Tuesday, November 16, 2004

NASA + Active Genome Mapping

NASA isn't just about rockets and Mars-crawling robots... The NASA Ames Research Facility just published a very interesting genomics study. They designed High-density Microarrays, based on the recently "finished" Human Genome Project, using their Maskless Array Synthesizer (MAS) system (manufacture of Affymetrix arrays use mask-based lithography). 134 arrays and 52 millions unique probes (spaced on average 46 nucleotides apart, spanning 1.5 Gb of non-repetitive sense and antisense genomic DNA) later, they had a "map" of the entire genome. These tiling arrays were then used to determine experimentally and with great precision the regions expressed as RNA (in liver tissue), corresponding to genes (and all their splicing variants) and microRNAs (or something else yet to be identified).

Transcription was detected from 64%, 57% and 35% of known genes from RefSeq, Ensembl, and predicted genes by GenScan. Not every gene is expressed in every tissue (~50% of known genes seem about right, from my experience with Affy arrays and CD4+ T cells); the low percentage from GenScan prediction may indicate a lot of false positives by the gene prediction algorithm. They also identified 10,595 transcriptionally active regions (TARs) not present in databases. They confirmed 90 (out of 96 tested) of these by RT-PCR. By BLAST analysis, they found that many of their novel TARs (24%) had significant homology with mouse Genome sequences. 14% of the novel TARs, when translated to protein in all 6 reading frames, showed significant homology with mouse proteins. Their "expression map" is quite an achievement... you can read the original paper here.

Recent NASA Ames Genome Research Facility publications
Coverage by SpaceFlight Now

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