22 March 2010

Last week in Nature: sequencing, sequencing...

A brief review describes the results of two publications from the latest issues of the journals Nature and Nature Genetics.

Transcriptome sequencing: more information about mutations that cause human diseasesIn the article Transcriptome genetics using second generation sequencing in a Caucasian population, published on March 10 in the online version of the journal Nature, a group of European scientists, led by Emmanouil Dermitzakis, cites the results of sequencing mRNA (RNA serving as a matrix for protein synthesis) from transcriptomes of 60 Europeans, information about which is contained in a publicly available database HapMap (we wrote about this project in the article "Human Evolution continues: new evidence").

With the help of second-generation sequencing technology, scientists have found that about 10 million sequences (one-time "reads" of nucleotide sequences) are equivalent to the results obtained using microchip analysis, with the difference that sequencing allows obtaining quantitatively more accurate data on alternative and abundant transcripts. (Alternative transcripts are mRNA molecules formed from a single RNA molecule during alternative splicing, a process in which coding RNA regions (exons) are cut out and assembled in various combinations, generating several different mature mRNA molecules, according to which proteins are subsequently synthesized.)

The correlation of the results of mRNA sequencing with snips allowed the researchers to detect a greater number of expressed genome regions associated with the so-called polygenic trait loci (quantitative trait loci, QTLs) compared to the results of microarray analysis. Signs associated with the interaction of several genes include, for example, eye color. Many hereditary human diseases also have a polygenic nature, because they arise as a result of a violation of the interaction of several genes.

The presented study demonstrated the new capabilities of the latest generation sequencing technologies: they make it possible to detect new properties of genetic effects in transcriptomes, which, in turn, makes it possible to study in more depth the effect of genetic changes on cellular processes.

Localized genetic predisposition to ulcerative colitisIn the online version of the journal Nature Genetics, an international group of scientists, led by Andre Franke from Germany, published on March 14 an article Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL), which presents the results of an associative genome study aimed at determining genetic predisposition to ulcerative colitis (chronic inflammatory disease of the rectum and colon).

Scientists analyzed 1,897,764 single nucleotide polymorphisms (SNPs) found in German residents, of whom 1,043 were ill with ulcerative colitis, and 1,703 people did not suffer from this disease, and found changes in genome regions localized on chromosome 7q22 (rs7809799) and on chromosome 22q13 in IL17REL (rs5771069) associated with an increased risk of ulcerative colitis. The researchers confirmed the relationship between the found loci and ulcerative colitis in six populations of residents of different regions of Europe, comprising a total of 2,539 patients with ulcerative colitis and 5,428 people from control groups.


Daria Chervyakova
Portal "Eternal Youth" based on Genomeweb materials: This Week in Nature, March 18, 201022.03.2010

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