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DisambiGuation of common HLA ambiGuities

15 laboratories of the HLA-NET BM0803 Action participated in this comprehensive study aimed at resolving three of the most common ambiguous group of alleles (HLA-B*44:02:01G, -DRB1*14:01:01G and -DQB1*03:01:01G) encountered during HLA typing. Almost 5100 individuals from 12 European countries were analyzed, providing the most detailed record to date on these ambiguities (relative ratios of alleles, linkage disequilibrium with other HLA loci, …).

Because these ambiguities are due to polymorphisms located outside of the exons coding for the peptide binding region, they may not be recognized by alloreactive T-cells. However, because of strong linkage disequilibrium (LD), mismatches for these ambiguous groups are associated to DRB3-, and C-mismatches. These results are thus very informative for algorithms searching unrelated hematopoietic stem cell donors. Furthermore, the introduction of human leukocyte antigen (HLA)-typing strategies that allow resolving exon 4 (for class I) and exon 3 (for class II) polymorphisms can be expected to contribute significantly to population genetics studies.

Read the article on Tissue Antigens website

Reference
Vidan-Jeras, B., S. Buhler, V. Dubois, Z. Grubic, M. Ivanova, T. Jaatinen, D. Ligeiro, et al. “Resolution of HLA-B*44:02:01G, -DRB1*14:01:01G and -DQB1*03:01:01G Reveals a High Allelic Variability among 12 European Populations.” Tissue Antigens, September 1, 2014. doi:10.1111/tan.12422.

Summertime

The 28th EFI conference seems now faraway, yet for us summertime still not here.

The days are getting already getting shorter and, before they get too short, we finally upload two photos from the session were HLA-net became public.

IMG_5814

The session started right in time, after lunch, and lasted long, but participants were so brave that they resisted to sleep.

open meeting photo

Or so we believe.

With this souvenir we thank to all participants, present or not. If summer is not too bad, a few new gadgets will be on the site by the end of August. Until then; have a nice summer.

HLA Imputation: the verdict is not guilty.

It is my opinion that 28th EFI conference poster P225
EVALUATION OF IMPUTATION METHODS FOR CLASSICAL HLA-DRB1 USING A
FINNISH DATASET
would have deserved selection for oral presentation to give it a broader audience, and pass an important message.

Anyway, this Finnish study shows, by using data obtained independently of the imputation study, that only 25% of alleles are correctly imputed. In other words; imputation is disproved.

Now it is time to enjoy Stockholm.

A Skål to the organisers!

New special issue of Human Heredity /// Genetic Diversity in European Populations: Evolutionary Evidence and Medical Implications

Cover_Human_Heredity_76_3-4_2013

A special issue of Human Heredity entitled “Genetic Diversity in European Populations: Evolutionary Evidence and Medical Implications” has just been published. It has been stimulated by a scientific meeting held in Geneva, Switzerland, in January 2013 as the closing conference of the European COST Action (BM0803, HLA-NET), also supported by the Swiss National Science Foundation.

www.karger.ch/Book/Home/261488

Hard Work in Athens

Although most people would see an oxymoron in the title, we can swear it is not the case. Of course, the weather is terrific, we could not taste all the wonderful “petit plats” people presented to us, the view of the Ακρόπολη Αθηνών is magnificent (though we can’t see it from the meeting room, only from the bar), but the server breakage stressed us a lot and made our nights not so sleepy. But it’s done!

And our first HLA-net server emergency ended up quite well.

Thanks to all in Geneva.

royal-olympic-restaurant

στην υγειά μας

When wrong is right

When developing complex applications, such as HLA-net, it is tempting to make everything alike, to the point were rational thinking is erased with copy-modify. The funny is that, sometimes, the system itself (the program, the web application) reacts and generates bugs. Then you can correct them. Or you can read them, and think twice, and see that the bug is not a bug.

What follows is part of an email exchange among the HLA-net core developpers.

>>> 3. ces valeurs ne sont pas encore remises à zéro après la soumission
>>> -> si vous revenez sur le formulaire, les champs sont toujours complétés
> Peut-être que cette remise à zéro n’est pas nécessaire. Si un utilisateur revient souvent, dans un court temps, sur cette même page, il est possible que la plupart des données soient identiques (identification, éthique. méthodes de typage, type d’étude. ,,,). C’est donc plutôt un avantage.

Hey cool…

“It’s not a bug, it’s a feature” :)

Love it.

So do we!