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González-Carracedo MA, Herrera-Luis E, Marco-Simancas M, Escuela-Escobar A, Martín-González E, Sardón-Prado O, Corcuera P, Hernández-Pérez JM, Lorenzo-Díaz F, Pérez-Pérez JA. Haplotype-Aware Detection of SERPINA1 Variants by Nanopore Sequencing. J Mol Diagn 2024:S1525-1578(24)00195-8. [PMID: 39276924 DOI: 10.1016/j.jmoldx.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 09/17/2024] Open
Abstract
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.
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Affiliation(s)
- Mario A González-Carracedo
- 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
| | - Esther Herrera-Luis
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - María Marco-Simancas
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain
| | - Ainhoa Escuela-Escobar
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain
| | - Elena Martín-González
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain
| | - Olaia Sardón-Prado
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain; Department of Pediatrics, University of the Basque Country, San Sebastián, Spain
| | - Paula Corcuera
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
| | - Jose M Hernández-Pérez
- Department of Respiratory Medicine, Hospital Universitario de N.S. de Candelaria, Tenerife, Spain
| | - Fabián Lorenzo-Díaz
- 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
| | - José A Pérez-Pérez
- 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.
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Matamala N, Gomez-Mariano G, Perez JA, Baladrón B, Torres-Durán M, Michel FJ, Saez R, Hernández-Pérez JM, Belmonte I, Rodriguez-Frias F, Blanco I, Strnad P, Janciauskiene S, Martinez-Delgado B. New cis-Acting Variants in PI*S Background Produce Null Phenotypes Causing Alpha-1 Antitrypsin Deficiency. Am J Respir Cell Mol Biol 2020; 63:444-451. [PMID: 32515985 DOI: 10.1165/rcmb.2020-0021oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is an inherited condition characterized by reduced levels of serum AAT due to mutations in the SERPINA1 (Serpin family A member 1) gene. The Pi*S (Glu264Val) is one of the most frequent deficient alleles of AATD, showing high incidence in the Iberian Peninsula. Herein, we describe two new alleles carrying an S mutation but producing a null phenotype: QOVigo and QOAachen. The new alleles were identified by sequencing the SERPINA1 gene in three patients who had lower AAT serum levels than expected for the initial genotype. These alleles are the result of combined mutations in cis in a PI*S allele. Sequencing detected the S mutation in cis with Tyr138Cys (S+Tyr138Cys) in two patients, whereas a third one had the S mutation in cis with Pro391Thr variant (S+Pro391Thr). When expressed in a cellular model, these variants caused strong AAT polymerization and very low AAT secretion to almost undetectable levels. The isoelectric focusing method for plasma AAT phenotyping did not show AAT protein encoded by the novel mutant alleles, behaving as null. We called these alleles PI*S-plus because the S variant was phased with another variant conferring more aggressive characteristics to the allele. The current data demonstrate that the clinical variability observed in AATD can be explained by additional genetic variation, such as dual cis-acting variants in the SERPINA1 gene. The possible existence of other unrevealed variants combined in the PI*S alleles should be considered to improve the genetic diagnosis of the patients.
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Affiliation(s)
- Nerea Matamala
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Gomez-Mariano
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Perez
- Área de Genética, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - Beatriz Baladrón
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - María Torres-Durán
- Servicio de Neumología, Hospital Álvaro Cunqueiro, Estructura Organizativa de Xestión Integrada Vigo, Pneumovigo I + i, Instituto de Investigación Sanitaria Galicia Sur, Vigo, Spain
| | | | - Raquel Saez
- Genetica e Inmunología, Hospital Universitario Donostia, País Vasco, Spain
| | | | - Irene Belmonte
- Biochemistry Department, Hospital Vall d'Hebron, Barcelona, Spain
| | | | - Ignacio Blanco
- Registro Español de Pacientes con Déficit de Alfa-1 Antitripsina, Fundación Española, de Pulmón, Respira, Sociedad Española de Neumología y Cirugía Torácica, Barcelona, Spain
| | - Pavel Strnad
- Department of Internal Medicine III, University Hospital Aachen, Aachen, Germany
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research, Hannover Medical School, Hannover, Germany; and
| | - Beatriz Martinez-Delgado
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
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Mattman A, Gilfix BM, Chen SX, DeMarco ML, Kyle BD, Parker ML, Agbor TA, Jung B, Selvarajah S, Barakauskas VE, Vaags AK, Estey MP, Nelson TN, Speevak MD. Alpha-1-antitrypsin molecular testing in Canada: A seven year, multi-centre comparison. Clin Biochem 2020; 81:27-33. [DOI: 10.1016/j.clinbiochem.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 10/24/2022]
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Chen S, DeMarco ML, Estey MP, Kyle B, Parker ML, Agbor TA, Kawada P, Speevak M, Nelson TN, Mattman A. Null Canada: A novel α 1-antitrypsin allele with in cis variants Glu366Lys and Ile100Asn. Clin Biochem 2020; 79:23-27. [PMID: 32087139 DOI: 10.1016/j.clinbiochem.2020.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/23/2020] [Accepted: 02/18/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND α1-Antitrypsin (A1AT) deficiency predisposes patients to pulmonary disease due to inadequate protection against human neutrophil elastase released during inflammatory responses. A1AT deficiency is caused by homozygosity or compound heterozygosity for A1AT variants; individuals with A1AT deficiency most commonly have at least one Z variant allele (c.1096G > A (Glu366Lys)). Null variants that result in complete absence of A1AT in the plasma are much rarer. With one recent exception, all reported A1AT variants are characterized by a single pathogenic variant. CASE An 8 years old patient from Edmonton, Alberta, Canada, was investigated for A1AT deficiency. His A1AT phenotype was determined to be M (wild type)/Null by isoelectric focusing (IEF) but M/Z by targeted genotyping. Gene sequencing revealed two heterozygous variants: Z and Ile100Asn (c.299 T > A). The Ile100Asn substitution is predicted to disrupt the secondary structure of an α-helix in which it resides and the neighbouring tertiary structure, resulting in intracellular degradation of A1AT prior to hepatocyte secretion. METHODS Family testing was conducted to verify potential inheritance of an A1AT allele carrying the two mutations in cis, as this arrangement of the mutations would explain "Z" detection by genotyping but not by IEF. Molecular modeling was used to assess the effect of the variants on A1AT structure and stability. DISCUSSION Carrier status for a novel variant NullCanada with in cis mutations (c.[299 T > A;1096G > A], p.[(Ileu100Asn;Glu366Lys)]) was confirmed. A sibling was identified as having A1AT deficiency on the basis of compound heterozygosity for two alleles: NullCanada and the common Z allele. A separate pedigree from the Maritimes was subsequently recognized as carrying NullCanada. CONCLUSION In cis mutations such as NullCanada may be more common than previously described due to failure to detect such mutations using historical testing methods. Combined approaches that include gene sequencing and segregation studies allow recognition of rare A1AT variants, including in cis mutations.
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Affiliation(s)
- Sharon Chen
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, BC, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada; Centre for Heart Lung Innovation, University of British Columbia, BC, Canada
| | - Mathew P Estey
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Barry Kyle
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Michelle L Parker
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Terence A Agbor
- DynaLIFE Medical Labs, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, AB, Canada
| | - Patricia Kawada
- Division of Pediatric Gastroenterology & Nutrition, Department of Pediatrics, University of Alberta, AB, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada; Department of Pathology and Laboratory Medicine, BC Children's & BC Women's Hospitals, BC, Canada
| | - Andre Mattman
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada.
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