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This Week in Nature: Jun 30, 2016

In this week's Nature Biotechnology, a multi-institute team of European researchers presents the results of a study comparing common methods for DNA methylation analysis that are compatible with routine clinical use, providing a resource for the use of such assays for biomarker development and patient care. In their study, the investigators shipped 32 reference samples to 18 labs in seven different countries, where they were analyzed using 21 locus-specific assays and six global assays. They found that most assays provide high accuracy and robustness, although some differences between assay types and laboratories were observed. Taken together, the findings can be used in the selection, optimization, and use of DNA methylation assays in large-scale validation studies, biomarker development, and clinical diagnostics. GenomeWeb has more on this and related studies here.

And in Nature Genetics, two independent research groups publish the results of studies using genomic techniques to examine Plasmodium vivax, a mosquito-borne pathogen responsible for malaria globally, but understudied compared with another cause of the disease, Plasmodium falciparum, due to its lower mortality. In the first, a group led by Wellcome Trust Sanger Institute investigators performs deep genome sequencing of more than 200 clinical samples of P. vivax across the Asia-Pacific region, and analyzed data on more than 300,000 SNPs and nine regions of the genome with large copy number variations. They uncovered a "dynamic landscape of local evolutionary adaptation in the parasite population," and provide data that can enable genomic surveillance to guide strategies for the control and elimination of P. vivax. In the second paper, a New York University-led team sequenced 182 clinical isolates of P. vivax samples from 11 countries. They confirmed previous reports of high genomic diversity in the pathogen versus P. falciparum, finding that regional populations of the former exhibited greater diversity than the latter's global population. Additionally, signals of natural selection suggested that P. vivax is evolving in response to antimalarial drugs and adapting to regional differences in human hosts and mosquito vectors.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.