Marcela Díaz-Matallana, Ignacio Briceño, Escilda Benavides-Benítez, Jaime E Bernal, Julio C Martínez-Lozano
{"title":"通过对哥伦比亚玻利瓦尔的一组样本进行 SNP 标记测序,确定镰状细胞病的分子特征,并对与β-球蛋白簇(HBB 基因)相关的主要单倍型进行分类。","authors":"Marcela Díaz-Matallana, Ignacio Briceño, Escilda Benavides-Benítez, Jaime E Bernal, Julio C Martínez-Lozano","doi":"10.1080/03014460.2024.2308714","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Colombia has a mestizo population and the prevalence of haemoglobin variants varies according to each region, but heterozygous carriers can be found in all of them.</p><p><strong>Aim: </strong>To characterise sickle cell disease (SCD) haematologically, biochemically, and molecularly, and detect classic haplotypes by DNA sequencing in a group of samples from Bolívar, Colombia.</p><p><strong>Subjects and methods: </strong>Blood samples were collected after informed consent from volunteers from eight communities in the Bolívar department, plus samples from the Pacific region, Providencia Island, and Bogotá were included. Data were obtained from: (1) haematological analyses; (2) biochemical tests: dHPLC was used to determine haemoglobin (Hb); and (3) DNA sequencing data through five SNPs.</p><p><strong>Results: </strong>101 samples were identified by <i>rs334</i> through Sanger's Sequencing, structural haemoglobinopathies <i>HbAS</i> (34.65%), <i>HbSS</i> (2.97%) and <i>HbAC</i> (1.98%) were found. When contrasting the Hb identification results between SNP <i>rs334</i> Vs. dHPLC/Isoelectric Focusing (IEF), a coincidence was found in 39/43 samples analysed, therefore, when comparing these techniques, a significant correlation was found (Pearson's correlation coefficient <i>r</i> = 0.998). 26 samples previously analysed by <i>rs334</i> were classified into classical haplotypes <i>CAR</i> (50.0%), <i>BEN</i> (30.76%), <i>CAM</i> (7.69%), <i>SEN</i> (3.84%), and <i>ATP-I</i> (7.69%).</p><p><strong>Conclusions: </strong>SCD characterisation and SNPs-based classification through Sanger's DNA sequencing have not been performed before in Colombia. The results of this work will make it possible to expand the data or records of carriers and those affected, which will benefit patients and their families.</p>","PeriodicalId":50765,"journal":{"name":"Annals of Human Biology","volume":null,"pages":null},"PeriodicalIF":1.2000,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Molecular characterisation of sickle cell disease and classification of major haplotypes associated with the β-globin cluster (HBB gene) by means of SNP marker sequencing in a group of samples from Bolívar, Colombia.\",\"authors\":\"Marcela Díaz-Matallana, Ignacio Briceño, Escilda Benavides-Benítez, Jaime E Bernal, Julio C Martínez-Lozano\",\"doi\":\"10.1080/03014460.2024.2308714\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Colombia has a mestizo population and the prevalence of haemoglobin variants varies according to each region, but heterozygous carriers can be found in all of them.</p><p><strong>Aim: </strong>To characterise sickle cell disease (SCD) haematologically, biochemically, and molecularly, and detect classic haplotypes by DNA sequencing in a group of samples from Bolívar, Colombia.</p><p><strong>Subjects and methods: </strong>Blood samples were collected after informed consent from volunteers from eight communities in the Bolívar department, plus samples from the Pacific region, Providencia Island, and Bogotá were included. Data were obtained from: (1) haematological analyses; (2) biochemical tests: dHPLC was used to determine haemoglobin (Hb); and (3) DNA sequencing data through five SNPs.</p><p><strong>Results: </strong>101 samples were identified by <i>rs334</i> through Sanger's Sequencing, structural haemoglobinopathies <i>HbAS</i> (34.65%), <i>HbSS</i> (2.97%) and <i>HbAC</i> (1.98%) were found. When contrasting the Hb identification results between SNP <i>rs334</i> Vs. dHPLC/Isoelectric Focusing (IEF), a coincidence was found in 39/43 samples analysed, therefore, when comparing these techniques, a significant correlation was found (Pearson's correlation coefficient <i>r</i> = 0.998). 26 samples previously analysed by <i>rs334</i> were classified into classical haplotypes <i>CAR</i> (50.0%), <i>BEN</i> (30.76%), <i>CAM</i> (7.69%), <i>SEN</i> (3.84%), and <i>ATP-I</i> (7.69%).</p><p><strong>Conclusions: </strong>SCD characterisation and SNPs-based classification through Sanger's DNA sequencing have not been performed before in Colombia. The results of this work will make it possible to expand the data or records of carriers and those affected, which will benefit patients and their families.</p>\",\"PeriodicalId\":50765,\"journal\":{\"name\":\"Annals of Human Biology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.2000,\"publicationDate\":\"2024-02-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Annals of Human Biology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1080/03014460.2024.2308714\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/2/20 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"ANTHROPOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Annals of Human Biology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1080/03014460.2024.2308714","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/2/20 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"ANTHROPOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
背景:目的:从血液学、生物化学和分子学方面描述镰状细胞病(SCD)的特征,并通过对哥伦比亚玻利瓦尔省的一组样本进行 DNA 测序来检测典型的单倍型:在征得知情同意后,从玻利瓦尔省八个社区的志愿者中采集了血液样本,此外还包括太平洋地区、普罗维登西亚岛和波哥大的样本。数据来自:(1) 血液学分析;(2) 生化测试:使用 dHPLC 测定血红蛋白(Hb);(3) 通过五个 SNPs 获得的 DNA 测序数据:结果:通过桑格测序法对 101 个样本进行了 rs334 鉴定,发现了结构性血红蛋白病 HbAS(34.65%)、HbSS(2.97%)和 HbAC(1.98%)。在对比 SNP rs334 与 dHPLC/等电聚焦(IEF)的血红蛋白鉴定结果时,发现 39/43 个分析样本的结果相同,因此,在对比这些技术时,发现了显著的相关性(皮尔逊相关系数 r = 0.998)。先前通过 rs334 分析的 26 个样本被归类为经典单倍型 CAR(50.0%)、BEN(30.76%)、CAM(7.69%)、SEN(3.84%)和 ATP-I(7.69%):哥伦比亚以前从未通过 Sanger DNA 测序进行过 SCD 特征描述和基于 SNPs 的分类。这项工作的结果将有助于扩大携带者和受影响者的数据或记录,从而使患者及其家属受益。
Molecular characterisation of sickle cell disease and classification of major haplotypes associated with the β-globin cluster (HBB gene) by means of SNP marker sequencing in a group of samples from Bolívar, Colombia.
Background: Colombia has a mestizo population and the prevalence of haemoglobin variants varies according to each region, but heterozygous carriers can be found in all of them.
Aim: To characterise sickle cell disease (SCD) haematologically, biochemically, and molecularly, and detect classic haplotypes by DNA sequencing in a group of samples from Bolívar, Colombia.
Subjects and methods: Blood samples were collected after informed consent from volunteers from eight communities in the Bolívar department, plus samples from the Pacific region, Providencia Island, and Bogotá were included. Data were obtained from: (1) haematological analyses; (2) biochemical tests: dHPLC was used to determine haemoglobin (Hb); and (3) DNA sequencing data through five SNPs.
Results: 101 samples were identified by rs334 through Sanger's Sequencing, structural haemoglobinopathies HbAS (34.65%), HbSS (2.97%) and HbAC (1.98%) were found. When contrasting the Hb identification results between SNP rs334 Vs. dHPLC/Isoelectric Focusing (IEF), a coincidence was found in 39/43 samples analysed, therefore, when comparing these techniques, a significant correlation was found (Pearson's correlation coefficient r = 0.998). 26 samples previously analysed by rs334 were classified into classical haplotypes CAR (50.0%), BEN (30.76%), CAM (7.69%), SEN (3.84%), and ATP-I (7.69%).
Conclusions: SCD characterisation and SNPs-based classification through Sanger's DNA sequencing have not been performed before in Colombia. The results of this work will make it possible to expand the data or records of carriers and those affected, which will benefit patients and their families.
期刊介绍:
Annals of Human Biology is an international, peer-reviewed journal published six times a year in electronic format. The journal reports investigations on the nature, development and causes of human variation, embracing the disciplines of human growth and development, human genetics, physical and biological anthropology, demography, environmental physiology, ecology, epidemiology and global health and ageing research.