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Cambridge Healthtech Institute’s Fourth Annual
Comprehending Copy Number and Structural Variation
Discovery. . .Data. . .Diseases. . .Diagnostics
March 5-7, 2012| Hilton San Diego Resort | San Diego, California 

Copy number and structural variations (CNVs and SVs) hold immense potential to explain genetic diversity, predict disease risk and diagnose complex genomic disorders. Advances in whole genome amplification, microarrays, and next-generation sequencing technologies have catalyzed the appreciation of CNVs/SVs in the genomic community. Studies linking insertions, deletions, and inversions to disease etiology continue to multiply. As these technologies become more prevalent in diagnostic laboratories, the major challenge becomes how to interpret accurately which variations are pathogenic in nature and which are benign.

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8:30 am Pre-Conference Short Course Registration


9:00 am-12:00 pm Recommended Pre-Conference Short Courses*

SC1: Epigenetics Toolbox

SC2: Sequencing 101

*Separate registration required.

12:00 - 2:00 pm Main Conference Registration


Data Drives Discovery 

2:00 Chairperson's Remarks

Jennifer Hogan, Ph.D., Vice President, Product Management, BIOBASE

2:10 A Genetic Survival Network for Glioblastoma Multiforme

Desmond J. Smith, Ph.D., Professor, Molecular and Medical Pharmacology, University of California, Los Angeles

To construct a survival network for glioblastoma multiforme, we identified correlated patterns of copy number alterations (CNAs) for distant genes using data from 301 tumors. We were able to obtain single gene specificity in the cancer network, and found 46 genes in the glioblastoma network that showed significant interactions with the epidermal growth factor receptor (EGFR) oncogene. This observation suggests that a flank attack strategy that strikes at both EGFR and its partner genes may be an effective approach to treatment of glioblastoma.

2:45 Bioinformatics for Copy Number Detection and Assessing the Impact of Genetic Variation on Gene Regulation

Roger Pique-Regi, Ph.D., Research Scientist, Department of Human Genetics, University of Chicago

Identification of copy number alteration and its potential impact in altering gene expression is a challenging problem that requires new and more sophisticated methods. New high-throughput experimental platforms offer the means for very high-resolution scans in large cohorts of samples to study human diseases. Insights into the utilization and detection capabilities of experimental platforms will be discussed.

Sponsored byBiobase 3:20 Assigning Functional Significance to Human Genome VariationsJennifer Hogan, Ph.D., Vice President, Product Management, BIOBASEHigh-throughput sequencing enables a closer look at the mutations causing inherited disease and cancer than ever before, but with 3-4 million variants identified per genome it becomes a challenge to determine which count. We describe Genome Trax™, an important tool for mapping variants to published genomic features.

3:35 Networking Refreshment Break 

Sponsored by
4:00 Stepping Outside the Exome

Srinka Ghosh, Ph.D., Senior Bioinformatics Applications Manager, Complete Genomics

The landscape of DNA variation is complex, interspersed with SNPs, insertions, deletions and substitutions. Copy number and structural variants add another layer of genomic diversity. Stepping outside the exome is equal to exploring the genome without a map and compass. It is through whole genome sequencing that the evolution of a tumor genome can be understood or discoveries of rare causative variants can be made.

4:35 Inferring Causal Genomic Alterations in Breast Cancer Using Gene Expression Data

Linh M. Tran, Ph.D., Research Scientist, Molecular and Medical Pharmacology, University of California, Los Angeles

Many valuable studies lack genomic data to detect CNV; therefore, methods that are able to infer CNVs from gene expression data would help maximize the value of these studies. In this talk, we present an algorithm that systematically identifies first altered cancer genomic regions and then their causal driver genes using gene expression data.

» 5:10 Featured Speaker: 

Complex Structural Re-Arrangements and Somatic Copy Number Alterations Identified in Pediatric Cancer Genomes

Jinghui Zhang, Ph.D., Associate Member, Biotechnology and Computational Biology, St. Jude Children's Research Hospital

Chromosomal re-arrangements and copy number alterations are key somatic lesions contributing to cancer initiation and progression. To identify these gross somatic lesions in the NGS data at base-pair resolution, we developed two novel computational methods, CREST for structural variation and CONSERTING for copy number alteration. We have uncovered complex structural variations that arise by different mechanisms. The high accuracy and precision of these methods has also made it possible to infer chronological order of gross somatic alterations and sequence mutations based on allelic imbalance in regions of structural alterations.

5:45 Close of Day

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