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Eid OM, Eid MM, Farid M, Abdel Kader RMA, Mahrous R, El-Dessouky SH. MLPA as a genetic assay for the prenatal diagnosis of common aneuploidy: the first Egyptian experience. J Genet Eng Biotechnol 2022; 20:112. [PMID: 35900681 PMCID: PMC9334468 DOI: 10.1186/s43141-022-00402-8] [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: 02/13/2022] [Accepted: 07/14/2022] [Indexed: 11/24/2022]
Abstract
Background The prenatal diagnosis of syndromes caused by chromosomal abnormality is a long-established part of obstetric care. Several DNA-based molecular approaches have provided rapid prenatal diagnosis of of cytogenomic abnormalities. MLPA has become available for rapid aneuploidy detection of the most common chromosome abnormalities. Objectives The aim of this study is to introduce the MLPA technique as a method for the prenatal detection of aneuploidy in Egypt by its validation compared to the FISH technique. Methods Fifty AF samples were collected for this study and were subjected to MLPA and FISH assays to detect the most common prenatal chromosomal abnormality. Results and conclusions Our study confirmed previous reports that MLPA is analogous to FISH for detecting common aneuploidies and could be a quick and dependable tool for prenatal diagnosis. Therefore, initial prompt testing of AF samples for the copy number of the most common occurring aneuploidies is recommended.
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Affiliation(s)
- Ola M Eid
- Departments of Human Cytogenetics, National Research Centre, El Bohouth Street, Dokki, Cairo, 12311, Egypt.
| | - Maha M Eid
- Departments of Human Cytogenetics, National Research Centre, El Bohouth Street, Dokki, Cairo, 12311, Egypt
| | - Marwa Farid
- Departments of Human Cytogenetics, National Research Centre, El Bohouth Street, Dokki, Cairo, 12311, Egypt
| | - Rania M A Abdel Kader
- Departments of Human Cytogenetics, National Research Centre, El Bohouth Street, Dokki, Cairo, 12311, Egypt
| | - Rana Mahrous
- Departments of Human Cytogenetics, National Research Centre, El Bohouth Street, Dokki, Cairo, 12311, Egypt
| | - Sara H El-Dessouky
- Prenatal Diagnosis & Fetal Medicine, National Research Centre, El Bohouth Street, Dokki, Cairo, 12311, Egypt
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2
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Xie M, Li J, Hu H, Wang P, Cong X, Li J, Dai L, Lu Y, Zhang W. Development and validation of a novel 26-plex system for prenatal diagnosis with forensic markers. Int J Legal Med 2022; 136:527-537. [PMID: 35102446 DOI: 10.1007/s00414-022-02780-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
Short tandem repeat (STR) loci are commonly used in forensic casework, such as personal identification and paternity testing. In recent years, STR has also been widely used for rapid, accurate and automated prenatal diagnosis, known as quantitative fluorescent PCR (QF-PCR). Despite their usefulness, the current systems often lack the power to detect mosaicism for Turner syndrome. In this study, we developed a novel 26-plex system that combined the 22 STRs in chromosome 21/18/13/X, 3 sex loci and 1 quality control marker (TAF9L). The system was generated to achieve greater diagnostic power of trisomy 21/18/13 and sex chromosome abnormalities. Studies of the sensitivity, specificity, stability and accuracy were performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Compared with the results of the chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), the detection ratio of non-mosaic chromosome abnormalities of this system in the identification of chromosome 21/18/13/X/Y aneuploidies reached 100%, and the rate of negative results was consistently 100% based on 203 prenatal diagnosis sample analyses. In addition, our results suggested that this panel was a useful tool for mosaicism for Turner syndrome cases. Interestingly, we found one case with large segment loss of chromosome X, which indicated that we should be alert to this situation when the STR genotype of the parent-child is inconsistent in forensic genetics. In summary, this study demonstrated that our system is an accurate, cost-effective and rapid approach for the detection of chromosome numerical abnormalities in prenatal diagnosis.
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Affiliation(s)
- Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Huan Hu
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Panpan Wang
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Xueqi Cong
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Jingzhi Li
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Lei Dai
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Yang Lu
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Weishe Zhang
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China.
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3
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Seidman MA, Mitchell RN. Fundamental principles in cardiovascular genetics. Cardiovasc Pathol 2022. [DOI: 10.1016/b978-0-12-822224-9.00019-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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4
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Structural and numerical Y chromosomal variations in elderly men identified through multiplex ligation-dependent probe amplification. J Hum Genet 2021; 66:1181-1184. [PMID: 34108640 DOI: 10.1038/s10038-021-00943-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/09/2021] [Accepted: 05/27/2021] [Indexed: 11/08/2022]
Abstract
Human Y chromosomes frequently acquire structural and numerical alterations. Known alterations include germline copy-number variations (CNVs) in the azoospermia factor (AZF) region and somatic mosaic loss of the Y chromosome (mLOY). Here, we explored Y chromosomal variations in 160 Japanese men aged 75-90 years. Multiplex ligation-dependent probe amplification (MLPA) identified ten types of AZF-linked CNVs in 77 men and mLOY of various degrees in 37. Seventeen men carried both a CNV and mLOY. MLOY levels estimated by MLPA were closely correlated with those determined by droplet digital PCR. No association was found between AZF-linked CNVs and the frequency or levels of mLOY. These results emphasize the high frequency and large inter-individual variability of AZF-linked CNVs and mLOY, and demonstrate the usefulness of MLPA in the detection of these variations. More importantly, this study provides the first evidence that AZF-linked CNVs do not increase the risk of aging-related mLOY.
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5
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Three-dimensional digital PCR through light-sheet imaging of optically cleared emulsion. Proc Natl Acad Sci U S A 2020; 117:25628-25633. [PMID: 32999068 DOI: 10.1073/pnas.2002448117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The realization of the vast potential of digital PCR (dPCR) to provide extremely accurate and sensitive measurements in the clinical setting has thus far been hindered by challenges such as assay robustness and high costs. Here we introduce a lossless and contamination-free dPCR technology, termed CLEAR-dPCR, which addresses these challenges by completing the dPCR sample preparation, PCR, and readout all in one tube. Optical clearing of the droplet dPCR emulsion was combined with emerging light-sheet fluorescence microscopy, to acquire a three-dimensional (3D) image of a half million droplets sealed in a tube in seconds. CLEAR-dPCR provides ultrahigh-throughput readout results in situ and fundamentally eliminates the possibility of either sample loss or contamination. This approach exhibits improved accuracy over existing dPCR platforms and enables a greatly increased dynamic range to be comparable to that of real-time quantitative PCR.
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Ansar Z, Nasir A, Moatter T, Khan S, Kirmani S, Ibrahim S, Imam K, Ather A, Samreen A, Hasan Z. MLPA Analyses Reveal a Spectrum of Dystrophin Gene Deletions/Duplications in Pakistani Patients Suspected of Having Duchenne/Becker Muscular Dystrophy: A Retrospective Study. Genet Test Mol Biomarkers 2019; 23:468-472. [DOI: 10.1089/gtmb.2018.0262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Tariq Moatter
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sara Khan
- Department of Pediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Salman Kirmani
- Department of Pediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahnaz Ibrahim
- Department of Pediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Kahkashan Imam
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Anif Ather
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Azra Samreen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
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7
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Belvini D, Salviato R, Radossi P, Tagariello G. Multiplex ligation-dependent probe amplification as first mutation screening for large deletions and duplications in haemophilia. Haemophilia 2017; 23:e124-e132. [DOI: 10.1111/hae.13143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2016] [Indexed: 12/24/2022]
Affiliation(s)
- D. Belvini
- Transfusion Service; Haemophilia Centre and Haematology; Castelfranco Veneto Hospital; Castelfranco Veneto Italy
| | - R. Salviato
- Transfusion Service; Haemophilia Centre and Haematology; Castelfranco Veneto Hospital; Castelfranco Veneto Italy
| | - P. Radossi
- Transfusion Service; Haemophilia Centre and Haematology; Castelfranco Veneto Hospital; Castelfranco Veneto Italy
| | - G. Tagariello
- Transfusion Service; Haemophilia Centre and Haematology; Castelfranco Veneto Hospital; Castelfranco Veneto Italy
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8
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Basgalupp SP, Siebert M, Vairo FPE, Chami AM, Pinto LLDC, Carvalho GDS, Schwartz IVD. Use of a multiplex ligation-dependent probe amplification method for the detection of deletions/duplications in the GBA1 gene in Gaucher disease patients. Blood Cells Mol Dis 2016; 68:17-20. [PMID: 27825739 DOI: 10.1016/j.bcmd.2016.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/19/2016] [Indexed: 11/26/2022]
Abstract
Gaucher disease (GD) is caused by the deficient activity of β-glucocerebrosidase due to pathogenic mutations in the GBA1. This gene has a pseudogene (GBAP) with 96% of sequence homology. Recombination (Rec) events in the GBA1 seem to be facilitated by an increased degree of homology and proximity to the GBAP. The objectives of this study were to validate the P338-X1 GBA kit (MRC-Holland) for Multiplex Ligation-dependent Probe Amplification (MLPA) and to detect larger deletions/duplications present in GBA1 in GD patients from Brazil. Thirty-three unrelated Brazilian GD patients, previously genotyped by the Sanger method (both pathogenic alleles identified=29 patients, only one allele identified=3 patients, no pathogenic alleles identified=1 patient), were evaluated by the MLPA assay. MLPA was compatible with the previous results obtained by Sanger sequencing and identified an additional allele (a heterozygous deletion in intron 7 in one patient with only one mutation identified by Sanger). Our data suggest that, although larger deletions/duplications do not appear to be frequent in GD, the P338-X1 GBA kit for MLPA appears to be a good method for GBA1 analysis. Additional investigations should be performed in order to characterize the remaining four uncharacterized alleles of our sample.
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Affiliation(s)
- Suelen P Basgalupp
- Postgraduate Program in Medical Sciences, School of Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Basic Research and Advanced Investigations in Neurosciences (BRAIN) Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Marina Siebert
- Postgraduate Program in Sciences of Gastroenterology and Hepatology, School of Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Basic Research and Advanced Investigations in Neurosciences (BRAIN) Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; Molecular and Protein Analysis Unit, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Filippo Pinto E Vairo
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | | | | | - Ida Vanessa D Schwartz
- Postgraduate Program in Medical Sciences, School of Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Basic Research and Advanced Investigations in Neurosciences (BRAIN) Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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9
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Seidman M, Mitchell R. Fundamental Principles in Cardiovascular Genetics. Cardiovasc Pathol 2016. [DOI: 10.1016/b978-0-12-420219-1.00006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Chen X, Li H, Mao Y, Xu X, Lv J, Zhou L, Lin X, Tang S. Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations. Mol Cytogenet 2014; 7:96. [PMID: 25506396 PMCID: PMC4265491 DOI: 10.1186/s13039-014-0096-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/18/2022] Open
Abstract
Background Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping. Results Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions. Conclusions Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiangnan Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China
| | - Huanzheng Li
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Yijian Mao
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Xueqin Xu
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Jiaojiao Lv
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China
| | - Lili Zhou
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Xiaoling Lin
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Shaohua Tang
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China ; Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
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11
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Sun L, Fan Z, Weng X, Ye X, Long J, Fu K, Yan S, Wang B, Zhuo Y, Liu X, Lao K. Rapid detection of Down's syndrome using quantitative real-time PCR (qPCR) targeting segmental duplications on chromosomes 21 and 11. Gene 2014; 552:272-6. [PMID: 25256276 DOI: 10.1016/j.gene.2014.09.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/09/2014] [Accepted: 09/19/2014] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Development of a qPCR test for the detection of trisomy 21 using segmental duplications. METHODS Segmental duplications in the TTC3 gene on chromosome 21 and the KDM2A gene on chromosome 11 were selected as molecular markers for the diagnostic qPCR assay. A set of consensus primers selected from the conserved regions of these segmental duplications were used to amplify internal diverse sequences that were detected and quantified with different probes labeled with distinct fluorescence. The copy numbers of these two fragments were determined based on the ΔCq values of qPCR. The results of qPCR for prenatal and neonatal screening of Down's syndrome were compared with the conventional karyotype analysis by testing 82 normal individuals and 50 subjects with Down's syndrome. RESULTS The ΔCq values of segmental duplications on chr21 and 11 ranged between 0.33 and 0.75 in normal individuals, and between 0.91 and 1.18 in subjects with Down's syndrome. The ΔCq values of these two segmental duplications clearly discriminated Down's syndrome from normal individuals (P<0.001). Furthermore, the qPCR results were consistent with karyotype analysis. CONCLUSION Our qPCR can be used for rapid prenatal and neonatal screening of Down's syndrome.
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Affiliation(s)
- Lei Sun
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China.
| | - Zuqian Fan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Xunjin Weng
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Xuehe Ye
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Ju Long
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Kepeng Fu
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Shanhuo Yan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Bo Wang
- Genetics Laboratory, Hubei Maternal and Child Health Hospital, Hubei, China
| | - Yongguang Zhuo
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Xinxing Liu
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Kegan Lao
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
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12
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Ye Y, Yu P, Yong J, Zhang T, Wei X, Qi M, Jin F. Preimplantational genetic diagnosis and mutation detection in a family with duplication mutation of DMD gene. Gynecol Obstet Invest 2014; 78:272-8. [PMID: 25196347 DOI: 10.1159/000365083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 06/04/2014] [Indexed: 11/19/2022]
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disease caused by mutation in the DMD gene. A 38-year-old woman was referred to our hospital with her son who was diagnosed with DMD. Multiplex PCR failed to detect DMD mutations in the affected child. The female carrier underwent preimplantation genetic diagnosis by linkage analysis and gender determination. Eight embryos were biopsied after in vitro fertilization. Two healthy embryos determined both as females (E1 and E3) were transferred. Although the paternal allele was absent in E3, it was considered to be a result of allele dropout for the STR-49 marker. Surprisingly, a female and a male baby were delivered at 38 gestational weeks, suggesting that E3 was a male embryo with the allele dropout occurring at the SRY gene. Exon 2 duplication was detected in the DMD patient and the carrier mother using next-generation sequencing and multiple ligation-dependent probe amplification. Next, we verified the duplication of exon 2 by real-time PCR, using a special primer at 3' of intron 1, very close to exon 2. Finally, we confirmed that both newborns inherited the normal allele, using quantitative real-time PCR and linkage analysis.
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Affiliation(s)
- Yinghui Ye
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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13
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Kong X, Li L, Sun L, Fu K, Long J, Weng X, Ye X, Liu X, Wang B, Yan S, Ye H, Fan Z. Rapid diagnosis of aneuploidy using segmental duplication quantitative fluorescent PCR. PLoS One 2014; 9:e88932. [PMID: 24625828 PMCID: PMC3953018 DOI: 10.1371/journal.pone.0088932] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023] Open
Abstract
The aim of this study was use a simple and rapid procedure, called segmental duplication quantitative fluorescent polymerase chain reaction (SD-QF-PCR), for the prenatal diagnosis of fetal chromosomal aneuploidies. This method is based on the co-amplification of segmental duplications located on two different chromosomes using a single pair of fluorescent primers. The PCR products of different sizes were subsequently analyzed through capillary electrophoresis, and the aneuploidies were determined based on the relative dosage between the two chromosomes. Each primer set, containing five pairs of primers, was designed to simultaneously detect aneuploidies located on chromosomes 21, 18, 13, X and Y in a single reaction. We applied these two primer sets to DNA samples isolated from individuals with trisomy 21 (n = 36); trisomy 18 (n = 6); trisomy 13 (n = 4); 45, X (n = 5); 47, XXX (n = 3); 48, XXYY (n = 2); and unaffected controls (n = 40). We evaluated the performance of this method using the karyotyping results. A correct and unambiguous diagnosis with 100% sensitivity and 100% specificity, was achieved for clinical samples examined. Thus, the present study demonstrates that SD-QF-PCR is a robust, rapid and sensitive method for the diagnosis of common aneuploidies, and these analyses can be performed in less than 4 hours for a single sample, providing a competitive alternative for routine use.
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Affiliation(s)
- Xiangdong Kong
- Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Lin Li
- Department of Genetic Laboratory, Lin Yi People’s Hospital, Shandong, China
| | - Lei Sun
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
- * E-mail:
| | - Kepeng Fu
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Ju Long
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Xunjin Weng
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Xuehe Ye
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Xinxiong Liu
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Bo Wang
- Genetics Laboratory, Hubei Maternal and Child Health Hospital, Hubei, China
| | - Shanhuo Yan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Haiming Ye
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
| | - Zuqian Fan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Guangxi, China
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14
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Chromosomal Microarrays in Prenatal Diagnosis: Time for a Change of Policy? MICROARRAYS 2013; 2:304-17. [PMID: 27605194 PMCID: PMC5003441 DOI: 10.3390/microarrays2040304] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/19/2013] [Accepted: 11/27/2013] [Indexed: 01/26/2023]
Abstract
Microarrays have replaced conventional karyotyping as a first-tier test for unbalanced chromosome anomalies in postnatal cytogenetics mainly due to their unprecedented resolution facilitating the detection of submicroscopic copy number changes at a rate of 10-20% depending on indication for testing. A number of studies have addressed the performance of microarrays for chromosome analyses in high risk pregnancies due to abnormal ultrasound findings and reported an excess detection rate between 5% and 10%. In low risk pregnancies, clear pathogenic copy number changes at the submicroscopic level were encountered in 1% or less. Variants of unclear clinical significance, unsolicited findings, and copy number changes with variable phenotypic consequences are the main issues of concern in the prenatal setting posing difficult management questions. The benefit of microarray testing may be limited in pregnancies with only moderately increased risks (advanced maternal age, positive first trimester test). It is suggested to not change the current policy of microarray application in prenatal diagnosis until more data on the clinical significance of copy number changes are available.
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15
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Shaffer LG, Rosenfeld JA. Microarray-based prenatal diagnosis for the identification of fetal chromosome abnormalities. Expert Rev Mol Diagn 2013; 13:601-11. [PMID: 23895129 DOI: 10.1586/14737159.2013.811912] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The goal of prenatal cytogenetic testing is to provide reassurance to the couple seeking testing for their pregnancy, identify chromosome abnormalities in the fetus, if present, and provide treatments and medical management for affected babies. Cytogenetic analysis of banded chromosomes has been the standard for identifying chromosome abnormalities in the fetus for over 40 years. With chromosome analysis, whole chromosome aneuploidies and large structural rearrangements can be identified. The sequencing of the human genome has provided the resources to develop molecular tools that allow higher resolution observations of human chromosomes. The future holds the promise of sequencing that may identify chromosomal imbalances and deleterious single nucleotide variants. This review will focus on the use of genomic microarrays for the testing and identification of chromosome anomalies in prenatal diagnosis and will discuss the future directions of fetal testing.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA.
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Rapid and non invasive prenatal diagnosis. Balkan J Med Genet 2013; 15:39-43. [PMID: 24052742 PMCID: PMC3776684 DOI: 10.2478/v10034-012-0017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Sheath KL, Duffy L, Asquith P, Love DR, George AM. Bacterial artificial chromosomes (BACs)-on-Beads™ as a diagnostic platform for the rapid aneuploidy screening of products of conception. Mol Med Rep 2013; 8:650-4. [PMID: 23764829 DOI: 10.3892/mmr.2013.1519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/28/2013] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to evaluate the use of KaryoLite™ bacterial artificial chromosomes (BACs)‑on‑Beads™ (BoBs) technology for the rapid screening of products of conception (POC). Validation and prospective studies were carried out on 85 and 95 patient samples, respectively. Validation studies had previously been analyzed using routine culture and G-banded karyotyping. BoBs resulted in an abnormality detection frequency of 27%, with a failure rate of <3%. The time required for processing was significantly lower compared with that of tissue culture. In conclusion, BoBs technology decreased the failure rate, while increasing the analytical sensitivity compared with G-banded karyotype analysis alone. Additionally, significant cost savings may be achieved with regard to the time of processing and analysis of specimens.
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Affiliation(s)
- Karen L Sheath
- Diagnostic Genetics, LabPlus, Auckland City Hospital, Auckland 1148, New Zealand
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Shaffer LG, den Veyver IBV. New technologies for the assessment of chromosomes in prenatal diagnosis. Prenat Diagn 2012; 32:307-8. [DOI: 10.1002/pd.3858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Lisa G. Shaffer
- Signature Genomic Laboratories; PerkinElmer, Inc.; Spokane WA USA
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Genecology and the Department of Molecular and Human Genetics; Baylor College of Medicine; Houston TX USA
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