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Genomics In The Journals: Aug 16, 2012

NEW YORK (GenomeWeb News) – A pair of genome-wide association studies in Nature Genetics look at loci linked to type 2 diabetes and to blood sugar and insulin levels.

Through a multi-stage GWAS and meta-analysis involving nearly 35,000 cases and 115,000 unaffected controls who were genotyped at SNPs suspected of having ties to cardiovascular and/or metabolic traits with the Metabochip array, members of the Diabetes Genetics Replication and Meta-analysis, or DIAGRAM, consortium tracked down 10 new type 2 diabetes-linked loci. Among them were two loci with apparent sex-specific effects: a chromosome 12 site near the CCND2 gene that was more closely associated with type 2 diabetes in men, and a second locus upstream of the GIPR gene on chromosome 19 that was more significantly tied to the disease in women.

Across the 60 genes or regions implicated in type 2 diabetes in this and prior studies, the researchers' analyses indicate that there is an over-representation of loci expected to impact processes such as transcription, cell cycle regulation, and signaling by molecules released by fat tissue.

By combining existing data with new genotyping information generated on the same custom Metabochip array, another large international team uncovered almost three-dozen new loci linked to blood glucose levels during times of fasting, to blood glucose levels two hours after eating, or to fasting insulin concentrations. Of the 53 loci that have been significantly associated with these glycemic traits in the new study or in the past, authors of that study explained, 33 have also been implicated in type 2 diabetes risk. Moreover, the researchers found that some of the same sites influencing insulin levels in the blood have also been linked to insulin resistance-related traits, such as lipid levels or abdominal obesity.

"We observed some overlap between the regions we identified and genetic regions associated with abdominal obesity and various lipid levels, which are a hallmark of insulin resistance," University of Oxford researcher Inga Prokopenko, a co-senior author on the glycemic trait GWAS paper, said in a statement. "We hope that these studies will help to find gene networks with potential key modifiers for important metabolic processes and related diseases, such as type 2 diabetes."

Researchers from Germany and Ghana report on two new loci associated with susceptibility to serious complications following infection with the malaria parasite Plasmodium falciparum.

As it reported in Nature, the team initially tested 1,325 individuals from Ghana who had been diagnosed with severe malaria-related syndromes, including cerebral malaria and severe anemia, comparing genotyped and imputed SNPs in the patients' genomes with those found in 825 unaffected individuals from the same region. After testing the most promising variants in another 1,320 cases and 2,222 controls, researchers were left with four loci showing statistically significant ties to severe malaria. These included new loci on chromosomes 1 and 16 as well as previously described loci near blood group and sickle cell-related genes on chromosomes 9 and 11, respectively.

"Our findings underline the potential of the [genome-wide association] approach to provide candidates for the development of control measures against infectious diseases in humans," senior author Rolf Horstmann, with the Bernhard Nocht Institute for Tropical Medicine in Hamburg, and colleagues wrote.

Meanwhile, a study in Cell Host & Microbe describes distinct microRNA patterns in the red blood cells of individuals with sickle cell disease that seem to help subvert the action of the P. falciparum malaria parasite.

For that effort, researchers from Duke University used tiled low-density arrays and other validation methods to profile miRNA patterns in red blood cells of individuals with or without sickle cell anemia. Their results suggest that individuals carrying one or two copies of the sickle cell disease-causing allele in the hemoglobin gene have red blood cells containing unusual miRNA repertoires. In particular, researchers reported, red blood cells in sickle cell-affected individuals seem to contain especially high levels of two human miRNAs — miR-451 and let-7i — that bind to certain P. falciparum messenger RNAs and thwart the pathogen's growth.

"These microRNAs enriched in the sickle red cells reduce the parasite's ability to propagate, so that certain people stay more protected," Duke researcher Jen-Tsan Chi, the study's senior author, said in a statement, adding that this realization "should lead to greater understanding of the host-parasite interaction and parasite lifecycle, which may eventually develop into a new approach to therapy for malaria."

An American team outlines its strategy for using DNA to store digital information in a new Science study. The method relies on the use of oligonucleotides that contain shared sequences for DNA amplification and sequencing, along with distinct stretches of sequence that can be used to pinpoint their locations within a larger data set.

Using DNA microchips and tens of thousands of these oligos — each designed to code for 96 bits of data — researchers encoded a 5.27 megabit book containing more than 53,000 words, almost a dozen images, and a JavaScript program. They then read back the tome using DNA amplification and Illumina HiSeq sequencing.

This is not the first time that DNA has been employed as an information storage device: a study published more than a decade ago illustrated ways in which messages could be stored in genetic material. But the amount of information that researchers managed to cram into DNA this time far exceeds that described in the past. Based on their results so far, the team argued that DNA could ultimately serve as a tool for stable, high-density information storage, encoding one bit of data per DNA base in a form that can be accessed using existing and anticipated sequencing technologies.

"Our general approach of using addressed data blocks combined with library synthesis and consensus sequencing should be compatible with future DNA sequencing and synthesis technologies," senior author Sriram Kosuri, a researcher affiliated with the Wyss Institute for Biologically Inspired Engineering and Harvard Medical School, and co-authors wrote. "Reciprocally, large-scale use of DNA such as for information storage could accelerate development of synthesis and sequencing technologies."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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