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Prasad R, Sharma K, Bhutani K, Prasad S, Manhas S, Kishan J. Identification of Genetic Variants in Exon 4 of TP53 in Lung Carcinoma and in Silico Prediction of Their Significance. Indian J Clin Biochem 2024; 39:276-282. [PMID: 38577139 PMCID: PMC10987423 DOI: 10.1007/s12291-022-01099-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
Abstract
Lung cancer is a severe and the leading cause of cancer related deaths in men and women all over the world. Tumor suppressor protein (TP53) encoded by the TP53 gene which plays a pivotal role in various cellular tumor suppression processes viz cell cycle arrest and apoptosis. Henceforth, the present study was aimed to TP53 exon4 variants from lung carcinoma. Histopathologic and clinically proven 20 patients of lung cancer were enrolled in this study the average age of patients was 45 ± 8 years which categorized as early onset of lung cancer. Genomic DNA was isolated from the blood specimen of patients. Extracted DNA was subjected to PCR amplification for exon 4 of TP53 using appropriate primers and subsequently amplified products were applied to nucleotide alterations via using the DNA sanger sequencing. The genetic analysis documented five variants in exon4 of TP53 which include viz. 4 substitutions [c.215 > C at codon 72, C. 358-359AA > GG at codon 120] were highly prevalent, occurring in 63% and 25% frequency in patients. Other two variants viz. C. 358 A > C at codon 120, C. 365T > G at codon 122 were present at frequency of 15% whilst one deletion variant [152 del C] was found with 5% frequency. Furthermore, alterations on codon 72, 120,122 and 51 were characterized as possibly damaging by Poly Phen-2 and decreased stability using stability bioinformatic tool. Taken together all these findings infer that TP53 gene involved in modulation and susceptibility to lung cancer.
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Affiliation(s)
- Rajendra Prasad
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Kirti Sharma
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Karanpreet Bhutani
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Suvarna Prasad
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
- Department of Biochemistry, AIIMS, Deoghar, India
| | - Sunita Manhas
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Jai Kishan
- Department of Respiratory Medicine, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
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Sahib S, Yan J, Chen T. Application of duplex sequencing to evaluate mutagenicity of aristolochic acid and methapyrilene in Fisher 344 rats. Food Chem Toxicol 2024; 185:114512. [PMID: 38342231 DOI: 10.1016/j.fct.2024.114512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Duplex sequencing (DS) is an error-corrected next-generation sequencing (NGS) method that can overcome notorious high error rate from the process of NGS and detect ultralow-frequency mutations. In this study, we evaluated the mutagenicity of aristolochic acid, a known genotoxic carcinogen, and methapyrilene, a known nongenotoxic carcinogen using DS. Four male Fisher 344 rats were treated with aristolochic acid, methapyrilene, or the vehicle control for 6 weeks, liver tissues were collected one day after the treatment, and the DNA was isolated for analysis. The mutation frequency for the aristolochic acid-treated group was significantly increased over the vehicle control (44-fold), whereas no significant difference in the mutation frequency was observed between the methapyrilene-treated and the control groups. The primary type of mutation induced by aristolochic acid was A:T > T:A transversion, which occurred frequently at ApT sites, whereas the major type of mutation in the control and methapyrilene-treated groups was G:C > A:T transition, which occurred frequently at CpG sites. These findings are consistent with previously published data obtained with other in vivo mutation assays. Thus, our results suggest that the DS mutation assay is a promising technology for assessing mutagenicity of chemicals in vivo.
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Affiliation(s)
- Seaab Sahib
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Frohne A, Vrabel S, Laccone F, Neesen J, Roesch S, Dossena S, Schoefer C, Frei K, Parzefall T. Mutational spectrum in patients with dominant non-syndromic hearing loss in Austria. Eur Arch Otorhinolaryngol 2024:10.1007/s00405-024-08492-5. [PMID: 38400873 DOI: 10.1007/s00405-024-08492-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 02/26/2024]
Abstract
PURPOSE Hearing loss (HL) is often monogenic. The clinical importance of genetic testing in HL may further increase when gene therapy products become available. Diagnoses are, however, complicated by a high genetic and allelic heterogeneity, particularly of autosomal dominant (AD) HL. This work aimed to characterize the mutational spectrum of AD HL in Austria. METHODS In an ongoing prospective study, 27 consecutive index patients clinically diagnosed with non-syndromic AD HL, including 18 previously unpublished cases, were analyzed using whole-exome sequencing (WES) and gene panels. Novel variants were characterized using literature and bioinformatic means. Two additional Austrian medical centers provided AD HL mutational data obtained with in-house pipelines. Other Austrian cases of AD HL were gathered from literature. RESULTS The solve rate (variants graded as likely pathogenic (LP) or pathogenic (P)) within our cohort amounted to 59.26% (16/27). MYO6 variants were the most common cause. One third of LP/P variants were truncating variants in haploinsufficiency genes. Ten novel variants in HL genes were identified, including six graded as LP or P. In one cohort case and one external case, the analysis uncovered previously unrecognized syndromic presentations. CONCLUSION More than half of AD HL cases analyzed at our center were solved with WES. Our data demonstrate the importance of genetic testing, especially for the diagnosis of syndromic presentations, enhance the molecular knowledge of genetic HL, and support other laboratories in the interpretation of variants.
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Affiliation(s)
- Alexandra Frohne
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department for Cell and Developmental Biology, Center of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sybille Vrabel
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Juergen Neesen
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Sebastian Roesch
- Department of Otorhinolaryngology, Head and Neck Surgery, Paracelsus Medical University, Salzburg, Austria
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Christian Schoefer
- Department for Cell and Developmental Biology, Center of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Klemens Frei
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Danube Private University, Steiner Landstraße 124, 3500, Krems a.d. Donau, Austria
| | - Thomas Parzefall
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
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Dobrovolsky VN, Matsuda T, McKinzie P, Miranda J, Revollo JR. Whole-genome high-fidelity sequencing: A novel approach to detecting and characterization of mutagenicity in vivo. Mutat Res Genet Toxicol Environ Mutagen 2023; 891:503691. [PMID: 37770148 DOI: 10.1016/j.mrgentox.2023.503691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023]
Abstract
Direct DNA sequencing can be used for characterizing mutagenicity in simple and complex biological models. Recently we described a method of whole-genome sequencing for detecting mutations in simple models of cultured bacteria, mammalian cells, and nematode. In the current proof-of-concept study, we expand and improve our method for evaluating a more complex mammalian biological model in outbred mice. We detail the method by applying it to a small set of animals treated with a mutagen with known mutagenicity profiles, N-ethyl-N-nitrosourea (ENU), for consistency with the known data. Whole-genome high-fidelity sequencing (HiFi Sequencing) showed frequencies and spectra of background mutations in tissues of untreated mice that were consistent with normal ageing and characterized by spontaneous or enzymatic deamination of 5-methylcytosine. In mice treated with a single 40 mg/kg dose of ENU, the frequency of mutations in the genomic DNA of solid tissues increased up to 7-fold, with the greatest increase observed in the spleen and the smallest increase in the liver. The most common mutations detected in ENU-treated mice were T > A transitions and T > C transversions, consistent with the types of mutations caused by alkylating agents. The data suggest that HiFi Sequencing may be useful for characterizing mutagenicity of novel compounds in various biological models.
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Affiliation(s)
- Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson AR, USA.
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
| | - Page McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson AR, USA
| | - Jaime Miranda
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson AR, USA
| | - Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson AR, USA
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Maeda T, Shibai A, Yokoi N, Tarusawa Y, Kawada M, Kotani H, Furusawa C. Mutational property of newly identified mutagen l-glutamic acid γ-hydrazide in Escherichia coli. Mutat Res 2021; 823:111759. [PMID: 34304126 DOI: 10.1016/j.mrfmmm.2021.111759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
We previously found that an l-glutamine analog l-glutamic acid γ-hydrazide has high mutagenic activity through the high-throughput laboratory evolution of Escherichia coli. In this study, mutagenicity and mutational property of l-glutamic acid γ-hydrazide were examined by the Ames test and mutation accumulation experiments using E. coli. The Ames test revealed that l-glutamic acid γ-hydrazide showed higher mutagenic activity without metabolic activation than known mutagens 2-aminoanthracene, and cobalt(II) acetate tetrahydrate. This result indicates that l-glutamic acid γ-hydrazide does not require metabolic activation for mutagenic activity in E. coli. Mutation accumulation experiments and whole-genome sequencing analysis revealed the number and spectrum of the accumulated mutations with or without l-glutamic acid γ-hydrazide. In the presence of l-glutamic acid γ-hydrazide, MDS42 strain accumulated 392.3 ± 116.2 point mutations during 30 passages corresponding to 777 generations, while MDS42 strain accumulated 1.5 ± 2.5 point mutations without l-glutamic acid γ-hydrazide during 50 passages corresponding to 1341 generations. The mutational spectrum of l-glutamic acid γ-hydrazide was G/C to A/T transition (82.2 ± 4.3 %) and A/T to G/C transition (17.4 ± 4.3 %). These results indicated that l-glutamic acid γ-hydrazide has a strong mutagenic activity.
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Affiliation(s)
- Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Atsushi Shibai
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Naomi Yokoi
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yumeko Tarusawa
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Masako Kawada
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hazuki Kotani
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan; Department of Physics, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan; Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
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Tao Y, Han D, Shen H, Li X. Spectrum of PAH gene mutations and genotype-phenotype correlation in patients with phenylalanine hydroxylase deficiency from Shanxi province. Brain Dev 2021; 43:220-229. [PMID: 32893076 DOI: 10.1016/j.braindev.2020.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/04/2020] [Accepted: 08/18/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Phenylalanine hydroxylase deficiency (PAHD) is an autosomal recessive inborn error that affects phenylalanine (Phe) metabolism. It has a complex phenotype with many variants and genotypes among different populations. Shanxi province is a high-prevalence area of PAHD in China. METHODS In this study, eighty-nine PAHD patients were subjected to genetic testing using Sanger sequencing, followed by multiplex ligation-dependent probe amplification analysis (MLPA). Allelic and genotypic phenotype values (APV and GPV, respectively) were used for genotype-based phenotypic prediction. RESULTS Fifty-one types of variants, including three novel forms, were identified. The predominant variant was p.R243Q (22.09%), followed by p.R53H (10.47%), p.EX6-96A > G (9.30%), p.V399V (5.23%) and p.R413P (3.49%). Notably, mild hyperphenylalaninemia (MHP) has a high prevalence in this region (up to 45.76%), and the variant p.R53H was solely observed in patients of MHP. According to the genotype-phenotype prediction, the APV/GPV system was well correlated with the metabolic phenotype of most PAHD patients. CONCLUSION We have systematically constructed the mutational and phenotypic spectrum of PAH in Shanxi province. Hence, this study will help to further understand the genotype-phenotype associations in PAHD patients, and it may offer more reliable genetic counseling and management.
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Affiliation(s)
- Yilun Tao
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China
| | - Dong Han
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China
| | - Huiyi Shen
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China
| | - Xiaoze Li
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China.
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Abstract
Pathogenic variants of the CFTR gene are responsible for a broad phenotypic spectrum characterized by malfunction of some exocrine tissues, with an autosomal recessive mode of inheritance. More than 2,000 variants, distributed throughout the CFTR gene, have been identified, with different effects on the gene and protein expression and function. Genotype-phenotype correlation studies have associated severe variants with a typical multi-organ form of cystic fibrosis, while mild variants are involved in monosymptomatic or adult-onset diseases, called CFTR-related disorders. However, the interpretation of rare variants remains challenging. This review presents an overview of the epidemiology of CFTR variants worldwide and in France and describes the functional classification. Finally, some frequent cystic fibrosis-causing and mild CFTR variants are used as example to depict the molecular pathology of the CFTR locus. Finally, we give the recommendations concerning nomenclature and classification that are useful for appropriate genetic counseling. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- C Bareil
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - A Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France; EA7402 Laboratoire de Génétique de Maladies Rares, Institut Universitaire de Recherche Clinique, Université de Montpellier, Montpellier, France..
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Lin Y, Xu J, Li X, Sheng H, Su L, Wu M, Cheng J, Huang Y, Mao X, Zhou Z, Zhang W, Li C, Cai Y, Wu D, Lu Z, Yin X, Zeng C, Liu L. Novel variants and uncommon cases among southern Chinese children with X-linked hypophosphatemia. J Endocrinol Invest 2020; 43:1577-1590. [PMID: 32253725 DOI: 10.1007/s40618-020-01240-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/24/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE X-linked hypophosphatemia (XLH) is the most common inherited renal phosphate wasting disorder and is often misdiagnosed as vitamin D deficiency. This study aims to provide clinical and mutational characteristics of 65 XLH pediatric patients in southern China. METHODS In this work, a combination of DNA sequencing and qPCR analysis was used to study the PHEX gene in 80 pediatric patients diagnosed with hypophosphatemia. The clinical and laboratory data of confirmed 65 XLH patients were assessed and analyzed retrospectively. RESULTS In 65 XLH patients from 61 families, 51 different variants in the PHEX gene were identified, including 23 previously reported variants and 28 novel variants. In this cohort of XLH patients, the c.1601C>T(p.Pro534Leu) variant appears more frequently. Fourteen uncommon XLH cases were described, including four boys with de novo mosaic variants, eight patients with large deletions and a pair of monozygotic twins. The clinical manifestations in this cohort are very similar to those previously reported. CONCLUSION This study extends the mutational spectrum of the PHEX gene, which will contribute to accurate diagnosis. This study also suggests a supplementary qPCR or MLPA assay may be performed along with classical sequencing to confirm the gross insertion/deletion.
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Affiliation(s)
- Y Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - J Xu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - X Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - H Sheng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - L Su
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - M Wu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - J Cheng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - Y Huang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - X Mao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - Z Zhou
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - W Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - C Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - Y Cai
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - D Wu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - Z Lu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - X Yin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China
| | - C Zeng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China.
| | - L Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Rd., Guangzhou, 510623, China.
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Hoyer J, Vasileiou G, Uebe S, Wunderle M, Kraus C, Fasching PA, Thiel CT, Hartmann A, Beckmann MW, Lux MP, Reis A. Addition of triple negativity of breast cancer as an indicator for germline mutations in predisposing genes increases sensitivity of clinical selection criteria. BMC Cancer 2018; 18:926. [PMID: 30257646 PMCID: PMC6158817 DOI: 10.1186/s12885-018-4821-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 09/14/2018] [Indexed: 11/22/2022] Open
Abstract
Background Breast cancer is the most common cancer in women. 12–15% of all tumors are triple-negative breast cancers (TNBC). So far, TNBC has been mainly associated with mutations in BRCA1. The presence of other predisposing genes seems likely since DNA damage repair is a complex process that involves several genes. Therefore we investigated if mutations in other genes are involved in cancer development and whether TNBC is an additional indicator of mutational status besides family history and age of onset. Methods We performed a germline panel-based screening of 10 high and low-moderate penetrance breast cancer susceptibility genes (BRCA1, BRCA2, ATM, CDH1, CHEK2, NBN, PALB2, RAD51C, RAD51D and TP53) in 229 consecutive individuals affected with TNBC unselected for age, family history or bilateral disease. Within this cohort we compared the number of mutation carriers fulfilling clinical selection criteria with the total number of carriers identified. Results Age at diagnosis ranged from 23 to 80 years with an average age of 50.2 years. In 57 women (24.9%) we detected a pathogenic mutation, with a higher frequency (29.7%) in the group manifesting cancer before 60 years. Deleterious BRCA1 mutations occurred in 14.8% of TNBC patients. These were predominantly recurrent frameshift mutations (24/34, 70.6%). Deleterious BRCA2 mutations occurred in 5.7% of patients, all but one (c.1813dupA) being unique. While no mutations were found in CDH1 and TP53, 10 mutations were detected in one of the six other predisposition genes. Remarkably, neither of the ATM, RAD51D, CHEK2 and PALB2 mutation carriers had a family history. Furthermore, patients with non-BRCA1/2 mutations were not significantly younger than mutation negative women (p = 0.3341). Most importantly, among the 57 mutation carriers, ten (17.5%) would be missed using current clinical testing criteria including five (8%) with BRCA1/2 mutations. Conclusions In summary, our data confirm and expand previous studies of a high frequency of germline mutations in genes associated with ineffective repair of DNA damage in women with TNBCs. Neither age of onset, contralateral disease nor family history were able to discern all mutation positive individuals. Therefore, TNBC should be considered as an additional criterion for panel based genetic testing.
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Affiliation(s)
- Juliane Hoyer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Marius Wunderle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstr. 21-23, 91054, Erlangen, Germany
| | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstr. 21-23, 91054, Erlangen, Germany
| | - Christian T Thiel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstr. 21-23, 91054, Erlangen, Germany
| | - Michael P Lux
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstr. 21-23, 91054, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
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Chu XL, Zhang BW, Zhang QG, Zhu BR, Lin K, Zhang DY. Temperature responses of mutation rate and mutational spectrum in an Escherichia coli strain and the correlation with metabolic rate. BMC Evol Biol 2018; 18:126. [PMID: 30157765 PMCID: PMC6116381 DOI: 10.1186/s12862-018-1252-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/21/2018] [Indexed: 11/28/2022] Open
Abstract
Background Temperature is a major determinant of spontaneous mutation, but the precise mode, and the underlying mechanisms, of the temperature influences remain less clear. Here we used a mutation accumulation approach combined with whole-genome sequencing to investigate the temperature dependence of spontaneous mutation in an Escherichia coli strain. Experiments were performed under aerobic conditions at 25, 28 and 37 °C, three temperatures that were non-stressful for the bacterium but caused significantly different bacterial growth rates. Results Mutation rate did not differ between 25 and 28 °C, but was higher at 37 °C. Detailed analyses of the molecular spectrum of mutations were performed; and a particularly interesting finding is that higher temperature led to a bias of mutation to coding, relative to noncoding, DNA. Furthermore, the temperature response of mutation rate was extremely similar to that of metabolic rate, consistent with an idea that metabolic rate predicts mutation rate. Conclusions Temperature affects mutation rate and the types of mutation supply, both being crucial for the opportunity of natural selection. Our results help understand how temperature drives evolutionary speed of organisms and thus the global patterns of biodiversity. This study also lend support to the metabolic theory of ecology for linking metabolic rate and molecular evolution rate. Electronic supplementary material The online version of this article (10.1186/s12862-018-1252-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Lin Chu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, People's Republic of China.
| | - Bi-Ru Zhu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, 100875, People's Republic of China.
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Dong EL, Wang C, Wu S, Lu YQ, Lin XH, Su HZ, Zhao M, He J, Ma LX, Wang N, Chen WJ, Lin X. Clinical spectrum and genetic landscape for hereditary spastic paraplegias in China. Mol Neurodegener 2018; 13:36. [PMID: 29980238 PMCID: PMC6035405 DOI: 10.1186/s13024-018-0269-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background Hereditary spastic paraplegias (HSP) is a heterogeneous group of rare neurodegenerative disorders affecting the corticospinal tracts. To date, more than 78 HSP loci have been mapped to cause HSP. However, both the clinical and mutational spectrum of Chinese patients with HSP remained unclear. In this study, we aim to perform a comprehensive analysis of clinical phenotypes and genetic distributions in a large cohort of Chinese HSP patients, and to elucidate the primary pathogenesis in this population. Methods We firstly performed next-generation sequencing targeting 149 genes correlated with HSP in 99 index cases of our cohort. Multiplex ligation-dependent probe amplification testing was further carried out among those patients without known disease-causing gene mutations. We simultaneously performed a retrospective study on the reported patients exhibiting HSP in other Chinese cohorts. All clinical and molecular characterization from above two groups of Chinese HSP patients were analyzed and summarized. Eventually, we further validated the cellular changes in fibroblasts of two major spastic paraplegia (SPG) patients (SPG4 and SPG11) in vitro. Results Most patients of ADHSP (94%) are pure forms, whereas most patients of ARHSP (78%) tend to be complicated forms. In ADHSP, we found that SPG4 (79%) was the most prevalent, followed by SPG3A (11%), SPG6 (4%) and SPG33 (2%). Subtle mutations were the common genetic cause for SPG4 patients and most of them located in AAA cassette domain of spastin protein. In ARHSP, the most common subtype was SPG11 (53%), followed by SPG5 (32%), SPG35 (6%) and SPG46 (3%). Moreover, haplotype analysis showed a unique haplotype was shared in 14 families carrying c.334C > T (p.R112*) mutation in CYP7B1 gene, suggesting the founder effect. Functionally, we observed significantly different patterns of mitochondrial dynamics and network, decreased mitochondrial membrane potential (Δψm), increased reactive oxygen species and reduced ATP content in SPG4 fibroblasts. Moreover, we also found the enlargement of LAMP1-positive organelles and abnormal accumulation of autolysosomes in SPG11 fibroblasts. Conclusions Our study present a comprehensive clinical spectrum and genetic landscape for HSP in China. We have also provided additional evidences for mitochondrial and autolysosomal-mediated pathways in the pathogenesis of HSP. Electronic supplementary material The online version of this article (10.1186/s13024-018-0269-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- En-Lin Dong
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Chong Wang
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Shuang Wu
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Ying-Qian Lu
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Xiao-Hong Lin
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Hui-Zhen Su
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Miao Zhao
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Jin He
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Li-Xiang Ma
- Department of Anatomy, Histology and Embryology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China. .,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
| | - Xiang Lin
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China.
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Huang B, Han M, Wang G, Huang S, Zeng J, Yuan Y, Dai P. Genetic mutations in non-syndromic deafness patients in Hainan Province have a different mutational spectrum compared to patients from Mainland China. Int J Pediatr Otorhinolaryngol 2018; 108:49-54. [PMID: 29605365 DOI: 10.1016/j.ijporl.2018.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 02/11/2018] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To provide appropriate genetic testing and counseling for non-syndromic hearing impairment patients in Hainan Province, an island in the South China Sea. METHODS 299 unrelated students with non-syndromic hearing loss who attended a special education school in Hainan Province were enrolled in this study. Three prominent deafness-related genes (GJB2, SLC26A4, and mtDNA 12S rRNA) were analyzed using Sanger sequencing. RESULTS GJB2 mutations were detected in 32.78% (98/299) of the entire cohort; however, only 5.69% (17/299) had two confirmed pathogenic mutations. The most common mutation observed in this population was c.109G > A in the GJB2 gene, with an allelic frequency of 15.05% (90/598), which is significantly higher than that reported in previous cohorts. A total of 16 patients had two confirmed pathogenic SLC26A4 gene mutations, and 16 patients had one. The IVS7-2A > G mutation was the most commonly observed, with an allelic frequency of 3.51% (21/598). Three patients had a m.1555A > G mutation in the mtDNA 12S rRNA gene. CONCLUSIONS These results reveal that genetic etiology occurred in 11.71% (35/299) of patients, suggesting that Hainan province have a different mutational spectrum compare to Mainland China in non-syndromic deafness patients, which provide useful information to genetic counseling in Hainan province.
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Affiliation(s)
- Bangqing Huang
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya 572013, PR China
| | - Mingyu Han
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya 572013, PR China; Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China
| | - Guojian Wang
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China
| | - ShaSha Huang
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China
| | - Jialing Zeng
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya 572013, PR China
| | - Yongyi Yuan
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China.
| | - Pu Dai
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China.
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Cheng Z, Dai Y, Pang Y, Jiao Y, Zhao H, Wu S, Zhang L, Zhang Y, Wang X, Wang L, Ma D, Qin T, Hu N, Zhang Y, Hu K, Zhang Q, Shi J, Fu L. Clinical and Biological Implications of Mutational Spectrum in Acute Myeloid Leukemia of FAB Subtypes M0 and M1. Cell Physiol Biochem 2018; 47:1853-1861. [PMID: 29961066 DOI: 10.1159/000491065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 04/24/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND/AIMS Acute myeloid leukemia (AML) of French-American-British (FAB) subtypes M0 and M1 are both poorly differentiated AML, but their mutational spectrum and molecular characteristics remain unknown. This study aimed to explore the mutational spectrum and prognostic factors of AML-M0 and M1. METHODS Sixty-five AML patients derived from The Cancer Genome Atlas (TCGA) database were enrolled in this study. Whole-genome sequencing was performed to depict the mutational spectrum of each patient. Clinical characteristics at diagnosis, including peripheral blood (PB) white blood cell counts (WBC), blast percentages in PB and bone marrow (BM), FAB subtypes and the frequencies of known recurrent genetic mutations were described. Survival was estimated using the Kaplan-Meier methods and log-rank test. Univariate and multivariate Cox proportional hazard models were constructed for event-free survival (EFS) and overall survival (OS), using a limited backward elimination procedure. RESULTS Forty-six patients had more than five recurrent genetic mutations. FLT3 had the highest mutation frequency (n=20, 31%), followed by NPM1 (n=18, 28%), DNMT3A (n=16, 25%), IDH1 (n=14, 22%), IDH2 (n=12, 18%), RUNX1 (n=11, 17%) and TET2 (n=7, 11%). Univariate analysis showed that age ≥60 years and TP53 mutations had adverse effect on EFS (P=0.015, P=0.036, respectively) and OS (P=0.003, P=0.004, respectively), WBC count ≥50×109/L and FLT3-ITD negatively affected EFS (P=0.003, P=0.034, respectively), whereas NPM1 mutations had favorable effect on OS (P=0.035) and allogeneic hematopoietic stem cell transplantation (allo-HSCT) on EFS and OS (all P< 0.001). Multivariate analysis suggested that allo-HSCT and NPM1 mutations were independent favorable prognostic factors for EFS and OS (all P< 0.05), WBC count ≥50×109/L was an independent risk factor for EFS (P=0.002) and TP53 mutations for OS (P=0.043). CONCLUSIONS Our study provided new insights into the mutational spectrum and molecular signatures of AML-M0 and M1. We proposed that FLT3-ITD, NPM1 and TP53 be identified as markers for risk stratification of AML-M0 and M1. Patients with AML-M0 and M1 would likely benefit from allo-HSCT.
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MESH Headings
- Aged
- Biomarkers, Tumor/genetics
- Databases, Factual
- Disease-Free Survival
- Female
- Humans
- Leukemia, Myeloid, Acute/classification
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/therapy
- Male
- Middle Aged
- Mutation
- Neoplasm Proteins/genetics
- Nucleophosmin
- Risk Assessment
- Survival Rate
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Affiliation(s)
- Zhiheng Cheng
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, China
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
| | - Yifeng Dai
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou, China
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Yifan Pang
- Department of Medicine, William Beaumont Hospital, Royal Oak, Michigan, USA
| | - Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Hongmian Zhao
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Sun Wu
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Lingxiu Zhang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Yuan Zhang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Xiufeng Wang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Lihua Wang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Dong Ma
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
| | - Tong Qin
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Ning Hu
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Yijie Zhang
- Department of Respiratory, Huaihe Hospital of Henan University, Kaifeng, China
| | - Kai Hu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
| | - Qingyi Zhang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Department of Hematology of Air Force PLA General Hospital, Beijing, China
| | - Jinlong Shi
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, China
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, China
- Department of Medical Big Data, Chinese PLA General Hospital, Beijing, China
| | - Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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Meisel C, Sadowski CE, Kohlstedt D, Keller K, Stäritz F, Grübling N, Becker K, Mackenroth L, Rump A, Schröck E, Arnold N, Wimberger P, Kast K. Spectrum of genetic variants of BRCA1 and BRCA2 in a German single center study. Arch Gynecol Obstet 2017; 295:1227-38. [PMID: 28324225 DOI: 10.1007/s00404-017-4330-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/10/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Determination of mutation status of BRCA1 and BRCA2 has become part of the clinical routine. However, the spectrum of genetic variants differs between populations. The aim of this study was to deliver a comprehensive description of all detected variants. METHODS In families fulfilling one of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) criteria for genetic testing, one affected was chosen for analysis. DNA of blood lymphocytes was amplified by PCR and prescreened by DHPLC. Aberrant fragments were sequenced. All coding exons and splice sites of BRCA1 and BRCA2 were analyzed. Screening for large rearrangements in both genes was performed by MLPA. RESULTS Of 523 index patients, 121 (23.1%) were found to carry a pathogenic or likely pathogenic (class 4/5) mutation. A variant of unknown significance (VUS) was detected in 73/523 patients (13.9%). Two mutations p.Gln1756Profs*74 and p.Cys61Gly comprised 42.3% (n = 33/78) of all detected pathogenic mutations in BRCA1. Most of the other mutations were unique mutations. The most frequently detected mutation in BRCA2 was p.Val1283Lys (13.9%; n = 6/43). Altogether, 101 different neutral genetic variants were counted in BRCA1 (n = 35) and in BRCA2 (n = 66). CONCLUSION The two most frequently detected mutations are founder mutations in Poland and Czech Republic. More similarities seem to be shared with our direct neighbor countries compared to other European countries. For comparison of the extended genotype, a shared database is needed.
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15
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Fonseca H, Azevedo L, Serrano C, Sousa C, Marcão A, Vilarinho L. 3-Methylcrotonyl-CoA carboxylase deficiency: Mutational spectrum derived from comprehensive newborn screening. Gene 2016; 594:203-210. [PMID: 27601257 DOI: 10.1016/j.gene.2016.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 01/26/2023]
Abstract
The deficiency of 3-methycrotonyl-CoA carboxylase (3-MCC; EC 6.4.1.4) is an autosomal recessive organic aciduria that is included in the newborn screening programs of several countries. This study reports data mainly obtained from the Portuguese newborn screening program collected over a ten-year period. Analysis of the MCCC1 and MCCC2 genes yielded 26 previously unreported mutations and a variant of clinically unknown significance. These mutations are discussed in the context of their likely impact on the function of the 3-MCC enzyme, with a view to exploring whether a phenotype-genotype correlation might be discerned. Further, these mutations were analysed in the context of what is known of the MCCC1 and MCCC2 mutational spectra, information that will be useful in both clinical and laboratory practice.
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Affiliation(s)
- Helena Fonseca
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Porto, Portugal.
| | - Luisa Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Population Genetics and Evolution, Porto, Portugal; IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Catarina Serrano
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Population Genetics and Evolution, Porto, Portugal; IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Carmen Sousa
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Porto, Portugal
| | - Ana Marcão
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Porto, Portugal
| | - Laura Vilarinho
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Porto, Portugal
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Ferla MP. Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling. BMC Bioinformatics 2016; 17:152. [PMID: 27044645 PMCID: PMC4820924 DOI: 10.1186/s12859-016-0996-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/22/2016] [Indexed: 01/03/2023] Open
Abstract
Background Assessing library diversity is an important control step in a directed evolution experiment. To do this, a limited amount of colonies from a test library are sequenced and tested. In the case of an error-prone PCR library, the spectrum of the identified mutations — the proportions of mutations of a specific nucleobase to another— is calculated enabling the user to make more informed predictions on library diversity and coverage. However, the calculations of the mutational spectrum are severely affected by the limited sample sizes. Results Here an online program, called Mutanalyst, is presented, which not only automates the calculations, but also estimates errors involved. Specifically, the errors are calculated thanks to the complementarity of DNA, which means that a mutation has a complementary mutation on the other sequence. Additionally, in the case of determining the mean number of mutations per sequence it does so by fitting to a Poisson distribution, which is more robust than calculating the average in light of the small sampling size. Conclusion As a result of the added measures to keep into account of small sample size the user can better assess whether the library is satisfactory or whether error-prone PCR conditions should be adjusted. The program is available at www.mutanalyst.com.
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Affiliation(s)
- Matteo Paolo Ferla
- Formerly Department of Biochemistry, University of Otago, Dunedin, New Zealand. .,Present address: Biosyntia, DTU Centre for Biosustainability, Hørsholm, Denmark.
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Wang R, Yu Y, Ye J, Han L, Qiu W, Zhang H, Liang L, Gong Z, Wang L, Gu X. 21-hydroxylase deficiency-induced congenital adrenal hyperplasia in 230 Chinese patients: Genotype-phenotype correlation and identification of nine novel mutations. Steroids 2016; 108:47-55. [PMID: 26804566 DOI: 10.1016/j.steroids.2016.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 11/27/2022]
Abstract
Steroid 21-hydroxylase deficiency (21-OHD) caused by the CYP21A2 gene mutations accounts for more than 90% of congenital adrenal hyperplasia (CAH) cases. In this study, molecular defects of 230 patients with 21-OHD were investigated. Point mutations of CYP21A2 gene were analyzed by Sanger sequencing, and large gene deletions were detected by multiplex ligation-dependent probe amplification (MLPA). Nine micro-conversions and 18 spontaneous mutations accounted for 74.6% of alleles, while large gene deletions and large gene conversions accounted for 25.4% of alleles. The most frequent micro-conversion was c.292-13A/C>G (I2G) (35%), followed by p.I173N (14.3%), p.R357W (5.9%) and p.Q319* (4.6%). Nine novel mutations were identified in these patients, which were predicted to hamper the 21-hydroxylase protein function in varying degrees. Genotype and phenotype correlated well in 89.6% of our patients, but disparity in phenotypic appearance also appeared in a small portion of the patients. 16.1% of the patients carried homozygous genotypes while 83.9% of patients carried compound heterozygous mutations. We concluded that the frequency of CYP21A2 mutations in our study was slightly different from those reported for other ethnic groups. Micro-conversions were the main category of the mutation spectrum, while large deletions and large gene conversions could also cause 21-OHD. A large portion of different types of the compound heterozygous genotypes may partially contribute to the discordance in genotype-phenotype comparison. This study expanded the CYP21A2 mutation spectrum of Chinese patients and could be helpful in prenatal diagnosis and genetic counseling for 21-OHD patients.
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Affiliation(s)
- Ruifang Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Jun Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lili Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China.
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