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Clausen FB. Antenatal RHD screening to guide antenatal anti-D immunoprophylaxis in non-immunized D- pregnant women. Immunohematology 2024; 40:15-27. [PMID: 38739027 DOI: 10.2478/immunohematology-2024-004] [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: 05/14/2024]
Abstract
In pregnancy, D- pregnant women may be at risk of becoming immunized against D when carrying a D+ fetus, which may eventually lead to hemolytic disease of the fetus and newborn. Administrating antenatal and postnatal anti-D immunoglobulin prophylaxis decreases the risk of immunization substantially. Noninvasive fetal RHD genotyping, based on testing cell-free DNA extracted from maternal plasma, offers a reliable tool to predict the fetal RhD phenotype during pregnancy. Used as a screening program, antenatal RHD screening can guide the administration of antenatal prophylaxis in non-immunized D- pregnant women so that unnecessary prophylaxis is avoided in those women who carry a D- fetus. In Europe, antenatal RHD screening programs have been running since 2009, demonstrating high test accuracies and program feasibility. In this review, an overview is provided of current state-of-the-art antenatal RHD screening, which includes discussions on the rationale for its implementation, methodology, detection strategies, and test performance. The performance of antenatal RHD screening in a routine setting is characterized by high accuracy, with a high diagnostic sensitivity of ≥99.9 percent. The result of using antenatal RHD screening is that 97-99 percent of the women who carry a D- fetus avoid unnecessary prophylaxis. As such, this activity contributes to avoiding unnecessary treatment and saves valuable anti-D immunoglobulin, which has a shortage worldwide. The main challenges for a reliable noninvasive fetal RHD genotyping assay are low cell-free DNA levels, the genetics of the Rh blood group system, and choosing an appropriate detection strategy for an admixed population. In many parts of the world, however, the main challenge is to improve the basic care for D- pregnant women.
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Affiliation(s)
- Frederik B Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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2
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Wang J, Wang W, Zhou W, Zhou Y, Zhou L, Wang X, Yu B, Zhang B. Preliminary study of noninvasive prenatal screening for 22q11.2 deletion/duplication syndrome using multiplex dPCR assay. Orphanet J Rare Dis 2023; 18:278. [PMID: 37684689 PMCID: PMC10486099 DOI: 10.1186/s13023-023-02903-2] [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: 03/23/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVE This study aimed to establish a cell-free fetal DNA (cffDNA) assay using multiplex digital PCR (dPCR) for identifying fetuses at increased risk of 22q11.2 deletion/duplication syndrome. METHODS Six detection sites and their corresponding probes were designed for the 22q11.2 recurrent region. A dPCR assay for the noninvasive screening of 22q11.2 deletion/duplication syndrome was established. A total of 130 plasma samples from pregnant women (including 15 samples with fetal 22q11.2 deletion/duplication syndrome) were blindly tested for evaluating the sensitivity and specificity of the established assay. RESULTS DNA with different sizes of 22q11.2 deletion/duplication was detected via dPCR, indicating that the designed probes and detection sites were reasonable and effective. In the retrospective clinical samples, 11 out of 15 samples of pregnant women with 22q11.2 deletion/duplication were detected during the cffDNA assay, and accurate regional localization was achieved. Among the 115 normal samples, 111 were confirmed to be normal. Receiver operating characteristic curves were used for assessing the cut-off values and AUC for these samples. The sensitivity, specificity, and positive as well as negative predictive values were 73.3%, 96.5%, 73.3%, and 96.5%, respectively. CONCLUSION The cffDNA assay based on dPCR technology for the noninvasive detection of 22q11.2 recurrent copy number variants in fetuses detected most affected cases, including smaller but relatively common nested deletions, with a low false-positive rate. It is a potential, efficient and simple method for the noninvasive screening of 22q11.2 deletion/duplication syndrome.
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Affiliation(s)
- Jing Wang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Wei Wang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Wenbo Zhou
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Yan Zhou
- Xingzhi Biotechnology Co., LTD, Suzhou, 215000, Jiangsu Province, China
| | - Linna Zhou
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Xinyue Wang
- Xingzhi Biotechnology Co., LTD, Suzhou, 215000, Jiangsu Province, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China.
| | - Bin Zhang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China.
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3
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Li X, Lin YL, Shao JK, Wu XJ, Li X, Yao H, Shi FL, Li LS, Zhang WG, Chang ZY, Chai NL, Wang YL, Linghu EQ. Plasma exosomal hsa_circ_0079439 as a novel biomarker for early detection of gastric cancer. World J Gastroenterol 2023; 29:3482-3496. [PMID: 37389236 PMCID: PMC10303519 DOI: 10.3748/wjg.v29.i22.3482] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Due to the poor prognosis of gastric cancer (GC), early detection methods are urgently needed. Plasma exosomal circular RNAs (circRNAs) have been suggested as novel biomarkers for GC.
AIM To identify a novel biomarker for early detection of GC.
METHODS Healthy donors (HDs) and GC patients diagnosed by pathology were recruited. Nine GC patients and three HDs were selected for exosomal whole-transcriptome RNA sequencing. The expression profiles of circRNAs were analyzed by bioinformatics methods and validated by droplet digital polymerase chain reaction. The expression levels and area under receiver operating characteristic curve values of plasma exosomal circRNAs and standard serum biomarkers were used to compare their diagnostic efficiency.
RESULTS There were 303 participants, including 240 GC patients and 63 HDs, involved in the study. The expression levels of exosomal hsa_circ_0079439 were significantly higher in GC patients than in HDs (P < 0.0001). However, the levels of standard serum biomarkers were similar between the two groups. The area under the curve value of exosomal hsa_circ_0079439 was higher than those of standard biomarkers, including carcinoembryonic antigen, carbohydrate antigen (CA)19-9, CA72-4, alpha-fetoprotein, and CA125 (0.8595 vs 0.5862, 0.5660, 0.5360, 0.5082, and 0.5018, respectively). The expression levels of exosomal hsa_circ_0079439 were significantly decreased after treatment (P < 0.05). Moreover, the expression levels of exosomal hsa_circ_0079439 were obviously higher in early GC (EGC) patients than in HDs (P < 0.0001).
CONCLUSION Our results suggest that plasma exosomal hsa_circ_0079439 is upregulated in GC patients. Moreover, the levels of exosomal hsa_circ_0079439 could distinguish EGC and advanced GC patients from HDs. Therefore, plasma exosomal hsa_circ_0079439 might be a potential biomarker for the diagnosis of GC during both the early and late stages.
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Affiliation(s)
- Xiao Li
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
- Medical School of Chinese PLA, Beijing 100853, China
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Yan-Li Lin
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Jia-Kang Shao
- Medical School of Chinese PLA, Beijing 100853, China
| | - Xiao-Jie Wu
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiang Li
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - He Yao
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Fa-Liang Shi
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Long-Song Li
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
- Medical School of Chinese PLA, Beijing 100853, China
| | - Wen-Gang Zhang
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
- Medical School of Chinese PLA, Beijing 100853, China
| | | | - Ning-Li Chai
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - You-Liang Wang
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - En-Qiang Linghu
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
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Prior-de Castro C, Gómez-González C, Rodríguez-López R, Macher HC. Prenatal genetic diagnosis of monogenic diseases. ADVANCES IN LABORATORY MEDICINE 2023; 4:28-51. [PMID: 37359899 PMCID: PMC10197187 DOI: 10.1515/almed-2023-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 06/28/2023]
Abstract
Prenatal genetic diagnosis of monogenic diseases is a process involving the use of a variety of molecular techniques for the molecular characterization of a potential monogenic disease in the fetus during pregnancy. Prenatal genetic diagnosis can be performed through invasive and non-invasive methods. A distinction must be made between "NIPD" (non-invasive prenatal diagnosis), which is considered to be diagnostic, from "NIPT" (non-invasive prenatal test), which is a screening test that requires subsequent confirmation by invasive methods. The different techniques currently available aim at detecting either, previously characterized pathogenic mutations in the family, the risk haplotype associated with the familial mutation, or potential pathogenic mutation(s) in a gene associated with a diagnostic suspicion. An overview is provided of relevant aspects of prenatal genetic diagnosis of monogenic diseases. The objective of this paper is to describe the main molecular techniques currently available and used in clinical practice. A description is provided of the indications, limitations and analytical recommendations regarding these techniques, and the standards governing genetic counseling. Continuous rapid advances in the clinical applications of genomics have provided increased access to comprehensive molecular characterization. Laboratories are struggling to keep in pace with technology developments.
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Affiliation(s)
| | | | - Raquel Rodríguez-López
- Laboratorio de Genética, Servicio Análisis Clínicos, Consorcio Hospital General Universitario, Valencia, Spain
| | - Hada C. Macher
- Departamento de Bioquímica Clínica, Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain
- Instituto de Investigaciones Biomédicas de Sevilla, IBIS, Universidad de Sevilla, Sevilla, Spain
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Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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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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7
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Shekhawat DS, Sharma C, Singh K, Singh P, Bhardwaj A, Patwa P. Critical appraisal of droplet digital polymerase chain reaction application for noninvasive prenatal testing. Congenit Anom (Kyoto) 2022; 62:188-197. [PMID: 35662261 DOI: 10.1111/cga.12481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022]
Abstract
Maternal-fetal medicine (FM) is currently a highly demanding branch and is gaining importance as increasing number of genetic disorders rise in incidence. Prenatal testing helps to detect such abnormalities that could affect the health status of the developing fetus like birth defects or genetic disorders. Considering the rising trend of genetic disorders, there is a need for a highly sensitive way of noninvasive prenatal testing (NIPT) that may reduce the incidence of unnecessary invasive procedures and iatrogenic fetal loss. The concept of NIPT for screening of genetic disorders is continuously evolving over the last two decades and multiple techniques have come up to utilize this in the field of FM. The crucial factor which decides the accuracy of NIPS is cell free fetal DNA (cffDNA) that is present in extremely low fraction (10%-15%) in the maternal plasma. Among the available methods, the next generation sequencing (NGS) is considered as the gold standard. However, the higher cost diminishes its utility in low-resource settings. Droplet digital Polymerase chain reaction (ddPCR), a type of digital PCR is a novel technique that is frugal, equally sensitive, less labor intensive, less time-consuming and plain algorithm dependent method for detecting cffDNA fraction. Considering these impressive attributes of ddPCR, we decided to critically review the existing literature on ddPCR for NIPT whilst highlighting the clinical utility, challenges and its advantages over NGS.
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Affiliation(s)
| | - Charu Sharma
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | | | - Pratibha Singh
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | - Abhishek Bhardwaj
- Department of Dermatology, Venereology and Leprology, AIIMS, Jodhpur, India
| | - Payal Patwa
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
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8
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Tounsi WA, Lenis VP, Tammi SM, Sainio S, Haimila K, Avent ND, Madgett TE. Rh Blood Group D Antigen Genotyping Using a Portable Nanopore-based Sequencing Device: Proof of Principle. Clin Chem 2022; 68:1196-1201. [PMID: 35652461 DOI: 10.1093/clinchem/hvac075] [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: 02/03/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Nanopore sequencing is direct sequencing of a single-stranded DNA molecule using biological pores. A portable nanopore-based sequencing device from Oxford Nanopore Technologies (MinION) depends on driving a DNA molecule through nanopores embedded in a membrane using a voltage. Changes in current are then measured by a sensor, thousands of times per second and translated to nucleobases. METHODS Genomic DNA (gDNA) samples (n = 13) were tested for Rh blood group D antigen (RHD) gene zygosity using droplet digital PCR. The RHD gene was amplified in 6 overlapping amplicons using long-range PCR. Amplicons were purified, and the sequencing library was prepared following the 1D Native barcoding gDNA protocol. Sequencing was carried out with 1D flow cells R9 version. Data analysis included basecalling, aligning to the RHD reference sequence, and calling variants. Variants detected were compared to the results acquired previously by the Ion Personal Genome Machine (Ion PGM). RESULTS Up to 500× sequence coverage across the RHD gene allowed accurate variant calling. Exonic changes in the RHD gene allowed RHD allele determination for all samples sequenced except 1 RHD homozygous sample, where 2 heterozygous RHD variant alleles are suspected. There were 3 known variant RHD alleles (RHD*01W.02, RHD*11, and RHD*15) and 6 novel RHD variant alleles, as previously seen in Ion PGM sequencing data for these samples. CONCLUSIONS MinION was effective in blood group genotyping, provided enough sequencing data to achieve high coverage of the RHD gene, and enabled confident calling of variants and RHD allele determination.
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Affiliation(s)
- Wajnat A Tounsi
- Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Vasileios P Lenis
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
- School of Health and Life Sciences, Teesside University, Middlesbrough, Tees Valley, UK
| | - Silja M Tammi
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Susanna Sainio
- Blood Group Unit, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Katri Haimila
- Blood Group Unit, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Neil D Avent
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Tracey E Madgett
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
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Li YQ, Tan GJ, Zhou YQ. Digital PCR and its applications in noninvasive prenatal testing. Brief Funct Genomics 2022; 21:376-386. [PMID: 35923115 DOI: 10.1093/bfgp/elac024] [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: 02/14/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
In the past decade, digital PCR (dPCR), as a new nucleic acid absolute quantification technology, has been widely used in clinical research. dPCR does not rely on the standard curve and has a higher tolerance to inhibitors. Therefore, it is more accurate than quantitative real-time PCR (qPCR) for the absolute quantification of target sequences. In this article, we aim to review the application of dPCR in noninvasive prenatal testing (NIPT). We focused on the progress of dPCR in screening and identifying fetal chromosome aneuploidies and monogenic mutations. We introduced some common strategies for dPCR in NIPT and analyzed the advantages and disadvantages of different methods. In addition, we compared dPCR with qPCR and next-generation sequencing, respectively, and described their superiority and shortcomings in clinical applications. Finally, we envisaged what the future of dPCR might be in NIPT. Although dPCR can provide reproducible results with improved accuracy due to the digital detection system, it is essential to combine the merits of dPCR and other molecular techniques to achieve more effective and accurate prenatal diagnostic strategies.
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Affiliation(s)
- Yue-Qi Li
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Gong-Jun Tan
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Yu-Qiu Zhou
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
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Zhang H, Laššáková S, Yan Z, Wang X, Šenkyřík P, Gaňová M, Chang H, Korabecna M, Neuzil P. Digital polymerase chain reaction duplexing method in a single fluorescence channel. Anal Chim Acta 2022; 1238:340243. [DOI: 10.1016/j.aca.2022.340243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022]
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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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12
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Orzińska A, Krzemienowska M, Purchla-Szepioła S, Kopeć I, Guz K. Noninvasive diagnostics of fetal KEL*01.01 allele from maternal plasma of immunized women using digital PCR protocols. Transfusion 2022; 62:863-870. [PMID: 35191535 DOI: 10.1111/trf.16829] [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: 03/03/2021] [Revised: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022]
Abstract
Allo-antibodies produced by K-negative pregnant women against a fetal K antigen from the Kell blood group system may cause hemolytic disease of the fetus and newborn (HDFN). Predicting the fetal K antigen using noninvasive prenatal testing (NIPT) is important for decisions concerning management of pregnancies. Digital and droplet digital PCR techniques permit the detection of fetal single nucleotide variant with a higher specificity and sensitivity than real-time polymerase chain reaction (PCR). AIM The aim was to evaluate and compare protocols for fetal KEL*01.01 genotyping using different assays and digital PCR platforms. METHODS DNA isolated from 59 pregnant women (9-39 weeks of gestation, 49 with anti-K) was tested using home-made and custom-ordered KEL*01.01/KEL*02 assays with Droplet Digital™ and QuantStudio™3D. The results were compared with fetal/neonatal genotypes/phenotypes. RESULTS Fetal KEL*01.01 results using all tested protocols were concordant with fetal/neonatal KEL*01.01 genotypes/phenotypes. None of the tested combinations of assays or digital PCR platforms gave false KEL*01.01-negative results, but inconclusive KEL*01.01 reads were observed in all tested protocols. For 36 cases compared using two digital PCR platforms and assays, there were not statistically significant differences in a level of fetal KEL*01.01 fraction (p < .72). CONCLUSION Independent of the applied dPCR and ddPCR platforms and KEL*01.01 assays, prediction of the fetal KEL*01.01 is highly reliable. Before implementation in routine practice further validation of the KEL*01.01 protocol with a larger group of pregnant women should be performed.
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Affiliation(s)
- Agnieszka Orzińska
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Magdalena Krzemienowska
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Sylwia Purchla-Szepioła
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Izabella Kopeć
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Katarzyna Guz
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
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Deng C, Liu S. Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review. Front Pediatr 2022; 10:812781. [PMID: 35155308 PMCID: PMC8829468 DOI: 10.3389/fped.2022.812781] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.
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Affiliation(s)
- Cechuan Deng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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14
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Alhur NF, Al Qahtani NH, AlSuhaibani ES, Alsulmi E, Almandil NB, AbdulAzeez S, Borgio JF. Fetal Nucleated Red Blood Cells Preferable Than Cell-Free Fetal DNA for Early Determination of Gender Among Invasive and Non-Invasive Source Using Novel Four Genes Multiplex PCR. Int J Gen Med 2021; 14:9697-9705. [PMID: 34938099 PMCID: PMC8687708 DOI: 10.2147/ijgm.s345345] [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: 10/20/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
Background Deoxyribonucleic acid from invasive, non-invasive and 9th week embryo can be a resource for the determination of fetal sex using highly sensitive and specific multiplex PCR. Methods A total of 402 DNA samples were used to test the newly developed novel multiplex PCR including male specific (3 genes: SRY, DAZ2 and TSPY1) Y-biomarkers and internal control, ACTB. The study isolated cffDNA (Cell-free fetal DNA; n = 73) from mother’s plasma, serum and urine, fetal DNA from 9th week embryo and cord blood, and fetal DNA from CD71+ve nucleated red blood cells (fNRBC; n = 73). Paternal and maternal DNA from buccal cells (n = 20) and blood (n = 232) used for male and female confirmation. Results The study observed that SRY alone cannot be a suitable Y-biomarker. Confirmation from any two Y-biomarkers is mandatory for male fetus identification. Direct sequencing of the gel eluted multiplex and single amplicons confirmed the specific sequences. Presence of two out of 3 Y-biomarkers OR single Y-biomarker with >1,000,000 intensity is considered positive for male. The multiplex PCR is suitable for determining sex from all source of fetal DNA including highly degraded cffDNA and can detect the sex using 0.5ng DNA. Individual marker-based real-time qPCR followed by combined melt curve analysis showed distinguished melt curve peaks for the markers. Conclusion The multiplex PCR achieved 100% accuracy on fetal DNA from fNRBC for early determinations (<13 weeks) of gender. The developed novel and simple multiplex PCR and individual qPCR can be adopted in all types of laboratories for determining human fetal gender using fetal DNA from fNRBC. Early identification of gender can support to prepare for possible X-linked analysis, reduce anxiety in mother, strengthen a bond between mother and fetus, and effective decision making. Non-invasive source of fetal DNA from fNRBC preferred for identifying gender to reduce the risk of invasive procedures in early (8–13 weeks) pregnancy.
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Affiliation(s)
- Norah F Alhur
- College of Science, Zoology Department, King Saud University, Riyadh, Saudi Arabia
| | - Nourah H Al Qahtani
- Obstetrics and Gynecology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Eman Alsulmi
- Obstetrics and Gynecology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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15
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Gaňová M, Zhang H, Zhu H, Korabečná M, Neužil P. Multiplexed digital polymerase chain reaction as a powerful diagnostic tool. Biosens Bioelectron 2021; 181:113155. [PMID: 33740540 DOI: 10.1016/j.bios.2021.113155] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/13/2021] [Accepted: 03/06/2021] [Indexed: 01/30/2023]
Abstract
The digital polymerase chain reaction (dPCR) multiplexing method can simultaneously detect and quantify closely related deoxyribonucleic acid sequences in complex mixtures. The dPCR concept is continuously improved by the development of microfluidics and micro- and nanofabrication, and different complex techniques are introduced. In this review, we introduce dPCR techniques based on sample compartmentalization, droplet- and chip-based systems, and their combinations. We then discuss dPCR multiplexing methods in both laboratory research settings and advanced or routine clinical applications. We focus on their strengths and weaknesses with regard to the character of biological samples and to the required precision of such analysis, as well as showing recently published work based on those methods. Finally, we envisage possible future achievements in this field.
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Affiliation(s)
- Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Haoqing Zhang
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Hanliang Zhu
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Marie Korabečná
- 1st Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University and General University Hospital, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China; The Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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16
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Next-generation sequencing of 35 RHD variants in 16 253 serologically D- pregnant women in the Finnish population. Blood Adv 2021; 4:4994-5001. [PMID: 33057632 DOI: 10.1182/bloodadvances.2020001569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Fetal RHD screening for targeted routine antenatal anti-D prophylaxis has been implemented in many countries, including Finland, since the 2010s. Comprehensive knowledge of the RHD polymorphism in the population is essential for the performance and safety of the anti-D prophylaxis program. During the first 3 years of the national screening program in Finland, over 16 000 samples from RhD- women were screened for fetal RHD; among them, 79 samples (0.5%) containing a maternal variant allele were detected. Of the detected maternal variants, 35 cases remained inconclusive using the traditional genotyping methods and required further analysis by next-generation sequencing (NGS) of the whole RHD gene to uncover the variant allele. In addition to the 13 RHD variants that have been previously reported in different populations, 8 novel variants were also detected, indicating that there is more variation of RHD in the RhD- Finnish population than has been previously known. Three of the novel alleles were identified in multiple samples; thus, they are likely specific to the original Finnish population. National screening has thus provided new information about the diversity of RHD variants in the Finnish population. The results show that NGS is a powerful method for genotyping the highly polymorphic RHD gene compared with traditional methods that rely on the detection of specific nucleotides by polymerase chain reaction amplification.
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17
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Vodicka R, Bohmova J, Holuskova I, Krejcirikova E, Prochazka M, Vrtel R. Risk Minimization of Hemolytic Disease of the Fetus and Newborn Using Droplet Digital PCR Method for Accurate Fetal Genotype Assessment of RHD, KEL, and RHCE from Cell-Free Fetal DNA of Maternal Plasma. Diagnostics (Basel) 2021; 11:diagnostics11050803. [PMID: 33925253 PMCID: PMC8146004 DOI: 10.3390/diagnostics11050803] [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: 04/13/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/19/2022] Open
Abstract
The molecular pathology of hemolytic disease of the fetus and newborn (HDFN) is determined by different RHD, RHCE, and KEL genotypes and by blood group incompatibility between the mother and fetus that is caused by erythrocyte antigen presence/absence on the cell surface. In the Czech Republic, clinically significant antierythrocyte alloantibodies include anti-D, anti-K, anti C/c, and anti-E. Deletion of the RHD gene and then three single nucleotide polymorphisms in the RHCE and KEL genes (rs676785, rs609320, and rs8176058) are the most common. The aim of this study is to develop effective and precise monitoring of fetal genotypes from maternal plasma of these polymorphisms using droplet digital (dd)PCR. Fifty-three plasma DNA samples (from 10 to 18 weeks of gestation) were analyzed (10 RHD, 33 RHCE, and 10 KEL). The ddPCR methodology was validated on the basis of the already elaborated and established method of minisequencing and real-time PCR and with newborn phenotype confirmation. The results of ddPCR were in 100% agreement with minisequencing and real-time PCR and also with newborn phenotype. ddPCR can fully replace the reliable but more time-consuming method of minisequencing and real-time PCR RHD examination. Accurate and rapid noninvasive fetal genotyping minimizes the possibility of HDFN developing.
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Affiliation(s)
- Radek Vodicka
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
| | - Jana Bohmova
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
- Correspondence: ; Tel.: +42-058-844-4636
| | - Iva Holuskova
- Department of Blood Transfusion, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic;
| | - Eva Krejcirikova
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
| | - Radek Vrtel
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
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18
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Hyland CA, O'Brien H, Flower RL, Gardener GJ. Non-invasive prenatal testing for management of haemolytic disease of the fetus and newborn induced by maternal alloimmunisation. Transfus Apher Sci 2020; 59:102947. [PMID: 33115620 DOI: 10.1016/j.transci.2020.102947] [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] [Indexed: 01/08/2023]
Abstract
Anti-D immunoglobulin prophylaxis reduces the risk of RhD negative women becoming alloimmunised to the RhD antigen and is a major preventative strategy in reducing the burden of haemolytic disease of the fetus and newborn (HDFN). HDFN also arises from other maternal red cell antibodies, with the most clinically significant, after anti-D, being anti-K, anti-c and anti-E. Among the 39 human blood group systems advanced genomic technologies are still revealing novel or rare antigens involved in maternal alloimmunisation. Where clinically significant maternal antibodies are detected in pregnancy, non-invasive prenatal testing (NIPT) of cell-free fetal DNA provides a safe way to assess the fetal blood group antigen status. This provides information as to the risk for HDFN and thus guides management strategies. In many countries, NIPT fetal RHD genotyping as a diagnostic test using real-time PCR has already been integrated into routine clinical care for the management of women with allo-anti-D to assess the risk for HDFN. In addition, screening programs have been established to provide antenatal assessment of the fetal RHD genotype in non-alloimmunised RhD negative pregnant women to target anti-D prophylaxis to those predicted to be carrying an RhD positive baby. Both diagnostic and screening assays exhibit high accuracy (over 99 %). NIPT fetal genotyping for atypical (other than RhD) blood group antigens presents more challenges as most arise from a single nucleotide variant. Recent studies show potential for genomic and digital technologies to provide a personalised medicine approach with NIPT to assess fetal blood group status for women with other (non-D) red cell antibodies to manage the risk for HDFN.
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Affiliation(s)
- Catherine A Hyland
- Clinical Services and Research, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.
| | - Helen O'Brien
- Clinical Services and Research, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Robert L Flower
- Clinical Services and Research, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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19
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Two Reliable Methodical Approaches for Non-Invasive RHD Genotyping of a Fetus from Maternal Plasma. Diagnostics (Basel) 2020; 10:diagnostics10080564. [PMID: 32764529 PMCID: PMC7460148 DOI: 10.3390/diagnostics10080564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Noninvasive fetal RHD genotyping is an important tool for predicting RhD incompatibility between a pregnant woman and a fetus. This study aimed to assess a methodological approach other than the commonly used one for noninvasive fetal RHD genotyping on a representative set of RhD-negative pregnant women. The methodology must be accurate, reliable, and broadly available for implementation into routine clinical practice. A total of 337 RhD-negative pregnant women from the Czech Republic region were tested in this study. The fetal RHD genotype was assessed using two methods: real-time PCR and endpoint quantitative fluorescent (QF) PCR. We used exon-7-specific primers from the RHD gene, along with internal controls. Plasma samples were analyzed and measured in four/two parallel reactions to determine the accuracy of the RHD genotyping. The RHD genotype was verified using DNA analysis from a newborn buccal swab. Both methods showed an excellent ability to predict the RHD genotype. Real-time PCR achieved its greatest accuracy of 98.6% (97.1% sensitivity and 100% specificity (95% CI)) if all four PCRs were positive/negative. The QF PCR method also achieved its greatest accuracy of 99.4% (100% sensitivity and 98.6% specificity (95% CI)) if all the measurements were positive/negative. Both real-time PCR and QF PCR were reliable methods for precisely assessing the fetal RHD allele from the plasma of RhD-negative pregnant women.
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20
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Clausen FB, Barrett AN, Advani HV, Choolani M, Dziegiel MH. Impact of long-term storage of plasma and cell-free DNA on measured DNA quantity and fetal fraction. Vox Sang 2020; 115:586-594. [PMID: 32342989 DOI: 10.1111/vox.12923] [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] [Received: 12/09/2019] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Optimal sample storage conditions are essential for non-invasive prenatal testing of cell-free fetal and total DNA. We investigated the effect of long-term storage of plasma samples and extracted cfDNA using qPCR. MATERIALS AND METHODS Fetal and total cfDNA yield and fetal fraction were calculated before and after storage of plasma for 0-6 years at -25°C. Dilution experiments were performed to investigate PCR inhibition. Extraction with or without proteinase K was used to examine protein dissociation. Storage of extracted cfDNA was investigated by testing aliquots immediately, and after 18 months and 3 years of storage at -25°C. RESULTS We observed a marked increase in the levels of amplifiable fetal and total DNA in plasma stored for 2-3 years, and fetal fraction was slightly decreased after 3 years of storage. cfDNA detection was independent of proteinase K during DNA extraction in plasma samples stored >2 years, indicating a loss of proteins from DNA over time, which was likely to account for the observed increase in DNA yields. Measured fetal and total DNA quantities, as well as fetal fraction, increased in stored, extracted cfDNA. CONCLUSION Fetal and total cell-free DNA is readily detectable in plasma after long-term storage at -25°C. However, substantial variation in measured DNA quantities and fetal fraction means caution may be required when using stored plasma and extracted cfDNA for test development or validation purposes.
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Affiliation(s)
- Frederik Banch Clausen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Morten Hanefeld Dziegiel
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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21
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Eryilmaz M, Müller D, Rink G, Klüter H, Bugert P. Introduction of Noninvasive Prenatal Testing for Blood Group and Platelet Antigens from Cell-Free Plasma DNA Using Digital PCR. Transfus Med Hemother 2019; 47:292-301. [PMID: 32884502 DOI: 10.1159/000504348] [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] [Received: 08/08/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) for fetal antigens is a common standard for targeted immune prophylaxis in RhD-mediated hemolytic disease of the fetus and newborn, and is most frequently done by quantitative PCR (qPCR). A similar approach is considered for other blood group and human platelet alloantigens (HPA). Because of a higher sensitivity compared to qPCR for rare molecule detection, we established and validated digital PCR (dPCR) assays for the detection of RHD exons 3, 5 and 7, KEL1, HPA-1a, and HPA-5b from cell-free DNA (cfDNA) in plasma. The dPCR assays for the Y-chromosomal marker amelogenin and autosomal SNPs were implemented as controls for the proof of fetal DNA. Methods Validation was performed on dilution series of mixed plasma samples from volunteer donors with known genotypes. After preamplification of the target loci, two-color (FAM and VIC) TaqMan<sup>TM</sup> probe chemistry and chip-based dPCR were applied. The assays for RHD included GAPDH as an internal control. For the diallelic markers KEL1/2, HPA-1a/b, HPA-5a/b, and AMEL-X/Y and 3 autosomal SNPs, the probes enabled allelic discrimination in the two fluorescence channels. The dPCR protocol for NIPT was applied to plasma samples from pregnant women. Results The RHD exon 5 assay allowed the detection of a 0.05% RHD target in an RhD-negative background, whereas the exon 7 assay required at least a 0.25% target. The exon 3 assay showed the highest background and required at least a 2.5% RHD target for reliable detection. The dPCR assays for the diallelic markers revealed similar sensitivity and enabled the detection of at least a 0.5% target allele. The HPA-1a assay was the most sensitive and allowed target detection in plasma mixtures containing only 0.05% HPA-1a. The plasma samples from 13 pregnant women at different gestational ages showed unambiguous positive and negative results for the analyzed targets. Conclusion Analysis of cfDNA from maternal plasma using dPCR is suitable for the detection of fetal alleles. Because of the high sensitivity of the assays, the NIPT protocol for RhD, KEL1, and HPA can also be applied to earlier stages of pregnancy.
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Affiliation(s)
- Marion Eryilmaz
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Dennis Müller
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Gabi Rink
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Harald Klüter
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
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22
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Jacobsen D, Krog GR, Clausen FB. Early and Accurate Sex Determination by qPCR of Y Chromosome Repetitive Sequence (YRS) In Cell-Free Fetal DNA from Maternal Plasma. J Appl Lab Med 2019; 3:346-356. [PMID: 33636925 DOI: 10.1373/jalm.2018.026799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/17/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Circulating cell-free fetal DNA (cffDNA) provides the opportunity for noninvasive prenatal diagnosis. Early knowledge of the fetal sex is essential in cases with a risk of a sex-linked genetic disease. A reliable and highly sensitive sex determination test is required for first trimester testing because of the low amounts of cffDNA. METHODS First trimester blood samples from 326 pregnant women were analyzed by real-time quantitative polymerase chain reaction (qPCR) for the presence of Y chromosome repetitive sequence (YRS). Blood samples were collected from gestational weeks 4-12. Fetal sex was predicted on the basis of results from the YRS assay of cffDNA extracted from maternal plasma. The predicted sex was compared with the phenotypic sex of the newborn baby (n = 294). RESULTS There was high concordance between the test results from the YRS assay and the actual sex at birth. There were no false-positive results, indicating agreement between male YRS results and male sex at birth. Two results were false negative (from gestational weeks 4 and 6) predicting female fetuses, when the actual sex at birth was male. Overall, the sensitivity of the YRS assay was 98.6% (95% CI, 95.1%-99.8%), specificity was 100% (95% CI, 97.5%-100%), and accuracy was 99.3% (95% CI, 97.5%-99.9%). From 7 weeks of gestation, sensitivity, specificity, and accuracy were 100%. CONCLUSIONS This study shows that qPCR can be used to detect and quantify repetitive DNA sequences from 0.3 genome equivalents per milliliter of plasma. Prenatal sex determination by qPCR of YRS in cffDNA from maternal plasma was reliable and robust with cffDNA extracted from 1 mL of nonhemolyzed plasma, with a plasma equivalent per PCR of 167 μL. The YRS assay can be used for early noninvasive prenatal sex determination from a gestational age of 7 weeks.
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Affiliation(s)
- Ditte Jacobsen
- Faculty of Health and Technology, University College Copenhagen, Denmark
| | - Grethe Risum Krog
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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23
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Clausen FB. Cell‐free fetal
DNA
and fetal blood group genotyping: non‐invasive prenatal testing. ACTA ACUST UNITED AC 2019. [DOI: 10.1111/voxs.12521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics Department of Clinical Immunology Copenhagen University Hospital Copenhagen Denmark
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24
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Complete RHD next-generation sequencing: establishment of reference RHD alleles. Blood Adv 2019; 2:2713-2723. [PMID: 30337299 DOI: 10.1182/bloodadvances.2018017871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022] Open
Abstract
The Rh blood group system (ISBT004) is the second most important blood group after ABO and is the most polymorphic one, with 55 antigens encoded by 2 genes, RHD and RHCE This research uses next-generation sequencing (NGS) to sequence the complete RHD gene by amplifying the whole gene using overlapping long-range polymerase chain reaction (LR-PCR) amplicons. The aim was to study different RHD alleles present in the population to establish reference RHD allele sequences by using the analysis of intronic single-nucleotide polymorphisms (SNPs) and their correlation to a specific Rh haplotype. Genomic DNA samples (n = 69) from blood donors of different serologically predicted genotypes including R1R1 (DCe/DCe), R2R2 (DcE/DcE), R1R2 (DCe/DcE), R2RZ (DcE/DCE), R1r (DCe/dce), R2r (DcE/dce), and R0r (Dce/dce) were sequenced and data were then mapped to the human genome reference sequence hg38. We focused on the analysis of hemizygous samples, as these by definition will only have a single copy of RHD For the 69 samples sequenced, different exonic SNPs were detected that correlate with known variants. Multiple intronic SNPs were found in all samples: 21 intronic SNPs were present in all samples indicating their specificity to the RHD*DAU0 (RHD*10.00) haplotype which the hg38 reference sequence encodes. Twenty-three intronic SNPs were found to be R2 haplotype specific, and 15 were linked to R1, R0, and RZ haplotypes. In conclusion, intronic SNPs may represent a novel diagnostic approach to investigate known and novel variants of the RHD and RHCE genes, while being a useful approach to establish reference RHD allele sequences.
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25
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Shebanits K, Günther T, Johansson ACV, Maqbool K, Feuk L, Jakobsson M, Larhammar D. Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR. BMC Biotechnol 2019; 19:31. [PMID: 31164119 PMCID: PMC6549351 DOI: 10.1186/s12896-019-0523-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/30/2019] [Indexed: 01/08/2023] Open
Abstract
Background Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome. Results We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split. Conclusions We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation. Electronic supplementary material The online version of this article (10.1186/s12896-019-0523-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kateryna Shebanits
- Department of Neuroscience, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Anna C V Johansson
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Khurram Maqbool
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Johannesburg, South Africa
| | - Dan Larhammar
- Department of Neuroscience, SciLifeLab, Uppsala University, Uppsala, Sweden.
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Belandres D, Shamonki M, Arrach N. Current status of spent embryo media research for preimplantation genetic testing. J Assist Reprod Genet 2019; 36:819-826. [PMID: 30895497 DOI: 10.1007/s10815-019-01437-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years, a growing body of literature has emerged investigating the clinical utility of spent embryo media (SEM) for preimplantation genetic testing for aneuploidy (PGT-A) (Hammond et al. in Fertil Steril. 107(1):220-8, 2017; Xu et al. in Proc Natl Acad Sci USA. 113(42):11907-12, 2016; Shamonki et al. in Fertil Steril. 106(6):1312-8, 2016; Feichtinger et al. in Reprod BioMed Online. 34(6):583-9, 2017; Vera-Rodriguez et al. in Hum Reprod. 33(4):745-56, 2018; Kuznyetsov et al. in PLoS One. 13(5):e0197262, 2018; Ho et al. in Fertil Steril. 110(3):467-75, 2018; Capalbo et al. in Fertil Steril. 110(5):870-9, 2018). Most of these studies have reported moderate success rates, suggesting the need for improvements in sensitivity and specificity. The concordance between spent media and embryo biopsy or whole embryo was reported to be between 30.4 and 90%, with 50-70% correlation being the most representative (Xu et al. in Proc Natl Acad Sci USA. 113(42):11907-12, 2016; Shamonki et al. in Fertil Steril. 106(6):1312-8, 2016; Feichtinger et al. in Reprod BioMed Online. 34(6):583-9, 2017; Vera-Rodriguez et al. in Hum Reprod. 33(4):745-56, 2018; Kuznyetsov et al. in PLoS One. 13(5):e0197262, 2018; Ho et al. in Fertil Steril. 110(3):467-75, 2018). Here, we will analyze all spent media testing strategies including SEM collection methods, whole genome amplification (WGA) strategies, chromosome copy number detection, and bioinformatics analysis tools. We will propose improvements to further increase the accuracy and sensitivity of the assay before bringing PGT-A with SEM into the clinical sphere.
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Affiliation(s)
- Denice Belandres
- Progenesis Inc., 4150 Regents Park Row, Suite 245, La Jolla, CA, 92037, USA
| | - Mousa Shamonki
- Fertility and Surgical Associates of California, 325 Rolling Oaks Drive, Suite 110, Thousand Oaks, CA, 91361, USA.,University of California, Los Angeles, CA, 90095, USA
| | - Nabil Arrach
- Progenesis Inc., 4150 Regents Park Row, Suite 245, La Jolla, CA, 92037, USA.
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Milosevic D, Mills JR, Campion MB, Vidal-Folch N, Voss JS, Halling KC, Highsmith WE, Liu MC, Kipp BR, Grebe SKG. Applying Standard Clinical Chemistry Assay Validation to Droplet Digital PCR Quantitative Liquid Biopsy Testing. Clin Chem 2018; 64:1732-1742. [DOI: 10.1373/clinchem.2018.291278] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/23/2018] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Droplet digital PCR (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, assay performance criteria must be established in a standardized manner to harness this potential. We reasoned that standard protocols used in clinical chemistry assay validation should be able to fill this need.
METHODS
We validated KRAS, EGFR, and BRAF quantitative ddPCR assays based on the Clinical Laboratory Improvement Act regulations for laboratory-developed tests in clinical chemistry and the matching Clinical and Laboratory Standards Institute guidelines. This included evaluation of limit of the blank (LOB), limit of detection (LOD), limit of quantification (LOQ), intraassay and interassay imprecision, analytical range, dilution linearity, accuracy (including comparison with orthogonal platforms), reference range study, interference, and stability studies.
RESULTS
For the ddPCR assays, the LOB was 4 mutant copies, LODs were 12 to 22 copies, and LOQs were 35 to 64 copies. The upper limit of the dynamic range was 30000 copies, and dilutions were linear down to the LOQs with good accuracy of spike recovery of Horizon reference material. Method comparisons with next-generation sequencing and an alternative ddPCR platform showed complete qualitative agreement and quantitative concordance, with slopes of 0.73 to 0.97 and R2s of 0.83 to 0.99. No substantial interferences were discovered. Wild-type copy numbers in plasma ranged from 462 to 6169/mL in healthy individuals.
CONCLUSIONS
Standard clinical chemistry assay validation protocols can be applied to quantitative ddPCR assays. This should facilitate comparison of the performance of different assays and allow establishment of minimal significant change thresholds in monitoring applications.
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Affiliation(s)
- Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - Michael B Campion
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - W Edward Highsmith
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Minetta C Liu
- Department of Laboratory Meidicne and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
- Department of Oncology, Division of Medical Oncology Mayo Clinic, Rochester, MN
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Stefan K G Grebe
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
- Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester, MN
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Clausen FB. Lessons learned from the implementation of non-invasive fetalRHDscreening. Expert Rev Mol Diagn 2018; 18:423-431. [DOI: 10.1080/14737159.2018.1461562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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D'Aversa E, Breveglieri G, Pellegatti P, Guerra G, Gambari R, Borgatti M. Non-invasive fetal sex diagnosis in plasma of early weeks pregnants using droplet digital PCR. Mol Med 2018; 24:14. [PMID: 30134789 PMCID: PMC6016869 DOI: 10.1186/s10020-018-0016-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/15/2018] [Indexed: 12/11/2022] Open
Abstract
Background Fetal sex determination is useful for families at risk of X-linked disorders, such as Duchenne muscular dystrophy, adrenal hypoplasia, hemophilia. At first, this could be obtained through invasive procedures such as amniocentesis and chorionic villus sampling, having a 1% risk of miscarriage. Since the discovery of cell-free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing permits the early diagnosis of fetal sex through analysis of cffDNA. However, the low amount of cffDNA relative to circulating maternal DNA requires highly sensitive molecular techniques in order to perform noninvasive prenatal diagnosis. In this context we employed droplet digital PCR (ddPCR) in order to evaluate the earliest possible fetal sex determination from circulating DNA extracted from plasma of pregnant women at different gestational ages. Methods We identified the fetal sex on cffDNA extracted from 29 maternal plasma samples at early gestational ages, several of them not suitable for qPCR determination, using ddPCR designed for SRY gene target. Results All maternal plasma samples were determined correctly for SRY gene target using ddPCR even at very early gestational age (prior to 7 weeks). Conclusions The ddPCR is a robust, efficient and reliable technology for the earliest possible fetal sex determination from maternal plasma.
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Affiliation(s)
- Elisabetta D'Aversa
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Giulia Breveglieri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Patrizia Pellegatti
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, Via A. Moro, 8, 44100, Ferrara, Italy
| | - Giovanni Guerra
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, Via A. Moro, 8, 44100, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.,Biotechnology Center, University of Ferrara, Via Fossato di Mortara 64, 44121, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy. .,Biotechnology Center, University of Ferrara, Via Fossato di Mortara 64, 44121, Ferrara, Italy.
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Shebanits K, Andersson-Assarsson JC, Larsson I, Carlsson LMS, Feuk L, Larhammar D. Copy number of pancreatic polypeptide receptor gene NPY4R correlates with body mass index and waist circumference. PLoS One 2018; 13:e0194668. [PMID: 29621259 PMCID: PMC5886410 DOI: 10.1371/journal.pone.0194668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/07/2018] [Indexed: 01/14/2023] Open
Abstract
Multiple genetic studies have linked copy number variation (CNV) in different genes to body mass index (BMI) and obesity. A CNV on chromosome 10q11.22 has been associated with body weight. This CNV region spans NPY4R, the gene encoding the pancreatic polypeptide receptor Y4, which has been described as a satiety-stimulating receptor. We have investigated CNV of the NPY4R gene and analysed its relationship to BMI, waist circumference and self-reported dietary intake from 558 individuals (216 men and 342 women) representing a wide BMI range. The copy number for NPY4R ranged from 2 to 8 copies (average 4.6±0.8). Rather than the expected negative correlation, we observed a positive correlation between NPY4R copy number and BMI as well as waist circumference in women (Pearson’s r = 0.267, p = 2.65×10−7 and r = 0.256, p = 8×10−7, respectively). Each additional copy of NPY4R correlated with 2.6 kg/m2 increase in BMI and 5.67 cm increase in waist circumference (p = 2.8×10−5 and p = 6.2×10−5, respectively) for women. For men, there was no statistically significant correlation between CNV and BMI. Our results suggest that NPY4R genetic variation influences body weight in women, but the exact role of this receptor appears to be more complex than previously proposed.
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Affiliation(s)
| | | | - Ingrid Larsson
- Dept. of Gastroenterology and Hepatology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lena M. S. Carlsson
- Dept. of Molecular and Clinical Medicine, Sahlgrenska Academy at Gothenburg University, Gothenburg, Sweden
| | - Lars Feuk
- Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Dept. of Neuroscience, Uppsala University, Uppsala, Sweden
- * E-mail:
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Nectoux J. Current, Emerging, and Future Applications of Digital PCR in Non-Invasive Prenatal Diagnosis. Mol Diagn Ther 2017; 22:139-148. [DOI: 10.1007/s40291-017-0312-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Li T, Shao Y, Fu L, Xie Y, Zhu L, Sun W, Yu R, Xiao B, Guo J. Plasma circular RNA profiling of patients with gastric cancer and their droplet digital RT-PCR detection. J Mol Med (Berl) 2017; 96:85-96. [PMID: 29098316 DOI: 10.1007/s00109-017-1600-y] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/27/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
To observe the diagnostic values of circular RNAs (circRNAs), their expression profiles between gastric cancer patients' plasma and healthy controls were first assessed by circRNA microarray. Then, circRNA levels were measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR), respectively. A total of 343 differentially expressed circRNAs were found. The top 10 elevated circRNAs in patients were hsa_circ_0088300, hsa_circ_0075825, hsa_circ_0019172, hsa_circ_0000220, hsa_circ_0035277, hsa_circ_0000301, hsa_circ_0000189, hsa_circ_0090080, hsa_circ_0001888, and hsa_circ_0001874. The top 10 reduced circRNAs were hsa_circ_0004771, hsa_circ_0001190, hsa_circ_0061276, hsa_circ_0092337, hsa_circ_0058495, hsa_circ_0061274, hsa_circ_0075829, hsa_circ_0080845, hsa_circ_0001006, and hsa_circ_0003764. In cancer and dysplasia tissues, hsa_circ_0001017 and hsa_circ_0061276 were downregulated. Their levels were significantly associated with distal metastasis. The area under receiver operating characteristic curve in combinative use was 0.966 with 95.5% sensitivity and 95.7% specificity. Patients with low plasma hsa_circ_0001017 or hsa_circ_0061276 had a much shorter overall survival than those with high levels. Patients whose plasma hsa_circ_0001017 or hsa_circ_0061276 levels recovered to normal after operation had a longer disease-free survival. Finally, the in vitro model indicated gastric cancer cells secreting circRNAs into plasma. In conclusion, RT-ddPCR is a potent non-invasive and absolute quantification method for simultaneous detection of multiple circRNAs. Hsa_circ_0001017 and hsa_circ_0061276 are new potential biomarkers for gastric cancer. KEY MESSAGE A total of 343 circRNAs are differentially expressed between gastric cancer patients' plasma and healthy controls. Hsa_circ_0001017 and hsa_circ_0061276 are downregulated in gastric cancer tissues. The RT-ddPCR is a potent method for simultaneous detection of multiple circRNAs in plasma. Hsa_circ_0001017 and hsa_circ_0061276 are potential biomarkers for gastric cancer.
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Affiliation(s)
- Tianwen Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School, Ningbo University, Ningbo, 315211, China
| | - Yongfu Shao
- Department of Gastroenterology, the Affiliated Hospital of Medical School of, Ningbo University, Ningbo, 315020, China
| | - Liyun Fu
- Department of Hepatology, Ningbo No. 2 Hospital and the Affiliated Hospital, Medical School, Ningbo University, Ningbo, 315010, China
| | - Yi Xie
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School, Ningbo University, Ningbo, 315211, China
| | - Linwen Zhu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School, Ningbo University, Ningbo, 315211, China
| | - Weiliang Sun
- Ningbo Yinzhou People's Hospital and the Affiliated Hospital, Medical School, Ningbo University, Ningbo, 315040, China
| | - Rui Yu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School, Ningbo University, Ningbo, 315211, China
| | - Bingxiu Xiao
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School, Ningbo University, Ningbo, 315211, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School, Ningbo University, Ningbo, 315211, China.
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34
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Wong YK, Tsang HF, Xue VW, Chan CM, Au TC, Cho WC, Chan LW, Wong SC. Applications of digital PCR in precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2017.1347482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Y. K. Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - H. F. Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - V. W. Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - C. M. Chan
- Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - T. C. Au
- Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - W. C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China
| | - L. W. Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - S. C. Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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Sillence KA, Halawani AJ, Tounsi WA, Clarke KA, Kiernan M, Madgett TE, Avent ND. Rapid RHD Zygosity Determination Using Digital PCR. Clin Chem 2017; 63:1388-1397. [PMID: 28615230 DOI: 10.1373/clinchem.2016.268698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Paternal zygosity testing is used for determining homo- or hemizygosity of RHD in pregnancies that are at a risk of hemolytic disease of the fetus and newborn. At present, this is achieved by using real-time PCR or the Rhesus box PCR, which can be difficult to interpret and unreliable, particularly for black African populations. METHODS DNA samples extracted from 53 blood donors were analyzed using 2 multiplex reactions for RHD-specific targets against a reference (AGO1)2 to determine gene dosage by digital PCR. Results were compared with serological data, and the correct genotype for 2 discordant results was determined by long-range PCR (LR-PCR), next-generation sequencing, and conventional Sanger sequencing. RESULTS The results showed clear and reliable determination of RHD zygosity using digital PCR and revealed that 4 samples did not match the serologically predicted genotype. Sanger sequencing and long-range PCR followed by next-generation sequencing revealed that the correct genotypes for samples 729M and 351D, which were serologically typed as R1R2 (DCe/DcE), were R2r' (DcE/dCe) for 729M and R1r″ (DCe/dcE), R0ry (Dce/dCE), or RZr (DCE/dce) for 351D, in concordance with the digital PCR data. CONCLUSIONS Digital PCR provides a highly accurate method to rapidly define blood group zygosity and has clinical application in the analysis of Rh phenotyped or genotyped samples. The vast majority of current blood group genotyping platforms are not designed to define zygosity, and thus, this technique may be used to define paternal RH zygosity in pregnancies that are at a risk of hemolytic disease of the fetus and newborn and can distinguish between homo- and hemizygous RHD-positive individuals.
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Affiliation(s)
- Kelly A Sillence
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Amr J Halawani
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Wajnat A Tounsi
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Kirsty A Clarke
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Michele Kiernan
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Tracey E Madgett
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK.
| | - Neil D Avent
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
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Yu Q, Huang F, Zhang M, Ji H, Wu S, Zhao Y, Zhang C, Wu J, Wang B, Pan B, Zhang X, Guo W. Multiplex picoliter-droplet digital PCR for quantitative assessment of EGFR mutations in circulating cell-free DNA derived from advanced non-small cell lung cancer patients. Mol Med Rep 2017; 16:1157-1166. [PMID: 29067441 PMCID: PMC5562084 DOI: 10.3892/mmr.2017.6712] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/13/2017] [Indexed: 12/30/2022] Open
Abstract
To explore the possible diagnostic value of liquid biopsy, two multiplex panels using picoliter-droplet digital polymerase chain reaction (ddPCR) were established to quantitatively assess the epidermal growth factor receptor (EGFR) mutations in cell‑free DNA (cfDNA) extracted from the plasma of advanced non‑small cell lung cancer (NSCLC) patients. Plasma samples derived from 22 patients with stage IIIB/IV NSCLC harboring EGFR mutations in matched tumor tissues confirmed by amplification refractory mutation system (ARMS) analysis were subjected to two multiplex ddPCR panels to assess the abundance of tyrosine kinase inhibitor (TKI) ‑sensitive (19DEL, L858R) and TKI‑resistant (T790 M) mutations. Fluctuations in EGFR mutant abundance were monitored by either of the multiplex ddPCR panels for three patients undergoing EGFR‑TKI treatment, with serial plasma sample collections over 2 months. The multiplex ddPCR panels applied to plasma cfDNA from advanced NSCLC patients achieved a total concordance rate of 80% with the EGFR mutation profiles obtained by ARMS from matched biopsy tumor specimens (90% for 19DEL, 95% for L858R, 95% for T790M, respectively) and revealed additional mutant alleles in two subjects. The respective sensitivity and specificity were 90.9 and 88.9% for 19DEL, 87.5 and 100% for L858R, 100 and 93.8% for T790M. The fluctuations of EGFR mutant abundance in serial plasma cfDNA were in accordance with the changes in tumor size as assessed by imaging scans. The authors demonstrated the utility of multiplex ddPCR panels with ultra‑sensitivity for quantitative analysis of EGFR mutations in plasma cfDNA and obtained promising usefulness in EGFR‑TKI decision‑making for advanced NSCLC patients.
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Affiliation(s)
- Qian Yu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Meilin Zhang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Haiying Ji
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Shenchao Wu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ying Zhao
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jiong Wu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Baisheng Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Xin Zhang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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Four human Plasmodium species quantification using droplet digital PCR. PLoS One 2017; 12:e0175771. [PMID: 28423028 PMCID: PMC5396971 DOI: 10.1371/journal.pone.0175771] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/30/2017] [Indexed: 02/06/2023] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a partial PCR based on water-oil emulsion droplet technology. It is a highly sensitive method for detecting and delineating minor alleles from complex backgrounds and provides absolute quantification of DNA targets. The ddPCR technology has been applied for detection of many pathogens. Here the sensitive assay utilizing ddPCR for detection and quantification of Plasmodium species was investigated. The assay was developed for two levels of detection, genus specific for all Plasmodium species and for specific Plasmodium species detection. The ddPCR assay was developed based on primers and probes specific to the Plasmodium genus 18S rRNA gene. Using ddPCR for ultra-sensitive P. falciparum assessment, the lower level of detection from concentrated DNA obtained from a high volume (1 mL) blood sample was 11 parasites/mL. For species identification, in particular for samples with mixed infections, a duplex reaction was developed for detection and quantification P. falciparum/ P. vivax and P. malariae/ P. ovale. Amplification of each Plasmodium species in the duplex reaction showed equal sensitivity to singleplex single species detection. The duplex ddPCR assay had higher sensitivity to identify minor species in 32 subpatent parasitaemia samples from Cambodia, and performed better than real-time PCR. The ddPCR assay shows high sensitivity to assess very low parasitaemia of all human Plasmodium species. This provides a useful research tool for studying the role of the asymptomatic parasite reservoir for transmission in regions aiming for malaria elimination.
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Measuring circulating placental RNAs to non-invasively assess the placental transcriptome and to predict pregnancy complications. Prenat Diagn 2016; 36:997-1008. [DOI: 10.1002/pd.4934] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/08/2016] [Accepted: 09/30/2016] [Indexed: 11/07/2022]
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Butchbach MER. Applicability of digital PCR to the investigation of pediatric-onset genetic disorders. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:9-14. [PMID: 27990344 PMCID: PMC5154671 DOI: 10.1016/j.bdq.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be used to identify genes associated with pediatric-onset disorders, to identify copy number status of important disease-causing genes and variants and to quantify modifier genes. It is also a powerful technology to track changes in genomic biomarkers with disease progression. Based on its capability to accurately and reliably detect genomic alterations with high sensitivity and a large dynamic detection range, dPCR has the potential to become the tool of choice for the verification of pediatric disease-associated mutations identified by next generation sequencing, copy number determination and noninvasive prenatal screening.
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Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
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