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Genomics In The Journals: Jun 14, 2012

NEW YORK (GenomeWeb News) – Researchers from the US and Germany used transcriptional profiling, histopathology, and more to explore the relationship between chronic inflammation and cancer in a mouse model of inflammatory bowel disease.

As they report in the early, online version of the Proceedings of the National Academy of Sciences, the investigators followed mice infected with Helicobacter hepaticus for nearly five months, profiling the gene expression and pathological events associated with liver and colitis-like infections that set in after 10 weeks and with colon cancer, which often occurred in the mice by about 20 weeks after infection. Results from the study suggest the mouse immune system dials up DNA and tissue damage in response to infection. Coupled with an apparent dip in DNA repair gene activity seem in colon but not liver tissue, this immune response seems to increase colon cancer risk.

"It’s possible that we have kind of a double whammy [in the colon]," co-corresponding author Peter Dedon, a biological engineering researcher at the Massachusetts Institute of Technology, said in a statement. "You have this bacterium that suppresses DNA repair, at the same time that you have all this DNA damage happening in the tissue as a result of the immune response to the bacterium."


In PLoS Genetics, researchers from the Mayo Clinic in Jacksonville, Florida, the Mayo Clinic in Rochester, Minnesota, and elsewhere describe the expression-based genome-wide association approach they used to find variants with ties to Alzheimer's disease and other conditions.

Using 773 autopsied brain samples from around 400 individuals with Alzheimer's disease or other conditions affecting the brain, the team first profiled gene expression patterns in the cerebellum and temporal cortex regions of the brain. From there, they went on to do an expression GWAS looking for SNPs linked to transcript levels of nearby genes.

The search led to around 3,000 variants with apparent ties to the expression profiles of around 700 genes. Some 2,000 of these SNPs appeared to act as expression quantitative trait loci in both brain regions tested. And because many of the top eQTLs identified in the study overlapped with variants implicated in past disease studies, the study's authors argued that "[c]ombined assessment of expression and disease GWAS may provide complementary information in [the] discovery of human disease variants with functional implications."


A Science Translational Medicine study is highlighting the potential of using exome sequencing to find new disease-related genes and to clarify existing genetic diagnoses and treatment strategies in the clinic.

A team from the University of California at San Diego, the Broad Institute, and several other institutions around the world did whole-exome sequencing on 118 individuals from the Middle East, North Africa, or Central Asia who had difficult-to-diagnose or undiagnosed neurodevelopmental conditions. All of the cases came from consanguineous families, researchers noted, a feature that simplifies the search for recessive Mendelian disease culprits.

The team's analyses of patient exome sequences led to apparent disease-related alterations in 22 genes not previously implicated in these conditions. Around 19 percent of affected individuals had mutations in one of these newly identified genes, while another 8 percent carried mutations in known disease-related genes that did not match their original diagnoses.

"If we extrapolate these results to the general population seen in these clinics, we can infer that a large number of patients could possibly have their diagnosis and treatment modified by advanced genetic testing," UCSD neurogenetics researcher Joseph Gleeson, the study's co-senior author, said in a statement.


An international team led by investigators at the Wellcome Trust Sanger Institute and Oxford University has shown that it's possible to use deep sequencing on DNA found in blood samples from individuals with malaria to assess genetic variation in the malaria parasite Plasmodium falciparum.

Using hundreds of blood samples collected from malaria-infected individuals in Burkina Faso, Kenya, Cambodia, Thailand, and Mali, Papua New Guinea, researchers attempted to sequence P. falciparum DNA with or without an additional blood-culturing step. As they explain in Nature, P. falciparum sequence data generated for 120 directly-sequenced and 107 cultured samples helped the investigators track down more than 86,000 SNPs in the parasite's genome, providing new clues to infection patterns within specific parasite populations.

"If we want to control [drug] resistance, we first need to be able to monitor the genetic diversity of P. falciparum and identify hotspots of potential resistance as they occur," senior author Dominic Kwiatkowski, a researcher affiliated with the Wellcome Trust Sanger Institute and Oxford University, said in a statement.

"Rapid sequencing of parasite genomes from the blood of infected people is a powerful way of detecting changes in the parasite population," he added, "and potentially an important new surveillance tool in the armamentarium for controlling malaria."


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

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