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Detection of four rare thalassemia variants using Single-molecule realtime sequencing

Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing an...

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Autores principales: Luo, Shiqiang, Chen, Xingyuan, Zeng, Dingyuan, Tang, Ning, Yuan, Dejian, Liu, Bailing, Chen, Lizhu, Zhong, Qingyan, Li, Jiaqi, Liu, Yinyin, Chen, Jianping, Wang, Xiaoyuan, Yan, Tizhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9493964/
https://www.ncbi.nlm.nih.gov/pubmed/36159974
http://dx.doi.org/10.3389/fgene.2022.974999
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author Luo, Shiqiang
Chen, Xingyuan
Zeng, Dingyuan
Tang, Ning
Yuan, Dejian
Liu, Bailing
Chen, Lizhu
Zhong, Qingyan
Li, Jiaqi
Liu, Yinyin
Chen, Jianping
Wang, Xiaoyuan
Yan, Tizhen
author_facet Luo, Shiqiang
Chen, Xingyuan
Zeng, Dingyuan
Tang, Ning
Yuan, Dejian
Liu, Bailing
Chen, Lizhu
Zhong, Qingyan
Li, Jiaqi
Liu, Yinyin
Chen, Jianping
Wang, Xiaoyuan
Yan, Tizhen
author_sort Luo, Shiqiang
collection PubMed
description Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four rare variants that have not been identified by conventional diagnostic methods for thalassemia. We also performed genotype and phenotype analyses on family members of thalassemia patients. The SMRT technology detected five cases in which the proband had abnormal results by conventional diagnostic methods or inconsistencies between the genotype and phenotype. The variants included two cases of an α-globin gene cluster 27,311 bp deletion, --(27.3)/αα (hg38 chr16:158664-185974), one case of an HS-40 region 16,079 bp deletion (hg38 chr16:100600-116678), one case of a rearrangement of -α(3.7)α1α2 on one allele and one case of a ß-globin gene cluster HBG1-HBG2 4,924 bp deletion (hg38 chr11:5249345-5254268). This study clarified the hematological phenotypes of four rare variants and indicated the application value of SMRT in the diagnosis of rare α-globin and ß-globin gene cluster deletions, gene recombination and deletion breakpoints. The SMRT method is a comprehensive one-step technology for the genetic diagnosis of thalassemia and is particularly suitable for the diagnosis of thalassemia with rare deletions or genetic recombination.
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spelling pubmed-94939642022-09-23 Detection of four rare thalassemia variants using Single-molecule realtime sequencing Luo, Shiqiang Chen, Xingyuan Zeng, Dingyuan Tang, Ning Yuan, Dejian Liu, Bailing Chen, Lizhu Zhong, Qingyan Li, Jiaqi Liu, Yinyin Chen, Jianping Wang, Xiaoyuan Yan, Tizhen Front Genet Genetics Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four rare variants that have not been identified by conventional diagnostic methods for thalassemia. We also performed genotype and phenotype analyses on family members of thalassemia patients. The SMRT technology detected five cases in which the proband had abnormal results by conventional diagnostic methods or inconsistencies between the genotype and phenotype. The variants included two cases of an α-globin gene cluster 27,311 bp deletion, --(27.3)/αα (hg38 chr16:158664-185974), one case of an HS-40 region 16,079 bp deletion (hg38 chr16:100600-116678), one case of a rearrangement of -α(3.7)α1α2 on one allele and one case of a ß-globin gene cluster HBG1-HBG2 4,924 bp deletion (hg38 chr11:5249345-5254268). This study clarified the hematological phenotypes of four rare variants and indicated the application value of SMRT in the diagnosis of rare α-globin and ß-globin gene cluster deletions, gene recombination and deletion breakpoints. The SMRT method is a comprehensive one-step technology for the genetic diagnosis of thalassemia and is particularly suitable for the diagnosis of thalassemia with rare deletions or genetic recombination. Frontiers Media S.A. 2022-09-02 /pmc/articles/PMC9493964/ /pubmed/36159974 http://dx.doi.org/10.3389/fgene.2022.974999 Text en Copyright © 2022 Luo, Chen, Zeng, Tang, Yuan, Liu, Chen, Zhong, Li, Liu, Chen, Wang and Yan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Luo, Shiqiang
Chen, Xingyuan
Zeng, Dingyuan
Tang, Ning
Yuan, Dejian
Liu, Bailing
Chen, Lizhu
Zhong, Qingyan
Li, Jiaqi
Liu, Yinyin
Chen, Jianping
Wang, Xiaoyuan
Yan, Tizhen
Detection of four rare thalassemia variants using Single-molecule realtime sequencing
title Detection of four rare thalassemia variants using Single-molecule realtime sequencing
title_full Detection of four rare thalassemia variants using Single-molecule realtime sequencing
title_fullStr Detection of four rare thalassemia variants using Single-molecule realtime sequencing
title_full_unstemmed Detection of four rare thalassemia variants using Single-molecule realtime sequencing
title_short Detection of four rare thalassemia variants using Single-molecule realtime sequencing
title_sort detection of four rare thalassemia variants using single-molecule realtime sequencing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9493964/
https://www.ncbi.nlm.nih.gov/pubmed/36159974
http://dx.doi.org/10.3389/fgene.2022.974999
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