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Liu Y, Liu Y, Guo L, Wu Y, Wang Y, Xu L, Xu M, Huang S, Chen P, Wang T, Huang Q, Li Q. Multiplex Asymmetric PCR by Combining the Amplification Refractory Mutation System with the Homo-Tag-Assisted Nondimer System. Anal Chem 2024; 96:9200-9208. [PMID: 38771984 DOI: 10.1021/acs.analchem.4c01322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Asymmetric PCR is widely used to produce single-stranded amplicons (ss-amplicons) for various downstream applications. However, conventional asymmetric PCR schemes are susceptible to events that affect primer availability, which can be exacerbated by multiplex amplification. In this study, a new multiplex asymmetric PCR approach that combines the amplification refractory mutation system (ARMS) with the homo-Tag-assisted nondimer system (HANDS) is described. ARMS-HANDS (A-H) PCR utilizes equimolar-tailed forward and reverse primers and an excess Tag primer. The tailed primer pairs initiate exponential symmetric amplification, whereas the Tag primer drives linear asymmetric amplification along fully matched strands but not one-nucleotide mismatched strands, thereby generating excess ss-amplicons. The production of ss-amplicons is validated using agarose gel electrophoresis, sequencing, and melting curve analysis. Primer dimer alleviation is confirmed by both the reduced Loss function value and a 20-fold higher sensitivity in an 11-plex A-H PCR assay than in an 11-plex conventional asymmetric PCR assay. Moreover, A-H PCR demonstrates unbiased amplification by its allele quantitative ability in correct identification of all 31 trisomy 21 samples among 342 clinical samples. A-H PCR is a new generation of multiplex asymmetric amplification approach with various applications, especially when sensitive and quantitative detection is required.
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Affiliation(s)
- Ying Liu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yinghua Liu
- Centre for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China
| | - Liu Guo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yazhe Wu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yafang Wang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Lingzhen Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Mingzhu Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Siyu Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Ping Chen
- NHC Key Laboratory of Thalassemia Medicine, Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Ting Wang
- Centre for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
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Bergallo M, Montanari P, Loiacono E, Galliano I. A novel TaqMAMA assay for allelic discrimination of immunoproteasome subunit PSMB8 in pediatric patients. Minerva Pediatr (Torino) 2022; 74:301-307. [DOI: 10.23736/s2724-5276.16.04675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Simple and rapid detection of common fetal aneuploidies using peptide nucleic acid probe-based real-time polymerase chain reaction. Sci Rep 2022; 12:150. [PMID: 34996887 PMCID: PMC8742004 DOI: 10.1038/s41598-021-02507-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
To examine the detection performance of a peptide nucleic acid (PNA) probe-based real-time time polymerase chain reaction (PCR) assay to detect common aneuploidies. Using amniotic fluid samples, PNA probe based real-time PCR (Patio DEP Detection Kit; SeaSun Biomaterials, Korea) assay was performed. PNA probe was designed to hybridize to similar sequences located on different segments of target chromosomes (21, 18, and 13) and a reference chromosome. Amplification of target sequences and melting curve analysis was performed. When analyzing the melting curve, the ratio of the peak height of the target and reference chromosome was calculated and determined as aneuploidy if the ratio of peak height was abnormal. All the results from the PNA probe-based real-time PCR and melting curve analyses were compared to those from conventional karyotyping. Forty-two cases with common aneuploidies (24 of trisomy 21, 12 of trisomy 18, and 6 of trisomy 13) and 131 cases with normal karyotype were analyzed. When comparing the karyotyping results, the sensitivity and specificity of the PNA probe-based real-time PCR assay were both 100%. The level of agreement was almost perfect (k = 1.00). PNA real-time PCR assay is a rapid and easy method for detecting common aneuploidies.
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Sun L, Fan Z, Long J, Weng X, Tang W, Pang W. Rapid prenatal diagnosis of aneuploidy for chromosomes 21, 18, 13, X, and Y using segmental duplication quantitative fluorescent PCR (SD-QF-PCR). Gene 2017; 627:72-78. [PMID: 28603073 DOI: 10.1016/j.gene.2017.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/23/2017] [Accepted: 06/08/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND In our previous studies, the rapid diagnosis of aneuploidy has been achieved using the segmental duplication molecular markers-based SD-QF-PCR technique. However, it is also insufficient due to the drawbacks including less detection loci and incompetence in single-tube detection. METHODS In this paper, we developed 13 new segmental duplications as molecular markers, as well as designed 13 pairs of primers and 1 fluorescence-labeled universal primer, which could detect chromosome aneuploidies in one PCR tube. RESULTS Two hundred and thirty samples were detected using SD-QF-PCR, the samples were collected from individuals with trisomy 21 (n=16); trisomy 18 (n=4); trisomy 13 (n=3); 45,X (n=3); 47,XXY (n=2); 47,XYY (n=2); suspected mosaic 46,XX/46,XY (n=2); and unaffected controls (n=198). CONCLUSIONS The detection results of SD-QF-PCR were consistent with those of conventional karyotype analysis. SD-QF-PCR based on the newly developed segmental duplications enables the single-tube and multi-locus simultaneous detection on the number of chromosomes 13, 18, 21, X and Y. Therefore, this technique offers a new alternative for the diagnosis of chromosome aneuploidies.
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Affiliation(s)
- Lei Sun
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi 535005, PR China.
| | - Zuqian Fan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi 535099, PR China.
| | - Ju Long
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi 535099, PR China.
| | - Xunjin Weng
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi 535099, PR China.
| | - Weijun Tang
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi 535099, PR China.
| | - Wanrong Pang
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi 535099, PR China.
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Lou J, Sun M, Zhao Y, Ji Z, Liu F, Li D, Xu W, Lin Y, Liu Y. Rapid and simultaneous detection of common aneuploidies by quadruplex real-time polymerase chain reaction combined with melting curve analysis. PLoS One 2017; 12:e0171886. [PMID: 28241016 PMCID: PMC5328249 DOI: 10.1371/journal.pone.0171886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/29/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND During the prenatal period, the number variation of chromosomes 13, 18, 21, X and Y accounts for more than 80% of the clinically significant chromosomal abnormalities diagnosed. Rapid tests for prenatal diagnosis of these abnormalities can improve pregnancy management and alleviate parental anxiety. Here, we present a molecular alternative method for detecting common aneuploidies. METHODS This method is based on co-amplification of segmental duplications located on two different chromosomes using a single pair of primers. Segmental duplications have a high degree of sequence identity, but have single-nucleotide differences in some regions. These sequence differences can be quantified using melting curve analysis of dual-labeled probes to estimate the relative dosages of different chromosomes. We designed two quadruplex real-time PCR assays to detect aneuploidies of chromosomes 13, 18, 21, X and Y. RESULTS We examined 75 aneuploid DNA samples and 56 unaffected DNA control samples using these two assays and correctly identified all samples. Four cases of unbalanced translocation were also accurately detected. The observed averaged ratio for each chromosomal disorder was similar to the theoretically expected value. CONCLUSIONS Our real-time assay is a robust, rapid, and easy to conduct technique for prenatal diagnosis of common aneuploidies, representing a competitive alternative for use in diagnostic laboratories.
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MESH Headings
- Aneuploidy
- Case-Control Studies
- Chromosome Disorders/diagnosis
- Chromosome Disorders/genetics
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 21
- Chromosomes, Human, X
- Chromosomes, Human, Y
- DNA/analysis
- Female
- Fluorescent Dyes/chemistry
- Humans
- Karyotyping
- Male
- Nucleotides
- Pregnancy
- Real-Time Polymerase Chain Reaction
- Trisomy
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Affiliation(s)
- Jiwu Lou
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
| | - Manna Sun
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
| | - Ying Zhao
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
| | - Zhisong Ji
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
| | - Fenghua Liu
- Reproductive medicine Center, Guangdong Maternal and Child Health Hospital, Guangzhou, People's Republic of China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women & Children Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Wanfang Xu
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
| | - Yangyang Lin
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
| | - Yanhui Liu
- Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, People's Republic of China
- * E-mail:
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Mačkić-Đurović M, Projić P, Ibrulj S, Cakar J, Marjanović D. A comparative analysis of the effectiveness of cytogenetic and molecular genetic methods in the detection of Down syndrome. Bosn J Basic Med Sci 2014; 14:94-8. [PMID: 24856381 DOI: 10.17305/bjbms.2014.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The goal of this study was to examine the effectiveness of 6 STR markers application (D21S1435, D21S11, D21S1270, D21S1411, D21S226 and IFNAR) in molecular genetic diagnostics of Down syndrome (DS) and to compare it with cytogenetic method. Testing was performed on 73 children, with the previously cytogenetically confirmed Down syndrome. DNA isolated from the buccal swab was used. Previously mentioned loci located on chromosome 21 were simultaneously amplified using quantitative fluorescence PCR (QF PCR). Using this method, 60 previously cytogenetically diagnosed DS with standard type of trisomy 21 were confirmed. Furthermore, six of eight children with mosaic type of DS were detected. Two false negative results for mosaic type of DS were obtained. Finally, five children with the translocation type of Down syndrome were also confirmed with this molecular test. In conclusion, molecular genetic analysis of STR loci is fast, cheap and simple method that could be used in detection of DS. Regarding possible false results detected for certain number of mosaic types, cytogenetic analysis should be used as a confirmatory test.
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Affiliation(s)
- Mirela Mačkić-Đurović
- Center for genetics, Faculty of Medicine, University of Sarajevo, Čekaluša 90, 71 000 Sarajevo, Bosnia and Herzegovina
| | - Petar Projić
- Genos LTD, Hondlova 2, 10000 Zagreb, Croatia. 3Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Slavka Ibrulj
- Center for genetics, Faculty of Medicine, University of Sarajevo, Čekaluša 90, 71 000 Sarajevo, Bosnia and Herzegovina
| | - Jasmina Cakar
- Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanović
- Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
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Zhou Y, Xiao L, Wu Q, Zhang K, Guo Q. Rapid prenatal diagnosis of common numerical chromosomal abnormalities by high-resolution melting analysis of segmental duplications. Genet Test Mol Biomarkers 2013; 18:141-8. [PMID: 24321085 DOI: 10.1089/gtmb.2013.0373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Rapid aneuploidy detection (RAD) methods constitute important complements to karyotyping in prenatal diagnosis. We evaluated the effectiveness of a method called high-resolution melting analysis of segmental duplications (SD-HRM) to serve as an alternative RAD method in prenatal diagnosis of common numerical chromosomal abnormalities (NCAs). METHODS We designed eight primary SD-HRM assays for the detection of chromosomes 13, 18, 21, X, and Y; 50 chorionic villus, 1105 amniotic fluid, and 395 cord blood samples were examined using these eight assays. For diagnosing samples that could not be diagnosed using primary assays, additional assays were designed for each target chromosome. RESULTS The success rate of eight primary SD-HRM assays ranged from 99.7% to 100%. For the distinguishable analyses, these eight assays attained high diagnostic sensitivities (100%) and specificities (99.9-100%). We differentiated 53 cases of NCAs from 1550 clinical samples; subsequent reference tests revealed that these assays attained 100% clinical sensitivity and specificity. The mosaic ratio of a 45,X/46,XX sample was also precisely calculated. CONCLUSIONS The SD-HRM method was able to effectively detect common NCAs in 1550 prenatal samples. We propose that SD-HRM could serve as an effective alternative option to the currently used prenatal RAD methods.
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Affiliation(s)
- Yulin Zhou
- 1 Molecular Diagnostics Laboratory, Department of Medical Genetics, Prenatal Diagnosis Center of Xiamen, Maternal and Child Health Hospital , Xiamen, China
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Guo Q, Xiao L, Zhou Y. Rapid Diagnosis of Aneuploidy by High-Resolution Melting Analysis of Segmental Duplications. Clin Chem 2012; 58:1019-25. [PMID: 22431896 DOI: 10.1373/clinchem.2011.178475] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Several molecular methods, such as quantitative fluorescence PCR and multiplex ligation-dependent probe amplification, currently serve as important adjuncts to traditional karyotyping for the diagnosis of aneuploidy; however, the performance or throughput limitations of these methods hinder their use for routine prenatal diagnosis and population-based postnatal screening. We developed a novel approach, called “high-resolution melting analysis of segmental duplications,” to detect common aneuploidies.
METHODS
In this method, similar sequences located on different chromosomes are amplified simultaneously with a single primer set; the PCR products are then analyzed by high-resolution melting. Aneuploidy-associated dosage abnormalities produce different ratios of similar amplicons, which produce melting curves that are detectably different from those of samples from unaffected individuals. We applied this method to DNA samples isolated from individuals with trisomy 21 (n = 48), trisomy 18 (n = 10), trisomy 13 (n = 3), 45,X (n = 8), and 47,XXY (n = 14), and from unaffected controls (n = 48).
RESULTS
As judged by the karyotyping results, our method attained 100% diagnostic sensitivity and 99.6% diagnostic specificity. Moreover, our method was able to detect a change in chromosome dosage as low as 1.05-fold.
CONCLUSIONS
This novel method clearly differentiates samples of patients with common aneuploidies from those of unaffected controls, while markedly simplifying the assays and reducing time and costs. The assay has sufficient throughput to meet the demands of large-scale testing, such as population-based postnatal screening, and is thus suitable for routine use.
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Affiliation(s)
- Qiwei Guo
- Molecular Diagnostics Laboratory, Department of Medical Genetics, Prenatal Diagnosis Center of Xiamen, Maternal and Child Health Hospital, Xiamen, Fujian, China
| | - Li Xiao
- Molecular Diagnostics Laboratory, Department of Medical Genetics, Prenatal Diagnosis Center of Xiamen, Maternal and Child Health Hospital, Xiamen, Fujian, China
| | - Yulin Zhou
- Molecular Diagnostics Laboratory, Department of Medical Genetics, Prenatal Diagnosis Center of Xiamen, Maternal and Child Health Hospital, Xiamen, Fujian, China
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9
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Silva VL, Loschi RH. Test, estimation and model comparison for the meiosis I nondisjunction fraction in trisomies. BRAZ J PROBAB STAT 2012. [DOI: 10.1214/10-bjps125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Cho CKJ, Diamandis EP. Application of proteomics to prenatal screening and diagnosis for aneuploidies. Clin Chem Lab Med 2011; 49:33-41. [DOI: 10.1515/cclm.2011.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Guo Q, Zhou Y, Wang X, Li Q. Simultaneous Detection of Trisomies 13, 18, and 21 with Multiplex Ligation-Dependent Probe Amplification–Based Real-Time PCR. Clin Chem 2010; 56:1451-9. [DOI: 10.1373/clinchem.2010.146472] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND
Trisomies 13, 18, and 21 account for the majority of chromosomal aneuploidies detected in prenatal diagnosis. Diagnosis of these trisomies relies mainly on karyotype analysis. Several molecular methods have been developed for trisomy detection, but performance or throughput limitations of these methods currently constrain their use in routine testing.
METHODS
We developed multiplex ligation-dependent probe amplification–based real-time PCR (MLPA/rtPCR) to simultaneously detect these 3 trisomy conditions with a single reaction. We applied the method to DNA isolated from 144 blinded clinical samples that included 32 cases of trisomy 21, 11 cases of trisomy 18, 1 case of trisomy 13, and 100 unaffected control samples; results were compared with karyotype analysis.
RESULTS
As judged by the results of the karyotype analysis, MLPA/rtPCR correctly detected all 44 cases of trisomy in the analysis of the blinded clinical samples. The method was able to detect a change in chromosome dosage as low as 1.2-fold.
CONCLUSIONS
This novel PCR-based technology simultaneously identified 3 types of trisomy in a single reaction and accurately detected trisomy with mosaicism, while reducing assay times and costs compared with conventional methods. The MLPA/rtPCR approach may have applicability in noninvasive prenatal diagnosis with maternal blood samples.
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Affiliation(s)
- Qiwei Guo
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen, China
- Molecular Diagnostics Laboratory, Department of Genetics, Prenatal Diagnosis Center of Xiamen, Maternal and Child Health Hospital of Xiamen, Xiamen, China
| | - Yulin Zhou
- Molecular Diagnostics Laboratory, Department of Genetics, Prenatal Diagnosis Center of Xiamen, Maternal and Child Health Hospital of Xiamen, Xiamen, China
| | - Xiaobo Wang
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen, China
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Abstract
LightCycler technology combines rapid-cycle polymerase chain reaction with real-time fluorescent monitoring and melting curve analysis. Since its introduction in 1997, it is now used in many areas of molecular pathology, including oncology (solid tumors and hematopathology), inherited disease, and infectious disease. By monitoring product accumulation during rapid amplification, quantitative polymerase chain reaction in a closed-tube system is possible in 15 to 30 minutes. Furthermore, melting curve analysis of probes and/or amplicons provides genotyping and even haplotyping. Novel mutations are identified by unexpected melting temperature or curve shape changes. Melting probe designs include adjacent hybridization probes, single labeled probes, unlabeled probes, and snapback primers. High-resolution melting allows mutation scanning by detecting all heterozygous changes. This review describes the major advances throughout the last 15 years regarding LightCycler technology and its application in clinical laboratories.
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Affiliation(s)
- Elaine Lyon
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
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13
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Loschi RH, Monteiro JVD, Souto CS. A Misclassification Model for the Non-Disjunction Fraction in Meiosis I. Biom J 2008; 50:940-53. [DOI: 10.1002/bimj.200810477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Abstract
A method that quickly and inexpensively differentiates crime scene samples from multiple donors would expedite casework analysis by allowing the selection of probative items requiring comprehensive testing. This new method need not be perfectly definitive nor give a complete 13 locus short tandem repeat (STR) profile; it simply must be able to differentiate between most victim and suspect samples. We describe the development of multiplex, single nucleotide polymorphism (SNP), fluorescence resonance energy transfer-based real-time polymerase chain reaction (PCR) assays to fulfill this need. Dual probes, one fluorescently labeled and the other labeled with a quencher, are monitored during a melt analysis to reveal an increase in fluorescence, which allows the assessment of the two SNP alleles. Two alternate 6-plex assays (with and without gender determination) have been developed for the six-color RG6000 real-time instrument (Corbett Robotics, Inc.) and one seven SNP plus gender assay (performed as two 4-plex assays, one with gender the other without) have been developed for use in four/five color real-time instruments. This technique can discriminate between 95% and 99% of samples from different individuals. This assay is fast (approximately 2 h), much less expensive than STR analysis, and uses a real-time PCR instrument which is found in most forensic and molecular biology labs.
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Affiliation(s)
- Janice A Nicklas
- Vermont Forensic Laboratory, Department of Public Safety, 103 S. Main St., Waterbury, VT 05671, USA
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15
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Storbeck KH, Swart AC, Snyman MA, Swart P. Two CYP17 genes in the South African Angora goat (Capra hircus) - the identification of three genotypes that differ in copy number and steroidogenic output. FEBS J 2008; 275:3934-43. [PMID: 18616460 DOI: 10.1111/j.1742-4658.2008.06539.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mammals, cytochrome P450 17alpha-hydroxylase/17-20 lyase (CYP17), which is encoded by a single gene, plays a critical role in the production of mineralocorticoids, glucocorticoids and androgens by the adrenal cortex. Two CYP17 isoforms with unique catalytic properties have been identified in the South African Angora goat (Capra hircus), a subspecies that is susceptible to cold stress because of the inability of the adrenal cortex to produce sufficient levels of cortisol. A real-time-based genotyping assay was used in this study to identify the distribution of the two CYP17 alleles in the South African Angora population. These data revealed that the two CYP17 isoforms were not the product of two alleles of the same gene, but two separate CYP17 genes encoding the two unique CYP17 isoforms. This novel finding was subsequently confirmed by quantitative real-time PCR. Goats were divided into three unique genotypes which differed not only in the genes encoding CYP17, but also in copy number. Furthermore, in vivo assays revealed that the identified genotypes differed in their ability to produce cortisol in response to intravenous insulin injection. This study clearly demonstrates the presence of two CYP17 genes in the South African Angora goat, and further implicates CYP17 as the primary cause of the observed hypocortisolism in this subspecies.
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16
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Ding C. ‘Other’ applications of single nucleotide polymorphisms. Trends Biotechnol 2007; 25:279-83. [PMID: 17493698 DOI: 10.1016/j.tibtech.2007.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 03/07/2007] [Accepted: 04/26/2007] [Indexed: 11/16/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are the most frequent form of sequence variation in the human genome, occurring on average every 300 base pairs. Owing to their high density, SNPs are considered useful for identifying the genes associated with complex diseases. The focus of this Opinion article is the recent applications of SNPs that fall outside of disease association studies. These applications are diverse, ranging from using SNPs as qualitative markers for distinguishing individuals in mixed samples to using SNPs for quantitative genomic DNA and RNA transcript dosage assessment. These are possible owing to the millions of validated SNPs and the variety of robust SNP analysis platforms.
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Affiliation(s)
- Chunming Ding
- Stanley Ho Centre for Emerging Infectious Diseases and Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
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17
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Dhallan R, Guo X, Emche S, Damewood M, Bayliss P, Cronin M, Barry J, Betz J, Franz K, Gold K, Vallecillo B, Varney J. A non-invasive test for prenatal diagnosis based on fetal DNA present in maternal blood: a preliminary study. Lancet 2007; 369:474-81. [PMID: 17292767 DOI: 10.1016/s0140-6736(07)60115-9] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Use of free fetal DNA to diagnose fetal chromosomal abnormalities has been hindered by the inability to distinguish fetal DNA from maternal DNA. Our aim was to establish whether single nucleotide polymorphisms (SNPs) can be used to distinguish fetal DNA from maternal DNA-and to determine the number of fetal chromosomes-in maternal blood samples. METHODS Formaldehyde-treated blood samples from 60 pregnant women and the stated biological fathers were analysed. Maternal plasma fractions were quantified at multiple SNPs, and the ratio of the unique fetal allele signal to the combined maternal and fetal allele signal calculated. The mean ratios of SNPs on chromosomes 13 and 21 were compared to test for potential fetal chromosomal abnormalities. FINDINGS The mean proportion of free fetal DNA was 34.0% (median 32.5%, range 17.0-93.8). We identified three samples with significant differences in the fetal DNA ratios for chromosome 13 and chromosome 21, indicative of trisomy 21; the remaining 57 samples were deemed to be normal. Amniocentesis or newborn reports from the clinical sites confirmed that the copy number of fetal chromosomes 13 and 21 was established correctly for 58 of the 60 samples, identifying 56 of the 57 normal samples, and two of the three trisomy 21 samples. Of the incorrectly identified samples, one was a false negative and one was a false positive. The sensitivity and positive predictive value were both 66.7% (95% CI 12.5-98.2) and the specificity and negative predictive values were both 98.2% (89.4-99.9). INTERPRETATION The copy number of chromosomes of interest can be directly established from maternal plasma. Such a non-invasive prenatal test could provide a useful complement to currently used screening tests.
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Sun X, Yan M, Zhang Y, Zhou X, Wang C, Zheng F, Xiong C. Practical application of fluorescent quantitative PCR on Trisomy 21 in Chinese Han population. Mol Biol Rep 2006; 33:167-73. [PMID: 16850185 DOI: 10.1007/s11033-006-0013-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 03/08/2006] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To apply the fluorescent quantitative PCR method on the detection of Trisomy 21 by D21S11 locus and make a foundation for rapid prenatal diagnosis of Trisomy 21. METHODS About 409 controls (39 amniotic fluid samples and 370 peripheral blood samples) and 35 patients (4 amniotic fluid samples and 31 peripheral blood samples) with Trisomy 21 were tested using fluorescent quantitative PCR by amplification of DNA fragment on D21S11 STR locus. The results were compared with conventional cytogenetic analysis to confirm the utility of this method. And the allele frequency distributions of D21S11 STR locus were analyzed. RESULTS The 95% reference interval of fluorescent intensity ratios of peak heights of PCR products amplified from two alleles on D21S11 locus ranged from 0.84 to 1.42 (1.13 +/- 0.29) in heterozygous controls. About 19 out of 35 patients showed a "diallelic" pattern and their height ratio of fluorescent peaks of PCR products amplified from two alleles in patients with "diallelic" patterns were all outside of the 95% reference range of controls. The PCR products of DNA from 12 patients presented the third allele. No sample with the "monoallelic" pattern was found. Four chimeras diagnosed by cytogenetic method could not be diagnosed by this method. There were 17 and 11 alleles found in controls and patients, respectively. About 343 out of 409 controls were heterozygous and the heterozygosity was 83.86%. We did not find any significant differences in the frequency distributions of alleles on D21S11 locus between controls and patients. But there were significant differences in the frequency distributions of alleles on D21S11 locus between controls and patients. But there were significant differences in the frequency distributions of alleles on D21S11 locus among different populations. CONCLUSIONS The fluorescent quantitative polymerase chain reaction method was rapid, accurate, and only small amount of starting material was needed, it could be applied in rapid prenatal diagnosis of Trisomy 21. D21S11 was a good marker with high heterozygosity for the screening of Trisomy 21. And the frequency distributions of alleles on D21S11 locus were significantly related to ethnic background.
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Affiliation(s)
- Xiaobo Sun
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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Huang DJ, Nelson MR, Zimmermann B, Dudarewicz L, Wenzel F, Spiegel R, Nagy B, Holzgreve W, Hahn S. Reliable detection of Trisomy 21 using MALDI-TOF mass spectrometry. Genet Med 2006; 8:728-34. [PMID: 17108765 DOI: 10.1097/01.gim.0000245573.42908.34] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Current diagnostic methods for chromosomal abnormalities rely mainly on karyotyping and occasionally fluorescent in situ hybridization or quantitative polymerase chain reaction. We describe an alternative molecular method for the detection of trisomy 21 involving mass spectrometric analysis of single nucleotide polymorphisms. METHODS In collaboration with Sequenom, Inc., 350 blinded amniotic fluid, amniocyte culture, chorionic villus, or amniotic fluid supernatant samples were analyzed for trisomy 21 using SNP analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Peak ratios were calculated for heterozygous genotypes and compared to control values generated from known euploid samples. An analytical algorithm using standard deviations from control values was used to determine the probability of a sample being affected or unaffected. RESULTS Seventy-three trisomy 21 samples from among the 350 blinded samples were correctly identified. There were no false-positive or false-negative results among the complete trisomy 21 samples. One sample exhibiting mosaicism for trisomy 21 was identified as being unaffected. CONCLUSIONS MALDI-TOF mass spectrometry is a robust and reproducible method for the detection of trisomy 21. Its amenability to high-throughput analysis and high degree of multiplexing make it a potential future diagnostic tool for the detection of other aneuploidies as well.
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Affiliation(s)
- Dorothy J Huang
- Laboratory for Prenatal Medicine University Women's Hospital, Department of Research Spitalstrasse 21, CH4031 Basel, Switzerland
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Rapid prenatal diagnosis of trisomy 21 by fluorescent quantitative multiplex polymerase chain reaction. Chin Med J (Engl) 2006. [DOI: 10.1097/00029330-200603020-00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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21
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Tsui NBY, Chiu RWK, Ding C, El-Sheikhah A, Leung TN, Lau TK, Nicolaides KH, Lo YMD. Detection of Trisomy 21 by Quantitative Mass Spectrometric Analysis of Single-Nucleotide Polymorphisms. Clin Chem 2005; 51:2358-62. [PMID: 16306096 DOI: 10.1373/clinchem.2005.056978] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nancy B Y Tsui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Special Administrative Region, China
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Mattarucchi E, Marsoni M, Binelli G, Passi A, Lo Curto F, Pasquali F, Porta G. Different real time PCR approaches for the fine quantification of SNP's alleles in DNA pools: assays development, characterization and pre-validation. BMB Rep 2005; 38:555-62. [PMID: 16202235 DOI: 10.5483/bmbrep.2005.38.5.555] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are becoming the most common type of markers used in genetic analysis. In the present report a SNP has been chosen to test the applicability of Real Time PCR to discriminate and quantify SNPs alleles on DNA pools. Amplification Refractory Mutation System (ARMS) and Mismatch Amplification Mutation Assay (MAMA) has been applied. Each assay has been pre-validated testing specificity and performances (linearity, PCR efficiency, interference limit, limit of detection, limit of quantification, precision and accuracy). Both the approaches achieve a precise and accurate estimation of the allele frequencies on pooled DNA samples in the range from 5 % to 95 % and don't require standard curves or calibrators. The lowest measurement that could be significantly distinguished from the background noise has been determined around the 1 % for both the approaches, allowing to extend the range of quantifications from 1 % to 99 %. Furthermore applicability of Real Time PCR assays for general diagnostic purposes is discussed.
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Affiliation(s)
- Elia Mattarucchi
- Department of Experimental and Clinical Biomedical Sciences, University of Insubria, Varese, Italy
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Nagy B, Bán Z, Lázár L, Nagy RG, Papp C, Tóth-Pál E, Papp Z. Rapid determination of trisomy 21 from amniotic fluid cells using single-nucleotide polymorphic loci. Prenat Diagn 2005; 25:1138-41. [PMID: 16231333 DOI: 10.1002/pd.1288] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Rapid detection of trisomy 21 is an important goal for prenatal genetic centers. Fluorescent-PCR and DNA fragment analysis was developed a decade ago and thousands of samples were analyzed in routine practice using this method. Quantitative real-time PCR with melting curve analysis using SNP markers for trisomy 21 detection was described recently. We studied the reliability of this method on a cohort of samples of Hungarian patients. METHODS DNA was isolated with silica adsorption method from amniotic fluid cells. We investigated 67 trisomy 21 and 62 diploid samples in the study. Quantitative real-time PCR was performed using hybridization probes combined with melting curve analysis. Peak areas under the derivative curves were determined and analyzed. RESULTS The SNP marker WIAF 899 was informative in 41.86% of cases and WIAF 2643 in 48.83%. The melting curve area ratios were significantly different between trisomic and normal cases for WIAF 899 (trisomic 0.5246 +/- 0.2498 vs 0.8347 +/- 0.5234; p < 0.001), while in the case of WIAF 2643, they were not different. CONCLUSION Combined and selected SNP markers could be valuable tools for rapid trisomy 21 detection in prenatal genetic screening.
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Affiliation(s)
- Bálint Nagy
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary.
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Current awareness in prenatal diagnosis. Prenat Diagn 2003. [DOI: 10.1002/pd.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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