SNP-SIG 2012: Identification and annotation of SNPs in the context of structure, function, and disease

Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations

Authors: Yana Bromberg and Emidio Capriotti

Collective judgment predicts disease-associated single nucleotide variants

In recent years the number of human genetic variants deposited into the publicly available databases has been increasing exponentially. The latest version of dbSNP, for example, contains ~50 million validated ...

Authors: Emidio Capriotti, Russ B Altman and Yana Bromberg

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of spec...

Authors: Hannah Carter, Christopher Douville, Peter D Stenson, David N Cooper and Rachel Karchin

The SAAP pipeline and database: tools to analyze the impact and predict the pathogenicity of mutations

Understanding and predicting the effects of mutations on protein structure and phenotype is an increasingly important area. Genes for many genetically linked diseases are now routinely sequenced in the clinic....

Authors: Nouf S Al-Numair and Andrew CR Martin

A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations

The body of disease mutations with known phenotypic relevance continues to increase and is expected to do so even faster with the advent of new experimental techniques such as whole-genome sequencing coupled w...

Authors: Thomas A Peterson, DoHwan Park and Maricel G Kann

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation

SNPs&GO is a method for the prediction of deleterious Single Amino acid Polymorphisms (SAPs) using protein functional annotation. In this work, we present the web server implementation of SNPs&GO (WS-SNPs&GO)....

Authors: Emidio Capriotti, Remo Calabrese, Piero Fariselli, Pier Luigi Martelli, Russ B Altman and Rita Casadio

Assessment of computational methods for predicting the effects of missense mutations in human cancers

Recent advances in sequencing technologies have greatly increased the identification of mutations in cancer genomes. However, it remains a significant challenge to identify cancer-driving mutations, since most...

Authors: Florian Gnad, Albion Baucom, Kiran Mukhyala, Gerard Manning and Zemin Zhang

Revealing selection in cancer using the predicted functional impact of cancer mutations. Application to nomination of cancer drivers

Every malignant tumor has a unique spectrum of genomic alterations including numerous protein mutations. There are also hundreds of personal germline variants to be taken into account. The combinatorial divers...

Authors: B Reva

Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia

It is a great challenge of modern biology to determine the functional roles of non-synonymous Single Nucleotide Polymorphisms (nsSNPs) on complex phenotypes. Statistical and machine learning techniques establi...

Authors: Li Xie, Clara Ng, Thahmina Ali, Raoul Valencia, Barbara L Ferreira, Vincent Xue, Maliha Tanweer, Dan Zhou, Gabriel G Haddad, Philip E Bourne and Lei Xie

GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS

It has been hypothesized that multivariate analysis and systematic detection of epistatic interactions between explanatory genotyping variables may help resolve the problem of "missing heritability" currently ...

Authors: Benjamin Goudey, David Rawlinson, Qiao Wang, Fan Shi, Herman Ferra, Richard M Campbell, Linda Stern, Michael T Inouye, Cheng Soon Ong and Adam Kowalczyk

Pathway analysis of genome-wide data improves warfarin dose prediction

Many genome-wide association studies focus on associating single loci with target phenotypes. However, in the setting of rare variation, accumulating sufficient samples to assess these associations can be diff...

Authors: Roxana Daneshjou, Nicholas P Tatonetti, Konrad J Karczewski, Hersh Sagreiya, Stephane Bourgeois, Katarzyna Drozda, James K Burmester, Tatsuhiko Tsunoda, Yusuke Nakamura, Michiaki Kubo, Matthew Tector, Nita A Limdi, Larisa H Cavallari, Minoli Perera, Julie A Johnson, Teri E Klein…