Rapid High-Resolution Typing of Class I HLA Genes by Nanopore Sequencing

Author(s):  
Chang Liu ◽  
Rick Berry
2020 ◽  
Author(s):  
Valery Cheranev ◽  
Irina Bulusheva ◽  
Valery Vechorko ◽  
Dmitriy Korostin ◽  
Denis Rebrikov

AbstractHLA genes play a pivotal role in an immune response via the presentation of pathogen peptides in a complex on the surface of cells of a host organism. Here, we studied the association of class I and class II genes with the severity of COVID-19 infection and HLA allele variants.We performed high-resolution sequencing of class I and class II HLA genes using the sample population of 147 patients who died of COVID-19 and statistically compared our results with the frequencies of the HLA genotypes in a control population of 270 samples.The obtained data demonstrated that 51:05 and 15:18 alleles from locus B* are statistically significantly associated with COVID-19 severity, while C*14:02 allele correlates with the probability of death from COVID-19 for patients without comorbidities.


Author(s):  
Karlijn Doorenspleet ◽  
Lara Jansen ◽  
Saskia Oosterbroek ◽  
Oscar Bos ◽  
Pauline Kamermans ◽  
...  

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA based techniques and especially environmental DNA (eDNA) metabarcoding from seawater is becoming a powerful monitoring tool. However, current approaches are based on genetic target regions of <500 nucleotides, which offer limited taxonomic resolution. This study aims to develop and validate a long read nanopore sequencing method for eDNA that enables improved identification of fish species. We designed a universal primer pair targeting a 2kb region covering the 12S and 16S rRNA genes of fish mitochondria. eDNA was amplified and sequenced using the Oxford Nanopore MiniON. Sequence data was processed using the new pipeline Decona, and accurate consensus identities of above 99.9% were retrieved. The primer set efficiency was tested with eDNA from a 3.000.000 L zoo aquarium with 31 species of bony fish and elasmobranchs. Over 55% of the species present were identified on species level and over 75% on genus level. Next, our long read eDNA metabarcoding approach was applied to North Sea eDNA field samples collected at ship wreck sites, the Gemini Offshore Wind Farm, the Borkum Reef Grounds and a bare sand bottom. Here, location specific fish and vertebrate communities were obtained. Incomplete reference databases still form a major bottleneck in further developing high resolution long read metabarcoding. Yet, the method has great potential for rapid and accurate fish species monitoring in marine field studies.


2018 ◽  
Vol 19 (2) ◽  
pp. 136-146 ◽  
Author(s):  
Takahiro Mimori ◽  
Jun Yasuda ◽  
Yoko Kuroki ◽  
Tomoko F. Shibata ◽  
Fumiki Katsuoka ◽  
...  

2004 ◽  
Vol 65 (9-10) ◽  
pp. S96
Author(s):  
David Sidebottom ◽  
Jack Lai ◽  
Liang Peng ◽  
Joanne Kurtzberg ◽  
Lee Ann Baxter-Lowe

2010 ◽  
Vol 62 (11-12) ◽  
pp. 773-780 ◽  
Author(s):  
Melisa L. Budde ◽  
Roger W. Wiseman ◽  
Julie A. Karl ◽  
Bozena Hanczaruk ◽  
Birgitte B. Simen ◽  
...  

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 973-973 ◽  
Author(s):  
Gesine Koegler ◽  
Juergen Enczmann ◽  
Vanderson Rocha ◽  
Eliane Gluckman ◽  
Peter Wernet

Abstract The CB Bank Düsseldorf has provided to date (July 2004) 224 CB units (216 unrelated and 8 related, 29% adults, 71% children) to transplant centers worldwide. Until now no correlation could be detected between the number of HLA-mismatches based on low resolution (LR) typing for HLA-A and-B and high resolution typing (HR) for DRB1 and the incidence of aGvHD as published previously by us and other groups. The lack of correlation between aGvHD occurrence and donor/recipient HLA diversity in patients given an unrelated CBT could be explained by the fact that some mismatches for HLA class I antigens (A, B and C) are not detected by LR typing. In order to determine the impact of HLA high resolution typing with outcomes, mainly aGvHD after UCBT we analysed DNA samples of 115 CB recipients (86 children; 29 adults; 66 male, 49 female; diagnosis ALL=43, AML=19, SecAL =1, MDS=5, CML=10, NHL=5, Hodgkin=1, AA=7, genetic and metabolic diseases= 24) and their unrelated CB grafts were HLA-typed for HLA-class I (A, B, C) and HLA-class II (DRB1 and DQB1) by sequencing. The transplant centers used their own protocols for GvHD prophylaxis, the most commonly used was the combination of CsA and steroids alone (60%), CsA alone (15%), or the combination with MTX (6%). 55 of 115 patients did not develop aGvHD (grade 0= 48%), 26 patients developed grade I (23%), 12 patients developed grade II (10%), 10 patients grade III (9%) and 12 patients grade IV (10%). When mismatches (MM) were analysed for HLA-A, B based on LR-typing and -DRB1 based on HR-typing in concordance with all published data so far, the following mismatch situation resulted: No MM (16 pairs, 13.9%), one MM (47 pairs, 40.9%), two MM (41 pairs, 35.7%), three MM (5 pairs, 4.3%), four MM (3 pairs, 2.6%). If the MM for A and B alleles detected by HR-typing were included, the situation was as follows: 0 MM (6 pairs, 5.2%), 1 MM (35 pairs, 30.4%), 2 MM (54 pairs, 47%), 3MM (14 pairs, 12.2%), 4 MM (5 pairs, 4.3%), 5 MM (1 pair, 0.9%). If analysing A, B, C, DR and DQ based on HR typing a high additional frequency of MM occurred: No MM (4 pairs, 3.5%), 1 MM (13 pairs, 11.3%), 2 MM (19 pairs, 16.5%), 3 MM (24 pairs, 20.9%), 4 MM (30 pairs, 26.1%), 5 MM (14 pairs, 12.2%), 6 MM (6 pairs, 5.2 %), 6 MM (6 pairs, 5.2%), 7 MM (3 pairs, 2.6%), 8 MM (2 pairs, 1.7%). There was no significant correlation between the number of MM (also analysed in GvHD or rejection direction) using high-resolution level for HLA-A, B and DRB1 as well as for HLA-A, B, C, DRB1 and DQB1 and the development of aGvHD grade III-IV. More interestingly, we have not found any significant correlation between numbers of MM with 2-year survival probability. Although the heterogeneity and number of patients analysed, it shows that the degree of mismatching is even higher than expected, also in comparison to unrelated BMT. It also shows that additional subtyping for HLA-A, B, C and DQ, not performed on a routine basis at present, does not improve the 2-year survival rate.


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