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Won D, Yeom E, Shin S, Lee ST, Rak Choi J. Comparison of exon-level copy number variants in CytoScan XON assay and next-generation sequencing in clinical samples. Clin Chim Acta 2024:119703. [PMID: 38763467 DOI: 10.1016/j.cca.2024.119703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/12/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
BACKGROUND AND AIMS Next-generation sequencing (NGS)-based copy number variants (CNVs) have high false-positive rates. The fewer the exons involved, the higher the false-positive rate. A CytoScan XON assay was developed to assess exon-level CNVs. MATERIALS AND METHODS Twenty-three clinically relevant exon-level CNVs in 20 patient blood samples found in previous NGS studies were compared with the results from the CytoScan XON and multiplex ligation-dependent probe amplification (MLPA). RESULTS Fifteen of the 23 exon-level CNVs were consistent with the NGS results. Among these, eight were confirmed using MLPA. In six out of eight discrepancies between the CytoScan Xon and NGS, MLPA was performed, and three were negative, indicating that the CNVs in NGS were false positives. The CytoScan XON exhibits a sensitivity of 72.7% for small exon-level CNVs, along with a specificity of 100%. The assay could not detect the three exon-level CNVs in PKD1 and TSC2 that were detected using both NGS and MLPA. This could be due to the distribution of the probes in some areas, and the CNV-calling regions containing multiple exons. CONCLUSION The CytoScan XON assay is a promising complementary tool for the detection of exon-level CNVs, provided that the users carefully examine the distribution of probes and calling regions.
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Affiliation(s)
- Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea
| | - Eunju Yeom
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea.
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Sun H, Zheng J, Zhang Q, Ying F, Fu Y, Guan Y, Wu J, Zhou Y, Dong J, Xu M, Yang F, An N, Shi N, Zhang L, Zhu S, Liu J, Li M. Screening of Spinal Muscular Atrophy Carriers and Prenatal Diagnosis in Pregnant Women in Yancheng, China. Biochem Genet 2024:10.1007/s10528-024-10775-9. [PMID: 38581475 DOI: 10.1007/s10528-024-10775-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/06/2024] [Indexed: 04/08/2024]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder with an autosomal recessive inheritance pattern. Patients with severe symptoms may suffer respiratory failure, leading to death. The homozygous deletion of exon 7 in the SMN1 gene accounts for nearly 95% of all cases. Population carrier screening for SMA and prenatal diagnosis by amniocentesis for high-risk couples can assist in identifying the risk of fetal disease. We provided the SMA carrier screening process to 55,447 pregnant women in Yancheng from October 2020 to December 2022. Among them, 8185 participated in this process, with a participation rate of around 14.76% (95% CI 14.47-15.06%). Quantitative real-time polymerase chain reaction (qPCR) was used to detect deletions of SMN1 exons 7 and 8 (E7, E8) in screened pregnant women. 127 were identified as carriers (111 cases of E7 and E8 heterozygous deletions, 15 cases of E7 heterozygous deletions, and 1 case of E7 heterozygous deletions and E8 homozygous deletions), resulting in a carrying rate of around 1.55% (95% CI 1.30-1.84%). After genetic counseling, 114 spouses of pregnant women who tested positive underwent SMA carrier screening; three of them were screened as SMA carriers. Multiplexed ligation-dependent probe amplification (MLPA) was used for the prenatal diagnosis of the fetuses of high-risk couples. Two of them exhibited two copies of SMN1 exon 7 (normal), and the pregnancy was continued; one exhibited no copies of SMN1 exon 7 and exon 8 (SMA patient), and the pregnancy was terminated. Analyzing SMN1 mutations in Yancheng and provide clinical evidence for SMA genetic counseling and birth defect prevention. Interventional prenatal diagnosis for high-risk families can promote informed reproductive selection and prepare for the fetus's early treatment.
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Affiliation(s)
- Huilin Sun
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jianli Zheng
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Qing'e Zhang
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Feifei Ying
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Yadong Fu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Yongjuan Guan
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jing Wu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Yueyun Zhou
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jingjing Dong
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Mengjun Xu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Fangfang Yang
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Ning An
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Ning Shi
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Lu Zhang
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Shu Zhu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jianbing Liu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China.
| | - Min Li
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China.
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Jiang Y, Xia Z, Zhou Y, Lu X, Du X, Guo Q. Comparison of the accuracy of multiplex digital PCR versus multiplex ligation-dependent probe amplification in quantification of the survival of motor neuron genes copy numbers. Clin Chim Acta 2024; 553:117708. [PMID: 38097128 DOI: 10.1016/j.cca.2023.117708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
For over two decades, multiplex ligation-dependent probe amplification (MLPA) has served as the gold standard for genetic testing of spinal muscular atrophy. However, there is emerging evidence questioning the reliability of MLPA in determining the copy numbers (CNs) of the survival of motor neuron (SMN) gene in certain cases. Recently, digital polymerase chain reaction (dPCR) has shown potential for better performance in copy number variant detection. This study aimed to compare MLPA and dPCR in quantifying SMN1 and SMN2 CNs, identify reasons for observed discrepancies, and explore the clinical implications of false results. A total of 733 DNA samples, previously subjected to MLPA analysis, were tested using multiplex droplet dPCR assays. Samples exhibiting inconsistent results between the two methods underwent repeated dPCR assays. When inconsistencies persisted, a third method was employed for verification. Digital PCR yielded results consistent with those of MLPA in 94.4% (692/733) of samples. Forty-one cases exhibited quantitative disparities in SMN1 and/or SMN2 CNs between the two methods. Confirmatory tests revealed that 37 inaccurate results were produced by the MLPA analysis, whereas four were attributed to the dPCR method. The dPCR technique exhibits better accuracy than MLPA and is qualified for SMA genetic testing across various clinical scenarios.
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Affiliation(s)
- Yu Jiang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China; Biobank, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, PR China.
| | - Zhongmin Xia
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China; Biobank, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Xingxiu Lu
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Xiaohan Du
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China.
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Floriani MA, Santos AS, Diniz BL, Glaeser AB, Gazzola Zen PR, Machado Rosa RF. 22q11 Copy Number Variations in a Brazilian Cohort of Children with Congenital Heart Disorders. Mol Syndromol 2023; 14:1-10. [PMID: 36777701 PMCID: PMC9911999 DOI: 10.1159/000525247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/19/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction Congenital heart disease (CHD) is the most common type of congenital defect reported to be one of the leading causes of mortality in the first year of life. Microdeletion and microduplication syndromes (MMS) are associated with cardiac malformations. Understanding which genetic factors are involved in these conditions directly impacts treatment decisions. We aimed to identify the occurrence of genetic alterations and their association with MMS in CHD pediatric patients evaluated in a reference service of Southern Brazil. Methods Participants were recruited during 2010 in the intensive care unit of a pediatric hospital. MMs and regions of chromosome 22 were screened by SALSA MLPA Probemix P245 Microdeletion Syndromes-1A kit for detection of copy number variations (CNVs). Results MMS were detected in 11 from 207 patients (5.3%). Heterozygous deletion in the 22q11.2 chromosome region was the most prevalent CNV (5 from 11 patients). Also, atypical RTDR1 deletion and 22q11.2 duplication were detected. MLPA was able to reveal microdeletions in SNRPN and NF1 genes in patients with a normal karyotype and FISH. Conclusion Our study reports the prevalence and variability of genomic alterations associated with MMS in CHD pediatric patients. The results by MLPA are of great help in planning and specialized care.
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Affiliation(s)
- Maiara A. Floriani
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | | | - Bruna L. Diniz
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | - Andressa B. Glaeser
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | - Paulo R. Gazzola Zen
- Department of Internal Medicine, Clinical Genetics, UFCSPA, Porto Alegre, Brazil,Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, Brazil
| | - Rafael F. Machado Rosa
- Department of Internal Medicine, Clinical Genetics, UFCSPA, Porto Alegre, Brazil,Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, Brazil,*Rafael Fabiano Machado Rosa,
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Almeida VT, Chehimi SN, Gasparini Y, Nascimento AM, Carvalho GF, Montenegro MM, Zanardo ÉA, Dias AT, Assunção NA, Kim CA, Kulikowski LD. Cri-du-Chat Syndrome: Revealing a Familial Atypical Deletion in 5p. Mol Syndromol 2023; 13:527-536. [PMID: 36660031 PMCID: PMC9843554 DOI: 10.1159/000524371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 03/29/2022] [Indexed: 01/22/2023] Open
Abstract
Introduction Cri-du-chat syndrome is generally diagnosed when patients present a high-pitched cry at birth, microcephaly, ocular hypertelorism, and prominent nasal bridge. The karyotype is useful to confirm deletions in the short arm of chromosome 5 (5p-) greater than 10 Mb. In cases of smaller deletions, it is necessary to resort to other molecular techniques such as fluorescence in situ hybridization, multiplex ligation-dependent probe amplification (MLPA) or genomic array. Case Presentation We report a family with an atypical deletion in 5p (mother and 2 children) and variable phenotypes compared with the literature. We applied a P064 MLPA kit to evaluate 5p- in the mother and the 2 children, and we used the Infinium CytoSNP-850K BeadChip genomic array to evaluate the siblings, an 11-year-old boy and a 13-year-old girl, to better define the 5p breakpoints. Both children presented a high-pitched cry at birth, but they did not present any of the typical physical features of 5p- syndrome. The MLPA technique with 5 probes for the 5p region revealed that the patients and their mother presented an atypical deletion with only 4 probes deleted (TERT_ex2, TERT_ex13, CLPTM1L, and IRX4). The genomic array performed in the siblings' samples revealed a 6.2-Mb terminal deletion in 5p15.33p15.32, which was likely inherited from their mother, who presented similar molecular features, seen in MLPA. Discussion The sparing of the CTNND2 gene, which is associated with cerebral development, in both siblings may explain why these 2 patients had features such as better communication skills which most patients with larger 5p deletions usually do not present. In addition, both patients had smaller deletions than those found in patients with a typical 5p- phenotype. This report demonstrates the utility of genomic arrays as a diagnostic tool to better characterize atypical deletions in known syndromes such as 5p- syndrome, which will allow a better understanding of the genotype-phenotype correlations.
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Affiliation(s)
- Vanessa T. Almeida
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil,*Vanessa T. Almeida,
| | - Samar N. Chehimi
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Yanca Gasparini
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Amom M. Nascimento
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Gleyson F.S. Carvalho
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Marília M. Montenegro
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Évelin Aline Zanardo
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Alexandre T. Dias
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Nilson A. Assunção
- Departamento de Química, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Chong A. Kim
- Unidade de Genetica, Departamento de Pediatria, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leslie D. Kulikowski
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
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Takkar A, Arora V, Saxena R, Kumar P, Verma IC. Reversal of Clinical Phenotype of Sotos Syndrome Due to Microduplication of NSD1 Gene. Indian J Pediatr 2022; 89:1137-1139. [PMID: 35925544 DOI: 10.1007/s12098-022-04325-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/27/2022] [Indexed: 11/05/2022]
Abstract
Sotos syndrome is caused by heterozygous pathogenic variants or deletions in the long arm of chromosome 5 encompassing NSD1. The cardinal features of this condition are overgrowth, macrocephaly, and intellectual disability. Conversely, duplications leading to an extra copy of NSD1 result in a reverse phenotype that is observed in duplication/microduplication of the 5q region. An 11-y-old boy was referred to the genetics clinic in view of global developmental delay and general tonic-clonic seizures. Whole-exome sequencing revealed the presence of likely pathogenic copy number variation, a contiguous duplication of size ~4.11 Mb spanning genomic location chr5: g.(?_171773956)_(175880045_?)dup. After validation by multiplex ligation-dependent probe amplification (MLPA) and phenotypic correlation, a diagnosis of reverse Sotos syndrome was confirmed. As far as the authors know, this is the first patient report of reverse Sotos syndrome from India. It highlights the peculiar presentation of this disorder as well as discusses the increasing potential of exome sequencing to screen for copy number variations (CNVs).
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Affiliation(s)
- Aashita Takkar
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Veronica Arora
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India.
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Praveen Kumar
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - I C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
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Anno M, Izawa S, Fujioka Y, Matsuzawa K, Saito K, Hikita K, Makishima K, Nosaka K, Takenaka A, Usui T, Yamamoto K. Retroperitoneal paraganglioma with loss of heterozygosity of the von Hippel-Lindau gene: a case report and review of the literature. Endocr J 2022; 69:1137-1147. [PMID: 35466127 DOI: 10.1507/endocrj.ej21-0611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant disease related to germline mutations in VHL. In VHL disease, pheochromocytoma develops in 10%-20% of patients because of germline mutations and loss of heterozygosity of VHL. However, the rate of paraganglioma associated with VHL is low compared with that of pheochromocytoma, and the reason is unknown. In this study, we performed germline and somatic mutation analyses of retroperitoneal paraganglioma that developed in a patient with clinically diagnosed VHL disease and investigated the tumorigenic mechanism of paraganglioma. The patient was a 25-year-old woman who was considered to have VHL disease on the basis of her family history. She was referred to our clinic to investigate a tumor at the bifurcation of the common iliac artery. The tumor was diagnosed as retroperitoneal paraganglioma by clinical evaluations. A left renal cell carcinoma was also suspected. Polymerase chain reaction direct sequencing analysis and polymorphic microsatellite analysis within the VHL locus suggested that loss of heterozygosity of VHL was associated with paraganglioma and renal cell carcinoma. Multiplex ligation-dependent probe amplification analysis showed a loss of the copy number of VHL exons in paraganglioma. These results suggest that VHL disease contributes to the development of paraganglioma. A literature review showed no reported common missense variants involved in the progression of paraganglioma. The loss of heterozygosity of VHL can be a tumorigenic mechanism of retroperitoneal paraganglioma in VHL disease. However, the low rate of paraganglioma compared with pheochromocytoma is not explained by their genetic background alone.
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Affiliation(s)
- Mari Anno
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Shoichiro Izawa
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Yohei Fujioka
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kazuhiko Matsuzawa
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kohei Saito
- Center for Diabetes, Endocrinology and Metabolism, Shizuoka Prefectural Hospital, Shizuoka 420-8527, Japan
| | - Katsuya Hikita
- Division of Urology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Karen Makishima
- Division of Pathology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kanae Nosaka
- Division of Pathology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Atsushi Takenaka
- Division of Urology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Takeshi Usui
- Research Support Center, Shizuoka Prefectural Hospital, Shizuoka 420-8527, Japan
- Shizuoka Graduate University of Public Health, Shizuoka 420-0881, Japan
| | - Kazuhiro Yamamoto
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
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Zamani GR, Mohammadi MF, Tavasoli AR, Ashrafi MR, Hosseinpour S, Ghabeli H, Pourbakhtyaran E, Haghighi R, Hosseiny SMM, Mohammadi P, Heidari M. Genetic Analysis of Forty MLPA-Negative Duchenne Muscular Dystrophy Patients by Whole-Exome Sequencing. J Mol Neurosci 2022. [PMID: 35218518 DOI: 10.1007/s12031-022-01980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
Abstract
This manuscript aimed to determine the underlying point mutations causing Duchenne muscular dystrophy (DMD) in a heterogeneous group of Iranian patients, who are clinically suspected. Whole-exome sequencing was utilized to detect disease-causing variants in 40 MLPA-negative DMD patients. Disease-causing variants were detected in the DMD gene in 36/40 of the patients (90%), and 4/40 of them (10%) remained undiagnosed. WES analysis revealed that nonsense variant was the most common type in our study (23/36 of the cases). Besides, 12/36 of the cases had frameshift variant, and one of the patients had a likely pathogenic splice variant in the DMD gene. Carrier testing revealed that 21/40 of the mothers had the identified variant. Therefore, most variants were inherited (58.3%), while 19/40 were de novo (41. 7%). The present study has demonstrated the importance of performing WES to detect disease-causing point mutations in MLPA-negative DMD patients and to identify carrier females. Due to regulatory challenges, the clinical development of therapeutic approaches is time-consuming and may not be available to all patients shortly. Therefore, it appears that the techniques used to accurately detect disease-causing variants in carrier mothers are a more efficient solution to prevent the increased prevalence of DMD.
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Lau NKC, Lee HHC, Chen SPL, Ng CWY, Mak CM, Chong YK, Tong TTY, Leung MT, Shek CC, Yuen YP, Ching CK. In-house multiplex ligation-dependent probe amplification assay for citrin deficiency: analytical validation and novel exonic deletions in SLC25A13. Pathology 2021; 53:867-874. [PMID: 34045052 DOI: 10.1016/j.pathol.2021.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/11/2021] [Accepted: 02/05/2021] [Indexed: 11/26/2022]
Abstract
Citrin deficiency is one of the most common inborn errors of metabolism in East Asians, which may manifest as neonatal cholestasis, failure to thrive and dyslipidaemia, or recurrent hyperammonaemic encephalopathy. Its molecular diagnosis requires confirmation of the presence of biallelic pathogenic variants in SLC25A13 gene by sequencing, and analysis for a common insertion IVS16ins3kb. However, patients with compatible biochemical features but only one monoallelic pathogenic variant have remained a diagnostic challenge. Here we report the development, validation and application of a multiplex ligation-dependent probe amplification (MLPA) assay using an in-house oligonucleotide probemix and a customised Coffalyer.NET worksheet for detection of exonic copy number variations in SLC25A13. With this MLPA assay, we successfully identified the presence of a heterozygous exonic deletion in SLC25A13 in three of 15 (20%) unrelated individuals with only one monoallelic pathogenic variant detected using conventional methods. Three exonic deletions, two novel involving exon 14 and one reported involving exon 5, were subsequently confirmed with Sanger sequencing. In summary, we developed, evaluated, and demonstrated the clinical utility of an in-house MLPA assay to look for exonic deletions in SLC25A13 in patients with citrin deficiency. With the discovery of novel deletions, MLPA should be considered a test of choice for molecular diagnosis of citrin deficiency when the sequencing result is inconclusive.
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Affiliation(s)
- Nike Kwai Cheung Lau
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Hencher Han Chih Lee
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Sammy Pak Lam Chen
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Candy Wai Yan Ng
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Chloe Miu Mak
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Yeow Kuan Chong
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Tammy Tsz Yan Tong
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Mei Tik Leung
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Chi Chung Shek
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Yuet Ping Yuen
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Chor Kwan Ching
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China.
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Srinivasan VK, Naseem S, Varma N, Lad DP, Malhotra P. Genomic alterations in chronic lymphocytic leukemia and their correlation with clinico-hematological parameters and disease progression. Blood Res 2020; 55:131-138. [PMID: 32747613 PMCID: PMC7536571 DOI: 10.5045/br.2020.2020080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/29/2020] [Accepted: 07/01/2020] [Indexed: 01/07/2023] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, which is attributed to differences in the genetic characteristics of the leukemic clone. We studied the genomic profile of 52 treatment-naïve CLL patients. Methods Genetic analysis was performed by multiplex ligation-dependent probe amplification (MLPA) using the SALSA P038 Probemix (MRC Holland, Amsterdam), which contains probes for 2p (MYCN,ALK,REL), 6q, 8p (TNFRSF10A/B), 8q (EIF3H,MYC), 9p21 (CDKN2A/B), 10q (PTEN), 11q (ATM, RDX, PPP2R1B, CADM1), chromosome 12, 13q14 (RB1, DLEU1/2/7, KCNRG, MIR15A), 14q, 17p (TP53) and chromosome 19, and for NOTCH1 7541-7542delCT, SF3B1 K700E, and MYD88 L265P mutations. Results The median age was 65 years (malefemale=21). The median hemoglobin, total leuko- cyte, and platelet counts were 12.4 g/dL, 57.7×109/L, and 176.5×109/L, respectively. At least one genetic abnormality was observed in 34 (65%) patients. The most common abnormality was del(13q14) (deleted DLEU2 and DLEU1/RB1 genes), which was observed in 22 (42%) cases, followed by trisomy 12 [7 (13%) cases]. Del(11q) (deleted ATM, RDX11/PPP2R1B-4) and del(17p) (deleted TP53) were present in 5 (10%) and 2 (4%) cases, respectively. 19p13.2 (CDKN2D-2) amplification and NOTCH1 mutation were found in one case each. Conclusion Genetic abnormalities are commonly (65%) observed in CLL patients. Del(13q), which is associated with DLEU2 and DLEU1/RB1 gene deletion, was the most common. Compared with other abnormalities, del(11q) and del(17p) patients presented with cytopenia and higher Binet stage, while those with del(13q14) had a longer time to first treatment.
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Affiliation(s)
- Vishrut K Srinivasan
- Departments of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shano Naseem
- Departments of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Varma
- Departments of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepesh P Lad
- Departments of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Departments of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Aoto Y, Kise T, Nakanishi K, Nagano C, Horinouchi T, Yamamura T, Ishiko S, Sakakibara N, Shima Y, Morisada N, Iijima K, Nozu K. A case with somatic and germline mosaicism in COL4A5 detected by multiplex ligation-dependent probe amplification in X-linked Alport syndrome. CEN Case Rep 2020; 9:431-436. [PMID: 32621070 DOI: 10.1007/s13730-020-00503-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/28/2020] [Indexed: 01/19/2023] Open
Abstract
X-linked Alport syndrome (XLAS) is a progressive hereditary kidney disease caused by mutations in the COL4A5 gene encoding the type IV collagen α5 chain. To date, 11 cases having somatic mosaic variants in COL4A5 have been reported; however, all of them involved single-nucleotide variations (SNVs). Here, we report a female XLAS patient with somatic mosaicism identified by copy number variation (CNV) in COL4A5. The case was a 35-year-old female, the mother of the proband, whose only clinical symptom was hematuria. The proband, who was the son of this patient, was diagnosed with XLAS by gene testing, which showed a large hemizygous deletion from exon 3-51 in COL4A5 detected by next-generation sequencing and then confirmed by multiplex ligation-dependent probe amplification (MLPA). Then, MLPA analysis revealed that the female patient had the same deletion with only a 20% copy number reduction compared with a normal female control; she was thus diagnosed with XLAS with somatic mosaicism. CNVs in COL4A5 are relatively rare and, to the best of our knowledge, somatic mosaic variants with CNVs have never been reported. This case clearly featured a germline variant because the patient's son exhibited XLAS. This is thus the first case report on an XLAS patient having CNV in COL4A5 with somatic mosaicism. The obtained findings were very important for the genetic counseling of this family.
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Affiliation(s)
- Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - Tomoo Kise
- Division of Pediatric Nephrology, Okinawa Prefectural Nanbu Medical Center, Children's Medical Center, 118-1 Arakawa, Haebaru-cho, Simajiri-gun, Okinawa, 901-1105, Japan
| | - Koichi Nakanishi
- Department of Pediatrics, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Nakagami-gun, Okinawa, 903-0125, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
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Franchim CS, Soares-Junior JM, Serafini PC, Monteleone PAA, Coccuzza MS, Zanardo EA, Montenegro MM, Dias AT, Kulikowski LD, Baracat EC. Efficacy of MLPA for detection of Y-chromosome microdeletions in infertile Brazilian patients. J Assist Reprod Genet 2020; 37:1251-9. [PMID: 32394194 DOI: 10.1007/s10815-020-01777-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 04/08/2020] [Indexed: 10/24/2022] Open
Abstract
PURPOSE Worldwide publications follow the gold standard method-the polymerase chain reaction (PCR)-for detecting Y-chromosome microdeletions; however, markers are frequently variable between the studies. Can we detect the deletions by another molecular method with more genomic coverage? The Y chromosome harbors several different genes responsible for testicular development and spermatogenesis, and its repetitive conformation predisposes it to complex rearrangements that have clinical impact. Our aim was to evaluate a molecular diagnostic method, the Multiplex Ligand Probe-dependent Amplification (MLPA), which is also a valuable ancillary method for the identification of deletions, duplications, and rearrangements in a single and faster reaction, leading to a better comprehension of patients' phenotypes, and should be considered a useful tool for detection of Y chromosome deletions. METHODS This is a study of diagnostic accuracy (transversal prospective study) conducted to investigate Y-chromosome deletions in 84 individuals through PCR and MLPA methods. Forty-three infertile men (azoospermic and oligozoospermic) and 41 controls (40 fertile men and 1 normal karyotyped woman) were analyzed by PCR and MLPA techniques. RESULTS We diagnosed seven (7) deletions (16.2%) by PCR and 9 with MLPA (21%). In addition, we found five (5) duplications and a suggestive mosaic. CONCLUSION Our results demonstrate that MLPA technique is valuable in the investigation of microdeletions and microduplications. Besides deletions, duplications can cause instability of chromosome genes, possibly leading to infertility. Both studied techniques provide an advantageous diagnostic strategy, thus enabling a better genetic counseling.
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Lu MY, Wang WC, Hou TC, Kuo CY, Lai YC. Methylation Statuses of H19DMR and KvDMR at WT2 in Wilms Tumors in Taiwan. Pathol Oncol Res 2020; 26:2153-9. [PMID: 32157637 DOI: 10.1007/s12253-020-00802-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/04/2020] [Indexed: 12/12/2022]
Abstract
Wilms tumor is the most common pediatric renal malignancy. Several genetic loci have been shown to be associated with its formation. Genetic or epigenetic aberrations at WT1 and WT2 loci have been implicated in the etiology of the majority of sporadic Wilms tumors. In our previous study, most Wilms tumors tested negative for both constitutional mutations and somatic mutations in the WT1 gene. Thus, WT2 may play an important role in these tumors. In the present study, we analyzed the methylation statuses of WT2 at 11p15 using methylation sensitive multiplex ligation-dependent probe amplification in six Wilms tumors. Paternal uniparental disomy at WT2 was observed in two Wilms tumors with epithelial components due to hypermethylation at H19DMR and hypomethylation at KvDMR. Our findings highlight the benefits of testing for 11p15 epigenetic abnormalities to identify Wilms tumors with epithelial components.
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Zhang J, Ma D, Liu G, Wang Y, Liu A, Li L, Luo C, Hu P, Xu Z. Genetic analysis of 62 Chinese families with Duchenne muscular dystrophy and strategies of prenatal diagnosis in a single center. BMC Med Genet 2019; 20:180. [PMID: 31727011 DOI: 10.1186/s12881-019-0912-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/25/2019] [Indexed: 12/11/2022]
Abstract
Background Duchenne muscular dystrophy (DMD) is a severe X-linked recessive neuromuscular disorder. Patients with DMD usually have severe and fatal symptoms, including progressive irreversible muscle weakness and atrophy complicated with gastrocnemius muscle pseudohypertrophy. DMD is caused by mutations in the dystrophin-encoding DMD gene, including large rearrangements and point mutations. This retrospective study was aimed at supplying information on our 4-year clinical experience of DMD genetic and prenatal diagnosis at the Department of Prenatal Diagnosis in Women’s Hospital of Nanjing Medical University. Methods Multiplex ligation-dependent probe amplification (MLPA) was used to detect the exon deletions or duplications. And Ion AmpliSeq™ panel for inherited disease was used as the next-generation sequencing (NGS) method to identify the point mutations in exons of DMD gene, but the introns were not sequenced. Results In this study, the large deletions and duplications of DMD gene were detected in 32 (51.6%) of the 62 families, while point mutations were detected in 20 families (32.3%). The remaining 10 families with a negative genetic diagnosis need to be reevaluated for clinical symptoms or be detected by other molecular methods. Notably, six novel mutations were identified, including c.412A > T(p.Lys138*), c.2962delT(p.Ser988Leufs*16), c.6850dupA (p.Ser2284Lysfs*7), c.5139dupA (p.Glu 1714Argfs*5), c.6201_6203delGCCins CCCA(p.Val2069Cysfs*14) and c.10705A > T (p.Lys3569*). In 52 families with positive results, 45 mothers (86.5%) showed positive results during carrier testing and de novo mutations arose in 7 probands. The prenatal diagnosis was offered to 34 fetuses whether the pregnant mother was a carrier or not. As a result, eight male fetuses were affected, three female fetuses were carriers, and the remaining fetuses had no pathogenic mutation. Conclusions This study reported that MLPA and NGS could be used for screening the DMD gene mutations. Furthermore, the stepwise procedure of prenatal diagnosis of DMD gene was shown in our study, which is important for assessing the mutation type of fetuses and providing perinatal care in DMD high-risk families.
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Kim HJ, Kim SK, Yoo KY, Lee KO, Yun JW, Kim SH, Kim HJ, Park SK. Molecular Genetics of von Willebrand Disease in Korean Patients: Novel Variants and Limited Diagnostic Utility of Multiplex Ligation-Dependent Probe Amplification Analyses. Ann Lab Med 2019; 39:545-551. [PMID: 31240882 PMCID: PMC6660331 DOI: 10.3343/alm.2019.39.6.545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/01/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND von Willebrand disease (VWD), characterized by quantitative or qualitative defects of von Willebrand factor (VWF), is the most common inheritable bleeding disorder. Data regarding the genetic background of VWD in Korean patients is limited. To our knowledge, this is the first comprehensive molecular genetic investigation of Korean patients with VWD. METHODS Twenty-two unrelated patients with VWD were recruited from August 2014 to December 2017 (age range 28 months-64 years; male:female ratio 1.2:1). Fifteen patients had type 1, six had type 2, and one had type 3 VWD. Blood samples were collected for coagulation analyses and molecular genetic analyses from each patient. Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed. In patients without sequence variants, multiplex ligation-dependent probe amplification (MLPA) was performed to detect dosage variants. We adapted the American College of Medical Genetics and Genomics guidelines for variant interpretation and considered variants of uncertain significance, likely pathogenic variants, and pathogenic variants as putative disease-causing variants. RESULTS VWF variants were identified in 15 patients (68%): 14 patients with a single heterozygous variant and one patient with two heterozygous variants. The variants consisted of 13 missense variants, one small insertion, and one splicing variant. Four variants were novel: p.S764Efs*16, p.C889R, p.C1130Y, and p.W2193C. MLPA analysis in seven patients without reportable variants revealed no dosage variants. CONCLUSIONS This study revealed the spectrum of VWF variants, including novel ones, and limited diagnostic utility of MLPA analyses in Korean patients with VWD.
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Affiliation(s)
- Hee Jung Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Laboratory Medicine, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, Korea
| | - Soon Ki Kim
- Department of Pediatrics, College of Medicine, Inha University Hospital, Incheon, Korea
| | | | - Ki O Lee
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Jae Won Yun
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Hee Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Sang Kyu Park
- Department of Pediatrics, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea.
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Luo D, Linpeng S, Zeng L, Tan H, Li Z, Wu L. Molecular genetic study of 59 Chinese Oculocutaneous albinism families. Eur J Med Genet 2019; 62:103709. [PMID: 31229681 DOI: 10.1016/j.ejmg.2019.103709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/24/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Oculocutaneous albinism is an autosomal recessive disorder characterized by either a complete lack of or reduction in melanin biosynthesis in the skin, hair, and eyes. The aim of the present study was to identify the molecular basis for 59 Chinese OCA families. In this study, compound heterozygous or homozygous pathogenic variants were found in 53 families, 4 families possessed only one heterozygous variant, and the pathogenic variants of 2 families remain undiscovered by using Sanger sequencing, whole exome sequencing and multiplex ligation-dependent probe amplification. We have identified a total of 55 variants including 21 novel variants in TYR, OCA2, SLC45A2, SLC24A5, and HPS1. The 21 novel variants include 11 missense changes, 4 nonsense changes, 2 splice site changes, 1 frameshift and 3 gross deletions. Forty-six variants including 14 novel variants were segregated with the phenotype in 37 families. We conducted RT-PCR of the novel splicing site variant (c.399-14G > A) of HPS1 and verified that the variant would result in the inclusion of 12 bp of intronic material in exon 6 of HPS1. The results of platelet whole mount electron microscopy further confirmed the diagnosis of HPS1. These novel variants identified in our study expand the mutational spectrum of the disease, which contributes to prenatal diagnosis and genetic counselling.
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Affiliation(s)
- Dan Luo
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Siyuan Linpeng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lanlan Zeng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Hu Tan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Zhuo Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lingqian Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
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Wang W, Qin W, Ge H, Kong X, Xie C, Tang Y, Li M. Clinical and molecular characteristics of thirty NF1 variants in Chinese patients with neurofibromatosis type 1. Mol Biol Rep 2019; 46:4349-4359. [PMID: 31201679 DOI: 10.1007/s11033-019-04888-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/15/2019] [Indexed: 01/29/2023]
Abstract
Neurofibromatosis type 1 (NF1) is a common autosomal dominant tumor-predisposition disorder that mainly impacts the nervous system and skin. Since the full clinical presentation of NF1 depends on age, it can be difficult to make an early and definite diagnosis in paediatric patients without family history who only exhibited multiple cafè-au-lait spots, highlighting the need for mutational analysis. A combination of techniques was conducted in 30 families with NF1, including multi-gene panels, direct sequencing, cDNA sequencing and multiplex ligation-dependent probe amplification. Thirty variants were identified in 36 patients from the 30 families, among which ten variants were novel. As a result, we confirmed that the combination of techniques were highly accurate and sensitive for identifying pathogenic variants in patients clinically suspected of having NF1, in particular, for patients who only present with multiple cafè-au-lait spots.
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Affiliation(s)
- Wen Wang
- Departments of Dermatology and Venereology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Hongsong Ge
- Departments of Dermatology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
| | | | - Chao Xie
- Department of Paediatrics, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China.
| | - Ming Li
- Departments of Dermatology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Liu Y, Wang M, Chen Q, Zheng Q, Li G, Cheng Q, Liu S, Ye S. A novel heterozygous large deletion of MSH6 gene in a Chinese family with Lynch syndrome. Gene 2019; 704:103-112. [PMID: 30974197 DOI: 10.1016/j.gene.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/27/2022]
Abstract
Lynch syndrome (LS) is a common cancer syndrome that is inherited in an autosomal dominant manner. Its pathogenesis is thought to be closely related to germline mutations of mismatch repair (MMR) genes such as the MLH1, MSH2, PMS2 and MSH6 genes. This study identifies a Chinese family with LS clinically diagnosed according to the Amsterdam II criteria. In these patients, immuno-histochemical staining showed negative MSH6 expressions but positive MLH1, MSH2, and PMS2 expressions. In order to further explore the molecular biology of this LS family, we used targeted next-generation sequencing (NGS) and Multiplex ligation dependent probe amplification (MLPA) to identify the mutation and verify the authenticity of the mutation in 15 family members. For NGS, two panels have been used, one is of MLH1, MSH2, PMS2 and MSH6 genes, the other one is of 139 cancer genetic susceptibility genes. And for the large deletions/duplications can also be identified by NGS panel, an adjusted data analysis strategy of NGS has been used. As a result, we identified a novel heterozygous large deletion in MSH6 gene that was found to be co-segregated among affected family members. This deletion results in the loss of a 3246 bp-sized fragment in MSH6 gene exons 5-9 which represents the coding regions of the MSH6 ATPase domain. This novel mutation has yet to be documented in the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database. This mutation resulted in MSH6 protein losing gene mismatch repair function, and further caused the microsatellite instable. We speculate that this mutation may significantly impact MMR function through impaired ATP domain function. Theoretically, this proband would likely benefit from PD-1 immune check-point blockade therapy, but conversely, we observed that tumors appeared to rapidly progress after 4 sessions of anti-PD-1 treatment. Further studies to validate the effectiveness of anti-PD-1 treatments in carriers of this mutation are necessary.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biobank, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Mingwei Wang
- Department of Pathology, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Qiongrong Chen
- Department of Pathology, Zhongnan Hospital, 169 Donghu Road, Wuhan, Hubei, China
| | - Qiaosong Zheng
- Beijing Genetron Health Co., Ltd, Changping, Beijing, China
| | - Guangyu Li
- Beijing Genetron Health Co., Ltd, Changping, Beijing, China
| | - Qian Cheng
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Sanhe Liu
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Shengwei Ye
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China.
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Capkova P, Srovnal J, Capkova Z, Staffova K, Becvarova V, Trkova M, Adamova K, Santava A, Curtisova V, Hajduch M, Prochazka M. MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PeerJ 2019; 6:e6183. [PMID: 30647996 PMCID: PMC6330045 DOI: 10.7717/peerj.6183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 11/28/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. METHOD We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. RESULT Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)-likely pathogenic, 10 VOUS-uncertain, and 58 VOUS-likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS-likely pathogenic, and six designated as VOUS-likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS-likely pathogenic, or VOUS-uncertain in multiple patients. Moreover, the studied ASD cohort exhibited significant (p < 0.05) enrichment of duplications encompassing DOCK8. CONCLUSION Multiplex ligation-dependent probe amplification and CMA yielded concordant results for 12 patients bearing CNV designated pathogenic or VOUS-likely pathogenic. Unambiguous diagnoses were achieved for eight patients (corresponding to 8.7% of the total studied population) by both MLPA and CMA, for one (1.09%) patient by karyotyping, and for one (1.09%) patient by FRAXA testing. MLPA and CMA thus achieved identical reliability with respect to clinically relevant findings. As such, MLPA could be useful as a fast and inexpensive test in patients with syndromic autism. The detection rate of potentially pathogenic variants (VOUS-likely pathogenic) achieved by CMA was higher than that for MLPA (13.04% vs. 4.35%). However, there was no corresponding difference in the rate of unambiguous diagnoses of ASD patients. In addition, the results obtained suggest that DOCK8 may play a role in the etiology of ASD.
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Affiliation(s)
- Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Katerina Staffova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | | | | | - Katerina Adamova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Alena Santava
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
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20
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Abstract
Genome diversity comprises single nucleotide polymorphisms, deletions, insertions, and duplications. These gains and losses of DNA segments leading to rearrangements of sequences are termed copy number variations (CNVs). CNVs may disrupt genes and/or alter gene dosage and, thereby, have an impact on both protein-coding and noncoding genes. Accordingly, they affect the activity of various signaling pathways and influence the cell phenotype. They are associated with risks for several severe diseases, in particular cancer. In the current chapter, I introduce a rapid profiling method to identify CNVs in circulating, cell-free DNA by multiplex ligation-dependent probe amplification (MLPA). MLPA represents an efficient method for the detection of CNVs among numerous genes on various chromosomal regions in serum.
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Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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21
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Lu C, Li LX, Dong HL, Wei Q, Liu ZJ, Ni W, Gitler AD, Wu ZY. Targeted next-generation sequencing improves diagnosis of hereditary spastic paraplegia in Chinese patients. J Mol Med (Berl) 2018; 96:701-712. [PMID: 29934652 DOI: 10.1007/s00109-018-1655-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/01/2018] [Accepted: 05/07/2018] [Indexed: 12/30/2022]
Abstract
Hereditary spastic paraplegia (HSP) is a heterogeneous group of neurodegenerative diseases characterized by progressive weakness and spasticity of lower limbs. To clarify the genetic spectrum and improve the diagnosis of HSP patients, targeted next-generation sequencing (NGS) was applied to detect the culprit genes in 55 Chinese HSP pedigrees. The classification of novel variants was based on the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. Patients remaining negative following targeted NGS were further screened for gross deletions/duplications by multiplex ligation-dependent probe amplification (MLPA). We made a genetic diagnosis in 61.8% (34/55) of families and identified 33 mutations, including 14 known mutations and 19 novel mutations. Of them, one was de novo mutation (NIPA1: c.316G>A). SPAST mutations (22/39, 56.4%) are the most common in Chinese AD-HSP followed by ATL1 (4/39, 10.3%). Moreover, we identified the third BSCL2 mutation (c.1309G>C) related to HSP by further functional studies and first reported the KIF1A mutation (c.304G>A) in China. Our findings broaden the genetic spectrum of HSP and improve the diagnosis of HSP patients. These results demonstrate the efficiency of targeted NGS to make a more rapid and precise diagnosis in patients with clinically suspected HSP. KEY MESSAGES We made a genetic diagnosis in 61.8% of families and identified 33 mutations. SPAST mutations are the most common in Chinese AD-HSP followed by ATL1. Our findings broaden the genetic spectrum and improve the diagnosis of HSP.
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Affiliation(s)
- Cong Lu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Li-Xi Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Hai-Lin Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Qiao Wei
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Zhi-Jun Liu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
- Joint Institute for Genetics and Genome Medicine Between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China.
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22
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Kim B, Lee ST, Kim S, Choi JR, Kim HO. Application of Multiplex Ligation-Dependent Probe Amplification Assay for Genotyping Major Blood Group Systems Including DEL Variants in the D-Negative Korean Population. Ann Lab Med 2018; 38:32-38. [PMID: 29071816 PMCID: PMC5700144 DOI: 10.3343/alm.2018.38.1.32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/02/2017] [Accepted: 08/31/2017] [Indexed: 01/22/2023] Open
Abstract
Background The DEL blood type, a very weak D variant, is a major concern in the field of transfusion medicine because of its potential to cause anti-D alloimmunization. We investigated the molecular basis of serologically D-negative phenotypes, including the DEL type, and the distribution of other blood group systems in the Korean population using the recently developed multiplex ligation-dependent probe amplification (MLPA) assay. Methods Blood group genotyping using the MLPA assay and RhCE phenotyping were performed on randomly selected 95 D-negative red blood cell products. The MLPA results were verified by multiplex PCR for the RHD promoter, exons 4, 7, and 10 and by direct sequencing of RHD exon 9. Results Out of 95 cases, total deletion of the RHD was observed in 74 cases (77.9%) and four cases (4.2%) had an RHD-CE-D hybrid allele. The other 17 cases (17.9%) had an RHD(1227G>A) allele, which was further confirmed by sequencing analysis. The RhCE phenotypes of RHD(1227G>A) alleles were composed of 14 Cce and 3 CcEe, and all 60 cases of the ce phenotype were revealed to have a total deletion of the RHD. Genotyping results and allele distribution of the other 17 blood group systems were consistent with previous reports on the East Asian population. Conclusions MLPA assay correctly determined RHD genotype, including RHD-CE-D hybrid alleles or RHD(1227G>A) allele, and other clinically relevant blood group genotypes in D-negative Koreans. The use of MLPA assay on serologically D-negative individuals may help improve transfusion safety by preventing anti-D alloimmunization.
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Affiliation(s)
- Banseok Kim
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Seung Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Ok Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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23
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Sonoda K, Ohno S, Ozawa J, Hayano M, Hattori T, Kobori A, Yahata M, Aburadani I, Watanabe S, Matsumoto Y, Makiyama T, Horie M. Copy number variations of SCN5A in Brugada syndrome. Heart Rhythm 2018; 15:1179-1188. [PMID: 29574140 DOI: 10.1016/j.hrthm.2018.03.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND Loss-of-function mutations in SCN5A are associated in ∼20% of Brugada syndrome (BrS) patients. Copy number variations (CNVs) have been shown to be associated with several inherited arrhythmia syndromes. OBJECTIVE The purpose of this study was to investigate SCN5A CNVs among BrS probands. METHODS The study cohort consisted of 151 BrS probands who were symptomatic or had a family history of BrS, sudden death, syncope, or arrhythmic diseases. We performed sequence analysis of SCN5A by the Sanger method. For detecting CNVs in SCN5A, we performed multiplex ligation-dependent probe amplification analysis of the 151 BrS probands. RESULTS We identified pathogenic SCN5A mutations in 20 probands by the Sanger method. In 140 probands in whom multiplex ligation-dependent probe amplification was successfully performed, 4 probands were found to present different CNVs (deletion in 3 and duplication in 1). Three of them had fatal arrhythmia events; the remaining 1 was asymptomatic but had a family history. Mean age at diagnosis was 23 ± 14 years. All of the baseline 12-lead electrocardiograms showed PQ-interval prolongation. The characteristics of these 4 probands with CNVs were similar to those of the probands with mutations leading to premature truncation of the protein or missense mutations causing peak INa reduction >90%. CONCLUSION We identified SCN5A CNVs in 2.9% of BrS probands who were symptomatic or had a family history.
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Affiliation(s)
- Keiko Sonoda
- Department of Cardiovascular Biology and Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Department of Molecular Biology, National Cerebral and Cardiovacular Center, Suita, Japan
| | - Seiko Ohno
- Department of Molecular Biology, National Cerebral and Cardiovacular Center, Suita, Japan; Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Otsu, Japan; Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Junichi Ozawa
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Mamoru Hayano
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tetsuhisa Hattori
- Department of Molecular Biology, National Cerebral and Cardiovacular Center, Suita, Japan; Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Atsushi Kobori
- Department of Cardiovascular Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Mitsuhiko Yahata
- Department of Cardiovascular Medicine, Shizuoka General Hospital, Shizuoka, Japan
| | - Isao Aburadani
- Department of Cardiovascular Medicine, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Seiichi Watanabe
- Department of Pediatrics, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Yuichi Matsumoto
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan.
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24
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Lin Y, Zheng Z, Sun W, Fu Q. A novel compound heterozygous variant identified in GLDC gene in a Chinese family with non-ketotic hyperglycinemia. BMC Med Genet 2018; 19:5. [PMID: 29304759 PMCID: PMC5755286 DOI: 10.1186/s12881-017-0517-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022]
Abstract
Background Non-ketotic hyperglycinemia (NKH) is a rare, devastating autosomal recessive disorder of glycine metabolism with a very poor prognosis. Currently, few studies have reported genetic profiling of Chinese NKH patients. This study aimed to identify the genetic mutations in a Chinese family with NKH. Methods A Chinese family of Han ethnicity, with three siblings with NKH was studied. Sanger sequencing and multiplex ligation-dependent probe amplification combined with SYBR green real-time quantitative PCR was used to identify potential mutations in the GLDC, AMT and GCSH genes. The potential pathogenicity of the identified missense mutation was analyzed using SIFT, PolyPhen-2, PROVEAN and MutationTaster software. Results All patients exhibited severe and progressive clinical symptoms, including lethargy, hypotonia and seizures, and had greatly elevated glycine levels in their plasma and CSF. Molecular genetic analysis identified compound heterozygous variants in the GLDC gene in these three siblings, including a novel missense variant c.2680A > G (p.Thr894Ala) in exon 23 and a heterozygous deletion of exon 3, which were inherited respectively from their parents. In silico analysis, using several different types of bioinformatic software, predicted that the novel variant c.2680A > G in the GLDC gene was pathogenic. Moreover, the deletion of exon 3 was identified for the first time in a Chinese population. Conclusions A novel missense variant and a previously reported deletion in GLDC gene were identified. The two variants of GLDC gene identified probably underlie the pathogenesis of non-ketotic hyperglycinemia in this family, and also enrich the mutational spectrum of GLDC gene. Electronic supplementary material The online version of this article (10.1186/s12881-017-0517-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Zhenzhu Zheng
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Wenjia Sun
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, Zhejiang Province, 310007, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China.
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25
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Thergaonkar RW, Narang A, Gurjar BS, Tiwari P, Puraswani M, Saini H, Sinha A, Varma B, Mukerji M, Hari P, Bagga A. Targeted exome sequencing in anti-factor H antibody negative HUS reveals multiple variations. Clin Exp Nephrol 2017; 22:653-660. [PMID: 28939980 DOI: 10.1007/s10157-017-1478-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/03/2017] [Indexed: 02/01/2023]
Abstract
BACKGROUND Genetic susceptibility to atypical hemolytic uremic syndrome (aHUS) may lie within genes regulating or activating the alternate complement and related pathways converging on endothelial cell activation. METHODS We tested 32 Indian patients of aHUS negative for antibodies to complement factor H for genetic variations in a panel of 15 genes, i.e., CFH, CFHR1-5, CFI, CFB, C3, CD46, MASP2, DGKE, ADAMTS13, THBD and PLG using next-generation DNA sequencing and for copy number variation in CFHR1-3. RESULTS Despite absence of a public database of exome variations in the Indian population and limited functional studies, we could establish a genetic diagnosis in 6 (18.8%) patients using a stringent scheme of prioritization. One patient carried a likely pathogenic variation. The number of patients carrying possibly pathogenic variation was as follows: 1 variation: 5 patients, 2 variations: 9 patients, 3 variations: 5 patients, 4 variations: 9 patients, 5 variations: 2 patients and 6 variations: 2 patients. Homozygous deletion of CFHR1-3 was present in five patients; none of these carried a diagnostic genetic variation. Patients with or without diagnostic variation did not differ significantly in terms of enrichment of genetic variations that were rare/novel or predicted deleterious, or for possible environmental triggers. CONCLUSION We conclude that genetic testing for multiple genes in patients with aHUS negative for anti-FH antibodies reveals multiple candidate variations that require prioritization. Population data on variation frequency of the Indian population and supportive functional studies are likely to improve diagnostic yield.
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Affiliation(s)
- R W Thergaonkar
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ankita Narang
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Pradeep Tiwari
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mamta Puraswani
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Himanshi Saini
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Aditi Sinha
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Binuja Varma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pankaj Hari
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arvind Bagga
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India.
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26
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Atanesyan L, Steenkamer MJ, Horstman A, Moelans CB, Schouten JP, Savola SP. Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA. Am J Clin Pathol 2017; 147:60-68. [PMID: 28122725 PMCID: PMC5848216 DOI: 10.1093/ajcp/aqw205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES Molecular genetic analysis of formalin-fixed, paraffin-embedded (FFPE) tissues is of great importance both for research and diagnostics. Multiplex ligation-dependent probe amplification (MLPA) is a widely used technique for gene copy number determination, and it has been successfully used for FFPE tissue-extracted DNA analysis. However, there have been no studies addressing the effect of tissue fixation procedures and DNA extraction methods on MLPA. This study therefore focuses on selecting optimal preanalytic conditions such as FFPE tissue preparation conditions and DNA extraction methods. METHODS Healthy tissues were fixed in buffered or nonbuffered formalin for 1 hour, 12 to 24 hours, or 48 to 60 hours at 4 °C or at room temperature. DNA extracted from differently fixed and subsequently paraffin-embedded tissues was used for MLPA. Four commercial DNA extraction kits and one in-house method were compared. RESULTS Tissues fixed for 12 to 24 hours in buffered formalin at room temperature produced DNA with the most optimal quality for MLPA. The in-house FFPE DNA extraction method was shown to perform as efficient as or even superior to other methods in terms of suitability for MLPA, time and cost-efficiency, and ease of performance. CONCLUSIONS FFPE-extracted DNA is well suitable for MLPA analysis, given that optimal tissue fixation and DNA extraction methods are chosen.
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Affiliation(s)
- Lilit Atanesyan
- From the MRC-Holland BV, Amsterdam, the Netherlands
- Corresponding author: Lilit Atanesyan, PhD, MRC-Holland, Willem Schoutenstraat 1, Amsterdam, the Netherlands; . Disclaimer: Lilit Atanesyan, Maryvonne Steenkamer, Suvi Savola, and Jan Schouten are employees of MRC-Holland
| | | | | | - Cathy B. Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
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Ribera J, Zamora L, García O, Hernández-Rivas JM, Genescà E, Ribera JM. [Copy number alterations in adult patients with mature B acute lymphoblastic leukemia treated with specific immunochemotherapy]. Med Clin (Barc) 2016; 147:488-491. [PMID: 28126143 DOI: 10.1016/j.medcli.2016.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/21/2016] [Accepted: 07/24/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE Unlike Burkitt lymphoma, molecular abnormalities other than C-MYC rearrangements have scarcely been studied in patients with mature B acute lymphoblastic leukemia (B-ALL). The aim of this study was to analyze the frequency and prognostic significance of copy number alterations (CNA) in genes involved in lymphoid differentiation, cell cycle and tumor suppression in adult patients with B-ALL. PATIENTS AND METHODS We have analyzed by multiplex ligation-dependent probe amplification the genetic material from bone marrow at diagnosis from 25 adult B-ALL patients treated with rituximab and specific chemotherapy. RESULTS The most frequent CNA were alterations in the 14q32.33 region (11 cases, 44%) followed by alterations in the cell cycle regulator genes CDKN2A/B and RB1 (16%). No correlation between the presence of specific CNA and the clinical-biologic features or the response to therapy was found. CONCLUSIONS The high frequency of CNA in the 14q32.33 region, CDKN2A/B and RB1 found in our study could contribute to the aggressiveness and invasiveness of mature B-ALL.
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Affiliation(s)
- Jordi Ribera
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Barcelona, España
| | - Lurdes Zamora
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Barcelona, España
| | - Olga García
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Barcelona, España
| | - Jesús-María Hernández-Rivas
- Hematology Department, Hospital Universitario de Salamanca, IBSAL, IBMCC, Centre for Cancer Research Universidad de Salamanca-CSIC, Salamanca, España
| | - Eulàlia Genescà
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Barcelona, España.
| | - Josep-Maria Ribera
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de Barcelona, Badalona, Barcelona, España
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28
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Chung B, Park C, Cho SY, Shin S, Yim SH, Jung GY, Lee DG, Chung YJ. Multiplex identification of drug-resistant Gram-positive pathogens using stuffer-free MLPA system. Electrophoresis 2016; 37:3079-3083. [PMID: 27573990 DOI: 10.1002/elps.201600372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 11/09/2022]
Abstract
Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture-based methods require relatively longer time to identify drug-resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug-resistant Gram-positive pathogens, we developed a method by using stuffer-free multiplex ligation-dependent probe amplification (MLPA) coupled with high-resolution CE single-strand conformation polymorphisms (CE-SSCP) system. We designed three probe sets for genes specific to Gram-positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram-positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain-specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target-specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug-resistant Gram-positive pathogens from sepsis patients' blood.
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Affiliation(s)
- Boram Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Seon-Hee Yim
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
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29
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Uno N, Araki N, Kaku N, Kosai K, Hasegawa H, Yanagihara K. Clinical application of a ligation-independent pathway of multiplex ligation-dependent probe amplification for the determination of quinolone susceptibility of Streptococcus pneumoniae. J Microbiol Methods 2016; 128:13-15. [PMID: 27343683 DOI: 10.1016/j.mimet.2016.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
We previously uncovered a ligation-independent pathway of multiplex ligation-dependent probe amplification (MLPA) through which products of MLPA could be amplified without both hybridization and ligation reactions. Here, we utilized this pathway to detect an antibiotic resistance mutation of quinolones in Streptococcus pneumoniae.
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Affiliation(s)
- Naoki Uno
- Department of Laboratory Medicine, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Nobuko Araki
- Department of Laboratory Medicine, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University, Graduate School of Biomedical Sciences, Nagasaki, Japan
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Hentschel J, Tatun D, Parkhomchuk D, Kurth I, Schimmel B, Heinrich-Weltzien R, Bertzbach S, Peters H, Beetz C. Identification of the first multi-exonic WDR72 deletion in isolated amelogenesis imperfecta, and generation of a WDR72-specific copy number screening tool. Gene 2016; 590:1-4. [PMID: 27259663 DOI: 10.1016/j.gene.2016.05.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/29/2016] [Indexed: 01/18/2023]
Abstract
Amelogenesis imperfecta (AI) is a clinically and genetically heterogeneous disorder of tooth development which is due to aberrant deposition or composition of enamel. Both syndromic and isolated forms exist; they may be inherited in an X-linked, autosomal recessive, or autosomal dominant manner. WDR72 is one of ten currently known genes for recessive isolated AI; nine WDR72 mutations affecting single nucleotides have been described to date. Based on whole exome sequencing in a large consanguineous AI pedigree, we obtained evidence for presence of a multi-exonic WDR72 deletion. A home-made multiplex ligation-dependent probe amplification assay was used to confirm the aberration, to narrow its extent, and to identify heterozygous carriers. Our study extends the mutational spectrum for WDR72 to include large deletions, and supports a relevance of the previously proposed loss-of-function mechanism. It also introduces an easy-to-use and highly sensitive tool for detecting WDR72 copy number alterations.
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Affiliation(s)
- Julia Hentschel
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Dana Tatun
- Institute of Medical and Human Genetics, Charité, Universitaetsmedizin Berlin, Germany
| | - Dmitri Parkhomchuk
- Institute of Medical and Human Genetics, Charité, Universitaetsmedizin Berlin, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Bettina Schimmel
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | | | | | - Hartmut Peters
- Institute of Medical and Human Genetics, Charité, Universitaetsmedizin Berlin, Germany; ChariteVivantes GmbH, Berlin, Germany
| | - Christian Beetz
- Department of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Jena, Germany.
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Vieitez I, Gallano P, González-Quereda L, Borrego S, Marcos I, Millán JM, Jairo T, Prior C, Molano J, Trujillo-Tiebas MJ, Gallego-Merlo J, García-Barcina M, Fenollar M, Navarro C. Mutational spectrum of Duchenne muscular dystrophy in Spain: Study of 284 cases. Neurologia 2016; 32:377-385. [PMID: 26968818 DOI: 10.1016/j.nrl.2015.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/09/2015] [Accepted: 12/12/2015] [Indexed: 10/22/2022] Open
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD) is a severe X-linked recessive neuromuscular disease that affects one in 3500 live-born males. The total absence of dystrophin observed in DMD patients is generally caused by mutations that disrupt the reading frame of the DMD gene, and about 80% of cases harbour deletions or duplications of one or more exons. METHODS We reviewed 284 cases of males with a genetic diagnosis of DMD between 2007 and 2014. These patients were selected from 8 Spanish reference hospitals representing most areas of Spain. Multiplex PCR, MLPA, and sequencing were performed to identify mutations. RESULTS Most of these DMD patients present large deletions (46.1%) or large duplications (19.7%) in the dystrophin gene. The remaining 34.2% correspond to point mutations, and half of these correspond to nonsense mutations. In this study we identified 23 new mutations in DMD: 7 large deletions and 16 point mutations. CONCLUSIONS The algorithm for genetic diagnosis applied by the participating centres is the most appropriate for genotyping patients with DMD. The genetic specificity of different therapies currently being developed emphasises the importance of identifying the mutation appearing in each patient; 38.7% of the cases in this series are eligible to participate in current clinical trials.
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Affiliation(s)
- I Vieitez
- Grupo de Patología Neonatal y Pediátrica, Enfermedades raras, Instituto de Investigación Biomédica de Ourense-Pontevedra-Vigo (IBI), Vigo, España; Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, España
| | - P Gallano
- Departamento de Genética, Hospital de la Santa Creu i Sant Pau, Barcelona, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - L González-Quereda
- Departamento de Genética, Hospital de la Santa Creu i Sant Pau, Barcelona, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - S Borrego
- Departamento de Genética, Reproducción y Medicina fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - I Marcos
- Departamento de Genética, Reproducción y Medicina fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - J M Millán
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario La Fe, Valencia, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - T Jairo
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario La Fe, Valencia, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - C Prior
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, Madrid, España
| | - J Molano
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, Madrid, España
| | - M J Trujillo-Tiebas
- Departamento de Genética, Hospital Universitario Fundación Jiménez Díaz, Madrid, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - J Gallego-Merlo
- Departamento de Genética, Hospital Universitario Fundación Jiménez Díaz, Madrid, España; CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), Instituto de Salud Carlos III, Madrid, España
| | - M García-Barcina
- Unidad de Genética, Hospital Universitario de Basurto, Vizcaya, España
| | - M Fenollar
- Sección de Genética Clínica, Servicio de Análisis Clínicos, Hospital Clínico San Carlos, Madrid, España
| | - C Navarro
- Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, España.
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Marcinkowska-Swojak M, Handschuh L, Wojciechowski P, Goralski M, Tomaszewski K, Kazmierczak M, Lewandowski K, Komarnicki M, Blazewicz J, Figlerowicz M, Kozlowski P. Simultaneous detection of mutations and copy number variation of NPM1 in the acute myeloid leukemia using multiplex ligation-dependent probe amplification. Mutat Res 2016; 786:14-26. [PMID: 26894557 DOI: 10.1016/j.mrfmmm.2016.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/30/2015] [Accepted: 02/02/2016] [Indexed: 01/13/2023]
Abstract
The NPM1 gene encodes nucleophosmin, a protein involved in multiple cell functions and carcinogenesis. Mutation of the NPM1 gene, causing delocalization of the protein, is the most frequent genetic lesion in acute myeloid leukemia (AML); it is considered a founder event in AML pathogenesis and serves as a favorable prognostic marker. Moreover, in solid tumors and some leukemia cell lines, overexpression of the NPM1 gene is commonly observed. Therefore, the purpose of this study was to develop a new method for the detection of NPM1 mutations and the simultaneous analysis of copy number alterations (CNAs), which may underlie NPM1 gene expression deregulation. To address both of the issues, we applied a strategy based on multiplex ligation-dependent probe amplification (MLPA). A designed NPM1mut+ assay enables the detection of three of the most frequent NPM1 mutations: A, B and D. The accuracy of the assay was tested using a group of 83 samples from Polish patients with AML and other blood-proliferative disorders. To verify the results, we employed traditional Sanger sequencing and next-generation transcriptome sequencing. With the use of the NPM1mut+ assay, we detected mutations A, D and B in 14, 1 and 0 of the analyzed samples, respectively. All of these mutations were confirmed by complementary sequencing approaches, proving the 100% specificity and sensitivity of the proposed test. The performed sequencing analysis allowed the identification of two additional rare mutations (I and ZE). All of the mutations were identified exclusively in AML cases, accounting for 25% of those cases. We did not observe any CNAs (amplifications) of the NPM1 gene in the studied samples, either with or without the mutation. The presented method is simple, reliable and cost-effective. It can be easily introduced into clinical practice or developed to target both less-frequent mutations in the NPM1 gene and other cancer-related genes.
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Affiliation(s)
- Malgorzata Marcinkowska-Swojak
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Luiza Handschuh
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland; Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznan, Poland.
| | - Pawel Wojciechowski
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Michal Goralski
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Kamil Tomaszewski
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Maciej Kazmierczak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznan, Poland.
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznan, Poland.
| | - Mieczyslaw Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznan, Poland.
| | - Jacek Blazewicz
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Marek Figlerowicz
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Piotr Kozlowski
- European Center of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
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Abstract
Uveal melanoma is the most common primary intraocular tumor in adults, and it has a strong potential to metastasize. Traditionally, clinicopathological features of these tumors were used to provide a limited prediction of the metastatic risk. However, early genetic studies using karyotype analysis, fluorescence in situ hybridization, and comparative genetic hybridization of posterior uveal melanoma samples identified multiple chromosomal abnormalities associated with a higher risk of fatal metastasis. This correlation between specific genetic abnormalities in uveal melanoma and a patient's risk for development of metastasis has recently been widely studied, and the development of new prognostic tests has allowed clinicians to predict this metastatic risk with increased accuracy. Such novel tests include gene expression profiling, which analyzes the RNA expression patterns of tumor cells, and multiplex ligation-dependent probe amplification, which detects deletions or and amplifications of DNA in tumor cells. This review discusses the current status of prognostic testing techniques available to clinicians and patients for posterior uveal melanomas.
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Affiliation(s)
- Victoria J Schopper
- University of Cincinnati College of Medicine, Medical Arts Building, 222 Piedmont Avenue, Suite 1500, Cincinnati, OH 45209 USA
| | - Zelia M Correa
- University of Cincinnati College of Medicine, Medical Arts Building, 222 Piedmont Avenue, Suite 1500, Cincinnati, OH 45209 USA
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Imamura H, Muroya K, Tanaka E, Konomoto T, Moritake H, Sato T, Kimura N, Takekoshi K, Nunoi H. Sporadic paraganglioma caused by de novo SDHB mutations in a 6-year-old girl. Eur J Pediatr 2016; 175:137-41. [PMID: 26283294 DOI: 10.1007/s00431-015-2614-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 11/30/2022]
Abstract
UNLABELLED Germline mutations in the succinate dehydrogenase complex subunit B (SDHB) gene (SDHB) cause susceptibility to paragangliomas and pheochromocytomas; however, it is exceedingly rare in childhood and especially in sporadic cases. We report the first Japanese pediatric case of paraganglioma with a de novo mutation in the SDHB gene. A 6-year-old girl with convulsions and hypertension was found to have a paravertebral abdominal tumor. Urinary and blood examinations revealed markedly elevated levels of norepinephrine. Following treatment for hypertension, the tumor was removed completely and histological findings were consistent with paraganglioma. Immunohistochemistry studies demonstrated the absence of SDHB protein expression, indicating an underlying SDH mutation with high probability. Germline mutation analysis of the SDHB gene revealed a heterozygous splice site mutation in intron 4 (C.423 + 1G > A). Subsequently, a second somatic genetic change was confirmed by multiplex ligation-dependent probe amplification (MLPA) analysis, showing that deletion of the wild-type allele resulted in loss of function of SDHB. No germline mutations in SDHB were detected in her parents. CONCLUSION Genetic testing should be considered for pediatric patients with paragangliomas, even in the absence of familial history, as closer lifelong screening to detect the development of malignancy will be required for patients with SDHB mutations. WHAT IS KNOWN Most sporadic cases of paraganglioma with SDHB mutations occur between adolescence and adulthood. Screening methods for carriers of SDHB mutations assessing recurrence and detecting developing metastases are yet to be standardized. WHAT IS NEW The current case of an extra-adrenal paraganglioma with a de novo SDHB mutation had an onset at 6 years. We suggest much closer periodical observation for these high-risk children.
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Affiliation(s)
- Hideaki Imamura
- Division of Pediatrics, Department of Reproductive and Developmental Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Mutsukawa 2-138-4, Minami-ku, Yokohama, 232-8555, Japan.
| | - Etsuko Tanaka
- Division of Pediatrics, Department of Reproductive and Developmental Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Takao Konomoto
- Division of Pediatrics, Department of Reproductive and Developmental Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Hiroshi Moritake
- Division of Pediatrics, Department of Reproductive and Developmental Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Takeshi Sato
- Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Noriko Kimura
- Department of Clinical Research, Pathology Division, National Hospital Organization, Hakodate Hospital, 18-16 Kawahara, Hakodate, Hokkaido, 041-8512, Japan.
| | - Kazuhiro Takekoshi
- Division of Sports Science, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan.
| | - Hiroyuki Nunoi
- Division of Pediatrics, Department of Reproductive and Developmental Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
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Mittal R, Cherepanoff S, Thornton S, Kalirai H, Damato B, Coupland SE. Bilateral Diffuse Uveal Melanocytic Proliferation: Molecular Genetic Analysis of a Case and Review of the Literature. Ocul Oncol Pathol 2015; 2:94-9. [PMID: 27171825 DOI: 10.1159/000440766] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/28/2015] [Indexed: 11/19/2022] Open
Abstract
PURPOSE OF THE STUDY To describe the clinicopathological features, mutational and chromosomal copy number analysis, and 8-year follow-up of a case of bilateral diffuse uveal melanocytic proliferation (BDUMP) associated with clear-cell carcinoma of the endometrium. METHODS Histological evaluation, multiplex ligation-dependent probe amplification (MLPA) analysis and GNAQ/11 mutational analysis were performed in a 67-year-old female patient with the diagnosis of BDUMP. RESULTS Histological evaluation revealed proliferation of bland spindle cells, diffusely replacing the uveal tract, which showed a proliferation index of less than 1%. There was absence of mutations involving the codon 209 and 183 of GNAQ, and of GNA11. MLPA analysis showed disomy 3 with polysomy 8q for both eyes. The patient died 8 years later of an unrelated condition. CONCLUSIONS Although BDUMP is considered to be a benign proliferative disease, copy number alterations of unknown significance may occur in these lesions.
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Affiliation(s)
- Ruchi Mittal
- Dalmia Ophthalmic Pathology Services, L.V. Prasad Eye Institute, Bhubaneswar, India
| | | | - Sophie Thornton
- Pathology, Department of Clinical and Molecular Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Helen Kalirai
- Pathology, Department of Clinical and Molecular Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Bertil Damato
- Ocular Oncology Service, University of California, San Francisco, Calif., USA
| | - Sarah E Coupland
- Pathology, Department of Clinical and Molecular Cancer Medicine, University of Liverpool, Liverpool, UK
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Santa María L, Faundes V, Curotto B, Morales P, Morales K, Aliaga S, Pugin Á, Alliende MA. Comparison of two subtelomeric assays for the screening of chromosomal rearrangements: analysis of 383 patients, literature review and further recommendations. J Appl Genet 2015; 57:63-9. [PMID: 26069167 DOI: 10.1007/s13353-015-0295-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/11/2015] [Accepted: 05/26/2015] [Indexed: 12/01/2022]
Abstract
Intellectual disability (ID) and global development delay (GDD) are caused by genetic factors such as subtelomeric rearrangements (SR) in 25 % of patients. There are several assays currently available to detect SR, but subtelomeric fluorescence in situ hybridisation (Subt-FISH) and subtelomeric multiplex ligation-dependent probe amplification (Subt-MLPA) have been the most frequently used. However, the diagnostic yield of each technique has not been compared. We reviewed the results of SR screening over a ten-year period in Chilean patients with ID/GDD using Subt-FISH and/or Subt-MLPA, compared the diagnostic yield of both tools and reviewed the corresponding literature. A total of 383 cases were included in this study, of which 53.8 % were males. The overall diagnostic yield was 8.9 % between both methods, but Subt-MLPA showed a higher performance than Subt-FISH (p = 0.002). A total of 4,181 patients with ID/GDD have been studied worldwide with Subt-MLPA and other subtelomeric assays, and 244 (5.84 %) had a pathogenic SR. It is estimated that Subt-MLPA may detect 92.6 % of the total cases with SR. The capacity of detecting tandem duplication and other critical regions, as well as the use of two MLPA kits, may explain the higher performance of this tool over Subt-FISH. Therefore, we recommend the use of this subtelomeric method as a cost-effective way to study ID/GDD patients.
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Affiliation(s)
- Lorena Santa María
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Víctor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile.
| | - Bianca Curotto
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Paulina Morales
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Karla Morales
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile.,Escuela de Tecnología Médica, Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
| | - Solange Aliaga
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Ángela Pugin
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - María Angélica Alliende
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
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Vranic S, Marchiò C, Castellano I, Botta C, Scalzo MS, Bender RP, Payan-Gomez C, di Cantogno LV, Gugliotta P, Tondat F, di Celle PF, Mariani S, Gatalica Z, Sapino A. Immunohistochemical and molecular profiling of histologically defined apocrine carcinomas of the breast. Hum Pathol 2015. [PMID: 26208846 DOI: 10.1016/j.humpath.2015.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the marked improvement in the understanding of molecular mechanisms and classification of apocrine carcinoma, little is known about its specific molecular genetic alterations and potentially targetable biomarkers. In this study, we explored immunohistochemical and molecular genetic characteristics of 37 invasive apocrine carcinomas using immunohistochemistry (IHC), fluorescent in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA), and next-generation sequencing (NGS) assays. IHC revealed frequent E-cadherin expression (89%), moderate (16%) proliferation activity [Ki-67, phosphohistone H3], infrequent (~10%) expression of basal cell markers [CK5/6, CK14, p63, caveolin-1], loss of PTEN (83%), and overexpression of HER2 (32%), EGFR (41%), cyclin D1 (50%), and MUC-1 (88%). MLPA assay revealed gene copy gains of MYC, CCND1, ZNF703, CDH1, and TRAF4 in 50% or greater of the apocrine carcinomas, whereas gene copy losses frequently affected BRCA2 (75%), ADAM9 (54%), and BRCA1 (46%). HER2 gain, detected by MLPA in 38% of the cases, was in excellent concordance with HER2 results obtained by IHC/FISH (κ = 0.915, P < .001). TOP2A gain was observed in one case, while five cases (21%) exhibited TOP2A loss. Unsupervised hierarchical cluster analysis revealed two distinct clusters: HER2-positive and HER2-negative (P = .03 and .04, respectively). NGS assay revealed mutations of the TP53 (2 of 7, 29%), BRAF/KRAS (2 of 7, 29%), and PI3KCA/PTEN genes (7 of 7, 100%). We conclude that morphologically defined apocrine carcinomas exhibit complex molecular genetic alterations that are consistent with the "luminal-complex" phenotype. Some of the identified molecular targets are promising biomarkers; however, functional studies are needed to prove these observations.
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Affiliation(s)
- Semir Vranic
- Department of Medical Sciences, University of Turin, Turin 10126, Italy; Department of Pathology, Clinical Center, University of Sarajevo, Sarajevo 71000, Bosnia and Herzegovina.
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| | | | - Cristina Botta
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| | | | | | - Cesar Payan-Gomez
- Medical Genetics Center, Department of Cell Biology and Genetics, Center of Biomedical Genetics, Erasmus MC, Rotterdam 3015, the Netherlands; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 110010, Colombia
| | | | | | - Fabrizio Tondat
- Center for Experimental Research and Medical Studies, San Giovanni Battista Hospital, Turin 10100, Italy
| | - Paola Francia di Celle
- Center for Experimental Research and Medical Studies, San Giovanni Battista Hospital, Turin 10100, Italy
| | - Sara Mariani
- Center for Experimental Research and Medical Studies, San Giovanni Battista Hospital, Turin 10100, Italy
| | | | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin 10126, Italy.
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Abstract
Background Mutations in known causative genes and cytogenetically detectable chromosomal rearrangements account for a fraction of cases with 46,XY disorders of sex development (DSD). Recent advances in molecular cytogenetic technologies, including array-based comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA), have enabled the identification of copy-number variations (CNVs) in individuals with apparently normal karyotypes. Findings This review paper summarizes the results of 15 recent studies, in which aCGH or MLPA were used to identify CNVs. Several submicroscopic CNVs have been detected in patients with 46,XY DSD. These CNVs included deletions involving known causative genes such as DMRT1 or NR5A1, duplications involving NR0B1, deletions involving putative cis-regulatory elements of SOX9, and various deletions and duplications of unknown pathogenicity. Conclusions The results of recent studies highlight the significance of submicroscopic CNVs as the genetic basis of 46,XY DSD. Molecular cytogenetic analyses should be included in the diagnostic workup of patients with 46,XY DSD of unknown origin. Further studies using aCGH will serve to clarify novel causes of this condition.
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Affiliation(s)
- Masafumi Kon
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan. .,Department of Urology, Hokkaido University Graduate School of Medicine, North-15, West-7, Kita-ku, Sapporo, 060-8638, Japan.
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.
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Williams VS, Cresswell CJ, Ruspi G, Yang T, Atak TC, McLoughlin M, Ingram CD, Ramirez AH, Roden D, Armstrong M. Multiplex ligation-dependent probe amplification copy number variant analysis in patients with acquired long QT syndrome. Europace 2015; 17:635-41. [PMID: 25564553 DOI: 10.1093/europace/euu288] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/16/2014] [Indexed: 01/06/2023] Open
Abstract
AIMS Thirteen genetic loci map to families with congenital long QT syndrome (cLQT) and multiple single nucleotide mutations have been functionally implicated in cLQT. Studies have investigated copy number variations (CNVs) in the cLQT genes to ascertain their involvement in cLQT. In these studies 3-12% of cLQT patients who were mutation negative by all other methods carried CNVs in cLQT genes. Prolongation of the QT interval can also be acquired after exposure to certain drugs [acquired LQT (aLQT)]. Single nucleotide mutations in cLQT genes have also been associated with and functionally implicated in aLQT, but to date no studies have explored CNVs as an additional susceptibility factor in aLQT. The aim of this study was to explore the contribution of CNVs in determining susceptibility to aLQT. METHODS AND RESULTS In this study we screened the commonest cLQT genes (KCNQ1; KCNH2; SCN5A; KCNE1, and KCNE2) in a general population of healthy volunteers and in a cohort of subjects presenting with aLQT for CNVs using the multiplex ligation-dependent probe amplification method. Copy number variants were detected and confirmed in 1 of 197 of the healthy volunteers and in 1 of 90 subjects with aLQT. The CNV in the aLQT subject was functionally characterized and demonstrated impaired channel function. CONCLUSION Copy number variation is a possible additional risk factor for aLQT and should be considered for incorporation into pharmacogenetic screening of LQTS genes in addition to mutation detection to improve the safety of medication administration.
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Affiliation(s)
- Victoria S Williams
- AstraZeneca, Personalised Healthcare and Biomarkers, R&D Genetics, Alderley Park, UK
| | - Carl J Cresswell
- AstraZeneca, Personalised Healthcare and Biomarkers, R&D Genetics, Alderley Park, UK
| | - Gerhard Ruspi
- School of Biomedical Sciences, King's College London, London, UK
| | - Tao Yang
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Thomas C Atak
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Matthew McLoughlin
- AstraZeneca, Personalised Healthcare and Biomarkers, R&D Genetics, Alderley Park, UK
| | | | - Andrea H Ramirez
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Dan Roden
- Department of Medicine, Vanderbilt University, Nashville, TN, USA Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Martin Armstrong
- AstraZeneca, Personalised Healthcare and Biomarkers, R&D Genetics, Alderley Park, UK Shire AG, Business Park Terre-Bonne, Route de Crassier 7, 1262 Eysins, Switzerland
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40
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Akashi-Tanaka S, Watanabe C, Takamaru T, Kuwayama T, Ikeda M, Ohyama H, Mori M, Yoshida R, Hashimoto R, Terumasa S, Enokido K, Hirota Y, Okuyama H, Nakamura S. BRCAness predicts resistance to taxane-containing regimens in triple negative breast cancer during neoadjuvant chemotherapy. Clin Breast Cancer 2015; 15:80-5. [PMID: 25445419 DOI: 10.1016/j.clbc.2014.08.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 08/12/2014] [Accepted: 08/25/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND To provide optimal treatment of heterogeneous triple negative breast cancer (TNBC), we need biomarkers that can predict the chemotherapy response. PATIENTS AND METHODS We retrospectively investigated BRCAness in 73 patients with breast cancer who had been treated with taxane- and/or anthracycline-based neoadjuvant chemotherapy (NAC). Using multiplex, ligation-dependent probe amplification on formalin-fixed core needle biopsy (CNB) specimens before NAC and surgical specimens after NAC. BRCAness status was assessed with the assessor unaware of the clinical information. RESULTS We obtained 45 CNB and 60 surgical specimens from the 73 patients. Of the 45 CNB specimens, 17 had BRCAness (38.6% of all subtypes). Of the 23 TNBC CNB specimens, 14 had BRCAness (61% of TNBC cases). The clinical response rates were significantly lower for BRCAness than for non-BRCAness tumors, both for all tumors (58.8% vs. 89.3%, P = .03) and for TNBC (50% vs. 100%, P = .02). All tumors that progressed with taxane therapy had BRCAness. Of the patients with TNBC, those with non-BRCAness cancer had pathologic complete responses significantly more often than did those with BRCAness tumors (77.8% vs. 14.3%, P = .007). After NAC, the clinical response rates were significant lower for BRCAness than for non-BRCAness tumors in all subtypes (P = .002) and in TNBC cases (P = .008). After a median follow-up of 26.4 months, 6 patients-all with BRCAness-had developed recurrence. Patients with BRCAness had shorter progression-free survival than did those with non- BRCAness (P = .049). CONCLUSION Identifying BRCAness can help predict the response to taxane, and changing regimens for BRCAness TNBC might improve patient survival. A larger prospective study is needed to further clarify this issue.
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Sung JY, Bae EJ, Park S, Kim SY, Hyun YJ, Park SS, Seong MW. Large deletion in KCNQ1 identified in a family with Jervell and Lange-Nielsen syndrome. Ann Lab Med 2014; 34:395-8. [PMID: 25187895 PMCID: PMC4151011 DOI: 10.3343/alm.2014.34.5.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/23/2014] [Accepted: 06/24/2014] [Indexed: 11/19/2022] Open
Abstract
Long QT syndrome (LQTS) is a genetically heterogeneous disorder associated with sequence variations in more than 10 genes; in some cases, it is caused by large deletions or duplications among the main, known LQTS-associated genes. Here, we describe a 14-month-old Korean boy with congenital hearing loss and prolonged QT interval whose condition was clinically diagnosed as Jervell and Lange-Nielsen syndrome (JLNS), a recessive form of LQTS. Genetic analyses using sequence analysis and multiplex ligation-dependent probe amplification (MLPA) assay revealed a large deletion spanning exons 7-10 as well as a frameshift mutation (c.1893dup; p.Arg632Glnfs*20). To our knowledge, this is the first report of a large deletion in KCNQ1 identified in JLNS patients. This case indicates that a method such as MLPA, which can identify large deletions or duplications needs to be considered in addition to sequence analysis to diagnose JLNS.
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Affiliation(s)
- Ji Yeon Sung
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eun Jung Bae
- Department of Pediatrics, Seoul National University Hospital, Seoul, Korea
| | | | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Ye Jin Hyun
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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Larsen AC, Holst L, Kaczkowski B, Andersen MT, Manfé V, Siersma VD, Kolko M, Kiilgaard JF, Winther O, Prause JU, Gniadecki R, Heegaard S. MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma. Acta Ophthalmol 2014; 92:541-9. [PMID: 24373459 DOI: 10.1111/aos.12322] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 10/31/2013] [Indexed: 12/30/2022]
Abstract
PURPOSE To determine the association of microRNA expression and chromosomal changes with metastasis and survival in uveal melanoma (UM). METHODS Thirty-six patients with UM were selected based on the metastatic status, and clinicopathological data were collected. Multiplex ligation-dependent probe amplification (MLPA) was used to identify chromosomal changes. Chromosomal changes and clinicopathological data were correlated with survival and metastasis. The microRNA expression was analysed in 26 of the 36 archived UM samples. Unsupervised analysis, differential expression analysis and Cox regression analysis were performed to determine the association with metastasis and survival. RESULTS Metastasis and metastatic death occurred in 20 patients, two patients died of other causes and one patient of unknown causes. A significant association between increasing size category (p = 0.002, log-rank), extraocular extension (p = 0.001), chromosome 3 loss (p = 0.033) and 1p loss (p = 0.030) and development of metastases was observed. Tumour, node, metastasis (TNM) staging showed a significant association with survival (p < 0.0001, log-rank). Adjusting for gender and age TNM size category T4 (p = 0.016, Cox regression analysis), mixed (p = 0.029) and epithelioid (p = 0.0058) cell types, chromosome 3 loss (p = 0.014) and 8q gain (p = 0.010) were significant prognosticators for a poor survival. Hierarchical clustering divided the UM into three groups based on microRNA expression. The clusters showed no association with clinical or histopathological features, TNM staging, metastasis or survival. Differential expression analysis did not reveal microRNAs related to metastasis or survival. CONCLUSIONS The prognostic significance of chromosome 3 loss and 8q gain identified by MLPA analysis was confirmed in archived UM samples. The value of microRNA expression as a predictor of metastasis and survival in UM could not be confirmed.
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Affiliation(s)
| | - Line Holst
- Department of Dermatology; Bispebjerg Hospital; University of Copenhagen; Copenhagen Denmark
| | - Bogumil Kaczkowski
- Department of Biology; Biotech Research and Innovation Centre; University of Copenhagen; Copenhagen Denmark
| | - Morten T. Andersen
- Department of Clinical Genetics; Copenhagen University Hospital; Copenhagen Denmark
| | - Valentina Manfé
- Department of Dermatology; Bispebjerg Hospital; University of Copenhagen; Copenhagen Denmark
| | - Volkert D. Siersma
- The Research Unit and Section of General Practice; Institute of Public Health; University of Copenhagen; Copenhagen Denmark
| | - Miriam Kolko
- Department of Neuroscience and Pharmacology; University of Copenhagen; Copenhagen Denmark
- Department of Ophthalmology; Glostrup Hospital; University of Copenhagen; Copenhagen Denmark
| | - Jens F. Kiilgaard
- Department of Ophthalmology; Glostrup Hospital; University of Copenhagen; Copenhagen Denmark
| | - Ole Winther
- Department of Biology; Biotech Research and Innovation Centre; University of Copenhagen; Copenhagen Denmark
- DTU Informatics; Technical University of Denmark; Lyngby Denmark
| | - Jan U. Prause
- Eye Pathology Institute; University of Copenhagen; Copenhagen Denmark
| | - Robert Gniadecki
- Department of Dermatology; Bispebjerg Hospital; University of Copenhagen; Copenhagen Denmark
| | - Steffen Heegaard
- Eye Pathology Institute; University of Copenhagen; Copenhagen Denmark
- Department of Ophthalmology; Glostrup Hospital; University of Copenhagen; Copenhagen Denmark
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Ohno S, Omura M, Kawamura M, Kimura H, Itoh H, Makiyama T, Ushinohama H, Makita N, Horie M. Exon 3 deletion of RYR2 encoding cardiac ryanodine receptor is associated with left ventricular non-compaction. Europace 2014; 16:1646-54. [PMID: 24394973 DOI: 10.1093/europace/eut382] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
AIMS Ryanodine receptor gene (RYR2) mutations are well known to cause catecholaminergic polymorphic ventricular tachycardia (CPVT). Recently, RYR2 exon 3 deletion has been identified in patients with dilated cardiomyopathy (DCM) and/or CPVT. This study aimed to screen for the RYR2 exon 3 deletion in CPVT probands, characterize its clinical pathology, and confirm the genomic rearrangement. METHODS AND RESULTS Our cohort consisted of 24 CPVT probands. Polymerase chain reaction (PCR)-based conventional genetic analysis did not identify any mutations in coding exons of RYR2 in these probands. They were screened using multiplex ligation-dependent probe amplification (MLPA). In probands identified with RYR2 exon 3 deletion, the precise location of the deletion was identified by quantitative PCR and direct sequencing methods. We identified two CPVT probands from unrelated families who harboured a large deletion including exon 3. The probands were 9- and 17-year-old girls. Both probands had a history of syncope related to emotional stress or exercise, exhibited bradycardia, and were diagnosed with left ventricular non-compaction (LVNC). We examined 10 family members and identified six more RYR2 exon 3 deletion carriers. In total, there were eight carriers, of which seven were diagnosed with LVNC (87.5%). Two carriers under the age of 4 years remained asymptomatic, although they were diagnosed with LVNC. Using quantitative PCR and direct sequencing, we confirmed that the deletions were 1.1 and 37.7 kb in length. CONCLUSION RYR2 exon 3 deletion is frequently associated with LVNC. Therefore, detection of the deletion offers a new modality for predicting the prognosis of patients with LVNC with ventricular/atrial arrhythmias, particularly in children.
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Affiliation(s)
- Seiko Ohno
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Masato Omura
- Cardiovasacular Department, Saiseikai Shimonoseki General Hospital, Shimonoseki 759-6603, Japan
| | - Mihoko Kawamura
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Hiromi Kimura
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Hideki Itoh
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Hiroya Ushinohama
- Cardiovascular Department, Fukuoka Children's Hospital and Medical Center for infectious disease, Fukuoka 810-0063, Japan
| | - Naomasa Makita
- Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Science, Nagasaki 852-8523, Japan
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
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Shang Y, Zhu P, Xu W, Guo T, Tian W, Luo Y, Huang K. Single universal primer multiplex ligation-dependent probe amplification with sequencing gel electrophoresis analysis. Anal Biochem 2013; 443:243-8. [PMID: 24050969 DOI: 10.1016/j.ab.2013.09.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 10/26/2022]
Abstract
In this study, a novel single universal primer multiplex ligation-dependent probe amplification (SUP-MLPA) technique that uses only one universal primer to perform multiplex polymerase chain reaction (PCR) was developed. Two reversely complementary common sequences were designed on the 5' or 3' end of the ligation probes (LPs), which allowed the ligation products to be amplified through only a single universal primer (SUP). SUP-MLPA products were analyzed on sequencing gel electrophoresis with extraordinary resolution. This method avoided the high expenses associated with capillary electrophoresis, which was the commonly used detection instrument. In comparison with conventional multiplex PCR, which suffers from low sensitivity, nonspecificity, and amplification disparity, SUP-MLPA had higher specificity and sensitivity and a low detection limit of 0.1 ng for detecting single crop species when screening the presence of genetically modified crops. We also studied the effect of different lengths of stuffer sequences on the probes for the first time. Through comparing the results of quantitative PCR, the LPs with different stuffer sequences did not affect the ligation efficiency, which further increased the multiplicity of this assay. The improved SUP-MLPA and sequencing gel electrophoresis method will be useful for food and animal feed identification, bacterial detection, and verification of genetic modification status of crops.
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Affiliation(s)
- Ying Shang
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Chung B, Shin GW, Park CK, Choi W, Chung YJ, Yoon HK, Jung GY. Rapid and sensitive detection of lower respiratory tract infections by stuffer-free multiplex ligation-dependent probe amplification. Electrophoresis 2013; 35:511-4. [PMID: 24311198 DOI: 10.1002/elps.201300374] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/11/2013] [Accepted: 10/25/2013] [Indexed: 11/09/2022]
Abstract
Lower respiratory tract infection is one of the most common infectious diseases. However, conventional methods for detecting infectious pathogens are time-consuming, and generally have a limited impact on early therapeutic decisions. We previously reported a rapid and sensitive method for detecting such pathogens using stuffer-free multiplex ligation-dependent probe amplification coupled with high-resolution CE-SSCP. In this study, we report an application of this method to the detection of respiratory pathogens. As originally configured, this method was capable of simultaneously detecting seven bacterial species responsible for lower respiratory tract infections, but its detection limit and assay time were insufficient to provide useful information for early therapeutic decisions. To improve sensitivity and shorten assay time, we added a target-specific preamplification step, improving the detection limit from 50 pg of genomic DNA to 500 fg. We further decreased time requirements by optimizing the hybridization step, enabling the entire assay to be completed within 7 h while maintaining the same detection limit. Taken together, these improvements enable the rapid detection of infectious doses of pathogens (i.e. a few dozen cells), establishing the strong potential of the refined method, particularly for aiding early treatment decisions.
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Affiliation(s)
- Boram Chung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
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Sheng JQ, Cui WJ, Fu L, Jin P, Han Y, Li SJ, Fan RY, Li AQ, Zhang MZ, Li SR. APC gene mutations in Chinese familial adenomatous polyposis patients. World J Gastroenterol 2010; 16:1522-6. [PMID: 20333795 PMCID: PMC2846260 DOI: 10.3748/wjg.v16.i12.1522] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To study the characteristics of APC (adenomatous polyposis coli) gene germline mutation in Chinese patients with familial adenomatous polyposis (FAP).
METHODS: APC gene from 14 FAP families was amplified by polymerase chain reaction (PCR) and underwent direct sequencing to determine the micromutation type. For the samples without micromutation, the large fragment deletion of APC gene was examined by multiplex ligation-dependent probe amplification (MLPA).
RESULTS: There were gene micromutations in 9 families with a micromutation detection rate of 64.3% (9/14), including 6 frameshift mutations (66.7%), 1 nonsense mutation (11.1%) and 2 splicing mutations (22.2%). Large fragment deletions were detected by MLPA in 2 families. The total mutation detection rate of micromutations and large fragment deletions was 78.6% (11/14).
CONCLUSION: The detection rate of APC gene germline mutation can be improved by direct sequencing combined with MLPA large fragment deletion detection.
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