The European Molecular Biology Lab and Germany’s Resource Center/Primary Database (RZPD) have created a human genome chip set.
The groups announced Human Unigene Set-RZPD3, a two-slide DNA chip set that contains nearly the entire human genome in the form of 51,145 sequence-verified cDNAs based on NCBI’s UniGene clusters. Each clone represents one UniGene cluster. The chips include spike-in controls and labeled oligonucleotides.
The new chip enters an arena of ultra-high density human micro-arrays that includes the two-chip set made by Affymetrix; the three-chip set sold in Japan by Hitachi Software Engineering; Amersham’s CodeLink UniSet Human I Bioarray; and Agilent’s human oligo array. None, however, including this latest entrant, have miniaturized the process of attaching probes that mirror the human genome to the extent of being able to place it on one single slide. At least one manufacturer has indicated that 1-chip human genome microarrays may be available within five years as commercial products.
For this collaboration, RZPD of Heidelberg/Berlin created the collection of cDNA while EMBL performed quality checks and purification. RZPD was initially established within the German Human Genome Project (DHGP) at the department of Hans Lehrach, Max Planck Institute for Molecular Genetics (MPIMG), Berlin, and the department of Annemarie Poustka, at the German Cancer Research Center, (DKFZ), Heidelberg, in 1995. Its mission is to supply of researchers with high quality, standardized experimental material and clones and the collection and integration of data created with these materials. EMBL is a 29-year-old research institute funded by the states of the European Union, as well as Switzerland and Israel.
The content on the Human UniGene Set-RZPD3 was selected according to the following criteria:
• More than one sequence per cluster;
• As close as possible to the 3´end of the cDNA;
• Length of the insert between 500 and 1,200 bp.
The development process took nine months, said Christian Schwager, a scientist in the EMBL group of Wilhelm Ansorge, and cost, by rough estimate, €250,000 to produce.
The chip will not be freely available but Schwager said interested researchers could obtain access to the chip on a collaborative basis.
Of these clones, 32,000 have been sequence verified, and characterization of another 20,000 clones is in progress, the group said. CDNA inserts were PCR amplified, purified, and spotted on glass slides. Analysis of PCR fragments on agarose gels, documentation, control DNAs and Cy5- / Cy3-labeled oligos on the slides were provided to ensure quality.
“We think it is the best library you can access,” said Schwager. “Sequence is verified and each is at the spot as it should be.”
More information is available at http://www.ansorge-group.embl.de/human55kchip/.