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Aug 20, 2001
 |  BioCentury  |  Tools & Techniques

Not all happy about haplotypes

The first planning meetings for a public-private haplotype map have barely finished and already the kinds of disagreements that occurred during the sequencing of the human genome appear to be surfacing. Most likely, there will be separate projects running in parallel using different methodologies to create different maps.

Haplotypes are groups of genetic variation (SNPs) that tend to associate together. The value of haplotypes lies in their ability to be used as markers for disease susceptibility or drug response.

Though SNPs (single nucleotide polymorphisms) have essentially the same potential, the problem is that the task of sequencing every SNP in every patient is impractical. In order to circumvent that project, the idea of the haplotype map was born.

"The reason we are talking about a haplotype map is that we can't sequence everyone," said Aravinda Chakravarti, director of the Institute of Genetic Medicine at Johns Hopkins University. "The haplotype map will reduce the complexity of the genome by breaking it up into packages."

There appear to be four main groups working on haplotype maps: the public-private effort; Genaissance Pharmaceuticals Inc. (GNSC, New Haven, Conn.); Affymetrix Inc. spin-off Perlegen Sciences Inc. (Santa Clara, Calif.); and Celera Genomics Group (CRA, Rockville, Md.).

In addition, Variagenics Inc. (VGNX, Cambridge, Mass.); Orchid Biosciences Inc. (ORCH, Princeton, N.J.); and DNA Sciences Inc. (Fremont, Calif.) are separately identifying haplotypes associated with disease and drug response, and Interleukin Genetics Inc. (ILGN, Waltham, Mass.) is looking specifically at variations in the IL-1 gene that affect susceptibility to and drug responses in inflammatory disorders.

Building a haplotype map includes identifying a large number of individual SNPs and analyzing how often groups of SNPs associate together between individuals. If a group of four SNPs are always found together, they create a haplotype.

Theoretically, by creating a...

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