SNPs analysis: tools and applications
28 - 29 November 2003
Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain

Organisers:

Mercedes Robledo, Javier Benítez, Human Genetic Department, Centro Nacional de Investigaciones Oncológicas (CNIO), Spain
Joaquín Dopazo, Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Spain
http://bioinfo.cnio.es/meetings/ESFWorkshopSNPs03/

Report

Scientific Content

This workshop brought experts mainly from the areas of 1- bioinformatics and computer science to discuss advances in SNPs data management and analysis, and 2- evolutionists, biologists and clinical professionals that gave an overview regarding the applicability of SNPs on complex diseases analysis, on forensic genetics or for the study of the evolutionary history of human populations.

The workshop covered three major topics.

Topic 1. High-throughput technologies.
Estimations indicate that the human genome might contain more than 10 million SNPs. Clearly current SNP genotyping technologies are not sufficiently efficient and cost effective to deal with genotyping all these SNPs in even a limited number of individuals. In order to optimise the information gained from a study, the approach has to be adapted, for example by the use of haplotype tag-SNPs in candidate genes omitting the redundant SNPs. The platform and design of the study itself depend on the number of individuals and the number of SNPs. The workshop gave us the opportunity to go through pros and cons of main ultra-high, high or medium-throughput technologies.

Topic 2. Biostatistics, data analysis and bioinformatics
The workshop provided tools and algorithms that can help in the selection of what SNPs to genotype: 1) bioinformatic tools, 2) protein structure (FOLD-X), 3) sequence information (Tango), 4) because of their location: promoters (protein level), or 5) coding SNPs (changing stability, protein-protein interaction, etc...). One of the conclusion of the workshop was the needed of improving and unify the different data bases.

Topic 3. Applications
During the workshop researchers from different backgrounds (interested in evolution, drug resistance, forensic genetics or complex diseases) shared experiences, designs, technical solutions, etc. Different approaches were analyzed and discussed the most common problems that one finds working on this field.

The meeting offered 45 presentations, including 12 given by invited speakers, 18 oral communications, and 15 additional presentations as posters, related to some of the sessions

Final Programme

27th November
20:00 Welcome reception and registration
NH Abascal Hotel. (José Abascal 47, Madrid)

28th November
09:00 Registration at the CNIO

Welcome Address
09:15 Mercedes Robledo. Centro Nacional de Investigaciones Oncológicas, Madrid, Spain

Keynote address
09:30 Anthony J. Brookes. Karolinska Institute, Stockholm, Sweden
SNPs today and (mega-) SNPs tomorrow

Session I: State-of-the-art in high-throughput technologies
Chair: A.J. Brooks

10:00 Jörg D. Hoheisel. DKFZ, Heidelberg, Germany
Direct genotyping genomic DNA

10:30 Ivo Glynne Gut. Centre National de Génotypage, Evry, France
High-throughput SNP genotyping using multiple platforms

Coffee break and poster exhibition (11.00-11-30)

11:30 Matthias Wjst. GSF National Research Center for Environment and Health, Neuherberg/Munich, Germany
Rapid SNP selection with a bioinformatics pipeline and association screening by MALDI-TOF in pooled DNA samples

Oral communications

12:00 Gianluca De Bellis. Consiglio Nazionale delle Ricerche-ITB. Array Technology. Segrate, Italy
Investigation of human polymorphisms by Ligation Detection Reaction and Universal Array

12:15 Paul Bao. Nanosphere Inc. Northbrook, USA
Direct SNP Detection in Human Genomic DNA Based on Nano-Particle Probe Technology

12:30 Diego Tejedor. Universidad de Zaragoza. Zaragoza, Spain
DNA microarray for the detection of more than one hundred mutations causing Familial Hypercholesterolemia

12:45 Mark van Haaren. Keygene N.V. Bio Informatics. Wageningen, The Netherlands
Flexible multiplex SNP genotyping in Arabidopsis using SNPWaveTM

Lunch (13:00-14:30)

Session II: Biostatistics, data analysis and bioinformatics
Chair: J. Dopazo

14:30 Joost Schymkowitz. SWITCH Laboratory, Flemish Interuniversity Institute for Biotechnology, Brussels, Belgium
Predicting the effect of point mutations using FOLD-X

15:00 Xavier de la Cruz. IRBB-PCB Parc Cientific de Barcelona, Spain
Prediction of pathological mutations from sequence

Oral Communications

15:30 Holger Kirsten. University Leipzig. IKIT/BBZ/Ahnert. Leipzig, Germany
SNP selection and Assay Design for a candidate gene genotype-phenotype association study in Rheumatoid Arthritis

15:45 Francisco Barros. Universidad de Santiago. Santiago de Compostela, Spain
OligoTags, a software for automated design in SBE-Tags projects

16:00 Joaquín Dopazo. Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
In silico search of SNPs with potential phenotypic effect

Coffee break and poster exhibition (16:15-16:45)

16:45 Zandra Clark. Transgenomic Ltd, Cheshire, UK
Comprehensive gene scanning by DHPLC: efficient, highly sensitive mutation and SNP discovery and screening

17:05 Trevor Woodage. Applied Biosystems. Rockville, MD, USA
High Throughput Genotyping Strategies Using Validated SNP Data

17.25 Armin Winands. Illumina, Inc. San Diego, USA
Production-Scale Genetic Analysis Using BeadArrayTM Technology

Official Dinner (21:00)
Restaurant Zerain (Quevedo 3, Madrid)

29th November
Session III: Applications
Chair: J. Benítez

09:30 Anne-Christine Syvanen. Uppsala University, Sweden
Large-scale SNP genotyping using microarrays: quantitative applications

10:00 Bruce Ponder. University of Cambridge, UK
SNP typing to detect cancer susceptibility genes

10:30 Ángel Carracedo. University of Santiago de Compostela, Spain
SNP typing in Forensic Genetics

Coffee break and poster exhibition (11.00-11:30)

Oral communications

11:30 Tanja Pessi. Tampere University. Tampere, Finland
A common IL-1 complex haplotype associates with an increased risk of atopy

11:45 Isabel Ferreirós. Hospital Clínico Universitario de Santiago. Santiago de Compostela, Spain
Association of PDCD1 with susceptibility to systemic lupus erythematosus (SLE): evidence for population-specific effects

12:00 Pelayo González. Hospital Central de Asturias. Oviedo, Spain
Functional polymorphism in the promoter region of p27/kip1 is associated to early myocardial infarction

12:15 Arancha Cebrián. Cambridge University. Cambridge, UK
A member of the Sialyltransferase family is a new susceptibility gene for sporadic medullary thyroid carcinoma

12:30 Gloria Ribas. Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
Regulatory haplotypes in the DNA repair genes and their contribution to breast cancer

Lunch (13.00-14:30)

Session IV: Population approaches and Evolution
Chair: A. Carracedo

14:30 Krista Kruuv. Estonian Genome Project Foundation, Tartu, Estonia
Estonian Genome Project

15:00 Jesús Sáinz. deCODE Genetics, Reykjavik, Iceland
Genetic Analysis of the Icelandic Population

15:30 Jaume Bertranpetit. Universitat Pompeu Fabra, Barcelona, Spain
Is there a single haplotype map of the human genome? The population stratification of SNP variation

Coffee break and poster exhibition (16.00-16:30)

Oral communications

16:30 Michelle Gardner. University Pompeu Fabra, Barcelona, Spain
Analysis of Linkage Disequilibrium across the NRG1 gene in a worldwide population set

16:45 David Comas. Universitat Pompeu Fabra. Unitat de Biologia Evolutiva. Barcelona, Spain
Worldwide haplotype diversity and linkage disequilibrium at CTLA4 gene

17:00 Nicole Maca. Hospital Universitario Ntra. Sra. Candelaria. Santa Cruz de Tenerife, Spain
Ancient mtDNA analysis and the origin of the Guanches

Conclusions and departure (17:15)

Posters List related to sessions
(in alphabetical order of presenting author)

Session I

Estimation of SNP allele frequencies in pooled population samples by primer extension method
Ville Pimenoff. Laboratory of Forensic Biology. Helsinki, Finland

Parallel SNP study with immobilised PCR products on glassy surfaces
Susanne Schwonbeck. Fraunhofer Institut for Biomedical Engineering. AMBT. Bergholz-Rehbruecke, Germany

Session II

HMMH: Hidden Markov Modelling of Haplotype Structures: Report of an Ongoing Research
Fernando Martín-Sánchez. Instituto de Salud Carlos III, Madrid, Spain

Session III

Single Nucleotide Polymorphism at -308 site in TNF- α Gene Promoter in End Stage Renal Disease Patients from North India
Harish Changotra. Guru Nank Dev University. Amritsar, India

DHPLC analysis of the PKHD1 gene in patients with autosomal recessive polycystic kidney disease: identification of mutations and DNA polymorphisms.
Eliecer Coto García. Hospital Central de Asturias. Oviedo, Spain

CAPN10 haplotypes and Polycystic Ovary Syndrome
José J. Galán. Neocodex, SL. Structural Genomics. Sevilla, Spain

Infection, Immunity and Atopy; The First Complete Genetic Results From The ALSPAC Cohort
Renata M.J. Hamvas. Institute of Child Health, University College, London, UK

SNPs genotyping by real time PCR for diagnosis of gene duplications in the Charcot-Marie-Tooth type 1A disease
Clara Ruiz-Ponte. Universidad de Santiago de Compostela. Santiago de Compostela, Spain

Session IV

The origin of Mayans according to HLA genes and the uniqueness of Amerindians
A. Arnaiz-Villena. Universidad Complutense, Madrid, Spain

Y-chromosome SNP typing: application in the Balkan region
Elena Bosch. Universitat Pompeu Fabra. Barcelona, Spain

A Predominant European Ancestry of Paternal Lineages from Canary Islanders
Carlos Flores. Hospital Universitario Ntra. Sra Candelaria. Santa Cruz de Tenerife, Spain

Geographic stratification of linkage disequilibrium: a worldwide population study in a region of chromosome 22
Anna González. Universitat Pompeu Fabra. Barcelona, Spain

Geographic structure of variation at SNPs conferring risk for Coronary Heart Disease
Oscar Lao. Universitat Pompeu Fabra, Barcelona, Spain

SNP detection in the human mitochondrial genome
Stéphanie Plaza. Universitat Pompeu Fabra. Barcelona, Spain

Prion Susceptibility and Protective Alleles Exhibit Marked Geographic Differences
Marta Soldevilla. Universitat Pompeu Fabra. Barcelona, Spain

Assessment of the results and contributions

This workshop has provided an excellent vision of the field. One important factor for the exchange of information during this event was the active discussion during all sessions of the workshop. It was especially enriching the multidisciplinary character of the audience that promoted the exchange of experiences between researchers with different backgrounds.

One of the main conclusions was that as a result of the big genotyping projects, we are going back to the origin, the careful SNPs selection to work with. This fact has to be accompanied by the implementation of bioinformatic tools based on different characteristics of the SNP itself (protein structure, sequence information, functional character, etc) and the needed of improving and unify the different data bases.

As current estimations indicate that the human genome might contain more than 10 million SNPs, the available SNP genotyping technologies are not sufficiently efficient and cost effective to deal with genotyping all these SNPs in even a limited number of individuals. In order to optimise the information gained from a study, the approach has to be adapted, for example by the use of haplotype tag-SNPs in candidate genes omitting the redundant SNPs. The platform and design of the study depend on the number of individuals and the number of SNPs. The workshop gave us the opportunity to go through pros and cons of main high or medium-throughput technologies, based on TaqMan or Amplifluor chemistry, MALDI mass spectrometric detection, arrays, etc. It seems that there is not a single method for everything, and probably the most potent tools are yet to come for each type of projects.

There are several applications in which SNPs analysis is being crucial to understanding the mechanisms related to complex diseases or drug resistance. Some of the most common problems the researchers find working on this field were exposed during the workshop. In particular, regarding to polygenic disorders, it is not known how much of the effect results from common genetic variants which are ancient in the population (the 'common variant: common disease hypothesis'), and how much is the result of less common, more recent, and possibly stronger genetic variation. This distinction is of critical importance for strategies to find the susceptibility genes. In principle, ancient common variants can be found through comparisons of the frequency of variants in large series of disease cases and controls (association studies), whereas this approach will be much less efficient to detect multiple rare variants. One of the most important problems one finds working on complex diseases is the statistical power and the design of the approach for searching candidates genes or low penetrance genes associated to these polygenic disorders.

Preliminary conclusions of the HapMap project were discussed during the workshop, as some of the participants were involved. Recent data of haplotype diversity in a number of genomic segments in the human genome have suggested that the genome is distributed in haplotype "blocks" over which there is little evidence of recombination events. The determination of these blocks would facilitate future screenings of genome diversity, mainly in order to understand the genetic basis of complex diseases and ascertain individual susceptibility and drug use. The aim of HapMap project is to define the haplotypes for a large number of SNPs in three different populations. This information will allow decreasing the number of SNPs needed to capture the genetic differences among individual in these populations. Nonetheless, little is known about the amount of geographic or ethnic stratification of the haplotype map of the human genome. So far, it seems that there are more blocks than initially was thought, so it is necessary to include many diverse populations to interrogate for LD.

This workshop has been a first step to generate a European network on SNPs, and to consolidate existing national collaborations. In fact, one of the conclusions was the possibility of organizing a future "EuroSNPs workshop" to get a feedback and reviewing of the advances in this field.

List of participants

Arnaiz-Villena, Antonio Universidad Complutense
aav@efd.net Madrid, Spain

Baiget, Montse Hospital San Pau
mbaiget@hsp.santpau.es Barcelona Spain

Bao, Paul Nanosphere Inc.
pbao@nanosphere-inc.com Northbrook, USA

Barros, Francisco Universidad de Santiago de Compostela
apimlbar@usc.es Santiago de Compostela, Spain

Benítez, Javier CNIO
jbenitez@cnio.es Madrid, Spain

Bertranpetit, Jaume Universitat Pompeu Fabra
jaume.bertranpetit@cexs.upf.es Barcelona, Spain

Blaschke, Christian CNB/CSIC
blaschke@cnb.uam.es Madrid, Spain

Bosch, Elena Universitat Pompeu Fabra
elena.bosch@upf.edu Barcelona Spain

Brookes, Anthony J. Karolinska Institute
Anthony.Brookes@cgb.ki.se Stockholm, Sweden

Caballero, Rosalia Universidad de Salamanca
rosaliacvh@hotmail.com Salamanca, Spain

Carmona-Sáez, Pedro CNB-CSIC
pcarmona@cnb.uam.es Madrid, Spain

Carracedo, Angel Universidad de Santiago de Compostela
apimlang@usc.es Santiago de Compostela, Spain

Carretero, Marivi Applied Biosystems
marivi.carretero@eur.appliedbiosystems.com Madrid, Spain

Cebrian, Arancha University of Cambridge
arancha@srl.cam.ac.uk Cambridge, UK

Changotra, Harish Guru Nank Dev University
hchangotra@yahoo.com Amritsar, India

Clark, Zandra Transgenomic Ltd
zclark@transgenomic.co.uk Cheshire, United Kingdom

Comas, David Universitat Pompeu Fabra
david.comas@upf.edu Barcelona, Spain

Coto García, Eliecer Hospital Central Asturias
ecoto@hcas.sespa.es Oviedo, Spain

Cristina, Xavier Applied Biosystems
xavier.cristina@eur.appliedbiosystems.com Madrid, Spain

De Bellis, Gianluca CNR- ITB
gianluca.debellis@itb.cnr.it Segrate, Italy

de la Cruz, Xavier IRBB-PCB Parc Cientific
xavier@mmb.pcb.ub.es Barcelona, Spain

Díez, Orland Hospital San Pau
ODiez@hsp.santpau.es Barcelona, Spain

Dopazo, Joaquín CNIO
jdopazo@cnio.es Madrid, Spain

Ferreirós, Isabel Hospital Clinico Universitario
de Santiago
isafv@hotmail.com Santiago de Compostela, Spain

Gardner, Michelle Universitat Pompeu Fabra
michelle.gardner@upf.edu Barcelona, Spain

Gonzalez, Anna Universitat Pompeu Fabra
anna.gonzalez@upf.edu Barcelona, Spain

González, Rogelio Universidad de Salamanca
gonzalez@usal.es Salamanca, Spain

González, Pelayo Hospital Central de Asturias
layopelayo@mixmail.com Oviedo, Spain

Gut, Ivo Centre National de Génotypage
ivo.gut@cng.fr Evry, France

Hamvas, Renata Institute of Child Health
University College
r.hamvas@ich.ucl.ac.uk London, UK

Hoheisel, Jörg DKFZ
j.hoheisel@dkfz-heidelberg.de Heidelberg, Germany

Kirsten, Holger University Leipzig
hkirsten@medizin.uni-leipzig.de Leipzig, Germany

Kruuv, Krista Estonian Genome Project Foundation
Krista.Kruuv@geenivaramu.ee Tartu, Estonia

Lao, Oscar Universitat Pompeu Fabra
oscar.lao@upf.edu Barcelona, Spain

Lesueur, Fabienne University of Cambridge
fabienne@srl.cam.ac.uk Cambridge, UK

Maca, Nicole Hospital Universitario N.S. Candelaria
nmacame@ull.es Santa Cruz de Tenerife, Spain

Martín-Sánchez, Fernando Institute of Health "Carlos III"
fmartin@isciii.es Madrid, Spain

Monnier, Stéphanie International Agency for Research
on Cancer (IARC /CIRC)
monnier@iarc.fr Lyon, France

Montero, Cristina CNIO
cmontero@cnio.es Madrid, Spain

Osorio, Ana CNIO
aosorio@cnio.es Madrid, Spain

Padh, Harish B. V. Patel PERD Centre
hpadh@yahoo.com Ahmedabad, India

Perez-Tur, Jordi Institut de Biomedicina de València
CSIC
jpereztur@ibv.csic.es València, Spain

Pessi, Tanja Tampere University
tanja.pessi@uta.fi Tampere, Finland

Pimenoff, Ville University of Helsinki
ville.pimenoff@helsinki.fi Helsinki, Finland

Plaza,Stéphanie Universitat Pompeu Fabra
stephanie.plaza@upf.edu Barcelona, Spain

Pollan, Marina Institute of Health "Carlos III"
mpollan@isciii.es Madrid, Spain

Ponder, Bruce University of Cambridge
bajp@mole.bio.cam.ac.uk Cambridge, UK

Ribas, Gloria CNIO
gribas@cnio.es Madrid, Spain

Robledo, Mercedes CNIO
mrobledo@cnio.es Madrid, Spain

Rodriguez, Raquel CNIO
rrodriguez@cnio.es Madrid, Spain

Ruiz, Sergio CNIO
sruiz@cnio.es Madrid, Spain

Ruiz-Ponte, Clara Universidad de Santiago de Compostela
crponte@usc.es Santiago de Compostela, Spain

Sáinz, Jesús deCODE Genetics
sainz@decode.is Reykjavik, Iceland

Schwonbeck, Susanne Fraunhofer Institut for Biomedical
Engineering
susanne.schwonbeck@ibmt.fhg.de Bergholz-Rehbruecke, Germany

Schymkowitz, Joost Switch Laboratory, Flemish Interuniversity
Institute for Biotechnology
jschymko@vub.ac.be Brussels, Belgium

Sezerman, Osman Ugur Sabancini University
ugur@sabanciuniv.edu Istanbul, Turkey

Skipper, Magdalena Nature Reviews Genetics
m.skipper@nature.com London, UK

Soldevila, Marta Universitat Pompeu Fabra
marta.soldevila@cexs.upf.es Barcelona, Spain

Syvanen, Anne-Christine Uppsala University
Ann-Christine.Syvanen@medsci.uu.se Uppsala, Sweden

Tejedor, Diego Universidad de Zaragoza
419413@docto.unizar.es Zaragoza, Spain

van Haaren, Mark Keygene N.V.
mark.van-haaren@keygene.com Wageningen, The Netherlands

Winands, Armin Illumina, Inc.
awinands@illumina.com San Diego, USA

Wjst, Matthias GSF National Research Center for
Environment and Health
m@wjst.de; wjst@gsf.de Neuherberg, Germany

Woodage, Trevor Applied Biosystems
woodagtj@appliedbiosystems.com Rockville MD, USA