Fast PGx SNP assays Our Novallele™ genotyping assays detect genetic variations, single-nucleotide polymorphisms (SNPs) and both small and large indels, of the human genome using any thermocycler capable of high-resolution melting (HRM). The assays cover several research areas, including pharmacogenetics, and provide scientists a simple method to detect mutations of consequence. Learn more at www.canon-biomedical.com.
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Genome variation for non-geneticists p1297 doi:10.1038/ng.3716 Single-nucleotide variation (SNPs or SNVs) in the human genome is now being used by the public and by researchers interested in the functional mechanisms of genetic perturbation for the 3D structure and function of the nucleus in various cells and tissues, and for understanding human-microbiota interactions. We have some requests for authors that may help prevent misunderstanding as familiar genetic markers acquire new users.
p53 partners with RNA in the DNA damage response pp1298 - 1299 Maite Huarte doi:10.1038/ng.3702 Stabilization of p53 protein is a key step in the cellular response to DNA damage. A new study describes a long noncoding RNA, DINO, transcribed from the CDKN1A promoter region that induces stabilization of p53 protein and promotes efficient activation of p53 target genes in response to DNA damage.
Dangerous R loops form in the absence of H3K9 methylation pp1299 - 1300 Anna Elisabetta Salcini doi:10.1038/ng.3705 Methylation of histone H3 on lysine 9 (H3K9) is a hallmark of transcriptionally inactive heterochromatin that is deregulated in pathological conditions. A new study shows that complete loss of H3K9 methylation in Caenorhabditis elegans leads to derepression of repetitive elements and formation of DNA:RNA hybrids (R loops), resulting in increased rates of repeat-specific mutation.
The gut microbiome—an emerging complex trait pp1301 - 1302 Andrew K Benson doi:10.1038/ng.3707 As the first series of genetic analyses of gut microbiome composition in humans is now emerging, the results should be met with enthusiasm, but also with caution. Findings from the initial offerings demonstrate how population-scale approaches can provide deeper insights into host-microbiome interactions while at the same time illustrating that our understanding of the architecture of highly complex microbiome 'traits' is still rudimentary.
Chromatin structure-based prediction of recurrent noncoding mutations in cancer pp1321 - 1326 Kwoneel Kim, Kiwon Jang, Woojin Yang, Eun-Young Choi, Seong-Min Park et al. doi:10.1038/ng.3682 Jung Kyoon Choi and colleagues identify sets of regulatory mutations in breast and lung cancer samples that converge on the same gene target across individual samples. They use features of these mutation sets to develop a method for predicting functionally recurrent regulatory mutations that may function as drivers in cancer.
The genomic landscape of schwannoma pp1339 - 1348 Sameer Agnihotri, Shahrzad Jalali, Mark R Wilson, Arnavaz Danesh, Mira Li et al. doi:10.1038/ng.3688 Gelareh Zadeh, Kenneth Aldape and colleagues present an integrative genomic analysis of schwannomas. In addition to finding recurrent mutations in ARID1A, ARID1B and DDR1, they identify a recurrent SH3PXD2A-HTRA1 fusion that confers increased proliferation, invasion and in vivo transformation, and is associated with sensitivity to MEK inhibition.
An inducible long noncoding RNA amplifies DNA damage signaling pp1370 - 1376 Adam M Schmitt, Julia T Garcia, Tiffany Hung, Ryan A Flynn, Ying Shen et al. doi:10.1038/ng.3673 Howard Chang and colleagues identify a long noncoding RNA, DINO, that is transcribed upstream of CDKN1A and induced by p53 in response to DNA damage. They show that DINO binds to p53 protein and promotes its stabilization, producing a feedback loop that amplifies DNA damage signaling.
The rate of meiotic gene conversion varies by sex and age pp1377 - 1384 Bjarni V Halldorsson, Marteinn T Hardarson, Birte Kehr, Unnur Styrkarsdottir, Arnaldur Gylfason et al. doi:10.1038/ng.3669 Bjarni Halldorsson, Kari Stefansson and colleagues use SNP array and whole-genome sequencing data to estimate the meiotic gene conversion rate (G) in humans. They find that G for SNPs is 7.0 conversions/Mb per generation, is 2.17 greater in mothers than in fathers, and increases with maternal age.
npj Precision Oncology is a new open access, online-only, peer-reviewed journal committed to publishing cutting-edge scientific research in all aspects of precision oncology from basic science to translational applications, to clinical medicine. The journal is part of the Nature Partner Journals series and published in partnership with The Hormel Institute, University of Minnesota.
The effect of host genetics on the gut microbiome pp1407 - 1412 Marc Jan Bonder, Alexander Kurilshikov, Ettje F Tigchelaar, Zlatan Mujagic, Floris Imhann et al. doi:10.1038/ng.3663 Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga and colleagues perform genome-wide association analysis for microbiome characteristics in a cohort with fully sequenced metagenomes and detailed diet and lifestyle data. They find loci significantly associated with different microbial species, pathways and genes and examine specific gene-diet interactions.
Association of host genome with intestinal microbial composition in a large healthy cohort pp1413 - 1417 Williams Turpin, Osvaldo Espin-Garcia, Wei Xu, Mark S Silverberg, David Kevans et al. doi:10.1038/ng.3693 Kenneth Croitoru, Andrew Paterson and colleagues perform genome-wide association analysis for gut microbiome composition. They identify 58 SNPs significantly associated with relative abundance of 33 taxa and replicate 4 of the associations in an independent cohort, providing further evidence that host genetics can influence the gut microbiota.
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq pp1430 - 1435 Björn Reinius, Jeff E Mold, Daniel Ramskold, Qiaolin Deng, Per Johnsson et al. doi:10.1038/ng.3678 Rickard Sandberg and colleagues use allele-sensitive single-cell RNA-seq on primary mouse fibroblasts and human T cells to study clonal and dynamic monoallelic expression patterns. They find that the majority of random monoallelic expression of autosomal genes occurs transiently within individual cells rather than being stably inherited within clonally related cells.
Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development pp1436 - 1442 Vincent Loubiere, Anna Delest, Aubin Thomas, Boyan Bonev, Bernd Schuettengruber et al. doi:10.1038/ng.3671 Giacomo Cavalli, Anne-Marie Martinez and colleagues identify a large set of genes that are bound by PRC1 in the absence of H3K27me3 in Drosophila larval tissues and in differentiated human cell lines. Many of these genes, which regulate cell proliferation, signaling and polarity, are upregulated in PRC1-mutant tissues and contribute to tumor formation in Drosophila.
Reference-based phasing using the Haplotype Reference Consortium panel pp1443 - 1448 Po-Ru Loh, Petr Danecek, Pier Francesco Palamara, Christian Fuchsberger, Yakir A Reshef et al. doi:10.1038/ng.3679 Po-Ru Loh, Alkes Price and colleagues present Eagle2, a reference-based phasing algorithm that allows for highly accurate and efficient phasing of genotypes across a broad range of cohort sizes. They demonstrate an approximately 10% improvement in accuracy and 20% improvement in speed compared to a competing method, SHAPEIT2.
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