Haplotype-Aware Detection of SERPINA1 Variants by Nanopore Sequencing.

Autor:	González-Carracedo MA; Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain., Herrera-Luis E; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland., Marco-Simancas M; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain., Escuela-Escobar A; Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain., Martín-González E; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain., Sardón-Prado O; Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain; Department of Pediatrics, University of the Basque Country, San Sebastián, Spain., Corcuera P; Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain., Hernández-Pérez JM; Department of Respiratory Medicine, Hospital Universitario de N.S. de Candelaria, Tenerife, Spain., Lorenzo-Díaz F; Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain., Pérez-Pérez JA; Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain. Electronic address: joanpere@ull.edu.es.
Jazyk:	angličtina
Zdroj:	The Journal of molecular diagnostics : JMD [J Mol Diagn] 2024 Nov; Vol. 26 (11), pp. 971-987. Date of Electronic Publication: 2024 Sep 12.
DOI:	10.1016/j.jmoldx.2024.08.002
Abstrakt:	α-1 Antitrypsin (AAT) is an acute-phase reactant with immunomodulatory properties that mainly inhibits neutrophil elastase. Low serum levels cause AAT deficiency (AATD), an underdiagnosed condition that predisposes to pulmonary and hepatic diseases. The SERPINA1 gene, which encodes AAT, contains >500 variants. PI∗Z and PI∗S alleles are the most diagnosed causes of AATD, but the role of the SERPINA1 haplotypes in AAT function remains unknown. SERPINA1 gene was PCR amplified from 94 patients with asthma, using primers with tails for indexing. Sequencing libraries were loaded into a MinION-Mk1C, and MinKNOW was used for basecalling and demultiplexing. Nanofilt and Minimap2 were used for filtering and mapping/alignment. Variant calling/phasing were performed with PEPPER-Margin-DeepVariant. SERPINA1 gene was 100% covered for all samples, with a minimum sequencing depth of 500×. A total of 75 single-nucleotide variants (SNVs) and 4 insertions/deletions were detected, with 45 and 2 of them highly polymorphic (minor allele frequency >0.1), respectively. Nine of the SNVs showed differences in allele frequencies when compared with the overall Spanish population. More than 90% of heterozygous SNVs were phased, yielding 91 and 58 different haplotypes for each SERPINA1 amplified region. Haplotype-based linkage disequilibrium analysis suggests that a recombination hotspot could generate variation in the SERPINA1 gene. The proposed workflow enables haplotype-aware genotyping of the SERPINA1 gene by nanopore sequencing, which will allow the development of novel AATD diagnostic strategies. Competing Interests: Disclosure Statement None declared. (Copyright © 2024 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu