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Genomics in the Journals: Jan 24, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, an international research team that included representatives from the St. Jude-Washington University Pediatric Cancer Genome Project presented findings from a genomic study of a childhood leukemia called hypodiploid acute lymphoblastic leukemia.

The researchers profiled samples from 124 children with the aggressive ALL subtype for the study. Based on gene expression and copy number data generated for patients' tumor and normal samples — coupled with whole-exome and/or whole-genome sequences for a subset of the cases — researchers identified potential treatment targets in the leukemia subtype. They also uncovered genetic patterns for further delineating hypodiploid ALL into two subgroups: a low hypodiploid ALL sub-type characterized by TP53 mutations and other genetic features overlapping with Li-Fraumeni syndrome and another sub-group called near haploid ALL.

"This approach led us to key insights about these leukemia subtypes that we would otherwise have missed," St. Jude pathology researcher Charles Mullighan, the study's corresponding author, said in a statement.


Adaptation to a starch-heavy diet that became available during the agricultural revolution contributed to dog domestication, according to a new study in Nature.

The Broad Institute's Kerstin Lindblad-Toh and her colleagues performed pooled genome sequencing on DNA from a dozen wolves and compared these sequences with those from 60 dogs belonging to 14 domestic breeds. Within these sequences, the researchers identified millions of genetic variants that they subsequently used to designate three-dozen stretches of genome sequence as suspected sites of domestication-related selection. Along with brain and nervous system-related genes believed to influence behavioral differences between dogs and wolves, these regions contained several genes mediating starch digestion, starch metabolisms, and fatty acid metabolism. Follow-up experiments — including copy number, gene expression, and genotyping analyses — confirmed that at least three starch digestion genes have undergone selection in domestic dogs, making the animals more able to digest starch-rich foods than their wild counterparts.

"Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs," Lindblad-Toh and her co-authors concluded.


A team from Finland, The Netherlands, and Serbia has identified ties between gut microbial diversity and risk of eczema in infants and toddlers.

As they reported in BMC Microbiology, the researchers assessed microbial diversity in fecal samples from 34 Finnish children between the ages of six and 18 months old, using a custom 16S ribosomal RNA microarray called HITChip that targets microbial phylogeny found in the human gut. Their findings highlighted gut microbial community shifts occurring as children got older, including a dip in the levels of bacteria from the Bifidobacterium genus. In the 15 children affected by eczema, though, gut microbial diversity tended to be higher at the 18-month-old mark, with microbial communities apparently taking on an adult-like composition somewhat earlier than usual.

"The number of bifidobacteria naturally falls with age, and in total we found 21 groups of bacteria which changed in this time period," the University of Turku's Lotta Nylund, corresponding author on the study, said in a statement. "However," she added, "it is the early change towards adult-type bacteria which seems to be a risk factor for eczema."


A Science Translational Medicine study reported that DNA methylation patterns vary between prostate cancers from different individuals, but remain relatively stable within metastatic tumors found in the same person.

In an effort to find methylation marks driving prostate cancer development and progression, researchers from Johns Hopkins University and Wake Forest University used an affinity enrichment and array-based method dubbed MBD-SNP to track genome-wide copy number and methylation profiles in 71 normal tissue samples or metastatic prostate cancer samples collected from 13 prostate cancer patients after death. The analysis uncovered methylation patterns that appear to be specific to cancer, including hypermethylation in and around genes linked to cancer-related processes in the past. When they considered metastases occurring within the same individual, the investigators saw consistent patterns at 1,000 or more DNA methylation marks.

"Our study shows that for prostate cancer, at least, each person develops his own path to cancer and metastasis," senior author Srinivasan Yegnasubramanian, an oncology researcher at Johns Hopkins University School of Medicine, said in a statement, "and we can find a signature of that path in the epigenetic marks within their tumors."


A study in the early, online edition of Science by a Dana Farber Cancer Institute-led team described two recurrent non-coding mutations in the promoter of a telomerase reverse transcriptase gene called TERT in malignant melanoma.

Researchers initially identified the somatic mutations when they sifted through existing genome sequence data for 19 malignant melanomas, where they saw non-coding mutations in 89 percent of samples. When the team sequenced additional samples to bring the tally of melanoma genomes up to 70, the TERT promoter mutations turned up in 71 percent of the tumor samples overall.

"Considered as a whole, these two TERT promoter mutations are even more common than BRAF mutations in melanoma," said senior author Levi Garraway, a researcher affiliated with Dana Farber, the Broad Institute, and Harvard Medical School, in a statement. "Altogether, this discovery could cause us to think more creatively about the possible benefits of targeting TERT in cancer treatment or prevention."


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

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