Author: José Manuel Nunes

[Publication] CWD catalogue form EFI-PG is out

HLA journal (formerly Tissue Antigens) published the first article resulting from the collaborative effort of the EFI population genetics working group: an EFI labs based catalogue of Common and Well Documented alleles.
The study compares this new catalogue with the former ASHI, and identifies a number of alleles that are not commun in Europe and others that altough common in Europe were absent form ASHi’s catalogue.
The link for the paper is http://onlinelibrary.wiley.com/doi/10.1111/tan.12956/full and all comments are appreciated.

[Publication] Mapping the HLA diversity of the Iberian Peninsula

Mapping the HLA diversity of the Iberian Peninsula
Iñigo Romòn, Carmen Montes, Dario Ligeiro, Hélder Trindade, Alicia Sanchez-Mazas, José Manuel Nunes, Stéphane Buhler
Human Immunology 2016, 77 (10): 832-40

… These results outline the genetic landscape of the Iberian Peninsula, and confirm that the analysis of the HLA polymorphism may reveal relevant signatures of past demographic events even when data from donor registries are used. This conclusion stimulates future developments of the Spanish registry, presented here for the first time.

There are some really nice graphs in the paper.

[Publication] Joint divergent asymmetric selection

Immunogenetics. 2016; 68: 401–416.
Published online 2016 May 27. doi: 10.1007/s00251-016-0918-x

HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection

… We thus propose that HLA-A and HLA-B evolved through a model of joint divergent asymmetric selection conferring all populations an equivalent immune potential…

It is on open access: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911380/
Enjoy.

EFI Population Genetics Working Group: Open meeting

Wednesday 11 May 201
Location: AEGLE B HALL

Population genetics at EFI
12:00: Alicia Sanchez-Mazas
Summary of current work, new objectives & challenges
12:10: Derek Middleton
Allelefrequencies.net
12:20: José Manuel Nunes
HLA-net

Ongoing HLA population studies
12:30: Thomas Goeury (Geneva)
From SSO to NGS in HLA population studies: the case of Mandenka
12:42: Iñigo Romón Alonso (Santander)
The HLA genetic landscape of the Iberian Peninsula
12:54: Sebastiaan Heidt (Leiden)
HLA population genetics in organ transplantation: EUROSTAM
13:06: Lisa Creary (Stanford)
HLA population Genetics in disease associations: schizophrenia

Questions & concluding remarks
13:20: Alicia Sanchez-Mazas

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!

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!

EFI SC PopGen WG Core meeting

On Tuesday 28 January 2014, the core of the WG on Population Genetics has met in Geneva. The report will be published in the next EFI Newsletter (June 2014).