In a paper published online in advance in Science this week, a large research collaboration led by investigators at the Johns Hopkins Kimmel Cancer Center describes the genetic landscape of medulloblastoma. Using high-density microarrays, the team investigated copy number alterations; the researchers also "sequenced all known protein-coding genes and miRNA genes using Sanger sequencing in a set of 22 MBs." Their resulting childhood brain cancer data set showed that, "on average, each tumor has 11 gene alterations," which is "five to 10 times fewer than in the adult solid tumors that have been sequenced to date," the authors write. The team also identified mutations of MLL2 or MLL3, histone-lysine N-methyltransferase genes, in 16 percent of the patient samples.
Researchers at the Memorial Sloan-Kettering Cancer Center, along with their collaborator at Columbia University, report that the structure of the DNA methyltransferase-1-DNA complex "reveals a role for autoinhibition in maintenance DNA methylation." Specifically, a linker between DNA and the active site of DNMT1 prevents de novo methylation, the Sloan-Kettering team shows. In this way, "occlusion of unmethylated CpG dinucleotides from de novo methylation ensures that only hemimethylated CpG dinucleotides gain access to the active site," the team concludes.
In Science Translational Medicine this week, Kari Stefansson et al. at DeCode Genetics, along with their international collaborators, propose a prostate-specific antigen diagnostic cut-off value, based on a patient's genotype, which they say physicians should consider "when deciding to perform a prostate biopsy." In a genome-wide association study of 15,757 Icelandic and 454 British men, all of whom had not been diagnosed with prostate cancer, the DeCode team found significant associations between PSA levels and SNPs at six loci. Of these, three alleles were associated with a heightened probability of a negative biopsy among 3,834 men who showed high PSA levels and underwent the procedure. Four of these loci, the authors add, are also associated with prostate cancer risk.
Though the first quantum machine took top honors as Science's breakthrough of the year, genomics research findings ranked highly among the runners-up. J. Craig Venter et al.'s synthetic genome, the Neandertal genome, and advances in next-gen sequencing all made the list. Exome sequencing to find the causes of Mendelian disorders and computational protein-folding simulations were also top contenders in the Science contest. In reflecting upon its 2009 winners, Science says that while induced-pluripotent stem cells still show much promise, real progress has yet to be made in "finding new treatments for more common conditions, say, Parkinson's disease or diabetes." Exome sequencing, though it has been vastly useful in revealing "the errant DNA underlying a dozen or so rare diseases," has only come so far in terms of "the missing heritability for common disorders," Science adds.