scholarly journals Phase-defined complete sequencing of the HLA genes by next-generation sequencing

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 355 ◽  
Author(s):  
Kazuyoshi Hosomichi ◽  
Timothy A Jinam ◽  
Shigeki Mitsunaga ◽  
Hirofumi Nakaoka ◽  
Ituro Inoue
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Hla Genes ◽  
Complete Sequencing ◽  
Generation Sequencing

OR46 Detecting low level clonal somatic mutation in HLA genes using next-generation sequencing in the presence of aplastic anemia

2016 ◽  
Vol 77 ◽  
pp. 39
Author(s):  
Jamie L. Duke ◽  
Daria V. Babushok ◽  
Hongbo M. Xie ◽  
Hilary Mehler ◽  
Yanping Huang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Aplastic Anemia ◽  
Somatic Mutation ◽  
Next Generation ◽  
Low Level ◽  
Hla Genes ◽  
Generation Sequencing

scholarly journals Population Frequencies Determined by Next-generation Sequencing Provide Strategies for Prospective HLA Epitope Matching for Transplantation

2020 ◽  
Author(s):  
Jenny Tran ◽  
Oliver Gunther ◽  
Karen Sherwood ◽  
Franz Fenninger ◽  
Lenka Allan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Renal Transplant ◽  
Human Leukocyte ◽  
Gene Complex ◽  
Next Generation ◽  
Leukocyte Antigen ◽  
Hla Genes ◽  
In Silico Mapping ◽  
High Degree ◽  
Generation Sequencing

Abstract Compatibility for human leukocyte antigen (HLA) genes between transplant donors and recipients improves graft survival but prospective matching is rarely performed due to the vast heterogeneity of this gene complex. To reduce complexity, we have combined next-generation sequencing and in silico mapping to determine population frequencies and matching probabilities of 150 antibody-binding eplets across all 11 classical HLA genes in 2000 ethnically heterogeneous renal patients and donors. We show that eplets are more common and more uniformly distributed between donors and recipients than the respective HLA isoforms. Simulation of targeted eplet matching shows that a high degree of overall compatibility, and perfect identity at the clinically important HLA class II loci, can be obtained within a patient waiting list of approximately 250 subjects. Internal epitope-based allocation is thus feasible for most major renal transplant programs, while regional or national sharing may be required for other solid organs.

scholarly journals Next generation sequencing HLA-typing of recipients and donors of allogeneic haematopoietic stem cells

2021 ◽  
Vol 66 (2) ◽  
pp. 206-217
Author(s):  
E. G. Khamaganova ◽  
A. R. Abdrakhimova ◽  
E. A. Leonov ◽  
S. P. Khizhinskiy ◽  
T. V. Gaponova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hla Class I ◽  
Class Ii ◽  
Hla Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Next Generation ◽  
Coding Regions ◽  
Hla Genes ◽  
Generation Sequencing

Introduction. The patient survival after allogeneic haematopoietic stem cell transplantation (allo-HSCT) from an unrelated or related haploidentical donor is improved in a donor–recipient match resolution at the level of non-coding region identity of HLA genes. Next-generation sequencing (NGS) allows detection of point substitutions in HLA non-coding regions.Aim — assessment of the NGS-based HLA-typing performance.Materials and methods. An NGS-based HLA-typing of 1,056 DNA samples from allo-HSCT recipients, their related and registry donors was performed with AllTypekit chemistry (OneLambda, USA). A parallel HLA-typing assay of 96 samples by 8 genes (A/B/C/DRB1/DRB3/DRB4/DRB5/DQB1) was accomplished within one working week.Results. HLA class I genes were typed at a 4-field (allelic), and HLA class II genes — 2–4-field (high to allelic) resolution. An allelic-resolution typing of HLA class I genes in a Russian population (657 registry donors) was conducted for the first time. The most frequent HLA alleles have been identified: А*02:01:01:01 in HLA-A (26.9 %), B*07:02:01:01 in HLA-B (12.5 %) and C*07:02:01:03 in HLA-C (12.6 %). The most frequent HLA class II variants were DRB1*07:01:01 (14.1 %), DRB3*02:01:01 (18.0 %), DRB4*01:03:01 (18.9  %), DRB5*01:01:01 (13.5  %), DQB1*03:01P (17.4  %).Conclusion. An NGS-geared HLA-typing has yielded low-ambiguity allelic and high-level resolution results in a parallel sequencing assay with a large number of samples. The method implemented detects genetic polymorphisms also in non-exonic non-coding regions of HLA genes and facilitates typing in candidate HSCT recipients, related and unrelated donors.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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