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Nature Papers Present Molecular Profiling Platform for Childhood Cancer, Algorithm for Long-Read Metagenomic Assembly, More

A molecular profiling platform for childhood cancer that combines germline and tumor whole-genome sequencing (WGS), RNA sequencing (RNAseq), and central nervous system methylome analysis is reported in this week's Nature Medicine. In the study, members of Australia's Zero Childhood Cancer Program apply the approach to 252 tumors from high-risk pediatric cancer patients, identifying a range of germline and somatic driver variants and contributing significantly to treatment recommendations. "The Zero Childhood Cancer Program is Australia's first national pediatric cancer precision medicine program, focused on real-time recruitment and analysis of patients with high-risk pediatric cancer," the study's authors write. "Our experience demonstrates that WGS and RNAseq offer the best opportunity to identify targetable driver genomic lesions" for these patients. GenomeWeb has more on this, here.

An algorithm for improved long-read metagenomic assembly is presented by a team led by University of California, San Diego, scientists in Nature Methods this week. Called metaFlye, the approach overcomes many of the challenges facing long-read metagenomics such as uneven bacterial composition and intra-species heterogeneity, according to its developers. Benchmarking metaFlye with simulated and mock bacterial communities shows it outperforms state-of-the-art long-read assemblers, while metaFlye assembly of the sheep microbiome results in 63 nearly complete bacterial contigs. Lastly, the researchers show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.

A genome resource for the wild plant green millet (Setaria viridis), a model species for the study of warm season C4 grasses, is presented in this week's Nature Biotechnology. A group led by HudsonAlpha Institute for Biotechnology investigators produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions. They use the assemblies to identify loci underlying three key traits including a loss-of-shattering trait that permits mechanical harvest. CRISPR-Cas9 genome editing was then used to validate a gene whose product controls shattering, and the scientists show that the orthologous gene in S. italica is disrupted by a transposon, indicating that the locus contributed to domestication.