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Genomics in the Journals: Jan 12, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, researchers from the US, UK, and Austria outline their efforts to catalog genetic variation in Arabidopsis thaliana accessions from around the world.

By genotyping each of the 1,307 accessions tested at some 250,000 sites in the genome, the group came up with what it calls the Regional Mapping, or RegMap, panel. Using this data, they went on to investigate everything from historical recombination hotspots in the A. thaliana genome to regions under selection and their ties to plant traits.

"Our genotyped accessions will be maintained as selfed lineages," University of Chicago ecology and evolution researcher Joy Bergelson, the study's senior author, and colleagues noted, "and it will soon be possible to impute the entire genome sequence from data being generated by the A. thaliana 1001 Genomes Project."


By sequencing the coding regions of more than 200 candidate genes in a chromosome 17 region previously implicated in prostate cancer, a US team has tracked down a potential risk gene for hereditary prostate cancer.

As they report online in the New England Journal of Medicine, the researchers sequenced the exons of 202 genes in individuals with prostate cancer from 94 families with a history of the disease.

The search unearthed a mutation in the HOXB13 gene that was shared by 18 men from four prostate cancer-affected families. When investigators looked for the mutation in another 5,083 unrelated men with prostate cancer and 1,401 unaffected controls, they found that 72 of those individuals had the same change in HOXB13. Results so far suggest the rare mutation is more common in men with early-onset, familial forms of the disease than in sporadic or late-onset prostate cancer cases.

"Although the variant accounts for a small fraction of all prostate cancers, this finding has implications for prostate-cancer risk assessment and may provide new mechanistic insights into this common cancer," co-senior author Kathleen Cooney from the University of Michigan Comprehensive Cancer Center, and colleagues wrote.


Members of the St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project report in Nature that they have sequenced matched tumor-normal genomes from a dozen children with an especially aggressive form of leukemia called early T-cell precursor acute lymphoblastic leukemia. The group subsequently screened for suspected mutations found in the tumor genomes in another 94 children with T-ALL, including 52 who had ETP-ALL and 42 with non-ETP-ALL. They also did transcriptome sequencing for two children with ETP-ALL who had their genomes sequenced, along with exome sequencing for three of the ETP-ALL cases in the replication group.

Together, the team's analyses suggest that ETP-ALL tumors often house mutations in cytokine receptor, RAS signaling, hematopoietic development, and histone modification pathway genes. The findings also hinted that ETP-ALL is more genetically similar to acute myeloid leukemia than it is to other ALL sub-types.

"The mutations and gene expression profile we identified in this study suggest that patients with ETP-ALL might benefit from treatment that includes drugs developed for treatment of acute myeloid leukemia," co-corresponding author Charles Mullighan, a pathology researcher at St. Jude, said in a statement.


In Nature Medicine, meanwhile, an international research group describes how it used array comparative genomic hybridization to discern new epigenetic pathway changes that seem to contribute to tumorigenesis in adult T-cell ALL.

From their aCGH experiments on tumor samples from 68 individuals, the researchers found that a quarter of the cases involved mutations to components of the Polycomb repressive complex 2. Their follow-up experiments in mouse models of the disease indicate that this PRC2 inactivation — which seems to be related to the excess NOTCH1 signaling pathway activity previously reported in T-cell ALL — leads to the loss of a histone modification that is usually repressive.

"These studies suggest a tumor suppressor role for PRC2 in human leukemia," the study authors wrote, "and suggest a hitherto unrecognized dynamic interplay between oncogenic NOTCH1 and PRC2 function for the regulation of gene expression and cell transformation."


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

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