Genomic Variation Program

About 99.5 percent of a person's DNA is the same as any unrelated person's DNA. Differences in the sequence of DNA among individuals are called genetic variation. Genomic variation explains some of the differences among people, such as eye color and blood group, as well as whether a person has a higher or lower risk for getting particular diseases. Variants in single genes cause some traits and diseases, such as the ABO blood group and cystic fibrosis. Complex interactions among multiple genes and the environment cause common diseases such as diabetes, heart disease, many cancers, stroke, Alzheimer's disease, Parkinson's disease, depression, arthritis, and asthma.

Currently, about 99 percent of variants with a frequency of 1 percent or higher have been found, with a false detection rate of 5 percent. About 96 percent of the genome can be studied with high confidence. More than 80 million variant sites in the genome have been found so far, including single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and other structural variants; these variants have been put onto haplotypes (phased), showing which variants at nearby sites are on the same chromosome. The program also seeks to relate there genetic variants to functional variation and phenotype.

The Genomic Variation Program supports large-scale studies of human genetic variation as part of projects such as the International HapMap Project and the 1000 Genomes Project. The program supports many studies developing data analysis methods for how to relate variation to traits, diseases, and responses to drugs and environmental factors, such as association and admixture approaches, and how to use patterns of variation to infer demographic history, selection, and other population genetic processes. The program also works with other programs to support experimental and analysis development studies and databases relating variation to differences in gene function and regulation and to clinical effects.

The Genomic Variation Program supports research aimed at:

• Discovering and typing single nucleotide polymorphisms (SNPs), indels, and other forms of genetic variation on a large scale across the genome.
• Developing high-resolution maps of genetic variation and haplotypes.
• Developing methods for the large-scale experimental and statistical analysis of SNPs, other forms of genetic variation, haplotypes, and complex traits.
• Developing statistical methods to relate genetic variation to phenotypes, disease, and function.

Information Related to the Genomic Variation Program

Non-Coding Variants Program (NoVa)

1000 Genomes: A Deep Catalog of Human Genetic Variation

An integrated map of genetic variation from 1,092 human genomes. 1000 Genomes Project Consortium (2012). Nature 491:56-65.

International HapMap Project

A haplotype map of the human genome. The International HapMap Consortium (2005). Nature 437: 1299-1320.

Databases for Variants:

NCBI:

• SNPs and Small Indels: dbSNP
• Structural Variants: dbVar
• Clinical and Phenotypic Information on Variants: ClinVar

Other:

• Clinical and Phenotypic Information on Variants: Clinical Genome Resource
• The NHGRI Large-Scale Sequencing Program

Meeting Reports Related to the Genomic Variation Program

July 28-29, 2014: Future Opportunities for Genome Sequencing and Beyond: A Planning Workshop for the National Human Genome Research Institute

June 5-6, 2012: Workshop on Establishing a Central Resource of Data from Genome Sequencing Projects

August 3-4, 2004: Executive Summary: Workshop on Characterizing Human Genetic Variation

July 18-19, 2001: Developing a Haplotype Map of the Human Genome for Finding Genes Related to Health and Disease