Lab mouse genome isn't simple
High-resolution study shows complex structure is bad news for QTL mapping
By Cathy Holding

The patterns of variation between genomes of standard laboratory inbred mice
are not as simple as generally believed, according to a team reporting in
PNAS. The results suggest that researchers will be forced to use other
methods in quantitative trait loci (QTL) mapping, as gene identification
will become "not impossible, but more challenging," said Richard Mott, who
led the study with Jonathan Flint at the Wellcome Trust Centre for Human
Genetics, Oxford.

"Inbred strains are great in the sense that they're completely homozygous,"
said Mott. But laboratory mice were bred originally by amateur scientists
who used anything they could catch, said Mott. "They weren't created,
generally speaking, for genetic research. The question is, if you look at
the genomes of these inbred strains in detail, how do they differ?"

Mott and his team sequenced about 12% of a 4.8-megabase region known to
contain a QTL affecting anxiety in each of eight inbred strains, in pieces
distributed fairly uniformly to ensure a good sampling of the region at high
resolution. "Essentially, we were sampling every 10 kb," said Mott.

Mott's team investigated whether the same group of strains of inbred mice
showed one variant while the other group showed a different variant-the
simplest picture of genome variation-based on data from low-level scans of
the mouse genomes.

Read the rest at The Scientist
http://www.biomedcentral.com/news/20040622/01

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