&lt;p&gt;Potential of next-generation sequencing to match blood group antigens for transfusion&lt;/p&gt;

Orzińska, Agnieszka; Guz, Katarzyna; Brojer, Ewa

doi:10.2147/ijctm.s175142

Cited by 10 publications

(6 citation statements)

References 82 publications

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“…Next generation sequencing is increasingly used for blood group genes [ 51 – 78 ]. In contrast to HLA [ 79 ], most blood group genes lack well documented long reference sequences associated with them [ 80 ].…”

Section: Discussionmentioning

confidence: 99%

Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

et al. 2021

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Background Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, using computerized genotype phasing, reported haplotype data. In contrast, we identified long reference sequences by analyzing the homozygous genomic regions in this online database, a concept that has rarely been reported since next generation sequencing data became available. Study design and methods Phased genotype data for a 80.6 kb region of chromosome 1 was downloaded for all 2,504 unrelated individuals of the 1000 Genome Project Phase 3 cohort. The data was centered on the ACKR1 gene and bordered by the CADM3 and FCER1A genes. Individuals with heterozygosity at a single site or with complete homozygosity allowed unambiguous assignment of an ACKR1 haplotype. A computer algorithm was developed for extracting these haplotypes from the 1000 Genome Project in an automated fashion. A manual analysis validated the data extracted by the algorithm. Results We confirmed 902 ACKR1 haplotypes of varying lengths, the longest at 80,584 nucleotides and shortest at 1,901 nucleotides. The combined length of haplotype sequences comprised 19,895,388 nucleotides with a median of 16,014 nucleotides. Based on our approach, all haplotypes can be considered experimentally confirmed and not affected by the known errors of computerized genotype phasing. Conclusions Tracts of homozygosity can provide definitive reference sequences for any gene. They are particularly useful when observed in unrelated individuals of large scale sequence databases. As a proof of principle, we explored the 1000 Genomes Project database for ACKR1 gene data and mined long haplotypes. These haplotypes are useful for high throughput analysis with next generation sequencing. Our approach is scalable, using automated bioinformatics tools, and can be applied to any gene.

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Section: Discussionmentioning

confidence: 99%

Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

et al. 2021

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“…There is also ongoing research on next generation sequencing (NGS). The above issues have been described by the authors in separate papers published in 2019 [16,17].…”

Section: Current Status Of Application Of Molecular Biology Methods Imentioning

confidence: 97%

“…If above described methods give no equivocal answers with regard to molecular basis of the antigen, additional tests are necessary which are mainly based on sequencing the antigen-encoding gene. The classical Sanger method is usually used, but such analyses can also be performed with next-generation sequencing (NGS) [17].…”

Section: Current Status Of Application Of Molecular Biology Methods Imentioning

confidence: 99%

Molecular biology methods for blood cell antigen genotyping in reference laboratories

Guz¹,

Orzińska²,

Michalewska³

et al. 2019

Journal of Transfusion Medicine

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The aim of the study is to present current applications of molecular biology methods in immunohematology as well as the status of their implementation in the Polish Blood Transfusion Service. Molecular biology methods are used for: analysis of molecular background of blood cell antigens in individuals with discrepant results of serological tests, identification of RhD antigen with weak expression undetectable by serological methods in blood donors, identification of weak D type antigen in recipients unsusceptible to alloimmunization. These methods are also used for noninvasive study of fetal genes in plasma samples of immunized pregnant women with serological incompatibilities and in RhD negative pregnant women for qualification to antenatal prophylactic administration of anti-D immunoglobulin. Molecular biology is also an important tool for diagnostics of patients with antibodies to high-frequency blood group antigens (HFA) or for patients immunized with HPA and HNA antigens and for identification of "antigen-negative" blood donors for such patients. In Poland, all these tests are available and in use.

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“…Przewagą technologii NGS jest wgląd w rzeczywistą sekwencję badanego regionu kodującego grupy krwi i wykrycie ewentualnych wariantów w jej obrębie, przy czym ta technologia jest obecnie w fazie badań naukowych [53][54]. Techniki NGS w oznaczaniu grup krwi zostały szczegółowo omówione przez autorów niniejszego artykułu w osobnej publikacji, która niedawno się ukazała [55].…”

Section: Sekwencjonowanie Nowej Generacji (Next Generation Sequencing)unclassified

Rozwój technologii opartych na metodach biologii molekularnej do oznaczania grup krwi

Guz

Orzińska

Brojer

2019

Journal of Transfusion Medicine

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Zakład Immunologii Hematologicznej i Transfuzjologicznej Instytutu Hematologii i Transfuzjologii w Warszawie Streszczenie W ciągu ostatnich lat obserwuje się gwałtowny rozwój technologii badań molekularnych stosowanych w immunohematologii. Na świecie są one obecnie używane nie tylko przez laboratoria referencyjne i wysokospecjalistyczne, lecz są wdrażane do badań masowych w centrach krwiodawstwa, gdzie służą przede wszystkim do genotypowania klinicznie istotnych antygenów w celu zwiększenia dostępności dawców dla chorych z alloprzeciwciałami. W nieodległej przyszłości będzie też możliwe dobieranie dla chorych zależnych od przetoczeń dawców zgodnych w najbardziej immunogennych antygenach, tak by zapobiegać alloimmunizacji. Z myślą o tak ambitnych planach, są opracowywane na świecie zaawansowane technologie, umożliwiające masowe genotypowanie antygenów komórek krwi. W niniejszym artykule zostaną omówione metody biologii molekularnej przydatne dla takich badań. Słowa kluczowe: genotypowanie antygenów komórek krwi, nanofluidowa/cyfrowa reakcja łańcuchowa polimerazy, mikromacierze, spekrometria masowa MALDI-TOF, multipleksowa amplifikacja zależna od ligacji sond (MLPA), sekwencjonowanie następnej generacji (NGS)

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<p>Potential of next-generation sequencing to match blood group antigens for transfusion</p>

Cited by 10 publications

References 82 publications

Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

Molecular biology methods for blood cell antigen genotyping in reference laboratories

Rozwój technologii opartych na metodach biologii molekularnej do oznaczania grup krwi

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