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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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2
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Qi XP, Zhao JQ, Fang XD, Lian BJ, Li F, Wang HH, Cao ZL, Zheng WH, Cao J, Chen Y. Spectrum of Germline RET variants identified by targeted sequencing and associated Multiple Endocrine Neoplasia type 2 susceptibility in China. BMC Cancer 2021; 21:369. [PMID: 33827484 PMCID: PMC8028819 DOI: 10.1186/s12885-021-08116-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
Background Germline RET mutations and variants are involved in development of multiple endocrine neoplasia type 2 (MEN2). The present study investigated a spectrum of RET variants, analyzed genotype-phenotype relationships, and evaluated their effect on the MEN2 phenotype in Han Chinese patients. Methods Targeted sequencing detected germline RET variants in 697 individuals, including 245 MEN2, 120 sporadic medullary thyroid cancer (MTC), and 15 pheochromocytoma (PHEO) patients and their 493 relatives. In silico analyses and classifications following ACMG-2015 were performed. Demographic, clinical variant types, and endocrine neoplasia molecular diagnosis records were also analyzed. Results Nineteen different RET mutations (18 point and 1 del/ins mutations) in 214 patients with MEN2A (97.7%) or MEN2B (2.3%) were found, of which exon 11/10 mutations accounted for 79% (169/214). Nineteen compound mutations were found in 31 patients with MEN2A. Twenty-three variants (18 single and 5 double base substitution/compound variants) non-classification were also found. Of these, 17 (3 of pathogenic, 10 of uncertain significance, 2 of likely benign and 2 as benign) were found in 31 patients with MTC/PHEO. The remaining 6 variants (4 of uncertain significance and 2 of likely benign) found in 8 carriers had no evidence of MEN2. The entire cohort showed MEN2A-related PHEO, all occurring in exons 11/10, particularly at C634. Kaplan-Meier curves showed age-dependent penetration rates of MTC and PHEO, and occurrence rates of PHEO in patients with exon 11 mutations were all higher than those within exon 10; these bilateral PHEO were always associated with exon 11 mutations (all P < 0.05). While patient offspring had PHEO, parents with MEN2A had none, the frequency was approximately 10%. Interestingly, at least 6.8% of families were adoptive. Also, 3 non-hotspot RET variants (R114H, T278N, and D489N) appeared with high frequency. Conversely, polymorphism S836S was absent. Conclusions These data are largely consistent with current evidence-based recommendations in the clinical practice guidelines. Diversity of RET variants or carriers may involve a different natural disease course. Further large-scale targeted sequencing studies will serve as an accurate and cost-effective approach to investigating MEN2 genotype-phenotype correlations for discovery of rare or unknown variants of RET.
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Affiliation(s)
- Xiao-Ping Qi
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China.
| | - Jian-Qiang Zhao
- Department of Head and Neck Surgery, Institute of Cancer Research and Basic Medical of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 1 East Banshan Road, Hangzhou, 310022, Zhejiang Province, China
| | - Xu-Dong Fang
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
| | - Bi-Jun Lian
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
| | - Feng Li
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
| | - Hui-Hong Wang
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
| | - Zhi-Lie Cao
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
| | - Wei-Hui Zheng
- Department of Head and Neck Surgery, Institute of Cancer Research and Basic Medical of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 1 East Banshan Road, Hangzhou, 310022, Zhejiang Province, China
| | - Juan Cao
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
| | - Yu Chen
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, 40 Jichang Road, Hangzhou, 310004, Zhejiang Province, China
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3
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Shi H, Niu W, Liu Y, Jin H, Song W, Shi S, Yao G, Xu J, Sun Y. A novel monogenic preimplantation genetic testing strategy for sporadic polycystic kidney caused by de novo PKD1 mutation. Clin Genet 2020; 99:250-258. [PMID: 33111320 DOI: 10.1111/cge.13871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/15/2022]
Abstract
Autosomal dominant hereditary polycystic kidney disease (ADPKD) is the most common inherited kidney disease that causes end-stage renal disease and kidney failure. Preimplantation genetic testing for monogenic (PGT-M) can effectively prevent the transmission of genetic diseases from parents to the offspring before pregnancy. However, PGT-M currently adopts the single nucleotide polymorphism (SNP) linkage analysis for embryo's pathogenic gene carrying status and linkage analysis requires proband of the family. Here we report a new PGT-M strategy using single sperm SNP linkage analysis for male patient with sporadic ADPKD caused by de novo PKD1 mutation. We recruited five couples with male patient with ADPKD caused by de novo PKD1 mutation, and 39 embryos from six PGT-M cycles were detected. The five couples had at least one embryo that does not carry the PKD1 mutation. Within these five couples, the accuracy of carrier status of embryos was confirmed by amniotic fluid gene detection of two couples and two couples successfully delivered healthy fetuses. Therefore, the new PGT-M strategy of using single sperm SNP linkage analysis was proved to be feasible and effective for male patient with ADPKD caused by de novo PKD1 mutation.
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Affiliation(s)
- Hao Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenbin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yidong Liu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haixia Jin
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenyan Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Senlin Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guidong Yao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawei Xu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Qi XP, Jin BY, Li PF, Wang S, Zhao YH, Cao ZL, Yu XH, Cheng J, Fang XD, Zhao JQ. RET S409Y Germline Mutation and Associated Medullary Thyroid Carcinoma. Thyroid 2019; 29:1447-1456. [PMID: 31364476 DOI: 10.1089/thy.2018.0385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background: Inherited medullary thyroid carcinoma (MTC) is primarily caused by RET mutations that are commonly localized in exons 5, 8, 10, 11, and 13-16. In this study, we report pedigrees for individuals with MTC that harbor a germline S409Y variant within exon 6 of the RET proto-oncogene. Methods: Targeted sequencing was used to diagnose four apparently sporadic MTC index cases carrying the germline RET S409Y (c.1226 C>A) variant. Subsequently, 27 relatives of these individuals underwent clinical and genetic assessments and/or thyroid surgery. Furthermore, in silico analyses and in vitro assays were performed to predict or verify the potential oncogenic activity of the S409Y variant. Results: Overall, 15 of 31 participants were found to carry the RET S409Y variant. Of these, 6 presented with isolated MTC (mean age 50.2 years; range 41-75 years), of which 3 presented with neck lymph node metastases and 2 presented with distant liver or lung metastases. Among the remaining 9 carriers, 3 (mean age 56 years; range 41-76 years) had elevated serum calcium-stimulated calcitonin (sCtn) or concurrent marginally elevated serum calcitonin (Ctn) levels, whereas the other 6 (mean age 37.5 years; range 14-52 years) exhibited typical Ctn/sCtn levels (p < 0.05). None of the 15 carriers in these 4 families presented clinical evidence of pheochromocytoma, hyperparathyroidism, or Hirschsprung's disease. In silico analyses revealed that S409Y was a "possibly damaging" mutation that could affect the RET protein inter-domain interface. An in vitro assay revealed that the phosphorylation level of RET tyrosine 905 was relatively higher in the RET S409Y mutant than in wild-type (WT) RET. Moreover, transfection of HEK 293 cells with S409Y enhanced the phosphorylation activity of AKT, ERK pathways, and it increased cell proliferation compared with WT RET, but to a lesser degree than that for the RET C618Y and C634Y mutations. Conclusions: This study demonstrates that the novel germline RET S409Y variant is likely pathogenic and is associated with lower penetrance of MTC than that for the C618Y and C634Y mutations. Individuals with S409Y should be managed using a personalized approach, and additionally, "at-risk" family members should be evaluated. Additional studies are needed to elucidate the correlation between the S409Y mutation and multiple endocrine neoplasia type 2-specific tumors.
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Affiliation(s)
- Xiao-Ping Qi
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, Hangzhou, China
| | - Bai-Ye Jin
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Peng-Fei Li
- Department of Research and Development, XY Biotechnology Co. Ltd., Hangzhou, China
| | - Sheng Wang
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Yi-Hua Zhao
- Department of Urologic Surgery, Yueqing People's Hospital, Wenzhou Medical University, Yueqing, China
| | - Zhi-Lie Cao
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, Hangzhou, China
| | - Xiu-Hua Yu
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, Hangzhou, China
| | - Jun Cheng
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, Hangzhou, China
| | - Xu-Dong Fang
- Department of Oncologic and Urologic Surgery, The 903rd PLA Hospital, Wenzhou Medical University, Hangzhou, China
| | - Jian-Qiang Zhao
- Department of Head and Neck Surgery, Zhejiang Cancer Hospital, Hangzhou, China
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5
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Mochizuki T, Teraoka A, Akagawa H, Makabe S, Akihisa T, Sato M, Kataoka H, Mitobe M, Furukawa T, Tsuchiya K, Nitta K. Mutation analyses by next-generation sequencing and multiplex ligation-dependent probe amplification in Japanese autosomal dominant polycystic kidney disease patients. Clin Exp Nephrol 2019; 23:1022-1030. [PMID: 30989420 DOI: 10.1007/s10157-019-01736-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/02/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD), one of the most common hereditary kidney diseases, causes gradual growth of cysts in the kidneys, leading to renal failure. Owing to the advanced technology of next-generation sequencing (NGS), genetic analyses of the causative genes PKD1 and PKD2 have been improved. METHODS We performed genetic analyses of 111 Japanese ADPKD patients using hybridization-based NGS and long-range (LR)-PCR-based NGS. Additionally, genetic analyses in exon 1 of PKD1 using Sanger sequencing because of an extremely low coverage of NGS and those using multiplex ligation-dependent probe amplification (MLPA) were performed. RESULTS The detection rate using NGS for 111 patients was 86.5%. One mutation in exon 1 of PKD1 and five deletions detected by MLPA were identified. When combined, the total detection rate was 91.9%. CONCLUSION Although NGS is useful, we propose the addition of Sanger sequencing for exon 1 of PKD1 and MLPA as indispensable for identifying mutations not detected by NGS.
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Affiliation(s)
- Toshio Mochizuki
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan. .,Clinical Research Division for Polycystic Kidney Disease, Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan.
| | - Atsuko Teraoka
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences (TIIMS), Tokyo, Japan
| | - Shiho Makabe
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Taro Akihisa
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayo Sato
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroshi Kataoka
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan.,Clinical Research Division for Polycystic Kidney Disease, Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Michihiro Mitobe
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Toru Furukawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences (TIIMS), Tokyo, Japan.,Department of Histopathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ken Tsuchiya
- Department of Blood Purification, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
| | - Kosaku Nitta
- Department of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, Japan
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6
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He WB, Xiao WJ, Tan YQ, Zhao XM, Li W, Zhang QJ, Zhong CG, Li XR, Hu L, Lu GX, Lin G, Du J. Novel mutations of PKD genes in Chinese patients suffering from autosomal dominant polycystic kidney disease and seeking assisted reproduction. BMC MEDICAL GENETICS 2018; 19:186. [PMID: 30333007 PMCID: PMC6192368 DOI: 10.1186/s12881-018-0693-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/24/2018] [Indexed: 01/24/2023]
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD), the commonest inherited kidney disease, is generally caused by heterozygous mutations in PKD1, PKD2, or GANAB (PKD3). Methods We performed mutational analyses of PKD genes to identify causative mutations. A set of 90 unrelated families with ADPKD were subjected to mutational analyses of PKD genes. Genes were analysed using long-range PCR (LR-PCR), direct PCR sequencing, followed by multiplex ligation-dependent probe amplification (MLPA) or screening of GANAB for some patients. Semen quality was assessed for 46 male patients, and the correlation between mutations and male infertility was analysed. Results A total of 76 mutations, including 38 novel mutations, were identified in 77 families, comprising 72 mutations in PKD1 and 4 in PKD2, with a positive detection rate of 85.6%. No pathogenic mutations of GANAB were detected. Thirty-seven patients had low semen quality and were likely to be infertile. No association was detected between PKD1 mutation type and semen quality. However, male patients carrying a pathogenic mutation in the Ig-like repeat domain of PKD1 had a high risk of infertility. Conclusion Our study identified a group of novel mutations in PKD genes, which enrich the PKD mutation spectrum and might help clinicians to make precise diagnoses, thereby allowing better family planning and genetic counselling. Men with ADPKD accompanied by infertility should consider intracytoplasmic sperm injection combined with preimplantation genetic diagnosis to achieve paternity and obtain healthy progeny. Electronic supplementary material The online version of this article (10.1186/s12881-018-0693-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen-Bin He
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Wen-Juan Xiao
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Xiao-Meng Zhao
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Wen Li
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Qian-Jun Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Chang-Gao Zhong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Xiu-Rong Li
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Guang-Xiu Lu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, 410078, People's Republic of China. .,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, 410078, People's Republic of China.
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7
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Ranjzad F, Aghdami N, Tara A, Mohseni M, Moghadasali R, Basiri A. Identification of Three Novel Frameshift Mutations in the PKD1 Gene in Iranian Families with Autosomal Dominant Polycystic Kidney Disease Using Efficient Targeted Next-Generation Sequencing. Kidney Blood Press Res 2018; 43:471-478. [PMID: 29590654 DOI: 10.1159/000488471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/14/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common inherited cystic kidney diseases caused by mutations in two large multi-exon genes, PKD1 and PKD2. High allelic heterogeneity and duplication of PKD1 exons 1-32 as six pseudo genes on chromosome 16 complicate molecular analysis of this disease. METHODS We applied targeted next-generation sequencing (NGS) in 9 non-consanguineous unrelated Iranian families with ADPKD to identify the genes hosting disease-causing mutations. This approach was confirmed by Sanger sequencing. RESULTS Here, we determined three different novel frameshift mutations and four previously reported nonsense mutations in the PKD1 gene encoding polycystin1 in heterozygotes. CONCLUSION This study demonstrates the effectiveness of NGS in significantly reducing the cost and time for simultaneous sequence analysis of PKD1 and PKD2, simplifying the genetic diagnostics of ADPKD. Although a probable correlation between the mutation types and phenotypic outcome is possible, however for more extensive studies in future, the consideration of renal hypouricemia (RHUC) and PKD1 coexistence may be helpful. The novel frameshift mutations reported by this study are p. Q1997X, P. D73X and p. V336X.
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Affiliation(s)
- Fariba Ranjzad
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ahmad Tara
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Moghadasali
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Abbas Basiri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med 2017; 20:855-866. [PMID: 29144510 PMCID: PMC6456263 DOI: 10.1038/gim.2017.192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/21/2023] Open
Abstract
PURPOSE: As massively parallel sequencing is increasingly being used for
clinical decision-making, it has become critical to understand parameters
that affect sequencing quality and to establish methods for measuring and
reporting clinical sequencing standards. In this report, we propose a
definition for reduced coverage regions and have
established a set of standards for variant calling in clinical sequencing
applications. METHODS: To enable sequencing centers to assess the regions of poor sequencing
quality in their own data, we optimized and used a tool
(ExCid) to identify reduced coverage loci within genes
or regions of particular interest. We used this framework to examine
sequencing data from 500 patients generated in ten projects from sequencing
centers in the NHGRI/NCI Clinical Sequencing Exploratory Research (CSER)
Consortium. RESULTS: This approach identified reduced coverage regions in clinically
relevant genes, including known clinically relevant loci that were uniquely
missed at individual centers, in multiple centers, and in all centers. CONCLUSIONS: This report provides a process roadmap for clinical sequencing
centers looking to perform similar analyses on their data.
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Mimura I, Tanaka T, Nangaku M. New insights into molecular mechanisms of epigenetic regulation in kidney disease. Clin Exp Pharmacol Physiol 2017; 43:1159-1167. [PMID: 27560313 DOI: 10.1111/1440-1681.12663] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 08/12/2016] [Accepted: 08/21/2016] [Indexed: 12/11/2022]
Abstract
The number of patients with kidney failure has increased in recent years. Different factors contribute to the progression of chronic kidney disease, including glomerular sclerosis, atherosclerosis of the renal arteries and tubulointerstitial fibrosis. Tubulointerstitial injury is induced by hypoxia and other inflammatory signals, leading to fibroblast activation. Technological advances using high-throughput sequencing has enabled the determination of the expression profile of almost all genes, revealing that gene expression is intricately regulated by DNA methylation, histone modification, changes in chromosome conformation, long non-coding RNAs and microRNAs. These epigenetic modifications are stored as cellular epigenetic memory. Epigenetic memory leads to adult-onset disease or ageing in the long term and may possibly play an important role in the kidney disease process. Herein we emphasize the importance of clarifying the molecular mechanisms underlying epigenetic modifications because this may lead to the development of new therapeutic targets in kidney disease.
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Affiliation(s)
- Imari Mimura
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
| | - Tetsuhiro Tanaka
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
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10
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Borràs DM, Vossen RHAM, Liem M, Buermans HPJ, Dauwerse H, van Heusden D, Gansevoort RT, den Dunnen JT, Janssen B, Peters DJM, Losekoot M, Anvar SY. Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing. Hum Mutat 2017; 38:870-879. [PMID: 28378423 PMCID: PMC5488171 DOI: 10.1002/humu.23223] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 01/23/2023]
Abstract
A genetic diagnosis of autosomal-dominant polycystic kidney disease (ADPKD) is challenging due to allelic heterogeneity, high GC content, and homology of the PKD1 gene with six pseudogenes. Short-read next-generation sequencing approaches, such as whole-genome sequencing and whole-exome sequencing, often fail at reliably characterizing complex regions such as PKD1. However, long-read single-molecule sequencing has been shown to be an alternative strategy that could overcome PKD1 complexities and discriminate between homologous regions of PKD1 and its pseudogenes. In this study, we present the increased power of resolution for complex regions using long-read sequencing to characterize a cohort of 19 patients with ADPKD. Our approach provided high sensitivity in identifying PKD1 pathogenic variants, diagnosing 94.7% of the patients. We show that reliable screening of ADPKD patients in a single test without interference of PKD1 homologous sequences, commonly introduced by residual amplification of PKD1 pseudogenes, by direct long-read sequencing is now possible. This strategy can be implemented in diagnostics and is highly suitable to sequence and resolve complex genomic regions that are of clinical relevance.
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Affiliation(s)
- Daniel M Borràs
- GenomeScan B.V, Leiden, The Netherlands.,Institut National de la Santé et de la Recherche Médicale (INSERM), Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Rolf H A M Vossen
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Michael Liem
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Henk P J Buermans
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hans Dauwerse
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Dave van Heusden
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ron T Gansevoort
- Department of Nephrology, University Hospital Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Johan T den Dunnen
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Monique Losekoot
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Seyed Yahya Anvar
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
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11
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Messa P, Alfieri CM, Montanari E, Ferraresso M, Cerutti R. ADPKD: clinical issues before and after renal transplantation. J Nephrol 2016; 29:755-763. [DOI: 10.1007/s40620-016-0349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/29/2016] [Indexed: 12/17/2022]
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12
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Xue C, Zhou CC, Wu M, Mei CL. The Clinical Manifestation and Management of Autosomal Dominant Polycystic Kidney Disease in China. KIDNEY DISEASES 2016; 2:111-119. [PMID: 27921038 DOI: 10.1159/000449030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/10/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic hereditary kidney disease characterized by progressive enlargement of renal cysts. The incidence is 1-2‰ worldwide. Mutations in two genes (PKD1 and PKD2) cause ADPKD. Currently, there is no pharmaceutical treatment available for ADPKD patients in China. Summary: This review focused on advances in clinical manifestation, gene diagnosis, risk factors, and management of ADPKD in China. There is an age-dependent increase in total kidney volume (TKV) and decrease in renal function in Chinese ADPKD patients. ADPKD is more severe in males than in females. Great progress has been made in molecular diagnosis in the last two decades. Nephrologists found many novel PKD mutations in Chinese ADPKD patients early through polymerase chain reaction, and then through liquid chromatography in 2000s, and recently through next-generation sequencing. Major predictive factors for ADPKD progression are age, PKD genotype, sex, estimated glomerular filtration rate (eGFR), and TKV. With respect to the management of ADPKD, inhibitors targeting mTOR and cAMP are the focus of clinical trials. Triptolide has been used to treat ADPKD patients in clinical trials in China. Triptolide significantly protected eGFR of ADPKD patients compared with placebo. KEY MESSAGES ADPKD affects about 1.5 million people in China. An additional PKD gene besides PKD1 and PKD2 was not found in the Chinese. The prevalence of intracranial aneurysm in Chinese ADPKD patients was 12.4%. The predictive factors for eGFR decrease in Chinese ADPKD patients are TKV, proteinuria, history of hypertension, and age. The treatment strategies in clinical trials for ADPKD patients in China are similar to those in the West except for triptolide. FACTS FROM EAST AND WEST (1) ADPKD is diagnosed globally by ultrasound detection of kidney enlargement and presence of cysts. Recent analyses of variants of the PKD1 and PKD2 genes by next-generation sequencing in Chinese and Western ADPKD patients might lead to the development of reliable genetic tests. (2) Besides lifestyle changes (low-salt diet, sufficient fluid intake, and no smoking), blood pressure control is the primary nonspecific treatment recommended by Kidney Disease - Improving Global Outcomes (KDIGO) for ADPKD patients. How low the blood pressure target should be and what the means of achieving it are remain open questions depending on the severity of chronic kidney disease and the age of the patients. In a recent Chinese study, diagnostic needle aspiration and laparoscopic unroofing surgery successfully improved infection, pain, and hypertension. Peritoneal dialysis was found to be a feasible treatment for most Chinese ADPKD patients with end-stage renal disease. In most Western centers, patients without contraindication are selected for peritoneal dialysis. Kidney transplantation with concurrent bilateral nephrectomy was successful in relieving hypertension and infection in Chinese ADPKD patients. In Western countries, sequential surgical intervention with kidney transplantation after nephrectomy, or the other way round, is preferred in order to reduce risks. (3) The vasopressin 2 receptor antagonist tolvaptan was approved in Europe, Canada, Japan, and Korea to slow down progression of kidney disease in ADPKD patients. Tolvaptan is not yet approved in the USA or in China. mTOR pathway-targeting drugs are currently under evaluation: mTOR inhibitors could slow down the increase in total kidney volume in a cohort of Western and Japanese ADPKD patients. Western studies as well as an ongoing study in China failed to show benefit from rapamycin. A study performed in Italy indicates protective effects of the somatostatin analog octreotide in ADPKD patients. Western and Chinese studies revealed a potential beneficial effect of triptolide, the active substance of the traditional Chinese medicine Tripterygium wilfordii (Lei Gong Teng) to prevent worsening in ADPKD patients.
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Affiliation(s)
- Cheng Xue
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chen-Chen Zhou
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ming Wu
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chang-Lin Mei
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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13
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Abstract
PURPOSE OF REVIEW Recent technological improvements have increased the use of genetic testing in the clinic. This review serves to summarize the many practical benefits of genetic testing, discusses various methodologies that can be used clinically, and exemplifies ways in which genetics is propelling the field forward in nephrology. RECENT FINDINGS The advent of next-generation sequencing and microarray technologies has heralded an unprecedented number of discoveries in the field of nephrology, providing many opportunities for incorporating genomic diagnostics into clinical care. The use of genetic testing, particularly in pediatrics, can provide accurate diagnoses in puzzling cases, resolve misclassification of disease, and identify subsets of individuals with treatable conditions. SUMMARY Genetic testing may have broad benefits for patients and their families. Knowing the precise molecular etiology of disease can help clinicians determine the exact therapeutic course, and counsel patients and their families about prognosis. Genetic discoveries can also improve the classification of kidney disease and identify new targets for therapy.
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14
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García-García G, Baux D, Faugère V, Moclyn M, Koenig M, Claustres M, Roux AF. Assessment of the latest NGS enrichment capture methods in clinical context. Sci Rep 2016; 6:20948. [PMID: 26864517 PMCID: PMC4750071 DOI: 10.1038/srep20948] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/13/2016] [Indexed: 12/30/2022] Open
Abstract
Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.
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Affiliation(s)
- Gema García-García
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Valérie Faugère
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Mélody Moclyn
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Michel Koenig
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
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15
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Lu QK, Zhao N, Lv YS, Gong WK, Wang HY, Tong QH, Lai XM, Liu RR, Fang MY, Zhang JG, Du ZF, Zhang XN. A novel CRX mutation by whole-exome sequencing in an autosomal dominant cone-rod dystrophy pedigree. Int J Ophthalmol 2015; 8:1112-7. [PMID: 26682157 DOI: 10.3980/j.issn.2222-3959.2015.06.06] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/30/2015] [Indexed: 11/02/2022] Open
Abstract
AIM To identify the disease-causing gene mutation in a Chinese pedigree with autosomal dominant cone-rod dystrophy (adCORD). METHODS A southern Chinese adCORD pedigree including 9 affected individuals was studied. Whole-exome sequencing (WES), coupling the Agilent whole-exome capture system to the Illumina HiSeq 2000 DNA sequencing platform was used to search the specific gene mutation in 3 affected family members and 1 unaffected member. After a suggested variant was found through the data analysis, the putative mutation was validated by Sanger DNA sequencing of samples from all available family members. RESULTS The results of both WES and Sanger sequencing revealed a novel nonsense mutation c.C766T (p.Q256X) within exon 5 of CRX gene which was pathogenic for adCORD in this family. The mutation could affect photoreceptor-specific gene expression with a dominant-negative effect and resulted in loss of the OTX tail, thus the mutant protein occupies the CRX-binding site in target promoters without establishing an interaction and, consequently, may block transactivation. CONCLUSION All modes of Mendelian inheritance in CORD have been observed, and genetic heterogeneity is a hallmark of CORD. Therefore, conventional genetic diagnosis of CORD would be time-consuming and labor-intensive. Our study indicated the robustness and cost-effectiveness of WES in the genetic diagnosis of CORD.
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Affiliation(s)
- Qin-Kang Lu
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Na Zhao
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Ya-Su Lv
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
| | - Wei-Kun Gong
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Hui-Yun Wang
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Qi-Hu Tong
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Xiao-Ming Lai
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Rong-Rong Liu
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
| | - Ming-Yan Fang
- BGI-Shenzhen, Shenzhen 518083, Guangdong Province, China
| | - Jian-Guo Zhang
- BGI-Shenzhen, Shenzhen 518083, Guangdong Province, China
| | - Zhen-Fang Du
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
| | - Xian-Ning Zhang
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
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17
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Polla DL, Cardoso MTO, Silva MCB, Cardoso ICC, Medina CTN, Araujo R, Fernandes CC, Reis AMM, de Andrade RV, Pereira RW, Pogue R. Use of Targeted Exome Sequencing for Molecular Diagnosis of Skeletal Disorders. PLoS One 2015; 10:e0138314. [PMID: 26380986 PMCID: PMC4575211 DOI: 10.1371/journal.pone.0138314] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/28/2015] [Indexed: 01/19/2023] Open
Abstract
Genetic disorders of the skeleton comprise a large group of more than 450 clinically distinct and genetically heterogeneous diseases associated with mutations in more than 300 genes. Achieving a definitive diagnosis is complicated due to the genetic heterogeneity of these disorders, their individual rarity and their diverse radiographic presentations. We used targeted exome sequencing and designed a 1.4Mb panel for simultaneous testing of more than 4,800 exons in 309 genes involved in skeletal disorders. DNA from 69 individuals from 66 families with a known or suspected clinical diagnosis of a skeletal disorder was analyzed. Of 36 cases with a specific clinical hypothesis with a known genetic basis, mutations were identified for eight cases (22%). Of 20 cases with a suspected skeletal disorder but without a specific diagnosis, four causative mutations were identified. Also included were 11 cases with a specific skeletal disorder but for which there was at the time no known associated gene. For these cases, one mutation was identified in a known skeletal disease genes, and re-evaluation of the clinical phenotype in this case changed the diagnoses from osteodysplasia syndrome to Apert syndrome. These results suggest that the NGS panel provides a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in a highly genetically heterogeneous set of disorders such as genetic skeletal disorders. The data also stress the importance of a thorough clinical evaluation before DNA sequencing. The strategy should be applicable to other groups of disorders in which the molecular basis is largely known.
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Affiliation(s)
- Daniel L. Polla
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria T. O. Cardoso
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
- Curso de Medicina, Universidade Católica de Brasília, Taguatinga, Distrito Federal, Brazil
| | - Mayara C. B. Silva
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Isabela C. C. Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Cristina T. N. Medina
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Rosenelle Araujo
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Alessandra M. M. Reis
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rosangela V. de Andrade
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rinaldo W. Pereira
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Robert Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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18
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Yu G, Qian X, Wu Y, Li X, Chen J, Xu J, Qi J. Analysis of gene mutations in PKD1/PKD2 by multiplex ligation-dependent probe amplification: some new findings. Ren Fail 2015; 37:366-71. [PMID: 26381842 DOI: 10.3109/0886022x.2015.1088349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a serious genetic disorder that can lead to chronic renal disease. Protein dysfunction caused by mutations in the genes polycystic kidney disease 1 (PKD1) and polycystic kidney disease 2 (PKD2) is an important factor in the pathogenesis of ADPKD. In the present study, 30 Chinese patients with confirmed diagnosis of ADPKD, based on ultrasound or computerized tomography (CT) findings were selected, and the exon copy numbers of PKD1 and PKD2 were determined using multiplex ligation-dependent probe amplification (MLPA). MLPA identified exon deletion in 1 case, suspected exon deletion in 4 cases, and suspected duplications in 3 cases. One case of suspected exon deletion was confirmed using quantitative real-time polymerase chain reaction (q-PCR) and sequencing (PKD2 exon 8). A missense mutation was observed in 1 case of exon deletion using q-PCR and sequencing (PKD1 exon 40, c.11333 C>A). The cases of suspected duplications were verified by q-PCR, and the copy number of exon 6 of PKD1 in 1 case of suspected duplication was 3.8 times greater than that in normal controls. Our findings provide new insights into ADPKD screening and mark a possibly meaningful step toward improved diagnosis and treatment of patients with ADPKD.
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Affiliation(s)
- Guopeng Yu
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China .,b Fudan Institute of Urology, Fudan University , Shanghai , P.R. China .,c Department of Urology , Huashan Hospital, Fudan University , Shanghai , P.R. China , and
| | - Xiaoqiang Qian
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Yu Wu
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Xinjuan Li
- d Medical examination center, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Jianhua Chen
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Jianfeng Xu
- b Fudan Institute of Urology, Fudan University , Shanghai , P.R. China .,c Department of Urology , Huashan Hospital, Fudan University , Shanghai , P.R. China , and
| | - Jun Qi
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
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19
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Mallett A, Patel C, Maier B, McGaughran J, Gabbett M, Takasato M, Cameron A, Trnka P, Alexander SI, Rangan G, Tchan MC, Caruana G, John G, Quinlan C, McCarthy HJ, Hyland V, Hoy WE, Wolvetang E, Taft R, Simons C, Healy H, Little M. A protocol for the identification and validation of novel genetic causes of kidney disease. BMC Nephrol 2015; 16:152. [PMID: 26374634 PMCID: PMC4570515 DOI: 10.1186/s12882-015-0148-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic renal diseases (GRD) are a heterogeneous and incompletely understood group of disorders accounting for approximately 10 % of those diagnosed with kidney disease. The advent of Next Generation sequencing and new approaches to disease modelling may allow the identification and validation of novel genetic variants in patients with previously incompletely explained or understood GRD. METHODS/DESIGN This study will recruit participants in families/trios from a multidisciplinary sub-specialty Renal Genetics Clinic where known genetic causes of GRD have been excluded or where genetic testing is not available. After informed patient consent, whole exome and/or genome sequencing will be performed with bioinformatics analysis undertaken using a customised variant assessment tool. A rigorous process for participant data management will be undertaken. Novel genetic findings will be validated using patient-derived induced pluripotent stem cells via differentiation to renal and relevant extra-renal tissue phenotypes in vitro. A process for managing the risk of incidental findings and the return of study results to participants has been developed. DISCUSSION This investigator-initiated approach brings together experts in nephrology, clinical and molecular genetics, pathology and developmental biology to discover and validate novel genetic causes for patients in Australia affected by GRD without a known genetic aetiology or pathobiology.
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Affiliation(s)
- Andrew Mallett
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia. .,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia. .,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia. .,Kidney Health Service, Level 9, Ned Hanlon Building, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia.
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Barbara Maier
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Michael Gabbett
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia.,School of Medicine, Griffith University, Brisbane, Australia
| | - Minoru Takasato
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Anne Cameron
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Peter Trnka
- Queensland Child and Adolescent Renal Service, Lady Cilento Children's Hospital, Brisbane, Australia
| | - Stephen I Alexander
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gopala Rangan
- Department of Nephrology, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michel C Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Georgina Caruana
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - George John
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Cathy Quinlan
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Hugh J McCarthy
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia.,Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Valentine Hyland
- Molecular Genetics Laboratory, Pathology Queensland and Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Wendy E Hoy
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ryan Taft
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Helen Healy
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Melissa Little
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
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20
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Iorio A, Polimanti R, Calandro M, Graziano ME, Piacentini S, Bucossi S, Squitti R, Lazzarin N, Scano G, Limbruno GM, Manfellotto D, Fuciarelli M. Explorative genetic association study of GSTT2B copy number variant in complex disease risks. Ann Hum Biol 2015. [PMID: 26207597 DOI: 10.3109/03014460.2015.1049206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Glutathione S-transferases (GSTs) are the main phase II enzymes involved in cellular detoxification. Through phase I and phase II detoxification reactions, the cell is able to detoxify endogenous and exogenous toxic compounds. AIMS This study focused attention on the GSTT2B copy number variant (CNV) in order to explore its involvement in the genetic pre-disposition to asthma, Alzheimer's disease (AD), allergic rhinitis (AR), essential hypertension (EH), hypothyroidism and recurrent miscarriage (RM). METHODS The study population consists of 1225 individuals divided into six case-control groups. The genotyping of the GSTT2B CNV was performed by using a duplex-PCR. Odds Ratios (ORs) were calculated, adjusting for the confounding variables, to estimate the association between GSTT2B CNV and the disease status. RESULTS The χ(2)-test and ORs did not show any association between this genetic marker and pathological phenotypes. CONCLUSION The data highlights that GSTT2B CNV is not associated with the investigated complex diseases in Italian patients. However, further investigations are necessary to replicate these findings in larger sample sizes and to explore other health-related phenotypes.
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Affiliation(s)
- Andrea Iorio
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Renato Polimanti
- b Department of Psychiatry , Yale University School of Medicine , West Haven , CT , USA
| | - Melania Calandro
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | | | - Sara Piacentini
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Serena Bucossi
- c Department of Clinical Neuroscience , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Isola Tiberina , Rome , Italy .,d Department of Neurology , 'Campus Bio-Medico' University , Rome , Italy
| | - Rosanna Squitti
- c Department of Clinical Neuroscience , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Isola Tiberina , Rome , Italy .,e Laboratorio Neurodegenerazione , IRCCS San Raffaele Pisana , Rome , Italy
| | | | - Giuseppina Scano
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Giancarlo Maria Limbruno
- g Clinical Pathology Department , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Rome , Italy
| | | | - Maria Fuciarelli
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
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21
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Mallett A, Corney C, McCarthy H, Alexander SI, Healy H. Genomics in the renal clinic - translating nephrogenetics for clinical practice. Hum Genomics 2015; 9:13. [PMID: 26104748 PMCID: PMC4485638 DOI: 10.1186/s40246-015-0035-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/16/2015] [Indexed: 01/21/2023] Open
Abstract
Genetic Renal Disease (GRD) presents to mainstream clinicians as a mixture of kidney-specific as well as multi-organ entities, many with highly variable phenotype-genotype relationships. The rapid increase in knowledge and reduced cost of sequencing translate to new and additional approaches to clinical care. Specifically, genomic technologies to test for known genes, the development of pathways to research potential new genes and the collection of registry data on patients with mutations allow better prediction of outcomes. The aim of such approaches is to maximise personal and health-system utility from genomics for those affected by nephrogenetic disorders.
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Affiliation(s)
- Andrew Mallett
- Kidney Health Service & Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia.
- Centre for Kidney Disease Research, CKD.QLD and Centre for Chronic Disease, School of Medicine, The University of Queensland, Brisbane, Australia.
- Centre for Rare Diseases Research, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
| | - Christopher Corney
- Kidney Health Service & Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia
- Centre for Kidney Disease Research, CKD.QLD and Centre for Chronic Disease, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Hugh McCarthy
- Department of Paediatric Nephrology, Children's Hospital at Westmead, Sydney, Australia
- Centre for Kidney Research, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- Department of Paediatric Nephrology, Children's Hospital at Westmead, Sydney, Australia
- Centre for Kidney Research, University of Sydney, Sydney, Australia
- Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Helen Healy
- Kidney Health Service & Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia
- Centre for Kidney Disease Research, CKD.QLD and Centre for Chronic Disease, School of Medicine, The University of Queensland, Brisbane, Australia
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22
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Hafizi A, Khatami SR, Galehdari H, Shariati G, Saberi AH, Hamid M. Exon sequencing of PKD1 gene in an Iranian patient with autosomal-dominant polycystic kidney disease. IRANIAN BIOMEDICAL JOURNAL 2015; 18:143-50. [PMID: 24842140 PMCID: PMC4048478 DOI: 10.6091/ibj.1317.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Introduction: Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic kidney disorders with the incidence of 1 in 1,000 births. ADPKD is genetically heterogeneous with two genes identified: PKD1 (16p13.3, 46 exons) and PKD2 (4q21, 15 exons). Eighty five percent of the patients with ADPKD have at least one mutation in the PKD1 gene. Genetic studies have demonstrated an important allelic variability among patients, but very few data are known about the genetic variation among Iranian populations. Methods: In this study, exon direct sequencing of PKD1 was performed in a seven-year old boy with ADPKD and in his parents. The patient’s father was ADPKD who was affected without any kidney dysfunction, and the patient’s mother was congenitally missing one kidney. Results: Molecular genetic testing found a mutation in all three members of this family. It was a missense mutation GTG>ATG at position 3057 in exon 25 of PKD1. On the other hand, two novel missense mutations were reported just in the 7-year-old boy: ACA>GCA found in exon 15 at codon 2241 and CAC>AAC found in exon 38 at codon 3710. For checking the pathogenicity of these mutations, exons 15, 25, and 38 of 50 unrelated normal cases were sequenced. Conclusion: our findings suggested that GTG>ATG is a polymorphism with high frequency (60%) as well as ACA>GCA and CAC>AAC are polymorphisms with frequencies of 14% and 22%, respectively in the population of Southwest Iran.
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Affiliation(s)
- Atousa Hafizi
- Dept. of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
| | - Saeid Reza Khatami
- Dept. of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
| | - Hamid Galehdari
- Dept. of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetic Laboratory, Ahvaz, Iran.,Dept. of Medical Genetics, Jundishapur University of Medical Science, Ahvaz, Iran
| | - Ali Hossein Saberi
- Narges Medical Genetic Laboratory, Ahvaz, Iran.,Dept. of Medical Genetics, Jundishapur University of Medical Science, Ahvaz, Iran
| | - Mohammad Hamid
- Research Center of Biotechnology, Pasteur Institute of Iran, Tehran, Iran
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23
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Liu W, Chen M, Wei J, He W, Li Z, Sun X, Shi Y. Modification of PCR conditions and design of exon-specific primers for the efficient molecular diagnosis of PKD1 mutations. Kidney Blood Press Res 2014; 39:536-45. [PMID: 25531466 DOI: 10.1159/000368464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Autosomal-dominant polycystic kidney disease (ADPKD) is a heterogeneous genetic disorder caused by mutations in the PKD1 and PKD2 genes. Currently, long-range PCR followed by nested PCR and sequencing (LRNS) is the gold standard approach for PKD1 testing. However, LRNS is complicated by the high structural and sequence complexity of PKD1, which makes the procedure for amplification and analysis of PKD1 difficult. METHODS Here in, we modified the PCR conditions and designed primers for efficient and specific amplification of both the long-range and individual exons of PKD1. RESULTS Using the modified system, seven long-range fragments were specifically amplified using two distinct sets of conditions, and all individual exon PCR assays were easily performed using a touch-down PCR method. Seven pathogenic or likely pathogenic variants, including two novel truncated frameshift indels and two novel likely pathogenic missense mutations, were identified in eight unrelated patients with or without histories of ADPKD disease (one variant was observed in two unrelated patients). Using combined bioinformatics tools, two indeterminate missense variants were identified in two sporadic patients. CONCLUSION Four novel PKD1 variants were identified in this study. We demonstrated that the modified LRNS method achieves high sensitivity and specificity for detecting pathogenic variants of ADPKD.
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Affiliation(s)
- WeiQiang Liu
- Graduate school, Southern Medical University, Guangzhou 510515, China
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24
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Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology. J Mol Diagn 2014; 16:639-47. [PMID: 25157971 DOI: 10.1016/j.jmoldx.2014.06.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/21/2014] [Accepted: 06/18/2014] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized genetic testing by enabling simultaneous analysis of unprecedented numbers of genes. However, genes with high-sequence homology pose challenges to current NGS technologies. Because diagnostic sequencing is moving toward exome analysis, knowledge of these homologous genes is essential to avoid false positive and negative results. An example is the STRC gene, one of >70 genes known to contribute to the genetic basis of hearing loss. STRC is 99.6% identical to a pseudogene (pSTRC) and therefore inaccessible to standard NGS methodologies. The STRC locus is also known to be a common site for large deletions. Comprehensive diagnostic testing for inherited hearing loss therefore necessitates a combination of several approaches to avoid pseudogene interference. We have developed a clinical test that combines standard NGS and NGS-based copy number assessment supplemented with a long-range PCR-based Sanger or MiSeq assay to eliminate pseudogene contamination. By using this combination of assays we could identify biallelic STRC variants in 14% (95% CI, 8%-24%) of individuals with isolated nonsyndromic hearing loss who had previously tested negative on our 70-gene hearing loss panel, corresponding to a detection rate of 11.2% (95% CI, 6%-19%) for previously untested patients. This approach has broad applicability because medically significant genes for many disease areas include genes with high-sequence homology.
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25
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Novel mutations of PKD genes in the Czech population with autosomal dominant polycystic kidney disease. BMC MEDICAL GENETICS 2014; 15:41. [PMID: 24694054 PMCID: PMC3992149 DOI: 10.1186/1471-2350-15-41] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 03/10/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary renal disorder caused by mutation in either one of two genes, PKD1 and PKD2. High structural and sequence complexity of PKD genes makes the mutational diagnostics of ADPKD challenging. The present study is the first detailed analysis of both PKD genes in a cohort of Czech patients with ADPKD using High Resolution Melting analysis (HRM) and Multiplex Ligation-dependent Probe Amplification (MLPA). METHODS The mutational analysis of PKD genes was performed in a set of 56 unrelated patients. For mutational screening of the PKD1 gene, the long-range PCR (LR-PCR) strategy followed by nested PCR was used. Resulting PCR fragments were analyzed by HRM; the positive cases were reanalyzed and confirmed by direct sequencing. Negative samples were further examined for sequence changes in the PKD2 gene by the method of HRM and for large rearrangements of both PKD1 and PKD2 genes by MLPA. RESULTS Screening of the PKD1 gene revealed 36 different likely pathogenic germline sequence changes in 37 unrelated families/individuals. Twenty-five of these sequence changes were described for the first time. Moreover, a novel large deletion was found within the PKD1 gene in one patient. Via the mutational analysis of the PKD2 gene, two additional likely pathogenic mutations were detected. CONCLUSIONS Probable pathogenic mutation was detected in 71% of screened patients. Determination of PKD mutations and their type and localization within corresponding genes could help to assess clinical prognosis of ADPKD patients and has major benefit for prenatal and/or presymptomatic or preimplantational diagnostics in affected families as well.
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26
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Identification of novel mutations of PKD1 gene in Chinese patients with autosomal dominant polycystic kidney disease by targeted next-generation sequencing. Clin Chim Acta 2014; 433:12-9. [PMID: 24582653 DOI: 10.1016/j.cca.2014.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 01/06/2023]
Abstract
BACKGROUND Mutations of PKD1 and PKD2 accounted for the most cases of autosomal dominant polycystic kidney disease (ADPKD). The presence of the large transcript, numerous exons and complex reiterated regions within the gene has significantly complicated the analysis of PKD1 with routine PCR-based approaches. METHODS We developed a strategy to analyze both the PKD1/PKD2 genes simultaneously using targeted next-generation sequencing (NGS). All coding exons plus the flanking sequences of PKD1 and PKD2 genes from probands were captured, individually barcoded and followed by HiSeq2000 sequencing. The candidate variants were validated by using classic Sanger sequencing. PKD1-specific primers were designed to amplify the replicated areas of PKD1 gene. RESULTS Five novel variations and one known mutation in PKD1 gene were detected in five familial and one sporadic Chinese ADPKD patients. Through pedigree and bioinformatic analysis, five of them were identified as pathogenic mutations (p.G1319R, p.Y3781*, p.W4122*, p.Val700Glyfs*14, and p.Leu3656Trpfs*28) and one was as polymorphism (p.T2420I). CONCLUSIONS Our result showed that targeted capture and NGS technology were effective for the gene testing of ADPKD disorder. Mutation study of PKD1 and PKD2 genes in Chinese patients may contribute to better understanding of the genetic diversity between different ethnic groups and enrich the mutation database in Asian population.
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27
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Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med 2014; 8:42-57. [PMID: 24384736 DOI: 10.1007/s11684-014-0303-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/30/2013] [Indexed: 12/23/2022]
Abstract
The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.
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28
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Claes KBM, De Leeneer K. Dealing with pseudogenes in molecular diagnostics in the next-generation sequencing era. Methods Mol Biol 2014; 1167:303-15. [PMID: 24823787 DOI: 10.1007/978-1-4939-0835-6_21] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this chapter, we focus on issues related to the application of next-generation sequencing (NGS) strategies for the analysis of genes with pseudogenes in a clinical setting. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences, which are characterized by higher mutation rates than their functional parental genes. For the target enrichment strategies, we describe advantages and disadvantages of PCR- and capture-based enrichment methodologies. For the mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some concrete examples of genes with known pseudogenes and associated with Mendelian disorders that were analyzed by NGS on various platforms and starting from different library preparations.
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29
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Tan AY, Michaeel A, Liu G, Elemento O, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H. Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing. J Mol Diagn 2013; 16:216-28. [PMID: 24374109 DOI: 10.1016/j.jmoldx.2013.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 12/29/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1 and PKD2. However, genetic analysis is complicated by six PKD1 pseudogenes, large gene sizes, and allelic heterogeneity. We developed a new clinical assay for PKD gene analysis using paired-end next-generation sequencing (NGS) by multiplexing individually bar-coded long-range PCR libraries and analyzing them in one Illumina MiSeq flow cell. The data analysis pipeline has been optimized and automated with Unix shell scripts to accommodate variant calls. This approach was validated using a cohort of 25 patients with ADPKD previously analyzed by Sanger sequencing. A total of 250 genetic variants were identified by NGS, spanning the entire exonic and adjacent intronic regions of PKD1 and PKD2, including all 16 pathogenic mutations. In addition, we identified three novel mutations in a mutation-negative cohort of 24 patients with ADPKD previously analyzed by Sanger sequencing. This NGS method achieved sensitivity of 99.2% (95% CI, 96.8%-99.9%) and specificity of 99.9% (95% CI, 99.7%-100.0%), with cost and turnaround time reduced by as much as 70%. Prospective NGS analysis of 25 patients with ADPKD demonstrated a detection rate comparable with Sanger standards. In conclusion, the NGS method was superior to Sanger sequencing for detecting PKD gene mutations, achieving high sensitivity and improved gene coverage. These characteristics suggest that NGS would be an appropriate new standard for clinical genetic testing of ADPKD.
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Affiliation(s)
- Adrian Y Tan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Alber Michaeel
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Genyan Liu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Jon Blumenfeld
- Department of Medicine, Weill Cornell Medical College, New York, New York; The Rogosin Institute, New York, New York
| | | | - Tom Parker
- The Rogosin Institute, New York, New York
| | | | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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30
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McInerney-Leo AM, Marshall MS, Gardiner B, Coucke PJ, Van Laer L, Loeys BL, Summers KM, Symoens S, West JA, West MJ, Paul Wordsworth B, Zankl A, Leo PJ, Brown MA, Duncan EL. Whole exome sequencing is an efficient, sensitive and specific method of mutation detection in osteogenesis imperfecta and Marfan syndrome. BONEKEY REPORTS 2013; 2:456. [PMID: 24501682 DOI: 10.1038/bonekey.2013.190] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/16/2013] [Accepted: 10/23/2013] [Indexed: 12/16/2022]
Abstract
Osteogenesis imperfecta (OI) and Marfan syndrome (MFS) are common Mendelian disorders. Both conditions are usually diagnosed clinically, as genetic testing is expensive due to the size and number of potentially causative genes and mutations. However, genetic testing may benefit patients, at-risk family members and individuals with borderline phenotypes, as well as improving genetic counseling and allowing critical differential diagnoses. We assessed whether whole exome sequencing (WES) is a sensitive method for mutation detection in OI and MFS. WES was performed on genomic DNA from 13 participants with OI and 10 participants with MFS who had known mutations, with exome capture followed by massive parallel sequencing of multiplexed samples. Single nucleotide polymorphisms (SNPs) and small indels were called using Genome Analysis Toolkit (GATK) and annotated with ANNOVAR. CREST, exomeCopy and exomeDepth were used for large deletion detection. Results were compared with the previous data. Specificity was calculated by screening WES data from a control population of 487 individuals for mutations in COL1A1, COL1A2 and FBN1. The target capture of five exome capture platforms was compared. All 13 mutations in the OI cohort and 9/10 in the MFS cohort were detected (sensitivity=95.6%) including non-synonymous SNPs, small indels (<10 bp), and a large UTR5/exon 1 deletion. One mutation was not detected by GATK due to strand bias. Specificity was 99.5%. Capture platforms and analysis programs differed considerably in their ability to detect mutations. Consumable costs for WES were low. WES is an efficient, sensitive, specific and cost-effective method for mutation detection in patients with OI and MFS. Careful selection of platform and analysis programs is necessary to maximize success.
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Affiliation(s)
- Aideen M McInerney-Leo
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia
| | - Mhairi S Marshall
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia
| | - Brooke Gardiner
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia
| | - Paul J Coucke
- Medical Genetics, The University Hospital Ghent , Gent, Belgium
| | - Lut Van Laer
- University of Antwerp, Antwerp University Hospital , Antwerp, Belgium
| | - Bart L Loeys
- University of Antwerp, Antwerp University Hospital , Antwerp, Belgium ; Department of Genetics, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Kim M Summers
- The Roslin Institute and R(D)SVS, University of Edinburgh , Midlothian, UK
| | - Sofie Symoens
- Medical Genetics, The University Hospital Ghent , Gent, Belgium
| | - Jennifer A West
- The University of Qld Northside Clinical School, Prince Charles Hospital , Chermside, Queensland, Australia
| | - Malcolm J West
- The University of Qld Northside Clinical School, Prince Charles Hospital , Chermside, Queensland, Australia
| | - B Paul Wordsworth
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Nuffield Orthopaedic Centre , Oxford, UK
| | - Andreas Zankl
- The University of Queensland, UQ Centre for Clinical Research , Herston, Queensland, Australia ; Sydney Medical School, University of Sydney , Sydney, New South Wales, Australia ; Academic Department of Medical Genetics, The Children's Hospital at Westmead , Sydney, New South Wales, Australia
| | - Paul J Leo
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia
| | - Matthew A Brown
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia
| | - Emma L Duncan
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia ; Department of Endocrinology, Royal Brisbane and Women's Hospital , Herston, Queensland, Australia
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31
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Németh AH, Kwasniewska AC, Lise S, Parolin Schnekenberg R, Becker EBE, Bera KD, Shanks ME, Gregory L, Buck D, Zameel Cader M, Talbot K, de Silva R, Fletcher N, Hastings R, Jayawant S, Morrison PJ, Worth P, Taylor M, Tolmie J, O’Regan M, Valentine R, Packham E, Evans J, Seller A, Ragoussis J. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain 2013; 136:3106-18. [PMID: 24030952 PMCID: PMC3784284 DOI: 10.1093/brain/awt236] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/28/2013] [Accepted: 06/20/2013] [Indexed: 12/23/2022] Open
Abstract
Many neurological conditions are caused by immensely heterogeneous gene mutations. The diagnostic process is often long and complex with most patients undergoing multiple invasive and costly investigations without ever reaching a conclusive molecular diagnosis. The advent of massively parallel, next-generation sequencing promises to revolutionize genetic testing and shorten the 'diagnostic odyssey' for many of these patients. We performed a pilot study using heterogeneous ataxias as a model neurogenetic disorder to assess the introduction of next-generation sequencing into clinical practice. We captured 58 known human ataxia genes followed by Illumina Next-Generation Sequencing in 50 highly heterogeneous patients with ataxia who had been extensively investigated and were refractory to diagnosis. All cases had been tested for spinocerebellar ataxia 1-3, 6, 7 and Friedrich's ataxia and had multiple other biochemical, genetic and invasive tests. In those cases where we identified the genetic mutation, we determined the time to diagnosis. Pathogenicity was assessed using a bioinformatics pipeline and novel variants were validated using functional experiments. The overall detection rate in our heterogeneous cohort was 18% and varied from 8.3% in those with an adult onset progressive disorder to 40% in those with a childhood or adolescent onset progressive disorder. The highest detection rate was in those with an adolescent onset and a family history (75%). The majority of cases with detectable mutations had a childhood onset but most are now adults, reflecting the long delay in diagnosis. The delays were primarily related to lack of easily available clinical testing, but other factors included the presence of atypical phenotypes and the use of indirect testing. In the cases where we made an eventual diagnosis, the delay was 3-35 years (mean 18.1 years). Alignment and coverage metrics indicated that the capture and sequencing was highly efficient and the consumable cost was ∼£400 (€460 or US$620). Our pathogenicity interpretation pathway predicted 13 different mutations in eight different genes: PRKCG, TTBK2, SETX, SPTBN2, SACS, MRE11, KCNC3 and DARS2 of which nine were novel including one causing a newly described recessive ataxia syndrome. Genetic testing using targeted capture followed by next-generation sequencing was efficient, cost-effective, and enabled a molecular diagnosis in many refractory cases. A specific challenge of next-generation sequencing data is pathogenicity interpretation, but functional analysis confirmed the pathogenicity of novel variants showing that the pipeline was robust. Our results have broad implications for clinical neurology practice and the approach to diagnostic testing.
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Affiliation(s)
- Andrea H. Németh
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- 2 Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Alexandra C. Kwasniewska
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Stefano Lise
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Ricardo Parolin Schnekenberg
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
- 4 School of Medicine, Universidade Positivo, Curitiba, Brazil
| | - Esther B. E. Becker
- 5 Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3QX, UK
| | - Katarzyna D. Bera
- 5 Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3QX, UK
| | - Morag E. Shanks
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Lorna Gregory
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - David Buck
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - M. Zameel Cader
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Kevin Talbot
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Rajith de Silva
- 6 Department of Neurology, Essex Centre for Neurological Sciences, Queen's Hospital, Romford, UK
| | | | - Rob Hastings
- 8 Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Sandeep Jayawant
- 9 Department of Paediatrics, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
| | - Patrick J. Morrison
- 10 School of Medicine, Dentistry and Biomedical Sciences, Queens University, Belfast, BT9 7BL, Northern Ireland, UK
| | - Paul Worth
- 11 Department of Neurology, Norfolk and Norwich University Hospital, Norwich, UK
| | - Malcolm Taylor
- 12 School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - John Tolmie
- 13 Department of Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Mary O’Regan
- 14 Fraser of Allander Neurosciences Unit, Royal Hospital for Sick Children, Glasgow G3 8SJ, UK
| | | | - Ruth Valentine
- 15 Thames Valley Dementia and Neurodegenerative Diseases Network, Oxford, UK
| | - Emily Packham
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Julie Evans
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Anneke Seller
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Jiannis Ragoussis
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
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QI XIAOPING, LIU WENTING, LI JINYU, DAI YUN, MA JUMING, ZHAO YAN, FEI JUN, LI FENG, SHEN MAO, JIN HANGYANG, CHEN ZHENGUANG, DU ZHENFANG, CHEN XIAOLING, ZHANG XIANNING. p.N78S and p.R161Q germline mutations of the VHL gene are present in von Hippel-Lindau syndrome in two pedigrees. Mol Med Rep 2013; 8:799-805. [PMID: 23842656 DOI: 10.3892/mmr.2013.1578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 07/04/2013] [Indexed: 11/06/2022] Open
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Shahzad M, Sivakumaran TA, Qaiser TA, Schultz JM, Hussain Z, Flanagan M, Bhinder MA, Kissell D, Greinwald JH, Khan SN, Friedman TB, Zhang K, Riazuddin S, Riazuddin S, Ahmed ZM. Genetic analysis through OtoSeq of Pakistani families segregating prelingual hearing loss. Otolaryngol Head Neck Surg 2013; 149:478-87. [PMID: 23770805 DOI: 10.1177/0194599813493075] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To identify the genetic cause of prelingual sensorineural hearing loss in Pakistani families using a next-generation sequencing (NGS)-based mutation screening test named OtoSeq. STUDY DESIGN Prospective study. SETTING Research laboratory. SUBJECTS AND METHODS We used 3 fluorescently labeled short tandem repeat (STR) markers for each of the known autosomal recessive nonsyndromic (DFNB) and Usher syndrome (USH) locus to perform a linkage analysis of 243 multigenerational Pakistani families segregating prelingual hearing loss. After genotyping, we focused on 34 families with potential linkage to MYO7A, CDH23, and SLC26A4. We screened affected individuals from a subset of these families using the OtoSeq platform to identify underlying genetic variants. Sanger sequencing was performed to confirm and study the segregation of mutations in other family members. For novel mutations, normal hearing individuals from ethnically matched backgrounds were also tested. RESULTS Hearing loss was found to co-segregate with locus-specific STR markers for MYO7A in 32 families, CDH23 in 1 family, and SLC26A4 in 1 family. Using the OtoSeq platform, a microdroplet PCR-based enrichment followed by NGS, we identified mutations in 28 of the 34 families including 11 novel mutations. Sanger sequencing of these mutations showed 100% concordance with NGS data and co-segregation of the mutant alleles with the hearing loss phenotype in the respective families. CONCLUSION Using NGS-based platforms like OtoSeq in families segregating hearing loss will contribute to the identification of common and population-specific mutations, early diagnosis, genetic counseling, and molecular epidemiology.
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Affiliation(s)
- Mohsin Shahzad
- Divisions of Ophthalmology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio USA
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Lee BR, Cho S, Song Y, Kim SC, Cho BK. Emerging tools for synthetic genome design. Mol Cells 2013; 35:359-70. [PMID: 23708771 PMCID: PMC3887862 DOI: 10.1007/s10059-013-0127-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 12/29/2022] Open
Abstract
Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives.
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Affiliation(s)
- Bo-Rahm Lee
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
| | - Suhyung Cho
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Yoseb Song
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Sun Chang Kim
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Byung-Kwan Cho
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
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