The 2011 annual scientific meeting of the Human Genome Variation Society (HGVS) was held on the 11th of October, in Montreal, Canada. The theme of this meeting was “Exome and Genome Analysis as a Tool for Disease Identification and Treatment.” In the last few years, there has been a substantial increase in the use of next-generation sequencing in identifying variants associated with both single-gene disorders and complex diseases. The advent of exome sequencing with the subsequent transition to whole genome sequencing will require methods to identify candidate causal variants both in coding and regulatory regions. As this technology slowly moves into the clinical diagnostic laboratory, the need to accurately predict the functional consequences of variants becomes more critical for the both the diagnosis and treatment of disease. This year's annual meeting focused on these issues. Hum Mutat 33:586–590, 2012. © 2011 Wiley Periodicals, Inc.