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Waye JS, Hanna M, Hohenadel BA, Nakamura L, Walker L, Eng B, Nfonsam LE. Newborn Screening for β-Thalassemia Identifies a Complex Genotype Involving a Novel β-Globin Gene Mutation ( HBB:c.336dup). Hemoglobin 2024; 48:113-115. [PMID: 38565194 DOI: 10.1080/03630269.2024.2328220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/02/2024] [Indexed: 04/04/2024]
Abstract
Newborn screening identified a Chinese-Canadian infant who was positive for possible β-thalassemia (β-thal). Detailed family studies demonstrated that the proband was a compound heterozygote for the Chinese Gγ(Aγδβ)0-thal deletion and a novel frameshift mutation within exon 3 (HBB:c.336dup), and heterozygous for the Southeast Asian α-thal deletion (--SEA/αα). This case illustrates the importance of follow-up molecular testing of positive newborn screening results to confirm the diagnosis and define risks for future pregnancies.
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Affiliation(s)
- John S Waye
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Meredith Hanna
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Betty-Ann Hohenadel
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Lisa Nakamura
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Lynda Walker
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Barry Eng
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Landry E Nfonsam
- Molecular Genetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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2
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Bao XQ, Wang JC, Qin DQ, Yao CZ, Liang J, Du L. A Novel 5 kb Deletion in the β-Globin Gene Cluster Identified in a Chinese Patient. Hemoglobin 2022; 46:245-248. [DOI: 10.1080/03630269.2022.2118604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Xiu-Qin Bao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Ji-Cheng Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Dan-Qing Qin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Cui-Ze Yao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Jie Liang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Li Du
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
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3
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Hu S, Zhan W, Wang J, Xie J, Zhou W, Yang X, Zeng Y, Hu T, Duan L, Chen K, Du L, Yin A, Luo M. Establishment and application of a novel method based on single nucleotide polymorphism analysis for detecting β-globin gene cluster deletions. Sci Rep 2020; 10:18298. [PMID: 33106596 PMCID: PMC7588424 DOI: 10.1038/s41598-020-75507-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/12/2020] [Indexed: 12/03/2022] Open
Abstract
β-Globin gene mutations reduce or terminate the production of beta globin chains, of which approximately 10% are large deletions within the β-globin gene cluster. Because gene deletion leads to loss of heterozygosity at single nucleotide polymorphism (SNP), a novel method for detecting β-globin gene cluster deletions based on SNP heterozygosity analysis was established in this study. The location range of SNPs was selected according to the breakpoint of β-globin gene cluster deletions. SNPs were screened using bioinformatics analysis and population sequencing data. A novel method which enables genotyping of multiplex SNPs based on tetra-primer ARMS-PCR was designed and optimized. Forty clinical samples were tested in parallel by this method and MLPA to verify the performance of this method for detecting β-globin gene cluster deletion. Six informative SNPs were obtained, achieving heterozygote coverage of 93.3% in normal individuals. Genotyping of six SNPs were successfully integrated into two multiplex tetra-primer ARMS-PCR reactions. The sensitivity, specificity, positive predictive value and negative predictive value of the method for detecting β-globin gene cluster deletion were 100%, 96.30%, 92.86%, and 100%, respectively. This is a simple, cost-effective and novel method for detecting β-globin gene cluster deletions, which may be suitable for use in combination with MLPA for thalassemia molecular testing.
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Affiliation(s)
- Siqi Hu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetics Center, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Wenli Zhan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jicheng Wang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jia Xie
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China
| | - Weiping Zhou
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiaohan Yang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yukun Zeng
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Tingting Hu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lei Duan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China
| | - Keyi Chen
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Li Du
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Aihua Yin
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Mingyong Luo
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China. .,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China.
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4
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Du L, Qin D, Wang J, Yu L, Yao C, Liu L, Zhang Y, Hu T, Yuan T, Liang J, Yin A. Genetic and phenotypic analysis of a rare asymptomatic case of a homozygous Chinese Gγ +( Aγδβ) 0-thalassemia deletion in a Chinese family. Clin Biochem 2019; 76:11-16. [PMID: 31765637 DOI: 10.1016/j.clinbiochem.2019.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 01/01/2023]
Abstract
OBJECTIVE The clinical and hematologic features of thalassemia are due to different factors, and patients with identical genotypes may regularly exhibit variable severity. In the present work, one homozygous Chinese Gγ+(Aγδβ)0-thalassemia case with an asymptomatic phenotype, which is contrary to traditional views, was identified. Analysis of the underlying causes of this rare clinical phenotype involved accurate genetic diagnosis and detection of several genetic modifications. METHODS Six members of the proband's family were enrolled in the study. Hematological parameters and hemoglobin analysis results were recorded. A suspension-array system, multiplex gap-polymerase chain reaction (gap-PCR) and multiplex ligation-dependent probe amplification (MLPA) were used together to characterize genotypes. Sanger sequencing was utilized to examine the KLF1 gene and four primary fetal hemoglobin (Hb F)-associated single-nucleotide polymorphisms (SNPs). RESULTS Four family members carried the Chinese Gγ+(Aγδβ)0-thalassemia mutation, and a homozygous state was ultimately diagnosed for the proband. All of the Chinese Gγ+(Aγδβ)0 mutation-positive cases were coinherited with the Southern Asian α-thalassemia deletion (- - SEA/αα). Two SNP variants, rs7776054 and rs9399137, in the HBS1L-MYB locus were detected in the proband. CONCLUSIONS Thus far, this is the first study to describe the molecular characterization of a homozygous Chinese Gγ+(Aγδβ)0-thalassemia patient who exhibits no clinical symptoms. Our findings suggest that coinheritance of α-thalassemia or HBS1L-MYB locus variants may affect the clinical severity of Chinese Gγ+(Aγδβ)0-thalassemia. We conclude that the molecular examination of genetic determinants known to be associated with clinical outcomes in Chinese Gγ+(Aγδβ)0-thalassemia should be emphasized.
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Affiliation(s)
- Li Du
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Danqing Qin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jicheng Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Lihua Yu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Cuize Yao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Ling Liu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yanxia Zhang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Tingting Hu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Tenglong Yuan
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jie Liang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China; Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China.
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5
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Zhu F, Wei X, Cai D, Pang D, Zhong J, Liang M, Zuo Y, Xu X, Shang X. A novel 223 kb deletion in the beta-globin gene cluster was identified in a Chinese thalassemia major patient. Int J Lab Hematol 2019; 41:456-460. [PMID: 30945812 DOI: 10.1111/ijlh.13021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/19/2019] [Accepted: 03/08/2019] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Although mutations in the human beta-globin gene cluster are essentially point mutations, several large deletions have been described in recent years. METHODS We have identified a novel 223 kb deletion in a Chinese patient by multiplex ligation-dependent probe amplification and characterized it by next-generation sequencing, Gap-PCR, and DNA sequence analysis. RESULTS The deletion extends from the 3'UTR of the δ globin gene (HBD) to 215 kb downstream of the HBB. Compound heterozygous with the typical β-thalassemia-CD41-42(-CTTT) mutation, the proband presented with microcytosis and hypochromic red cells, and required regulate transfusion. The patient was clinically diagnosed with thalassemia major. CONCLUSION Our study widens the mutation spectrum of β-thalassemia. In addition, this case may spark future studies of the regulatory regions of the beta-globin gene cluster.
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Affiliation(s)
- Fei Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Decheng Cai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Dejian Pang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jianmei Zhong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Min Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yangjin Zuo
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Genetics Testing Engineering Research Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Genetics Testing Engineering Research Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
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6
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He S, Qin Q, Lin L, Zuo Y, Chen Q, Wei H, Zheng C, Chen B, Qiu X. First Identification of the 3.5 kb Deletion (NC_000011.10: g.5224302-5227791del3490bp) on the β-Globin Gene Cluster in a Chinese Family. Hemoglobin 2019; 42:272-275. [PMID: 30612499 DOI: 10.1080/03630269.2018.1531018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sheng He
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Qian Qin
- Prenatal Diagnostic Centre, Baise Women and Children Care Hospital, Baise, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Li Lin
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Yangjin Zuo
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Qiuli Chen
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Honghwei Wei
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Chenguang Zheng
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Biyan Chen
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Xiaoxia Qiu
- Prenatal Diagnostic Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
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7
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He S, Wei Y, Lin L, Chen Q, Yi S, Zuo Y, Wei H, Zheng C, Chen B, Qiu X. The prevalence and molecular characterization of (δβ) 0 -thalassemia and hereditary persistence of fetal hemoglobin in the Chinese Zhuang population. J Clin Lab Anal 2017; 32. [PMID: 28763119 PMCID: PMC5888142 DOI: 10.1002/jcla.22304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/04/2017] [Indexed: 11/10/2022] Open
Abstract
Objective To reveal the prevalence and molecular characterization of (δβ)0‐thalassemia [(δβ)0‐thal] and hereditary persistence of fetal hemoglobin (HPFH) in the Chinese Zhuang population. Methods A total of 105 subjects with fetal hemoglobin (Hb F) level ≥5% from 14 204 unrelated ones were selected for the study. Multiplex ligation dependent probe amplification was firstly used to analyze dosage changes of the β‐globin gene cluster for associated with (δβ)0‐thal and HPFH mutations. The gap polymerase chain reaction was then performed to identify the deletions using the respective flanking primers. Hematologic data were recorded and correlated with the molecular findings. Results Twenty‐one (0.15%) subjects were diagnosed with Chinese Gγ(Aγδβ)0‐thal. Nine (0.06%) were diagnosed with Southeast Asia HPFH (SEA‐HPFH) deletion. Seventy‐five (0.53%) cases remained uncharacterized. Three genotypes for Chinese Gγ(Aγδβ)0‐thal and SEA‐HPFH deletion were identified, respectively. The genotype‐phenotype relationships were discussed. Conclusion Our study for the first time demonstrated that (δβ)0 and HPFH were not rare events, and molecular characterized Gγ(Aγδβ)0‐thal and HFPH mutations in the Chinese Zhuang population. The findings in our study will be useful in genetic counseling and prenatal diagnostic service of β‐thalassemia in this populations.
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Affiliation(s)
- Sheng He
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Yuan Wei
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Li Lin
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Qiuli Chen
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Shang Yi
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Yangjin Zuo
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Hongwei Wei
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Chenguang Zheng
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - Biyan Chen
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
| | - XiaoXia Qiu
- Prenatal Diagnosis Center, Guangxi Zhuang Autonomous Region Women and Children Care Hospital, Nanning, China
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8
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Ke LY, Chang JG, Chang CS, Hsieh LL, Liu TC. Rapid Screening for Deleted Form of β-thalassemia by Real-Time Quantitative PCR. J Clin Lab Anal 2017; 31. [DOI: 10.1002/jcla.22019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 06/07/2016] [Indexed: 11/11/2022] Open
Affiliation(s)
- Liang-Yin Ke
- Department of Laboratory Medicine; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- Department of Medical Laboratory Science and Biotechnology; KMU; Kaohsiung Taiwan
| | - Jan-Gowth Chang
- Department of Laboratory Medicine; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- Graduate Institute of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Chao-Sung Chang
- Graduate Institute of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Division of Hematology-Oncology; Department of Internal Medicine; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
| | - Li-Ling Hsieh
- Department of Laboratory Medicine; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
| | - Ta-Chih Liu
- Department of Laboratory Medicine; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- Graduate Institute of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Division of Hematology-Oncology; Department of Internal Medicine; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
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9
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De Angioletti M, Sabato V, Musollino G, Prezioso R, Carestia C, Lacerra G. South-Italy β°-thalassemia: a novel deletion not removing the γ-globin silencing element and with 3' breakpoint in a hsRTVL-H element, associated with β°-thalassemia and high levels of HbF. Haematologica 2013; 98:e98-e100. [PMID: 23812938 DOI: 10.3324/haematol.2013.089722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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10
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Cui J, Azimi M, Baysdorfer C, Vichinsky EP, Hoppe CC. Application of multiplex ligation-dependent probe amplification to screen for β-globin cluster deletions: detection of two novel deletions in a multi ethnic population. Hemoglobin 2013; 37:241-56. [PMID: 23577918 DOI: 10.3109/03630269.2013.782461] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) and δβ-thalassemia (δβ-thal) are heterogeneous disorders caused by deletions within the β-globin gene cluster. When combined with other β-thal mutations or structural hemoglobin (Hb) variants, these deletions give rise to clinical phenotypes ranging from an asymptomatic condition to β-thal major (β-TM). Overlap in hematological parameters and variability in expression of Hbs A2 and F make molecular testing necessary to distinguish clinically relevant deletions. Multiplex ligation-dependent probe amplification (MLPA) was used to screen for β-globin gene cluster deletions in 49 unresolved samples referred for a suspected β-thal anomaly. The 1.39 kb Black β(0), 3.5 kb Thai β(0), 118 kb Filipino β(0), 11.8 kb Black (δβ)(0), 13.4 kb Sicilian (δβ)(0), 35.8 kb Black ((A)γδβ)0, Hb Lepore-Boston-Washington (Hb LBW) and HPFH-2 deletions, and two novel deletions, a 61.7 kb Pakistani β(0) deletion and an ((A)γδβ)(0) deletion, were identified in 15 cases. Detection of both known and unknown deletional Hb disorders provides for appropriate clinical management and genetic counseling.
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Affiliation(s)
- Jialing Cui
- Hemoglobinopathy Reference Laboratory, Children's Hospital & Research Center Oakland, Oakland, California, USA
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11
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Tritipsombut J, Phylipsen M, Viprakasit V, Chalaow N, Sanchaisuriya K, Giordano PC, Fucharoen S, Harteveld CL. A Single-Tube Multiplex Gap-Polymerase Chain Reaction for the Detection of Eight β-Globin Gene Cluster Deletions Common in Southeast Asia. Hemoglobin 2012. [DOI: 10.3109/03630269.2012.747441] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Tharmarajah G, Faas L, Reiss K, Saftig P, Young A, Van Raamsdonk CD. Adam10 haploinsufficiency causes freckle-like macules in Hairless mice. Pigment Cell Melanoma Res 2012; 25:555-65. [DOI: 10.1111/j.1755-148x.2012.01032.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Phylipsen M, Chaibunruang A, Vogelaar IP, Balak JRA, Schaap RAC, Ariyurek Y, Fucharoen S, den Dunnen JT, Giordano PC, Bakker E, Harteveld CL. Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangements. Hum Mutat 2011; 33:272-80. [PMID: 21922597 DOI: 10.1002/humu.21612] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 08/26/2011] [Indexed: 12/21/2022]
Abstract
Implementation of multiplex ligation-dependent probe amplification (MLPA) for thalassemia causing deletions has lead to the detection of new rearrangements. Knowledge of the exact breakpoint sequences should give more insight into the molecular mechanisms underlying these rearrangements, and would facilitate the design of gap-PCRs. We have designed a custom fine-tiling array with oligonucleotides covering the complete globin gene clusters. We hybridized 27 DNA samples containing newly identified deletions and nine positive controls. We designed specific primers to amplify relatively short fragments containing the breakpoint sequence and analyzed these by direct sequencing. Results from nine positive controls showed that array comparative genomic hybridization (aCGH) is suitable to detect small and large rearrangements. We were able to locate all breakpoints to a region of approximately 2 kb. We designed breakpoint primers for 22 cases and amplification was successful in 19 cases. For 12 of these, the exact locations of the breakpoints were determined. Seven of these deletions have not been reported before. aCGH is a valuable tool for high-resolution breakpoint characterization. The combination of MLPA and aCGH has lead to relatively cheap and easy to perform PCR assays, which might be of use for laboratories as an alternative for MLPA in populations where only a limited number of specific deletions occur with high frequency.
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Affiliation(s)
- Marion Phylipsen
- Hemoglobinopathies Laboratory, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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14
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Chen JM, Férec C, Cooper DN. LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption. J Biomed Biotechnol 2010; 2006:56182. [PMID: 16877817 PMCID: PMC1510945 DOI: 10.1155/jbb/2006/56182] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
LINE-1 (L1) elements are the most abundant autonomous non-LTR retrotransposons in the human genome. Having recently performed a meta-analysis of L1 endonuclease-mediated retrotranspositional events causing human genetic disease, we have extended this study by focusing on two key issues, namely, mutation detection bias and the multiplicity of mechanisms of target gene disruption. Our analysis suggests that whereas an ascertainment bias may have generally militated against the detection of autosomal L1-mediated insertions, autosomal L1 direct insertions could have been disproportionately overlooked owing to their unusually large size. Our analysis has also indicated that the mechanisms underlying the functional disruption of target genes by L1-mediated retrotranspositional events are likely to be dependent on several different factors such as the type of insertion (L1 direct, L1 trans-driven Alu, or SVA), the precise locations of the inserted sequences within the target gene regions, the length of the inserted sequences, and possibly also their orientation.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- *Jian-Min Chen:
| | - Claude Férec
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- Hôpital Morvan, CHRU Brest, Laboratoire de
Génétique Moléculaire et d'Histocompatibilité, 29200 Brest, France
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine,
Cardiff University, Heath Park Campus, Cardiff CF14 4XN, UK
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15
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Voruganti I, Eng B, Waye JS. Molecular characterization of a novel 55.1 kb (G)gamma((A)gammadeltabeta)(0)-thalassemia deletion in two Canadian families. Hemoglobin 2009; 33:422-7. [PMID: 19958187 DOI: 10.3109/03630260903333088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We report two Canadian families in which there are four carriers of a novel (G)gamma((A)gammadeltabeta)(0)-thalassemia deletion. The patients all have mild microcytosis and hypochromia, and elevated levels of Hb F ranging from 9.7 to 17.3%. The precise endpoints of the deletion have been identified and are unique relative to other forms of (G)gamma((A)gammadeltabeta)(0)-thal reported in the literature. The deletion encompasses approximately 55.1 kb, beginning approximately 1.6 kb downstream of the (G)gamma-globin gene and extending approximately 29.0 kb downstream of the beta-globin gene.
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Affiliation(s)
- Indu Voruganti
- Molecular Diagnostic Genetics, Hamilton Regional Laboratory Medicine Program, Hamilton, ON, Canada
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16
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Liao C, Li DZ. Detection of unknown deletions in beta-globin gene cluster using PCR-reverse dot-blot method in prenatal diagnosis. Eur J Haematol 2009; 83:385-386. [PMID: 19519729 DOI: 10.1111/j.1600-0609.2009.01293.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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17
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Fucharoen S, Winichagoon P, Chaicharoen S, Wasi P. Different molecular defects of Gγ (Aγδβ)°-thalassaemia in Thailand. Eur J Haematol 2009. [DOI: 10.1111/j.1600-0609.1987.tb00746.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Srikanta D, Sen SK, Huang CT, Conlin EM, Rhodes RM, Batzer MA. An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. Genomics 2008; 93:205-12. [PMID: 18951971 DOI: 10.1016/j.ygeno.2008.09.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 09/15/2008] [Accepted: 09/26/2008] [Indexed: 11/18/2022]
Abstract
The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA).
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Affiliation(s)
- Deepa Srikanta
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
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19
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Sen SK, Huang CT, Han K, Batzer MA. Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res 2007; 35:3741-51. [PMID: 17517773 PMCID: PMC1920257 DOI: 10.1093/nar/gkm317] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
LINE-1 elements (L1s) are a family of highly successful retrotransposons comprising approximately 17% of the human genome, the majority of which have inserted through an endonuclease-dependent mechanism termed target-primed reverse transcription. Recent in vitro analyses suggest that in the absence of non-homologous end joining proteins, L1 elements may utilize an alternative, endonuclease-independent pathway for insertion. However, it remains unknown whether this pathway operates in vivo or in cell lines where all DNA repair mechanisms are functional. Here, we have analyzed the human genome to demonstrate that this alternative pathway for L1 insertion has been active in recent human evolution and characterized 21 loci where L1 elements have integrated without signs of endonuclease-related activity. The structural features of these loci suggest a role for this process in DNA double-strand break repair. We show that endonuclease-independent L1 insertions are structurally distinguishable from classical L1 insertion loci, and that they are associated with inter-chromosomal translocations and deletions of target genomic DNA.
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Affiliation(s)
| | | | | | - Mark A. Batzer
- *To whom correspondence should be addressed. +1 225 578 7102+1 225 578 7113
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20
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Koll F, Begel O, Belcour L. Insertion of short poly d(A) d(T) sequences at recombination junctions in mitochondrial DNA of Podospora. ACTA ACUST UNITED AC 2006; 209:630-2. [PMID: 17193717 DOI: 10.1007/bf00331176] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have characterized the DNA sequences at recombination points in the mitochondrial DNA of two independent mitochondrial mutants of Podospora anserina. These sequences reveal the presence of foreign DNA at each recombination border, consisting of short stretches of A and T residues. We discuss the possible origin of this DNA and suggest the involvement of a reverse transcriptase activity.
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Affiliation(s)
- F Koll
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, F-91190 Gif sur Yvette, France
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21
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Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN. Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum Mutat 2006; 25:207-21. [PMID: 15643617 DOI: 10.1002/humu.20133] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although gross insertions (>20 bp) comprise <1% of disease-causing mutations, they nevertheless represent an important category of pathological lesion. In an attempt to study these insertions in a systematic way, 158 gross insertions ranging in size between 21 bp and approximately 10 kb were identified using the Human Gene Mutation Database (www.hgmd.org). A careful meta-analytical study revealed extensive diversity in terms of the nature of the inserted DNA sequence and has provided new insights into the underlying mutational mechanisms. Some 70% of gross insertions were found to represent sequence duplications of different types (tandem, partial tandem, or complex). Although most of the tandem duplications were explicable by simple replication slippage, the three complex duplications appear to result from multiple slippage events. Some 11% of gross insertions were attributable to nonpolyglutamine repeat expansions (including octapeptide repeat expansions in the prion protein gene [PRNP] and polyalanine tract expansions) and evidence is presented to support the contention that these mutations are also caused by replication slippage rather than by unequal crossing over. Some 17% of gross insertions, all >or=276 bp in length, were found to be due to LINE-1 (L1) retrotransposition involving different types of element (L1 trans-driven Alu, L1 direct, and L1 trans-driven SVA). A second example of pathological mitochondrial-nuclear sequence transfer was identified in the USH1C gene but appears to arise via a novel mechanism, trans-replication slippage. Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene.
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Affiliation(s)
- Jian-Min Chen
- INSERM (Institut National de la Santé et de la Recherche Médicale) U613-Génétique Moléculaire et Génétique Epidémiologique, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France.
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22
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Chen JM, Stenson PD, Cooper DN, Férec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005; 117:411-27. [PMID: 15983781 DOI: 10.1007/s00439-005-1321-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
Diverse long interspersed element-1 (LINE-1 or L1)-dependent mutational mechanisms have been extensively studied with respect to L1 and Alu elements engineered for retrotransposition in cultured cells and/or in genome-wide analyses. To what extent the in vitro studies can be held to accurately reflect in vivo events in the human genome, however, remains to be clarified. We have attempted to address this question by means of a systematic analysis of recent L1-mediated retrotranspositional events that have caused human genetic disease, with a view to providing a more complete picture of how L1-mediated retrotransposition impacts upon the architecture of the human genome. A total of 48 such mutations were identified, including those described as L1-mediated retrotransposons, as well as insertions reported to contain a poly(A) tail: 26 were L1 trans-driven Alu insertions, 15 were direct L1 insertions, four were L1 trans-driven SVA insertions, and three were associated with simple poly(A) insertions. The systematic study of these lesions, when combined with previous in vitro and genome-wide analyses, has strengthened several important conclusions regarding L1-mediated retrotransposition in humans: (a) approximately 25% of L1 insertions are associated with the 3' transduction of adjacent genomic sequences, (b) approximately 25% of the new L1 inserts are full-length, (c) poly(A) tail length correlates inversely with the age of the element, and (d) the length of target site duplication in vivo is rarely longer than 20 bp. Our analysis also suggests that some 10% of L1-mediated retrotranspositional events are associated with significant genomic deletions in humans. Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France.
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23
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Audrézet MP, Chen JM, Raguénès O, Chuzhanova N, Giteau K, Le Maréchal C, Quéré I, Cooper DN, Férec C. Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms. Hum Mutat 2004; 23:343-57. [PMID: 15024729 DOI: 10.1002/humu.20009] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR/ABCC7). Despite the extensive and enduring efforts of many CF researchers over the past 14 years, up to 30% of disease alleles still remain to be identified in some populations. It has long been suggested that gross genomic rearrangements could account for these unidentified alleles. To date, however, only a few large deletions have been found in the CFTR gene and only three have been fully characterized. Here, we report the first systematic screening of the 27 exons of the CFTR gene for large genomic rearrangements, by means of the quantitative multiplex PCR of short fluorescent fragments (QMPSF). A well-characterized cohort of 39 classical CF patients carrying at least one unidentified allele (after extensive and complete screening of the CFTR gene by both denaturing gradient gel electrophoresis and denaturing high-performance liquid chromatography) participated in this study. Using QMPSF, some 16% of the previously unidentified CF mutant alleles were identified and characterized, including five novel mutations (one large deletion and four indels). The breakpoints of these five mutations were precisely determined, enabling us to explore the underlying mechanisms of mutagenesis. Although non-homologous recombination may be invoked to explain all five complex lesions, each mutation appears to have arisen through a different mechanism. One of the indels was highly unusual in that it involved the insertion of a short 41 bp sequence with partial homology to a retrotranspositionally-competent LINE-1 element. The insertion of this ultra-short LINE-1 element (dubbed a "hyphen element") may constitute a novel type of mutation associated with human genetic disease.
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Affiliation(s)
- Marie-Pierre Audrézet
- INSERM U613, Génétique Moléculaire et Génétique Epidémiologique, Centre Hospitalier Universitaire, Brest, France
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24
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Brouha B, Meischl C, Ostertag E, de Boer M, Zhang Y, Neijens H, Roos D, Kazazian HH. Evidence consistent with human L1 retrotransposition in maternal meiosis I. Am J Hum Genet 2002; 71:327-36. [PMID: 12094329 PMCID: PMC379165 DOI: 10.1086/341722] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2002] [Accepted: 05/10/2002] [Indexed: 11/04/2022] Open
Abstract
We have used a unique polymorphic 3' transduction to show that a human L1, or LINE-1 (long interspersed nucleotide element-1), retrotransposition event most likely occurred in the maternal primary oocyte during meiosis I. We characterized a truncated L1 retrotransposon with a 3' transduction that was inserted, in a Dutch male patient, into the X-linked gene CYBB, thereby causing chronic granulomatous disease. We used the unique flanking sequence to localize the precursor L1 locus, LRE3, to chromosome 2q24.1. In a cell culture assay, the retrotransposition frequency of LRE3 is greater than that for any other element that has been tested to date. The patient's mother had two LRE3 alleles that differed slightly in the 3'-flanking genomic DNA. The patient had a single LRE3 allele that was identical to one of the maternal alleles; however, the patient's insertion matched the maternal LRE3 allele that he did not inherit. Other data indicate that there is only a small chance that the father (unavailable for analysis) carries the precursor LRE3 allele. In addition, paternal origin of the insertion would have required that an LRE3 mRNA transcribed before meiosis II be carried separately from its precursor LRE3 allele in the fertilizing sperm. Since the mother carries a potential precursor allele and the insertion was on the patient's maternal X chromosome, it is highly likely that the insertion originated during maternal meiosis I.
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Affiliation(s)
- Brook Brouha
- Department of Genetics, University of Pennsylvania School of Medicine, 475 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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25
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Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, Taccioli GE, Batzer MA, Moran JV. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 2002; 31:159-65. [PMID: 12006980 DOI: 10.1038/ng898] [Citation(s) in RCA: 322] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long interspersed elements (LINE-1s) are abundant retrotransposons in mammalian genomes that probably retrotranspose by target site-primed reverse transcription (TPRT). During TPRT, the LINE-1 endonuclease cleaves genomic DNA, freeing a 3' hydroxyl that serves as a primer for reverse transcription of LINE-1 RNA by LINE-1 reverse transcriptase. The nascent LINE-1 cDNA joins to genomic DNA, generating LINE-1 structural hallmarks such as frequent 5' truncations, a 3' poly(A)+ tail and variable-length target site duplications (TSDs). Here we describe a pathway for LINE-1 retrotransposition in Chinese hamster ovary (CHO) cells that acts independently of endonuclease but is dependent upon reverse transcriptase. We show that endonuclease-independent LINE-1 retrotransposition occurs at near-wildtype levels in two mutant cell lines that are deficient in nonhomologous end-joining (NHEJ). Analysis of the pre- and post-integration sites revealed that endonuclease-independent retrotransposition results in unusual structures because the LINE-1s integrate at atypical target sequences, are truncated predominantly at their 3' ends and lack TSDs. Moreover, two of nine endonuclease-independent retrotranspositions contained cDNA fragments at their 3' ends that are probably derived from the reverse transcription of endogenous mRNA. Thus, our results suggest that LINE-1s can integrate into DNA lesions, resulting in retrotransposon-mediated DNA repair in mammalian cells.
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Affiliation(s)
- Tammy A Morrish
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, Michigan 48105-0618, USA
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26
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Abstract
L1 retrotransposons comprise 17% of the human genome. Although most L1s are inactive, some elements remain capable of retrotransposition. L1 elements have a long evolutionary history dating to the beginnings of eukaryotic existence. Although many aspects of their retrotransposition mechanism remain poorly understood, they likely integrate into genomic DNA by a process called target primed reverse transcription. L1s have shaped mammalian genomes through a number of mechanisms. First, they have greatly expanded the genome both by their own retrotransposition and by providing the machinery necessary for the retrotransposition of other mobile elements, such as Alus. Second, they have shuffled non-L1 sequence throughout the genome by a process termed transduction. Third, they have affected gene expression by a number of mechanisms. For instance, they occasionally insert into genes and cause disease both in humans and in mice. L1 elements have proven useful as phylogenetic markers and may find other practical applications in gene discovery following insertional mutagenesis in mice and in the delivery of therapeutic genes.
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Affiliation(s)
- E M Ostertag
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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27
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Xu XM, Li ZQ, Liu ZY, Zhong XL, Zhao YZ, Mo QH. Molecular characterization and PCR detection of a deletional HPFH: Application to rapid prenatal diagnosis for compound heterozygotes of this defect with ?-thalassemia in a Chinese family. Am J Hematol 2000. [DOI: 10.1002/1096-8652(200011)65:3%3c183::aid-ajh1%3e3.0.co;2-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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28
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Xu XM, Li ZQ, Liu ZY, Zhong XL, Zhao YZ, Mo QH. Molecular characterization and PCR detection of a deletional HPFH: application to rapid prenatal diagnosis for compound heterozygotes of this defect with beta-thalassemia in a Chinese family. Am J Hematol 2000; 65:183-8. [PMID: 11074532 DOI: 10.1002/1096-8652(200011)65:3<183::aid-ajh1>3.0.co;2-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) is one of the hemoglobinopathies in which the fetal gamma-globin genes remain active in adult life. Most HPFHs are caused by a large deletion involving a variable extent of DNA segment on the beta-globin gene cluster. We report the molecular defects associated with a deletional HPFH, which has previously been described in Cambodians and Vietnamese, in two unrelated Chinese individuals. To define the sequence around the breakpoints of the deletion, both the deletion junction fragment and the normal DNA across the breakpoints were cloned by PCR and sequenced. We found that the 5' breakpoint is located between nucleotides 986 and 987 upstream from the startpoint of the beta-globin gene, which further confirmed the Southeast Asian (SEA) HPFH deletion previously determined, whereas the 3' breakpoint, which is clarified for the first time by us, lies approximately 2.3 kb downstream from the 3' HS1 site of the beta-globin gene. It is suggested that deletions were the result of a non-homologous recombination event. Based on our novel sequence data, we designed a PCR amplification method with three primers bridging the 3' breakpoint. With this method and reverse dot blot (RDB) for detecting beta-thalassemia mutations, a Chinese family that had a 6-year-old propositus with severe thalassemia intermediate and that had requested prenatal diagnosis for the second pregnancy was found to be compound heterozygotes of HPFH defects with beta-thalassemia. The fetal genomic DNA diagnosis showed the same results as those in propositus, i.e., both of them inherited the deletion from their mother and inherited a codons 14-15 (+G) frameshift mutation causing beta-thalassemia from their father.
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Affiliation(s)
- X M Xu
- Department of Cellular Biology and Medical Genetics, First Military Medical University, Guangzhou, Peoples Republic of China.
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29
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Abstract
This review aims at providing a general understanding of how the multiple cytogenetic aberrations in cancer cells arise and exemplifies this by considering the specific role of chromosome 11q loci in carcinogenesis. Section I provides a theoretical molecular and structural framework for understanding the cytogenetic aberrations described in cancer. Given this background, Section II describes advances in the identification and localization of cancer susceptibility genes on chromosome 11q, highlighting ongoing areas of investigation.
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Affiliation(s)
- J Koreth
- University of Oxford, Nuffield Department of Pathology and Bacteriology, John Radcliffe Hospital, Headington, U.K
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30
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Taruscio D, Mantovani A. Human endogenous retroviral sequences: possible roles in reproductive physiopathology. Biol Reprod 1998; 59:713-24. [PMID: 9746718 DOI: 10.1095/biolreprod59.4.713] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Affiliation(s)
- D Taruscio
- Laboratories of Ultrastructure, Istituto Superiore di Sanità, 00161 Rome, Italy.
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31
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Lau YL, Chan LC, Chan YY, Ha SY, Yeung CY, Waye JS, Chui DH. Prevalence and genotypes of alpha- and beta-thalassemia carriers in Hong Kong -- implications for population screening. N Engl J Med 1997; 336:1298-301. [PMID: 9113933 DOI: 10.1056/nejm199705013361805] [Citation(s) in RCA: 162] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND The thalassemias are common in southern China. We determined the prevalence of heterozygous carriers of these genetic disorders in Hong Kong and assessed the feasibility of a community-based screening program. METHODS An educational and screening program for the thalassemias was carried out in three high schools with a total of 2420 students. Seventy-five percent of the students agreed to undergo screening, which consisted of blood counts, hemoglobin electrophoresis, serum ferritin measurements, and DNA analyses. RESULTS Of the 1800 blood samples tested, 150 (8.3 percent) had microcytosis (mean corpuscular volume, <80 microm3). Ninety students (5.0 percent) were carriers of alpha-thalassemia, of whom 81 (4.5 percent) were carriers of the Southeast Asian type of deletion, in which both alpha-globin genes on the same chromosome 16 are deleted. Sixty-one students (3.4 percent) were carriers of either beta-thalassemia or the mutation coding for hemoglobin E. Six students were carriers of both alpha- and beta-thalassemias. On the basis of these figures, the estimated numbers of pregnancies in Hong Kong in which the fetus is at risk for homozygous alpha-thalassemia and beta-thalassemia major or intermedia are 145 and 80 per year, respectively. In Hong Kong the actual numbers of women referred for prenatal diagnoses of these disorders are approximately 95 and 40 per year, respectively. CONCLUSIONS Despite the availability of hospital-based screening and prenatal diagnosis for many years in Hong Kong, many women carrying fetuses at risk for thalassemia are not referred for genetic counseling. A community-based program of education, screening, and counseling is needed in Hong Kong and southern China.
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Affiliation(s)
- Y L Lau
- Department of Pediatrics, University of Hong Kong and Queen Mary Hospital
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Rainville IR, Albertini RJ, Nicklas JA. Breakpoints and junctional regions of intragenic deletions in the HPRT gene in human T-Cells. SOMATIC CELL AND MOLECULAR GENETICS 1995; 21:309-26. [PMID: 8619128 DOI: 10.1007/bf02257466] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
DNA sequences of the deletion breakpoints of 24 human T-lymphocyte hprt gene mutations are reported. These independent deletions ranged in size from 18 to 15655 base pairs. Seven of the 21 in vivo mutations arose in normal adults, three in normal children, eight in radioimmunotherapy patients and three in platinum chemotherapy patients. One in vitro mutation was isolated after 93cGy radon exposure and two after 300cGy gamma radiation. The breakpoints were found to be non-random and a cluster of small deletions in exon 6 is reported. Ten of the mutations had 2-5bp direct repeats at the breakpoints. There was no excess of "deletion-associated" motifs over that expected by chance. Some breakpoints do occur at consensus topoisomerase II cleavage sites and the centromeric end of a Donehower sequence occurs exactly at a telomeric breakpoint. Three mutants had breakpoints at hairpins expected by the model of Glickman and Ripley.
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Affiliation(s)
- I R Rainville
- VCC Genetics Laboratory, University of Vermont, Burlington, Vermont 05401, USA
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33
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Abstract
The synthesis of fetal hemoglobin (HbF) is normally reduced to very low levels of less than 0.6% of the total hemoglobin in adults. The HbF is restricted to a sub-population of erythrocytes termed 'F-cells'; 85% of the normal adult population have 0.3% to 4.4% F-cells. The levels of HbF and F-cells vary by more than 10-fold in normal adults; family studies show that these levels are genetically controlled but the number and nature of these genetic factors are still poorly understood. HbF levels may be increased in adults in a number of inherited and acquired disorders, accompanied by an increase in both the number of F-cells and the amount of HbF per F-cell. The clinical significance of these conditions with raised HbF relates to their interaction in disorders such as sickle cell disease and beta thalassaemia in which raised levels of HbF can lead to considerable amelioration of disease severity. Study of the 'natural' mutants primarily associated with increased HbF has provided considerable insight into the understanding of the control of globin gene regulation and hemoglobin switching. Currently considerable effort is being channelled into clinical trials and the search for the 'ideal' therapeutic agents which could increase HbF in adult life with minimal drug toxicity.
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Affiliation(s)
- J Rochette
- MRC Molecular Haematology Unit, John Radcliffe Hospital, Headington, Oxford, UK
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34
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Gaensler KM, Kitamura M, Kan YW. Germ-line transmission and developmental regulation of a 150-kb yeast artificial chromosome containing the human beta-globin locus in transgenic mice. Proc Natl Acad Sci U S A 1993; 90:11381-5. [PMID: 8248258 PMCID: PMC47986 DOI: 10.1073/pnas.90.23.11381] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sequential expression of the genes of the human beta-globin locus requires the formation of an erythroid-specific chromatin domain spanning > 200 kb. Regulation of this gene family involves both local interactions with proximal cis-acting sequences and long-range interactions with control elements upstream of the locus. To make it possible to analyze the interactions of cis-acting sequences of the human beta-globin locus in their normal spatial and sequence context, we characterized two yeast artificial chromosomes (YACs) 150 and 230 kb in size, containing the entire beta-globin locus. We have now successfully integrated the 150-kb YAC into the germ line of transgenic mice as a single unrearranged fragment that includes the locus control region, structural genes, and 30 kb of 3' flanking sequences present in the native locus. Expression of the transgenic human beta-globin locus is tissue- and developmental stage-specific and closely follows the pattern of expression of the endogenous mouse beta-globin locus. By using homology-directed recombination in yeast and methods for the purification and transfer of YACs into transgenic mice, it will now be feasible to study the physiological role of cis-acting sequences in specifying an erythroid-specific chromatin domain and directing expression of beta-globin genes during ontogeny.
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Affiliation(s)
- K M Gaensler
- Department of Medicine, University of California, San Francisco 94143-0724
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35
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Yao R, Patterson D, Onodera K. Isolation and characterization of a DNA fragment containing various kinds of repetitive sequences located on human chromosome 21. THE JAPANESE JOURNAL OF HUMAN GENETICS 1993; 38:243-55. [PMID: 8260717 DOI: 10.1007/bf01874135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In order to investigate the repetitive sequences located on human chromosome 21, we have isolated DNA fragments containing Alu sequences. One of the clones, p1, was chosen for further study, because it contained repetitive sequences different from the Alu sequence. Nucleotide sequence analysis of p1 indicates that p1 contains L1 and O-family sequences. Interestingly, when the L1 sequence was used as a probe, a discrete band of 5 kb was seen in HindIII-digested DNA from somatic cell hybrids containing human chromosome 21 as the sole human chromosome. The L1 sequence was rearranged and was interrupted by O-family sequence, which was flanked by 6 bp target site duplications. Since all three repetitive sequences are known to act as retroposons, these results imply that there is an integration hot spot on human chromosome 21. The sequence was mapped within 21q11-21.
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Affiliation(s)
- R Yao
- Department of Agricultural Chemistry, University of Tokyo, Bunkyo-ku, Tokyo 113, Japan
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36
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Narita N, Nishio H, Kitoh Y, Ishikawa Y, Ishikawa Y, Minami R, Nakamura H, Matsuo M. Insertion of a 5' truncated L1 element into the 3' end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J Clin Invest 1993; 91:1862-7. [PMID: 8387534 PMCID: PMC288178 DOI: 10.1172/jci116402] [Citation(s) in RCA: 152] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We report here the second evidence of retrotransposition of L1, which was found inserted into the dystrophin gene of a patient, causing Duchenne muscular dystrophy (DMD). When the PCR was used to amplify a region of the dystrophin gene encompassing exon 44 from genomic DNA of two Japanese brothers with DMD, it was found to be approximately 600 bp larger than expected. Both the normal and the abnormally large products were amplified from the DNA of their mother. However, the maternal grandparents did not have the abnormal allele, and the mutation must therefore have occurred in the mother. Analysis of nucleotide sequence of the amplified product from a patient disclosed that the insertion was present zero to two bases upstream from the 3' end of exon 44 and that two to four bases of the exon sequence were deleted from the insertion site. The insertion sequence was found to be composed of 606-608 bp and to be almost identical to the inverse complement of 3' portion of the L1 retrotransposon consensus sequence. The dystrophin gene transcript from peripheral lymphocytes of one of the patients was analyzed by using reverse transcription/semi-nested PCR. The size of the amplified product encompassing exon 42 to 46 was smaller than expected. Sequencing of the amplified product disclosed that the sequence of exon 43 was directly joined to that of exon 45. Exon 44 of the transcript was thus shown to be skipped during splicing. This novel mutation of the dystrophin gene has important implications regarding retrotransposition of an active L1 element and provides a new insight into the origins of mutations in the dystrophin gene.
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Affiliation(s)
- N Narita
- Department of Pediatrics, Kobe University School of Medicine, Japan
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37
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Motum PI, Kearney A, Hamilton TJ, Trent RJ. Filipino beta zero thalassaemia: a high Hb A2 beta zero thalassaemia resulting from a large deletion of the 5' beta globin gene region. J Med Genet 1993; 30:240-4. [PMID: 7682618 PMCID: PMC1016308 DOI: 10.1136/jmg.30.3.240] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A large novel deletional beta zero thalassaemia mutation associated with unusually high levels of haemoglobin (Hb) A2 in heterozygotes is described in two unrelated subjects of Filipino background. The deletion was characterised by DNA mapping including pulsed field gel electrophoresis. Filipino beta zero thalassaemia extends for approximately 45 kb beginning approximately 1.5 kb 3' to the delta globin gene. It is the largest deletion to date which gives rise to the beta zero thalassaemia phenotype. This mutation, similar to previously described deletional beta zero thalassaemias associated with high Hb A2, removes sequences 5' to the beta globin gene promoter and emphasises the functional importance of the 5' beta globin region in eliciting the unusually high level of Hb A2. This example also suggests that it is the 3' sequences which are transposed rather than the actual deletion size which are significant in the raised fetal haemoglobin (Hb F) found with some of the thalassaemias.
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Affiliation(s)
- P I Motum
- Department of Molecular Genetics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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38
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Abstract
A novel 30 kb deletion of the beta-globin gene cluster associated with the phenotype of hereditary persistence of fetal hemoglobin (HPFH) is described in two unrelated individuals of Vietnamese background. The Vietnamese G gamma A gamma HPFH deletion has a unique 5' breakpoint 3.5 kb downstream of the delta-globin gene. The 3' breakpoint lies approximately 8 kb upstream from the HPFH-3 breakpoint (Henthorn et al., 1986) and in the region of the 3' breakpoints of HPFH-4 (Saglio et al., 1986), German and Belgian G gamma+ (A gamma delta beta)zero-thalassemias (Anagnou et al., 1988; Losekoot et al., 1991). Characterisation of the 3' breakpoint in the present study has enabled more precise localisation of other deletion breakpoints at this locus. Further evidence is provided that the 3' breakpoint region contains functionally important sequences and that the juxtaposition of these sequences to the gamma-globin genes is a significant factor in the increased fetal hemoglobin levels.
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Affiliation(s)
- P I Motum
- Department of Molecular Genetics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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39
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Gaensler KM, Burmeister M, Brownstein BH, Taillon-Miller P, Myers RM. Physical mapping of yeast artificial chromosomes containing sequences from the human beta-globin gene region. Genomics 1991; 10:976-84. [PMID: 1916829 DOI: 10.1016/0888-7543(91)90188-k] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The recently developed technique for cloning genomic DNA fragments of several hundred kilobases or more into yeast artificial chromosomes (YACs) makes it possible to isolate gene families while preserving their structural integrity. We have analyzed five independent yeast clones identified by PCR screening using oligonucleotides derived from the adult human beta-globin gene. Analysis of the five clones containing YACs by conventional and pulsed-field gel electrophoresis revealed that all of the clones include a YAC with sequences from the adult beta-globin gene as expected. One of the clones contains multiple, unstable YACs. Two other clones carry single YACs in which there are at least two unrelated human genomic inserts. The remaining two clones contain single YACs, 150 and 220 kb in size, that contain the entire beta-globin gene family and flanking regions in a single, structurally intact genomic fragment. These should prove useful in future studies of the regulation of expression of genes in the beta-globin gene cluster.
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Affiliation(s)
- K M Gaensler
- Department of Physiology, University of California, San Francisco 94143-0444
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40
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Cooper DN, Krawczak M. Mechanisms of insertional mutagenesis in human genes causing genetic disease. Hum Genet 1991; 87:409-15. [PMID: 1652548 DOI: 10.1007/bf00197158] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Examples of the insertion of less than 10 bp of DNA sequence into human gene-coding regions causing genetic disease were collated in order to study the underlying causative mechanisms. The nature of these insertions was found to be consistent with several mechanisms of mutagenesis including: (1) slipped mispairing mediated by direct repeats or runs of identical bases and (2) the templated misincorporation of bases by secondary-structure intermediates whose formation is facilitated by palindromic (inverted repeat) sequences, quasi-palindromic sequences or symmetric elements. Both the size and position of insertions were found to be non-random and highly dependent upon the surrounding DNA sequence. Inferred mechanisms of insertional mutagenesis thus appear to be very similar to those involved in the causation of gene deletions.
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Affiliation(s)
- D N Cooper
- Charter Molecular Genetics Laboratory, Thrombosis Research Institute, Chelsea, London, UK
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41
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42
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Fortina P, Delgrosso K, Werner E, Haines K, Rappaport E, Schwartz E, Surrey S. A greater than 200 kb deletion removing the entire beta-like globin gene cluster in a family of Irish descent. Hemoglobin 1991; 15:23-41. [PMID: 1717405 DOI: 10.3109/03630269109072482] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe a new deletional form of gamma delta beta-thalassemia segregating in two generations of a family of Irish descent. Affected family members present with a beta-thalassemia minor phenotype, normal Hb A2 and Hb F levels. Genomic blotting analyses on DNA from affected family members show heterozygosity for a large deletion beginning at least 15 kb upstream of the 5' endpoint of the gamma delta beta-thalassemia-1 deletion, extending through the entire beta-like globin gene cluster, and continuing for at least 10 kb beyond the 3' endpoint of the deletion associated with the Spanish form of delta beta 0-thalassemia. This deletion is among the largest described so far, and removes at least 205 kb encompassing the entire beta-like globin gene cluster on chromosome 11.
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Affiliation(s)
- P Fortina
- Division of Hematology, Children's Hospital of Philadelphia, PA
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43
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Forrester WC, Epner E, Driscoll MC, Enver T, Brice M, Papayannopoulou T, Groudine M. A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev 1990; 4:1637-49. [PMID: 2249769 DOI: 10.1101/gad.4.10.1637] [Citation(s) in RCA: 402] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Naturally occurring deletions that remove sequences located approximately 60 kb upstream of the human adult beta-globin gene result in the failure to transcriptionally activate the cis-linked globin genes in erythroid cells. In addition, transfection, transgenic, and somatic cell hybrid studies have revealed that sequences within this region are essential for the developmentally regulated high-level expression of cis-linked globin genes. This regulatory region located at the 5' end of the beta-globin locus has been termed the locus activation region (LAR). Using somatic cell hybrids, we have studied the chromatin structure and timing of DNA replication of the normal human beta-globin locus and a locus containing a de novo 25-kb deletion that removes elements of the LAR. As a result of this deletion, the entire beta-globin locus and sequences approximately 100 kb 5' and 3' of the adult beta-globin gene are DNase I-resistant and do not form characteristic distant hypersensitive sites. These sequences also replicate late in S phase in an erythroid cell background. In contrast, the sequences of the normal locus are DNase I sensitive and early replicating. These results suggest that the LAR is required for both the erythroid-specific chromatin structure and timing of DNA replication over a large physical distance.
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Affiliation(s)
- W C Forrester
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
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44
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Alpha-galactosidase A gene rearrangements causing Fabry disease. Identification of short direct repeats at breakpoints in an Alu-rich gene. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38851-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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45
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Translocation of an erythroid-specific hypersensitive site in deletion-type hereditary persistence of fetal hemoglobin. Mol Cell Biol 1990. [PMID: 1690839 DOI: 10.1128/mcb.10.4.1382] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) can involve large deletions which eliminate the 3' end of the beta-like globin gene cluster and more than 70 kilobases (kb) of flanking DNA. Blot hybridization revealed a DNase I-hypersensitive site extending from 1.1 to 1.4 kb downstream of the HPFH-1 3' deletion endpoint. The site was found in normal fetal and adult nucleated erythroid cells and in two erythroleukemia cell lines but not in nonerythroid cells and tissues. Simian virus 40 core enhancer-like sequences were found nonrandomly distributed within the boundaries of the site, which is contained in a fragment of known enhancer activity (E. A. Feingold and B. G. Forget, Blood, in press). A second hypersensitive site was found 0.5 kb upstream of the HPFH-1 3' deletion endpoint but was not erythroid specific. A third site, most prominent in fetal liver-derived erythroid cells, was found 1 kb upstream of the HPFH-2 deletion endpoint. As predicted by the locations of the deletion endpoints, the first two sites were translocated to within 12 kb of the A gamma gene in erythroid colonies derived from an HPFH-2 heterozygote and in hybrid mouse-human erythroid cells carrying the HPFH-2 deletion chromosome. Further analysis of this region showed that it was DNase I sensitive in erythroid and myeloid cells, indicating that it resides in an open chromatin domain. These observations suggest that alterations of chromatin structure flanking the fetal globin genes may contribute to abnormal gene regulation in deletion-type HPFH.
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46
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Elder JT, Forrester WC, Thompson C, Mager D, Henthorn P, Peretz M, Papayannopoulou T, Groudine M. Translocation of an erythroid-specific hypersensitive site in deletion-type hereditary persistence of fetal hemoglobin. Mol Cell Biol 1990; 10:1382-9. [PMID: 1690839 PMCID: PMC362240 DOI: 10.1128/mcb.10.4.1382-1389.1990] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) can involve large deletions which eliminate the 3' end of the beta-like globin gene cluster and more than 70 kilobases (kb) of flanking DNA. Blot hybridization revealed a DNase I-hypersensitive site extending from 1.1 to 1.4 kb downstream of the HPFH-1 3' deletion endpoint. The site was found in normal fetal and adult nucleated erythroid cells and in two erythroleukemia cell lines but not in nonerythroid cells and tissues. Simian virus 40 core enhancer-like sequences were found nonrandomly distributed within the boundaries of the site, which is contained in a fragment of known enhancer activity (E. A. Feingold and B. G. Forget, Blood, in press). A second hypersensitive site was found 0.5 kb upstream of the HPFH-1 3' deletion endpoint but was not erythroid specific. A third site, most prominent in fetal liver-derived erythroid cells, was found 1 kb upstream of the HPFH-2 deletion endpoint. As predicted by the locations of the deletion endpoints, the first two sites were translocated to within 12 kb of the A gamma gene in erythroid colonies derived from an HPFH-2 heterozygote and in hybrid mouse-human erythroid cells carrying the HPFH-2 deletion chromosome. Further analysis of this region showed that it was DNase I sensitive in erythroid and myeloid cells, indicating that it resides in an open chromatin domain. These observations suggest that alterations of chromatin structure flanking the fetal globin genes may contribute to abnormal gene regulation in deletion-type HPFH.
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Affiliation(s)
- J T Elder
- Department of Dermatology, University of Michigan, Ann Arbor 48109-0528
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47
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Molecular analysis of two mouse dilute locus deletion mutations: spontaneous dilute lethal20J and radiation-induced dilute prenatal lethal Aa2 alleles. Mol Cell Biol 1990. [PMID: 2300051 DOI: 10.1128/mcb.10.2.501] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dilute (d) coat color locus of mouse chromosome 9 has been identified by more than 200 spontaneous and mutagen-induced recessive mutations. With the advent of molecular probes for this locus, the molecular lesion associated with different dilute alleles can be recognized and precisely defined. In this study, two dilute mutations, dilute-lethal20J (dl20J) and dilute prenatal lethal Aa2, have been examined. Using a dilute locus genomic probe in Southern blot analysis, we detected unique restriction fragments in dl20J and Aa2 DNA. Subsequent analysis of these fragments showed that they represented deletion breakpoint fusion fragments. DNA sequence analysis of each mutation-associated deletion breakpoint fusion fragment suggests that both genomic deletions were generated by nonhomologous recombination events. The spontaneous dl20J mutation is caused by an interstitial deletion that removes a single coding exon of the dilute gene. The correlation between this discrete deletion and the expression of all dilute-associated phenotypes in dl20J homozygotes defines the dl20J mutation as a functional null allele of the dilute gene. The radiation-induced Aa2 allele is a multilocus deletion that, by complementation analysis, affects both the dilute locus and the proximal prenatal lethal-3 (pl-3) functional unit. Molecular analysis of the Aa2 deletion breakpoint fusion fragment has provided access to a previously undefined gene proximal to d. Initial characterization of this new gene suggests that it may represent the genetically defined pl-3 functional unit.
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48
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Henthorn PS, Smithies O, Mager DL. Molecular analysis of deletions in the human beta-globin gene cluster: deletion junctions and locations of breakpoints. Genomics 1990; 6:226-37. [PMID: 2307466 DOI: 10.1016/0888-7543(90)90561-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA fragments that contain the deletion junction regions of four independent deletions involving the human beta-globin gene cluster have been isolated and cloned. The fragments were isolated from individuals with the conditions referred to as Sicilian (delta beta)zero-thalassemia, Turkish G gamma+(A gamma delta beta)zero-thalassemia, Black G gamma+(A gamma delta beta)zero-thalassemia, and HPFH-2. The sequences of the deletion junctions and of the normal DNA surrounding their 3' breakpoints were determined and compared to the previously determined sequences of normal DNA surrounding their 5' breakpoints. These comparisons show that the deletions were the result of nonhomologous recombinational events. Two of the deletion junctions contain "orphan" nucleotides, while the other two show very limited amounts of "junctional homology." Both types of junctions are common among recombination events in mammalian cells and we discuss a simple joining scheme that could account for the junctions reported here. Unlike other deletions in this cluster and in other gene clusters, none of the eight deletion breakpoints examined here occurred within Alu family repeats. To examine the significance of deletion breakpoints within various sequence categories, we analyzed the data from a well-defined set of deletions within this locus. In contrast to deletions in the alpha-globin gene cluster, the occurrence of breakpoints in Alu family repetitive sequences is not statistically significant within the beta-globin gene cluster. However, breakpoints do occur within transcriptional units of the beta-globin gene cluster more frequently than expected by chance alone. We conclude from our analysis that the mechanisms of DNA joining are not locus or location specific, but at least a portion of the mechanisms of chromosomal breakages do show locus specificity.
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Affiliation(s)
- P S Henthorn
- Department of Human Genetics, University of Pennsylvania School of Medicine, Philadelphia 19104
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49
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Strobel MC, Seperack PK, Copeland NG, Jenkins NA. Molecular analysis of two mouse dilute locus deletion mutations: spontaneous dilute lethal20J and radiation-induced dilute prenatal lethal Aa2 alleles. Mol Cell Biol 1990; 10:501-9. [PMID: 2300051 PMCID: PMC360824 DOI: 10.1128/mcb.10.2.501-509.1990] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The dilute (d) coat color locus of mouse chromosome 9 has been identified by more than 200 spontaneous and mutagen-induced recessive mutations. With the advent of molecular probes for this locus, the molecular lesion associated with different dilute alleles can be recognized and precisely defined. In this study, two dilute mutations, dilute-lethal20J (dl20J) and dilute prenatal lethal Aa2, have been examined. Using a dilute locus genomic probe in Southern blot analysis, we detected unique restriction fragments in dl20J and Aa2 DNA. Subsequent analysis of these fragments showed that they represented deletion breakpoint fusion fragments. DNA sequence analysis of each mutation-associated deletion breakpoint fusion fragment suggests that both genomic deletions were generated by nonhomologous recombination events. The spontaneous dl20J mutation is caused by an interstitial deletion that removes a single coding exon of the dilute gene. The correlation between this discrete deletion and the expression of all dilute-associated phenotypes in dl20J homozygotes defines the dl20J mutation as a functional null allele of the dilute gene. The radiation-induced Aa2 allele is a multilocus deletion that, by complementation analysis, affects both the dilute locus and the proximal prenatal lethal-3 (pl-3) functional unit. Molecular analysis of the Aa2 deletion breakpoint fusion fragment has provided access to a previously undefined gene proximal to d. Initial characterization of this new gene suggests that it may represent the genetically defined pl-3 functional unit.
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Affiliation(s)
- M C Strobel
- Mammalian Genetics Laboratory, National Cancer Institute-Frederick Cancer Research Facility, Maryland 21701
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50
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Winichagoon P, Fucharoen S, Thonglairoam V, Wasi P. Thai G gamma (A gamma delta beta)zero-thalassemia and its interaction with a single gamma-globin gene on a chromosome carrying beta zero-thalassemia. Hemoglobin 1990; 14:185-97. [PMID: 2272841 DOI: 10.3109/03630269009046960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Clinical manifestations and hematologic data of thalassemia intermedia were observed in three siblings of a Thai family. Analyses of the hemoglobin of their parents and other siblings indicated that they inherited a delta beta-thalassemia gene from the father and a beta zero thalassemia gene from the mother. Globin gene mapping confirmed that they carry two abnormal beta-globin gene complexes. On one chromosome more than 70 kb of DNA was removed which resulted in G gamma (A gamma delta beta)zero-thalassemia. The deletion started at the Hind III site located just 3' to the G gamma gene, and extended downstream to a region recognized by the p3'N 2.8R probe which is located more than 45 kb from the 3' end of the beta gene. The other chromosome carried a beta zero thalassemia gene, and a 5 kb deletion between the G gamma and A gamma genes which produced a hybrid -GA gamma- gene. A synthetic oligonucleotide probe showed that this beta zero thalassemia arose from a C----T mutation at position 654 of IVS-II in the beta-globin gene.
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Affiliation(s)
- P Winichagoon
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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