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Human Single Nucleotide Polymorphisms & Disease
Gordon Research Conference

Understanding the Mechanisms of Variant Effects in the Era of Genome Sequencing
Note: This conference is currently known as "Human Genetic Variation & Disease".

Dates

June 12-17, 2016

Location

Mount Holyoke College
South Hadley, MA

Organizers

Chairs:
Anna R. Panchenko & Sean D. Mooney

Vice Chairs:
Rita Casadio & Rachel Karchin

Meeting Description

Reductions in the costs of DNA sequencing have enabled inexpensive whole human genome and exome sequencing, thereby opening the era of precision medicine. However, these new advances in genome sequencing are necessary but not sufficient for understanding the origins of allelic variation in human genes and mechanisms of human genetic diseases and phenotypes. Although the majority of variants are likely to be neutral, a substantial fraction of them may explain the origins of Mendelian inherited disorders, inherited complex traits and diseases, as well as diseases caused by somatic mutations. However, finding functionally important variants and separating them from neutral polymorphisms remains a significant challenge.

Many computational and experimental methods have been developed to estimate the phenotypic effects of variants and this Gordon Conference will discuss new developments and approaches in this field. In parallel, significant efforts are being invested to catalog naturally occurring genetic differences, those found in the general population and those known to be disease-associated. The rapid growth of these databases and the current status of collection and categorization of genomic variation data will be another important topic of the conference. Database developers and researchers will have the opportunity to get together and bridge their research.

Another aspect of the conference will be addressed by the researchers working in the field of biological networks and pathways. Indeed, a defect in a single gene may sometimes be pathological, while in other cases a series of mutations in different genes are responsible for a disease. Can our understanding of biomolecular interaction networks contribute to predictions of the effects of disease mutations on cellular function? The conference participants will be able to share ideas about the interplay between molecular characteristics of individual network elements, effects of variants and networks’ topological properties.

In summary, the goal of this conference is to bring together researchers that work on diverse experimental and computational aspects related to inferring and analyzing the effects of human mutations on cellular function and their role in causing different diseases. It will help to advance the field by merging genomics and proteomics approaches, and by bringing together scientists who work on the same problems from different perspectives. We especially aim to provide a stimulating environment where students, postdocs and junior investigators can present and discuss their research with the best minds in the field. We believe the meeting will have significant impact on the research and development in the fields of human genetics, bioinformatics, translational and precision medicine.

Contributors

Final Meeting Program

Sunday
2:00 pm - 9:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pmKeynote Session: Characterizing the Common Patterns of Genetic Variation
Discussion Leader: Natarajan Kannan (University of Georgia, USA)
7:40 pm - 7:50 pmOpening Remarks
7:50 pm - 8:00 pmIntroduction by Discussion Leader
8:00 pm - 8:35 pmRuth Nussinov (National Cancer Institute, NIH, USA)
"Oncogenic K-Ras: The Undruggable Protein"
8:35 pm - 8:45 pmDiscussion
8:45 pm - 9:20 pmChris Sander (Dana-Farber Cancer Institute, USA)
"Functional Fitness of Proteins Quantified Using Maximum Entropy Probability Models of Natural Sequence Variation"
9:20 pm - 9:30 pmDiscussion
Monday
7:30 am - 8:30 amBreakfast
8:30 amGroup Photo
9:00 am - 12:30 pmAssessing the Effects of Variations on Protein Biophysical Characteristics
Discussion Leader: Nir Ben-Tal (Tel Aviv University, Israel)
9:00 am - 9:10 amIntroduction by Discussion Leader
9:10 am - 9:40 amOlivier Lichtarge (Baylor College of Medicine, USA)
"Evolutionary Action Measures the Clinical Effect of Mutations on Fitness"
9:40 am - 9:50 amDiscussion
9:50 am - 10:20 amMarianne Rooman (Université Libre de Bruxelles, Belgium)
"Knowledge-Driven Prediction of Protein Stability for Assessing the Pathogenic Effect of Exomic Variants"
10:20 am - 10:30 amDiscussion
10:30 am - 10:50 amCoffee Break
10:50 am - 11:20 amDaniel Bolon (University of Massachusetts Medical School, USA)
"Utilizing EMPIRIC Mutational Scans to Investigate the Distinction Between Health and Disease"
11:20 am - 11:30 amDiscussion
11:30 am - 12:00 pmEmil Alexov (Clemson University, USA)
"Rescuing Disease-Causing Effects with Targeted Small Molecule Binding"
12:00 pm - 12:10 pmDiscussion
12:10 pm - 12:25 pmSelected from Poster Abstracts: Ogun Adebali (University of Tennessee, USA)
"Establishing the Precise Evolutionary History of a Gene Improves Predicting Disease-Causing Missense Mutations"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
3:00 pm - 4:00 pmPower Hour
The GRC Power Hour is an optional informal gathering open to all meeting participants. It is designed to help address the challenges women face in science and support the professional growth of women in our communities by providing an open forum for discussion and mentoring.
Organizers: Yana Bromberg (Rutgers University, USA) and Lilia Iakoucheva (University of California, San Diego, USA)
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmMutations, Protein Interaction Networks and Pathways
Discussion Leader: Ozlem Keskin (Koc University, Turkey)
7:30 pm - 7:40 pmIntroduction by Discussion Leader
7:40 pm - 8:10 pmNir Ben-Tal (Tel Aviv University, Israel)
"Navigating in Protein Space"
8:10 pm - 8:20 pmDiscussion
8:20 pm - 8:50 pmBruce Aronow (Cincinnati Children's Research Institute, USA)
"Multidimensional Network Analysis of Loss of Function and Non-Synonymous Variants"
8:50 pm - 9:00 pmDiscussion
9:00 pm - 9:15 pmSelected from Poster Abstracts: Viviane Labrie (Van Andel Research Institute, USA)
"Lactase Nonpersistence Is Directed by DNA-Variation-Dependent Epigenetic Aging"
9:15 pm - 9:20 pmDiscussion
9:20 pm - 9:30 pmGeneral Discussion
Tuesday
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmCharacterizing Variants in Cancer
Discussion Leader: Cristina Marino-Buslje (Leloir Institute, Argentina)
9:00 am - 9:10 amIntroduction by Discussion Leader
9:10 am - 9:40 amYue Xiong (University of North Carolina at Chapel Hill, USA)
"IDH Mutation, Mechanism and Therapeutics in Human Cancers"
9:40 am - 9:50 amDiscussion
9:50 am - 10:20 amLudmil Alexandrov (Los Alamos National Laboratory, USA)
"Signatures of Mutational Processes in Human Cancer"
10:20 am - 10:30 amDiscussion
10:30 am - 10:50 amCoffee Break
10:50 am - 11:20 amJinfeng Liu (Genentech, USA)
"Mining Somatic Mutations and Transcriptomic Alterations for Cancer Target Discovery"
11:20 am - 11:30 amDiscussion
11:30 am - 12:00 pmMaricel Kann (University of Maryland, Baltimore County, USA)
"Protein Domain Landscape of Cancer Genomes"
12:00 pm - 12:10 pmDiscussion
12:10 pm - 12:25 pmSelected from Poster Abstracts: Eva Berglund (Uppsala University, Sweden)
"The Mutational Spectrum in Acute Lymphoblastic Leukemia Uncovered by Deep Targeted Sequencing"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmComputational Prediction of Phenotypic Effects of Disease Mutations
Discussion Leader: Predrag Radivojac (Indiana University, USA)
7:30 pm - 7:40 pmIntroduction by Discussion Leader
7:40 pm - 8:10 pmMauno Vihinen (Lund University, Sweden)
"Towards Clinical Variation Interpretation - High-Performance Predictors"
8:10 pm - 8:20 pmDiscussion
8:20 pm - 8:50 pmYana Bromberg (Rutgers University, USA)
"Interpreting Genomic Variation to Inform Pathogenesis Pathways"
8:50 pm - 9:00 pmDiscussion
9:00 pm - 9:15 pmSelected from Poster Abstracts: Aimee Deaton (Amgen Inc, USA)
"Rationalizing Off-Target Screening in Drug Development Using Human Genetics"
9:15 pm - 9:20 pmDiscussion
9:20 pm - 9:30 pmGeneral Discussion
Wednesday
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmSNVs and Copy Number Variations in Complex Diseases
Discussion Leader: Bonnie Berger (Massachusetts Institute of Technology, USA)
9:00 am - 9:10 amIntroduction by Discussion Leader
9:10 am - 9:40 amIgor Rogozin (National Center for Biotechnology Information, National Library of Medicine, NIH, USA)
"Aberrant Translation as a Putative Causative Factor for Autism: Support from Medical Data Mining"
9:40 am - 9:50 amDiscussion
9:50 am - 10:20 amLilia Iakoucheva (University of California, San Diego, USA)
"Interpreting Genetic Variation in Psychiatric Diseases"
10:20 am - 10:30 amDiscussion
10:30 am - 10:50 amCoffee Break
10:50 am - 11:20 amJoseph Gecz (The University of Adelaide, Australia)
"Deciphering DNA Variation in PCDH19, an X-Chromosome Protocadherin Causing Female Limited Epilepsy, Intellectual Disability and Autism"
11:20 am - 11:30 amDiscussion
11:30 am - 12:00 pmGerhard Coetzee (Van Andel Research Institute, USA)
"Post-GWAS Functionality of Parkinson's Disease"
12:00 pm - 12:10 pmDiscussion
12:10 pm - 12:25 pmSelected from Poster Abstracts: Nobuko Katagiri (U.S. Food and Drug Administration, USA)
"The Importance of mRNA Structure in Determining the Pathogenicity of Synonymous and Non-Synonymous Mutations in X-Linked Genes"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
Nominations for the Next Vice Chair; Fill in Conference Evaluation Forms; Discuss Future Site and Scheduling Preferences; Election of the Next Vice Chair
7:30 pm - 9:30 pmVariants Causing Rare Diseases
Discussion Leader: Joel Bader (Johns Hopkins University, USA)
7:30 pm - 7:40 pmIntroduction by Discussion Leader
7:40 pm - 8:10 pmMichael Brudno (University of Toronto, Canada)
"Not the Same Old Broken Record: What a Genomics EHR Should Look Like"
8:10 pm - 8:20 pmDiscussion
8:20 pm - 8:50 pmSteven Brenner (University of California, Berkeley, USA)
"Diagnostic Role of Exome Sequencing in Immune Deficiency Disorders"
8:50 pm - 9:00 pmDiscussion
9:00 pm - 9:15 pmSelected from Poster Abstracts: Nishanth Nair (University of Maryland, USA)
"Driver Genes in Idiopathic Dilated Cardiomyopathy"
9:15 pm - 9:20 pmDiscussion
9:20 pm - 9:30 pmGeneral Discussion
Thursday
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmPrecision Medicine in Practice
Discussion Leader: Dmitry Korkin (Worcester Polytechnic Institute, USA)
9:00 am - 9:10 amIntroduction by Discussion Leader
9:10 am - 9:40 amNicholas Tatonetti (Columbia University, USA)
"Identifying Genomics Opportunities Using the EHR"
9:40 am - 9:50 amDiscussion
9:50 am - 10:20 amDana Crawford (Case Western Reserve University, USA)
"All In! Precision Medicine in Cleveland"
10:20 am - 10:30 amDiscussion
10:30 am - 10:50 amCoffee Break
10:50 am - 11:20 amMark Boguski (Precision Medicine Network, USA)
"Precision Diagnosis for Precision Medicine: Case Studies in Knowledge Visualization and Decision Support"
11:20 am - 11:30 amDiscussion
11:30 am - 12:00 pmRobert Hughes (Buck Institute for Research on Aging, USA)
"Natural Genetic Variation in Yeast Reveals Conserved Modifiers of PolyQ Aggregation"
12:00 pm - 12:10 pmDiscussion
12:10 pm - 12:25 pmSelected from Poster Abstracts: Carola Droge (Heinrich Heine University Düsseldorf, Germany)
"Sequencing of FIC1, BSEP, and MDR3 Revealed 139 Genetic Variants Including 63 New Ones in 389 Unrelated Patients with Suspected Intrahepatic Cholestasis"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmVariants and Pharmacogenomics
Discussion Leader: S. Banu Ozkan (Arizona State University, USA)
7:30 pm - 7:40 pmIntroduction by Discussion Leader
7:40 pm - 8:10 pmBissan Al-Lazikani (Institute of Cancer Research, United Kingdom)
"Integrative Chemogenomics for Drug Target Selection and Personalised Treatment"
8:10 pm - 8:20 pmDiscussion
8:20 pm - 8:50 pmDeanna Kroetz (University of California, San Francisco, USA)
"Genetic Predictors of Chemotherapy-Induced Toxicity"
8:50 pm - 9:00 pmDiscussion
9:00 pm - 9:15 pmSelected from Poster Abstracts: Lei Li (Indiana University - Purdue University Indianapolis, USA)
"To Quantify a DNA Photolesion via LC/MS and Immunoassay"
9:15 pm - 9:20 pmDiscussion
9:20 pm - 9:30 pmGeneral Discussion
Friday
7:30 am - 8:30 amBreakfast
9:00 amDeparture
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