What is the Hapmap Project?

The International HapMap Project is a project whose aim is to develop a haplotype map of the human genome, which will describe the common patterns of human genetic variation. In plain English, what they have done is taken blood samples from groups of related individuals from various regions of the planet and used these samples to catalog some of the common variations in their DNA which was extracted from a type of white blood cell called a lymphoblast. Because it would be far too expensive to sequence the full genomes of so many people, the HapMap project looks at sites of common variation in DNA sequence called Single Nucleotide Polymorphisms (SNPs).

All of the data has been sampled from related individuals, two parents and a child, these are referred to as “trios”. The reason this is done is that it allows researchers to investigate patters of heritability.

So essentially the raw data which the project has produced is genotype (SNP) data for trios of related individuals from from various regions around the world; for example what is referred to as the CEU subset of data are genotypes for 30 trios (2 parents, 1 child) who are residents of Utah of northern and western European decent. Similarly the YRI data are 30 adult-and-both-parents trios from Ibadan, Nigeria.

There have thus far been three “phases” to the project. They are essentially a combination of different samples (e.g. new geographic locations) and different genotyping technologies. For example Phase II has 270 samples between 4 geographic areas and is genotyped with 3.8 million SNPs per sample. Phase III has a greater number of samples (1,115) but is genotyped using a less sensitive technology (1.6 million SNPs per sample).

The data can be applied to studies such as genome wide association, where phenotypic traits (e.g. height, a disease etc.) are linked to SNPs to give an idea of which areas of the genome are responsible for what visible traits. Because the individuals who were samples are related the data can also be applied to heritability studies.

The HapMap website provides some analysis tools such as a genome browser that can be used to browse and visualise the data. The data is also available for bulk download.

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Till Next time.

2 Responses to “What is the Hapmap Project?”

  1. [...] Bioinformatics Tutorials Bioinformatics in Plain English « What is the Hapmap Project? [...]

  2. Is this map endorsed by the RSA?

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