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Genomics in the Journals: 2013.05.23

NEW YORK (GenomeWeb News) – In Nature Genetics, an international team led by investigators at the University of Minnesota described findings from a forward genetic screen aimed at uncovering mutations that drive the development of malignant peripheral nerve sheath tumors — a type of inherited or sporadically occurring sarcoma that affects cells from the Schwann cell lineage.

Using mutant mice carrying alterations that made them more cancer prone, the researchers did transposon-mediated mutagenesis with the Sleeping Beauty transposon to look for genetic contributions to the development of sarcomas that affect Schwann cells, which are supporting glial cells from the peripheral nervous system.

The group identified 87 common insertion sites in the 106 MPNSTs considered. Nearly 700 more common insertion sites were associated with the development of neurofibromas, which often precede full-blown MPNST.

By folding in existing data on human MPNST cases, meanwhile, the researchers narrowed in on apparent oncogenes involved in the condition as well as signaling and growth factor-related pathways that tend to become altered as MPNST develops.

Recent demographic events can produce genetic profiles within populations that are reminiscent of those used to uncover ancient population events, according to a study in Investigative Genetics.

Researchers from the Netherlands and Germany used Affymetrix arrays to genotype 999 individuals from 54 locales in the Netherlands. Within the Dutch population, their analyses revealed four genetic clusters coinciding with Netherlands geography.

By considering the genetic data in light of the country's archaeological and other data, the group determined that these profiles are likely not a consequence of extremely old population events. Instead, they seem to reflect well-documented migrations within the country over the past 2,000 years or less.

"Our results not only are of epidemiological and forensic relevance, but additionally highlight that future population history studies need to take into account recent demography before assuming all genetic variation observed is due to ancient events," the study's senior author, Erasmus University Medical Center researcher Manfred Kayser, said in a statement.

A team based at the Massachusetts General Hospital, Massachusetts Eye and Ear Infirmary, and other centers in the US has garnered evidence linking high genetic variability to relatively poor outcomes for individuals with head and neck cancer.

As they reported in the journal Cancer, the investigators evaluated exome sequence data for tumors from 74 individuals with head and neck squamous cell carcinoma, using a previously developed mutant-allele tumor heterogeneity, or MATH, approach to look at levels of genetic heterogeneity in the cancers.

When they added in survival data for the patients, the study's authors found that individuals whose tumors had the highest heterogeneity levels also tended to have significantly shorter survival times. Moreover, those genetically variable tumors tended to have other features implicated in poor outcomes in the past, such as TP53 mutations.

"Our findings will eventually allow better matching of treatments to individual patients, based on this characteristic of their tumors," said senior author Edmund Mroz, with the Massachusetts General Hospital's Center for Cancer Research, in a statement.

"This method of measuring heterogeneity can be applied to most types of cancer," he added, "so our work should help researchers determine whether a similar relationship between heterogeneity and outcome occurs in other tumors."

A study in the Journal of the American Medical Association suggested that a variant falling in the promoter region of the MUC5G gene may offer insights into survival outcomes for individuals with idiopathic pulmonary fibrosis.

The retrospective study, performed by a University of Colorado-led team, involved two IPF cohorts: a group of 438 IPF patients enrolled by members of the international INSPIRE consortium and another 148 individuals with IPF recruited at a University of Chicago clinic.

For the INSPIRE group, researchers brought together clinical data and survival outcome information with patients' genotype at a MUC5B promoter variant called rs35705950, which had been previously implicated in IPF risk. Their results indicated that there are survival differences depending on the allele present at the promoter site — a pattern that they further verified using data for the University of Chicago cohort.

"Among patients with IPF, a common risk polymorphism in MUC5B was significantly associated with improved survival," corresponding author David Schwartz, chair of the University of Colorado's medicine department, and his co-authors wrote. "Further research is needed to refine the risk estimates and to determine the clinical implications of these findings."

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

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