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Comprehending Copy Number Variation


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The resulting applications of newly developed whole-genome scanning technologies have catalyzed the appreciation of copy number variation (CNV) in the genomic community. Studies linking insertions, deletions, and inversions to disease etiology continue to multiply. As genome-wide scanning techniques become more widely used in diagnostic laboratories, the major challenge is how to accurately interpret which variations are pathogenic in nature and which are benign.

MONDAY, MARCH 15, 2010

8:30 am Short Course Registration


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



Thomas J. Downey, President, Partek, Inc.

Min Li, Ph.D., Field Application Specialist, Partek, Inc.

Click here for the complete short course description.

* Separate registration required 


1:00 pm Conference Registration


2:00 Chairperson’s Remarks
Charles Lee, Ph.D., Associate Professor, Brigham & Women's Hospital


James LupskiGenomic Disorders: Mechanisms and Assays for CNV Causing Neuropsychiatric Traits

James R. Lupski, Ph.D., Professor and Vice Chair, Molecular & Human Genetics & Pediatrics, Baylor College of Medicine

Whereas Watson-Crick DNA base pair changes have long been recognized as a mechanism for mutations, rearrangements of the human genome including deletions, duplications, and inversions have been appreciated only more recently as a significant source for human genetic variation. This presentation will discuss the study of the analyses of breakpoints in the proximal short arm of chromosome 17 (17p), which reveal nonallelic homologous recombination (NAHR) as a major mechanism for recurrent rearrangements, in comparison to nonhomologous end-joining (NHEJ), which can be responsible for many of the non-recurrent rearrangements.  We recently elucidated a DNA replication mechanism for nonrecurrent rearrangements that we termed FoSTeS – Fork Stalling and Template Switching.  A newer model, microhomology-mediated break-induced replication or MMBIR, provides further molecular mechanistic details and may be operative in all life forms as a means to process one-ended, double-stranded DNA generated by collapsed forks. Our study reveals that genomic rearrangements may cause Mendelian diseases and complex traits such as obesity and neurobehavioral phenotypes.


2:50 Use of Molecular Inversion Probes (MIPs) to Detect Copy Number Changes in the Cancer Genome

Joshua Schiffman, M.D., Medical Director, High Risk Pediatric Cancer Clinic, Pediatric Hematology/Oncology and Oncological Sciences, Huntsman Cancer Institute, University of Utah

In this talk, we will discuss the new Molecular Inversion Probe (MIP) technology which performs high-resolution, genome-wide copy number analysis. We will focus on the cancer genome and the distinct copy number alterations which have been identified using MIP technology. We also will discuss the use of MIPs to validate other high-resolution copy number platforms.

3:20 Networking Refreshment Break, Exhibit & Poster Viewing

4:00 Copy Number Variation in Common Disease

Steven McCarroll, Ph.D., Assistant Professor, Genetics, Harvard Medical School

Structural variants such as copy number variants are routinely assumed (because of their large size) to make a disproportionate contribution to human phenotypic variation. It is increasingly possible to test this hypothesis in a systematic way; I will describe the results of several broad-based tests of this hypothesis in various common diseases.

4:30 Glioblastoma Genomic Amplifications, Deletions and Mutations

Gregory J. Riggins, M.D., Ph.D., Professor, Neurosurgery & Oncology, Johns Hopkins University

Gene amplifications and deletions play a significant role in the development of human glioblastomas. An analysis of the copy number changes in over 200 glioblastomas reveal the contribution of copy number changes to tumor formation. Further evaluating copy number changes in glioblastomas together with large-scale mutation analysis, further reveals the synergistic contributions of copy number changes and mutations to tumor growth. Copy number analysis in these tumors provides important information for identifying and stratifying possible therapeutic targets.

5:00 Establishment and Characterization of a Cancer Cell Line Derived from an Aggressive Childhood Liver Tumor

Gail Tomlinson, Ph.D., Professor, Pediatrics, Greehey Children’s Cancer Research Institute, University of Texas San Antonio

5:30 – 7:00 Welcoming Reception in the Exhibit Hall