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This Week in Nucleic Acids Research: Feb 18, 2015

An international team turned to a combination of whole-genome bisulfite sequencing, array-based gene expression profiling, and high-definition microarrays to assess DNA methylation patterns in pediatric B-cell acute lymphoblastic leukemia cases. Based on information from samples from 227 children with B-ALL, the researchers described two types of differentially methylated regions in the blood cancer: newly methylated sites involving small functional regions that are normally hypomethylated and a decline in methylation across broader swaths of sequences in a subset of patients.

Using an approach called single molecule analysis of replicated DNA, or SMARD, a team from Brazil, the US, and the UK characterized DNA replication rates and dynamics in the sleeping sickness-causing parasite Trypanosoma brucei. The researchers tracked replication fork speeds in parasites from a fly vector and from the blood of an infected mammalian host. T. brucei had replication rates that resembled other eukaryotes at both stages of their life cycle, the study's authors say, though the parasite seemed to have more replication origins than anticipated.

Researchers from the University of Pennsylvania and the Children's Hospital of Philadelphia present a tool that uses a cross-sample normalization process to track down and analyze copy number variants from whole exome sequence data. The team validated this approach, dubbed CODEX, using exome sequences for individuals included in the 1000 Genomes Project, showing that it compared favorably with microarray-based CNV detection methods. In matched tumor and normal samples from 222 individuals with neuroblastoma, meanwhile, CODEX helped the investigators focus in on tumor-associated somatic deletions in a gene called ATRX.