SNP-SIG 2013: from coding to non-coding - new approaches for genomic variant interpretation
BMC Genomics volume 15, Article number: S1 (2014)
The last few years have seen an explosion in genomic sequencing and, consistently, exponential growth in the number of known variants . One of the variant repositories, the dbSNP database , currently contains over 62 million human single nucleotide polymorphisms (SNPs) and many other short genomic variants. These variants are interesting as both markers of evolution and for their phenotypic effects (e.g. characteristic traits and diseases). However, due to the high count of variants per-genome, an even larger number of potential variant set interactions, and relatively low levels of experimental annotation, variant interpretation is still severely limited.
In line with the continued strong interest of the computational biology community in genetic variation, the 3rd SNP Special Interest Group (SNP-SIG) meeting [3, 4] was held on July 19 at the ISMB/ECCB 2013 in Berlin (Germany). The meeting aimed to summarize the relevant (computational) research advances in the fields of "Annotation and prediction of structural/functional impacts of coding SNPs" and "SNPs and Personal Genomics: GWAS, populations and phylogenetic analysis". The SNP-SIG is a venue for the development of a research network of scientists, necessary for facilitating the exchange of ideas and establishing new collaborations. The 2013 SNP-SIG attracted over 100 participants, with seven research talks and five presentations from the leading scientists in the field.
The SIG topics covered in this proceedings issue address: the SNP annotation  from functional [6, 7] and structural [8, 9] perspectives, the prediction of pharmocogenomic variants  and new drug targets , the visualization of transcriptome genetic variants , and human population models to predict the rate of private variants .
[The complete program of SNP-SIG meeting 2013 with presentation and poster abstracts is available at http://snpsig.biofold.org/2013/docs/snp-sig-2013-programme.pdf].
The SNP-SIG is undergoing some changes, which will further promote our efforts in genome interpretation. SNP-SIG will change its name to VarI-SIG (Variant Interpretation Special Interest Group) to reach out to scientists investigating all the different types of genetic variants. We are currently working on the organization of VarI-SIG meeting (July 12, 2014) that will be held in the context of the ISMB 2014 (Boston, MA). Further information about the meeting is available on our web site (http://varisig.biofold.org). Additionally, we encourage the interested readers to join our effort to establish the VarI-COSI - Variant Interpretation Community of Special Interest - a hub for variation research-related year-round activity. VarI-COSI will be aimed at sharing relevant information, discussing ideas, and providing networks of training and support. We are in the initial stages of setting up our COSI presence on the web and look forward to input and participation from the variation interpretation community.
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Leggett , MacLean : Reference-free SNP detection dealing with the data deluge. BMC Genomics. 2014
Acuner-Ozbabacan : The Structural Network of Interleukin-10 and Its Implications in Inflammation and Cancer. BMC Genomics. 2014
Stade , et al: GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files. BMC Genomics. 2014
Giollo , et al: NeEMO: A Method Using Residue Interaction Networks to Improve Prediction of Protein Stability upon Mutation. BMC Genomics. 2014
Folkman , et al: Feature-based multiple models improve classification of mutation-induced stability changes. BMC Genomics. 2014
Li , et al: In silico comparative characterization of pharmacogenomic missense variants. BMC Genomics. 2014
Cao , Moult : GWAS and Drug targets. BMC Genomics. 2014
Naqvi , et al: Visualization of nucleotide substitutions in the (micro)transcriptome. BMC Genomics. 2014
Gao , Keinan : High burden of private mutations due to explosive human population growth and purifying selection. BMC Genomics. 2014
We are grateful to Sean Mooney (Buck Institute, Novato, CA) for serving as chair of the roundtable discussion held at the end of the meeting and to Steven Brenner (UC Berkley, CA) for presenting results of the CAGI experiment. We thank Frank Schacherer and BIOBASE International for their financial support. We acknowledge Sarah Headley and the editorial staff of BioMed Central for their help with releasing this issue. We would like to extend special thanks for all help to the ISMB organizational committee and specifically Steven Leard and Jeremy Hennig. We also thank the invited speakers: Paul Flicek (EMBL-EBI, Hinxton, UK), Alon Keinan (Cornell University, Ithaca, NY), Manolis Kellis (MIT, Cambridge, MA) and Ruth Nussinov (NCI, Fredrick, MD).
Finally, we are very grateful for the patience and help of our colleagues around the world who reviewed the submitted manuscripts. The SNP-SIG 2013 special issue would has not be possible without them:
Can Alkan (Bilkent University, Ankara, Turkey), Giovanni Busotti (EMBL-EBI, Hinxton, UK), Lucia Conde (University of Alabama at Birmingham, Birmingham, AL), Xavier de la Cruz (Vall d'Hebron Institute of Research, Barcelona, Spain), Yves Dehouck (Christian-Université Libre de Bruxelles, Bruxelles, Belgium), Hernan Dopazo (Universidad de Buenos Aires, Buenos Aires, Argentina), Juan Rocio Fernandez, (Institute for Research in Biomedicine, Barcelona, Spain), Christian Gilissen (Radboud University, Nijmegen, Netherland), Fereydoun Hormozdiari (University of Washington, Seattle, WA), Liang-Tsung Huang (Mingdao University, Changhua, Taiwan), Pierluigi Martelli (University of Bologna, Bologna, Italy), Majid Masso (George Mason University, Fairfax, VA), Ignacio Medina (MBL-EBI, Hinxton, UK), Giulio Pavesi (University of Milan, Milan, Italy), Alberto Riva (University of Florida, Gainesville, FL), Abel González Pérez (Universitat Pompeu Fabra, Barcelona, Spain), Britt-Sabina Petersen (Christian-Albrechts-University, Kiel, Germany), Hersh Sagreiyai (University of Pittsburgh, Pittsburgh, PA), Jacob Tennessen (Oregon State University, Corvallis, OR).
This article has been published as part of BMC Genomics Volume 15 Supplement 4, 2014: SNP-SIG 2013: Identification and annotation of genetic variants in the context of structure, function, and disease. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/15/S4
The authors declare they have no conflict of interests in relation to this SNP-SIG issue article.
YB and EC wrote the manuscript. Both authors read and approved the manuscript.
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Bromberg, Y., Capriotti, E. SNP-SIG 2013: from coding to non-coding - new approaches for genomic variant interpretation. BMC Genomics 15 (Suppl 4), S1 (2014). https://doi.org/10.1186/1471-2164-15-S4-S1