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This Week in Nature: Aug 24, 2017

In Nature Genetics this week, an international research team reports new details about the genetic drivers of Wilms tumors, the most common type of malignant kidney tumor in children. The scientists performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in over 100 Wilms tumors, followed by targeted sequencing of 651 additional tumors. They found a number of previously unidentified recurrent novel somatic and germline mutations, recurrent copy number changes, global mRNA and miRNA expression, and DNA methylation patterns associated with the disease. The investigators also propose a genetic framework for Wilms tumors within the context of early renal development.

The Scan's sister publication, GenomeWeb Daily News, has more on this study here.

In Nature Plants, a group of Chinese and German investigators publishes details of a novel haplotyping method based on genome assembly, which they used to produce a half haplotype-resolved sweet potato genome to reconstruct the crop plant's hexaploidization history. "Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes," the researchers write.

And in Nature Methods, collaborators from Stanford University and Harvard University present newly developed software for analyzing sparse chromatin accessibility data. By measuring the gain or loss of chromatin accessibility within sets of genomic features while controlling for known technical biases in epigenomic data, the tool — called ChromVAR — enables accurate clustering of single-cell ATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility, according to the researchers.