GRAde: a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism
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Published:2021-05
Issue:S10
Volume:22
Page:
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ISSN:1471-2105
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Container-title:BMC Bioinformatics
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language:en
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Short-container-title:BMC Bioinformatics
Author:
Wu Yu-Ching, Chen Chia-I, Chen Peng-Ying, Kuo Chun-Hung, Hung Yi-Hsuan, Peng Kang-Yung, Wu Vin-Cent, Tsai-Wu Jyy-Jih, Hsu Chia-LangORCID,
Abstract
Abstract
Background
Glucocorticoid-remediable aldosteronism (GRA) is a form of heritable hypertension caused by a chimeric fusion resulting from unequal crossing over between 11β‐hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2), which are two genes with similar sequences. Different crossover patterns of the CYP11B1 and CYP11B2 chimeric genes may be associated with a variety of clinical presentations. It is therefore necessary to develop an efficient approach for identifying the differences between the hybrid genes of a patient with GRA.
Results
We developed a long-read analysis pipeline named GRAde (GRA deciphering), which utilizes the nonidentical bases in the CYP11B1 and CYP11B2 genomic sequences to identify and visualize the chimeric form. We sequenced the polymerase chain reaction (PCR) products of the CYP11B1/CYP11B2 chimeric gene from 36 patients with GRA using the Nanopore MinION device and analyzed the sequences using GRAde. Crossover events were identified for 30 out of the 36 samples. The crossover sites appeared in the region exhibiting high sequence similarity between CYP11B1 and CYP11B2, and 53.3% of the cases were identified as having a gene conversion in intron 2. More importantly, there were six cases for whom the PCR products indicated a chimeric gene, but the GRAde results revealed no crossover pattern. The crossover regions were further verified by Sanger sequencing analysis.
Conclusions
PCR-based target enrichment followed by long-read sequencing is an efficient and precise approach to dissecting complex genomic regions, such as those involved in GRA mutations, which could be directly applied to clinical diagnosis. The scripts of GRAde are available at https://github.com/hsu-binfo/GRAde.
Funder
Ministry of Science and Technology, Taiwan National Taiwan University Hospital
Publisher
Springer Science and Business Media LLC
Subject
Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology
Reference37 articles.
1. Farrugia FA, Zavras N, Martikos G, Tzanetis P, Charalampopoulos A, Misiakos EP, Sotiropoulos D, Koliakos N. A short review of primary aldosteronism in a question and answer fashion. Endocr Regul. 2018;52(1):27–40. 2. Perez-Rivas LG, Williams TA, Reincke M. Inherited forms of primary hyperaldosteronism: new genes, new phenotypes and proposition of a new classification. Exp Clin Endocrinol Diabetes. 2019;127(2–03):93–9. 3. Zennaro MC, Boulkroun S, Fernandes-Rosa F. An update on novel mechanisms of primary aldosteronism. J Endocrinol. 2015;224(2):R63-77. 4. Mulatero P, Tizzani D, Viola A, Bertello C, Monticone S, Mengozzi G, Schiavone D, Williams TA, Einaudi S, La Grotta A, et al. Prevalence and characteristics of familial hyperaldosteronism: the PATOGEN study (Primary Aldosteronism in TOrino-GENetic forms). Hypertension. 2011;58(5):797–803. 5. Aglony M, Martinez-Aguayo A, Carvajal CA, Campino C, Garcia H, Bancalari R, Bolte L, Avalos C, Loureiro C, Trejo P, et al. Frequency of familial hyperaldosteronism type 1 in a hypertensive pediatric population: clinical and biochemical presentation. Hypertension. 2011;57(6):1117–21.
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