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Resolving Genotype-Phenotype Discrepancies of the Kidd Blood Group System Using Long-Read Nanopore Sequencing.
Gueuning, Morgan; Thun, Gian Andri; Trost, Nadine; Schneider, Linda; Sigurdardottir, Sonja; Engström, Charlotte; Larbes, Naemi; Merki, Yvonne; Frey, Beat M; Gassner, Christoph; Meyer, Stefan; Mattle-Greminger, Maja P.
Afiliación
  • Gueuning M; Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Rütistrasse 19, 8952 Schlieren, Switzerland.
  • Thun GA; Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Rütistrasse 19, 8952 Schlieren, Switzerland.
  • Trost N; Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Schneider L; Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Sigurdardottir S; Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Engström C; Department of Immunohematology, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Larbes N; Department of Immunohematology, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Merki Y; Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Frey BM; Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Rütistrasse 19, 8952 Schlieren, Switzerland.
  • Gassner C; Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Meyer S; Department of Immunohematology, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland.
  • Mattle-Greminger MP; Institute of Translational Medicine, Private University in the Principality of Liechtenstein, 9495 Triesen, Liechtenstein.
Biomedicines ; 12(1)2024 Jan 19.
Article en En | MEDLINE | ID: mdl-38275395
ABSTRACT
Due to substantial improvements in read accuracy, third-generation long-read sequencing holds great potential in blood group diagnostics, particularly in cases where traditional genotyping or sequencing techniques, primarily targeting exons, fail to explain serological phenotypes. In this study, we employed Oxford Nanopore sequencing to resolve all genotype-phenotype discrepancies in the Kidd blood group system (JK, encoded by SLC14A1) observed over seven years of routine high-throughput donor genotyping using a mass spectrometry-based platform at the Blood Transfusion Service, Zurich. Discrepant results from standard serological typing and donor genotyping were confirmed using commercial PCR-SSP kits. To resolve discrepancies, we amplified the entire coding region of SLC14A1 (~24 kb, exons 3 to 10) in two overlapping long-range PCRs in all samples. Amplicons were barcoded and sequenced on a MinION flow cell. Sanger sequencing and bridge-PCRs were used to confirm findings. Among 11,972 donors with both serological and genotype data available for the Kidd system, we identified 10 cases with unexplained conflicting results. Five were linked to known weak and null alleles caused by variants not included in the routine donor genotyping. In two cases, we identified novel null alleles on the JK*01 (Gly40Asp; c.119G>A) and JK*02 (Gly242Glu; c.725G>A) haplotypes, respectively. Remarkably, the remaining three cases were associated with a yet unknown deletion of ~5 kb spanning exons 9-10 of the JK*01 allele, which other molecular methods had failed to detect. Overall, nanopore sequencing demonstrated reliable and accurate performance for detecting both single-nucleotide and structural variants. It possesses the potential to become a robust tool in the molecular diagnostic portfolio, particularly for addressing challenging structural variants such as hybrid genes, deletions and duplications.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Tipo de estudio: Prognostic_studies Idioma: En Revista: Biomedicines Año: 2024 Tipo del documento: Article País de afiliación: Suiza Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Tipo de estudio: Prognostic_studies Idioma: En Revista: Biomedicines Año: 2024 Tipo del documento: Article País de afiliación: Suiza Pais de publicación: Suiza