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carrier rate Analysis of Single-Gene Disorders Based on 1000 Genome Project and Exome Aggregation Consortium Data

Reproductive and Developmental Medicine 2019年第4期3卷 235-242,I0001,I0002页

作者： Meng-Meng Duan Hua-Jun Zheng Laboratory of Medical Foods NHC Key Laboratory of Reproduction Regulation(Shanghai Institute of Planned Parenthood Research)School of Basic Medical SciencesFudan UniversityShanghai 200032China

Objective:Screening variants underlying the single-gene disorder in the general population can help reduce the incidences of birth defects.To determine the most prevalent pathogenic variants causing autosomal recessive diseases,we investigated the frequencies of these variants in six major geographic ancestry groups from Exome Aggregation Consortium(ExAC)database and 26 populations from the 1,000 Genome Project,including three Chinese ethnic groups.Methods:We selected 64 autosomal recessive diseases and collected corresponding causal genes and variants from ClinVar for the analysis.The RS(reference single-nucleotide polymorphism)IDs of these variants were used to search the corresponding VCF file from the 1,000 Genomes Project and ExAC databases.We calculated the frequencies of heterozygotes of each disease variants in the 1,000 Genomes Project and ExAC samples and compared the distribution of disease alleles among different populations.Results:Our analysis revealed that 1,151/212 variants were carried by 60,706/2,504 individuals sequenced in the ExAC/1,000 Genomes Project.The average number of autosomal recessive disease alleles carried by samples from ExAC and 1,000 Genomes Project were 0.53 and 0.68,respectively.These disease alleles showed differential distribution among populations,and some disease alleles were significantly enriched in certain ethnic groups.In addition,1-2 main pathogenic variants were identified in each disease.Meanwhile,several ClinVar variants with relatively high frequency(>1%)in the samples were found to be benign instead of“conflicting evaluations of pathogenicity.”Conclusions:Our observations revealed that main pathogenic variants existed in certain autosomal recessive disease,suggesting that screening of disease hypermutations in different populations is valuable in reducing the occurrence of birth defects.

关键词： Single-Gene Disorders Exome Aggregation Consortium 1,000 Genomes Project carrier rate

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Epidemiological Survey of Hemoglobinopathies Based on Next-Generation Sequencing Platform in Hunan Province,China

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Biomedical and Environmental Sciences 2023年第2期36卷 127-134页

作者： XI Hui LIU Qin XIE Dong Hua ZHOU Xu TANG Wang Lan TANG De Guo ZENG Chun Yan WANG Qiong NIE Xing Hui PENG Jin Ping GAO Xiao Ya WU Hong Liang ZHANG Hao Qing QIU Li FENG Zong Hui WANG Shu Yuan ZHOU Shu Xiang HE Jun ZHOU Shi Hao ZHOU Fa Qun ZHENG Jun Qing WANG Shun Yao CHEN Shi Ping ZHENG Zhi Fen MA Xiao Yuan FANG Jun Qun LIANG Chang Biao WANG Hua NHC Key Laboratory of Birth Defect for Research and Prevention Hunan Provincial Maternal and Child Health Care HospitalChangsha 410028HunanChina Yongzhou Hospital for Maternal and Child Health Care Yongzhou 425000HunanChina Changde Hospital for Maternal and Child Health Care Changde 415099HunanChina Hengyang Hospital for Maternal and Child Health Care Hengyang 421009HunanChina Shaoyang Hospital for Maternal and Child Health Care Shaoyang 422001HunanChina Yiyang Hospital for Maternal and Child Health Care Yiyang 413099HunanChina Yueyang Hospital for Maternal and Child Health Care Yueyang 414021HunanChina Center of Prenatal Diagnosis Chenzhou No.1 People’s HospitalChenzhou 423099HunanChina Loudi Hospital for Maternal and Child Health Care Loudi 417599HunanChina Huaihua Hospital for Maternal and Child Health Care Huaihua 418099HunanChina Xiangtan Hospital for Maternal and Child Health Care Xiangtan 411104HunanChina Zhuzhou Hospital for Maternal and Child Health Care Zhuzhou 412008HunanChina Changsha Hospital for Maternal and Child Health Care Changsha 410007HunanChina Xiangxi Tujia and Miao Autonomous Prefecture Hospital for Maternal and Child Health Care Jishou 416000HunanChina Zhang Jiajie Centre for maternal and child health family planning services Zhangjiajie 427299HunanChina BGI Genomics BGI-ShenzhenShenzhen 518083GuangdongChina Clinical Laboratory of BGI Health BGI-ShenzhenShenzhen 518083GuangdongChina BGI-Wuhan Clinical Laboratories BGI-ShenzhenWuhan 430074HubeiChina SEBIA Representative Office Shanghai 200001China

Objective This study was aimed at investigating the carrier rate of,and molecular variation in,α-andβ-globin gene mutations in Hunan Province.Methods We recruited 25,946 individuals attending premarital screening from 42 districts and counties in all 14 cities of Hunan Province.Hematological screening was performed,and molecular parameters were assessed.Results The overall carrier rate of thalassemia was 7.1%,including 4.83%forα-thalassemia,2.15%forβ-thalassemia,and 0.12%for bothα-andβ-thalassemia.The highest carrier rate of thalassemia was in Yongzhou(14.57%).The most abundant genotype ofα-thalassemia andβ-thalassemia was-α^(3.7)/αα(50.23%)andβ^(IVS-Ⅱ-654)/β^(N)(28.23%),respectively.Fourα-globin mutations[CD108(ACC>AAC),CAP+29(G>C),Hb Agrinio and Hb Cervantes]and sixβ-globin mutations[CAP+8(C>T),IVS-Ⅱ-848(C>T),-56(G>C),beta nt-77(G>C),codon 20/21(-TGGA)and Hb Knossos]had not previously been identified in China.Furthermore,this study provides the first report of the carrier rates of abnormal hemoglobin variants andα-globin triplication in Hunan Province,which were 0.49%and 1.99%,respectively.Conclusion Our study demonstrates the high complexity and diversity of thalassemia gene mutations in the Hunan population.The results should facilitate genetic counselling and the prevention of severe thalassemia in this region.

关键词： Thalassemia carrier rate Molecular spectrum Abnormal hemoglobin variants α-globin triplication

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APPLICATION OF GENETIC DEAFNESS GENE CHIP FOR DETECTION OF GENE MUTATION OF DEAFNESS IN PREGNANT WOMEN

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Journal of Otology 2014年第2期9卷 97-100页

作者： CHANG Liang ZHONG Su ZHAO Nan LIU Ping ZHAO Yangyu QIAO Jie Department of Obstetrics and Gynecology Peking University Third Hospital Key Laboratory of Assisted Reproduction Ministry of Education Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology

Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip. Methods The pregnant women in obstetric clinic without hearing impairment and hearing disorders family history were selected. The informed consent was signed. Peripheral blood was taken to extract genom- ic DNA. Application of genetic deafness gene chip for detecting 9 mutational hot spot of the most common 4 Chinese deafness genes, namely GJB2 （35delG, 176del16bp, 235delC, 299delAT）, GJB3 （C538T） ,SLC26A4 （ IVS72A〉G, A2168G） and mito- chondrial DNA 12S rRNA （A1555G, C1494T） . Further genetic testing were provided to the spouses and newborns of the screened carriers. Results Peripheral blood of 430 pregnant women were detected, detection of deafness gene mutation carri- ers in 24 cases（4.2%）, including 13 cases of the GJB2 heterozygous mutation, 3 cases of SLC26A4 heterozygous mutation, 1 cases of GJB3 heterozygous mutation, and 1 case of mitochondrial 12S rRNA mutation. 18 spouses and 17 newborns took further genetic tests, and 6 newborns inherited the mutation from their mother. Conclusion The common deafness genes muta- tion has a high carrier rate in pregnant women group, 235delC and IVS7-2A〉G heterozygous mutations are common.

关键词： Gene chip Hereditary deafness carrier rate Mutation detection

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