Author: José Manuel Nunes

Saludos from the 17IHIW

by Monterey Bay, California.

One thing that usually surprises Europeans is how much bigotry and creationism are spread in this paradise of science and technique that the USA are supposed to be.

Looks like astrology or lovetalk but in an opposite mode, that is, we don’t really read and use horoscopes, but we talk as if the subject deserved some credit. I start to believe that it is a general feature of this country’s culture. Here I’ve seen a lot of talk about population genetics but then no use of it.

If a sample does not conform with Hardy-Weinberg expectations then the sample frequencies are at most sample frequencies and certainly not *population* frequencies. If a sample is in Hardy-Weinberg equilibrium then it makes no sense to say that the population is composed of two or three different sub-populations, as, if it was the case, the Wahlund effect would ensure deviation from Hardy-Weinberg expectations: you can’t have simultaneously two exclusive situations.

[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 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:

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
12:20: José Manuel Nunes

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


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.


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
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.


στην υγειά μας