniques for genetic diseases include prenatal diagnosis and screening of neonatal genetic diseases. Applications of PCR techniques for cancer research include tumor-related gene detection. This chapter aimed to discuss about the different types of PCR techniques, including traditional PCR, quantitative PCR, digital PCR, etc., and their applications for rapid detection, mutation screen or diagnosis in infectious diseases, inherited diseases, cancer, and other diseases.
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Noninvasive Prenatal Screening for Common Fetal Aneuploidies Using Single-Molecule Sequencing. J Transl Med 2023; 103:100043. [PMID: 36870287 DOI: 10.1016/j.labinv.2022.100043] [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: 09/28/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Amplification biases caused by next-generation sequencing (NGS) for noninvasive prenatal screening (NIPS) may be reduced using single-molecule sequencing (SMS), during which PCR is omitted. Therefore, the performance of SMS-based NIPS was evaluated. We used SMS-based NIPS to screen for common fetal aneuploidies in 477 pregnant women. The sensitivity, specificity, positive predictive value, and negative predictive value were estimated. The GC-induced bias was compared between the SMS- and NGS-based NIPS methods. Notably, a sensitivity of 100% was achieved for fetal trisomy 13 (T13), trisomy 18 (T18), and trisomy 21 (T21). The positive predictive value was 46.15% for T13, 96.77% for T18, and 99.07% for T21. The overall specificity was 100% (334/334). Compared with NGS, SMS (without PCR) had less GC bias, a better distinction between T21 or T18 and euploidies, and better diagnostic performance. Overall, our results suggest that SMS improves the performance of NIPS for common fetal aneuploidies by reducing the GC bias introduced during library preparation and sequencing.
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Singh K. Prenatal Interventions for the Treatment of Congenital Disorders. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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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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Madgett TE. First Trimester Noninvasive Prenatal Diagnosis of Maternally Inherited Beta-Thalassemia Mutations. Clin Chem 2022; 68:1002-1004. [PMID: 35757992 DOI: 10.1093/clinchem/hvac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/08/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Tracey E Madgett
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
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