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- Efficient labeling of limited genomic material using CYTAG® SuperCGH
- High quality data for previously undetected CNVs in amniotic fluid and postnatal samples
- Results indicating superior DLR scores
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TABLE OF CONTENTS
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April 2018 Volume 50, Issue 4 |
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| Editorial Correspondence News & Views Brief Communications Letters Articles Analysis | |
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Focal Point on Japan's Designated National University Initiative Japan's radical new program to boost just a handful of universities has precedents across the world Access free online | | | |
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Genome Variation in Precision Medicine 2018 The aim of this conference is to take advantage of the past decade of enormous progress in understanding the human genome and the flourishing discoveries in clinical genetics and genetic epidemiology in order to identify and match therapeutic strategies more accurately to the people and populations that are best suited to benefit from them. May 25-27, 2018 | Chengdu, China | | | |
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Editorial | |
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FAIR to the community p473 doi:10.1038/s41588-018-0103-2 |
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Correspondence | |
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Plain-language medical vocabulary for precision diagnosis pp474 - 476 Nicole A. Vasilevsky, Erin D. Foster, Mark E. Engelstad, Leigh Carmody, Matt Might et al. doi:10.1038/s41588-018-0096-x |
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News & Views | |
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Brief Communications | |
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Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice pp483 - 486 Zoƫ N. Rogers, Christopher D. McFarland, Ian P. Winters, Jose A. Seoane, Jennifer J. Brady et al. doi:10.1038/s41588-018-0083-2 In vivo analysis of pairwise combinations of tumor suppressor losses using a barcode-based assay in mice identifies unpredicted genetic interactions and shows that the effects of tumor suppressor alterations can be context-dependent. |
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Letters | |
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Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence pp487 - 492 Jakob M. Goldmann, Vladimir B. Seplyarskiy, Wendy S. W. Wong, Thierry Vilboux, Pieter B. Neerincx et al. doi:10.1038/s41588-018-0071-6 Analysis of whole-genome sequencing data from 1,291 parentoffspring trios identifies patterns of clustered de novo mutations. Clusters increase in number with maternal age and are associated with DNA double-strand-break processes. |
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Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs pp493 - 497 Monique G. P. van der Wijst, Harm Brugge, Dylan H. de Vries, Patrick Deelen, Morris A. Swertz et al. doi:10.1038/s41588-018-0089-9 Single-cell RNA sequencing (scRNA-seq) of ~25,000 peripheral blood mononuclear cells from 45 donors identifies new celltype-specific cis-eQTLs and genetic variants that significantly alter co-expression relationships ('co-expression QTLs'). |
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Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding pp498 - 503 Gabriella E. Martyn, Beeke Wienert, Lu Yang, Manan Shah, Laura J. Norton et al. doi:10.1038/s41588-018-0085-0 The fetal globin gene repressors BCL11A and ZBTB7A directly bind ?-globin gene promoter regions. Repressor binding is disrupted by naturally occurring point mutations located upstream of the transcriptional start site that are associated with hereditary persistence of fetal hemoglobin. |
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A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins pp504 - 509 JoaquĆn Letelier, Elisa de la Calle-Mustienes, Joyce Pieretti, Silvia Naranjo, Ignacio Maeso et al. doi:10.1038/s41588-018-0080-5 The authors study the cis-regulatory evolution of the Shh locus in vertebrates. Using genomic editing and chromatin profiling, they conclude that paired fins emerged through the co-option of developmental programs for the median fins of gnathostomes. |
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Highly parallel genome variant engineering with CRISPRCas9 pp510 - 514 Meru J. Sadhu, Joshua S. Bloom, Laura Day, Jake J. Siegel, Sriram Kosuri et al. doi:10.1038/s41588-018-0087-y The authors present a CRISPR-library-based approach for highly efficient and precise genome-wide variant engineering. They examine the functional consequences of premature termination codons within all annotated essential genes in yeast. |
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Do you have a career question? The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. Hosted on the Naturejobs blog, the podcast is also available on iTunes and Soundcloud. Listen today! | | | |
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Articles | |
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Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma pp515 - 523 Rhamy Zeid, Matthew A. Lawlor, Evon Poon, Jaime M. Reyes, Mariateresa Fulciniti et al. doi:10.1038/s41588-018-0044-9 This study investigates the effects of MYCN on the chromatin and transcriptional landscape of neuroblastoma. The authors find that, at oncogenic levels, MYCN binds to canonical E-boxes at promoters and invades enhancers, leading to transcriptional amplification. |
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Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes pp524 - 537 Rainer Malik, Ganesh Chauhan, Matthew Traylor, Muralidharan Sargurupremraj, Yukinori Okada et al. doi:10.1038/s41588-018-0058-3 Multiancestry genome-wide association analyses identify new risk loci for stroke and stroke subtypes. Fine mapping and bioinformatics analyses of these risk loci point to mechanisms not previously implicated in stroke pathophysiology. |
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Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights pp538 - 548 Alexander Gusev, Nicholas Mancuso, Hyejung Won, Maria Kousi, Hilary K. Finucane et al. doi:10.1038/s41588-018-0092-1 A transcriptome-wide association study integrating genome-wide association data with expression data from brain, blood and adipose tissues identifies new candidate susceptibility genes for schizophrenia, providing a step toward understanding the underlying biology. |
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Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis pp549 - 558 Eleni Zengini, Konstantinos Hatzikotoulas, Ioanna Tachmazidou, Julia Steinberg, Fernando P. Hartwig et al. doi:10.1038/s41588-018-0079-y Genome-wide association study for osteoarthritis using data from UK Biobank identifies loci for knee- and hip-specific disease. Functional analyses of chondrocytes provide further insight into candidate causal genes. |
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Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes pp559 - 571 Anubha Mahajan, Jennifer Wessel, Sara M. Willems, Wei Zhao, Neil R. Robertson et al. doi:10.1038/s41588-018-0084-1 Trans-ethnic analyses of exome array data identify new risk loci for type 2 diabetes. Fine-mapping analyses using genome-wide association data show that the index coding variants represent the likely causal variants at only a subset of these loci. |
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Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition pp572 - 580 Kerrin S. Small, Marijana Todorcevic, Mete Civelek, Julia S. El-Sayed Moustafa, Xiao Wang et al. doi:10.1038/s41588-018-0088-x Analysis of the imprinted KLF14 locus shows that the type 2 diabetes risk alleles in this region act in adipocytes to reduce KLF14 expression and modulate the expression of almost 400 genes in trans, leading to a shift in body-fat distribution and insulin resistance specifically in females. |
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Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy pp581 - 590 Hiroyuki Ishiura, Koichiro Doi, Jun Mitsui, Jun Yoshimura, Miho Kawabe Matsukawa et al. doi:10.1038/s41588-018-0067-2 This study identifies TTTCA- and TTTTA-repeat expansions in benign adult familial myoclonic epilepsy. Cortical neurons from affected people exhibit RNA foci containing these expanded repeats, suggesting RNA toxicity as the mechanism underlying disease pathogenesis. |
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DNA methylation loss in late-replicating domains is linked to mitotic cell division pp591 - 602 Wanding Zhou, Huy Q. Dinh, Zachary Ramjan, Daniel J. Weisenberger, Charles M. Nicolet et al. doi:10.1038/s41588-018-0073-4 Whole-genome DNA methylation profiling and analysis of normal tissues from both human and mouse reveal that hypomethylation within partially methylated, late-replicating domains depends on sequence context, starts early in development, accumulates with cell divisions and progresses with organismal aging. |
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CRISPRCas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity pp603 - 612 Nicholas J. Kramer, Michael S. Haney, David W. Morgens, Ana Jovicic, Julien Couthouis et al. doi:10.1038/s41588-018-0070-7 A genome-wide CRISPR screen for suppressors and enhancers of C9ORF72 dipeptide-repeat protein toxicity identifies candidate genes involved in nucleocytoplasmic transport and other pathways including RNA processing and chromatin modification. |
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A global transcriptional network connecting noncoding mutations to changes in tumor gene expression pp613 - 620 Wei Zhang, Ana Bojorquez-Gomez, Daniel Ortiz Velez, Guorong Xu, Kyle S. Sanchez et al. doi:10.1038/s41588-018-0091-2 Analysis of whole-genome sequences and transcription data from tumors identifies noncoding loci in which mutations affect target gene expression. These somatic eQTLs can classify tumors into pathway-based subtypes and are disrupted in 88% of tumors. |
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Analysis | |
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Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types pp621 - 629 Hilary K. Finucane, Yakir A. Reshef, Verneri Anttila, Kamil Slowikowski, Alexander Gusev et al. doi:10.1038/s41588-018-0081-4 A new method tests whether disease heritability is enriched near genes with high tissue-specific expression. The authors use gene expression data together with GWAS summary statistics for 48 diseases and traits to identify disease-relevant tissues. |
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Ionis Pharmaceuticals, Nature Structural and Molecular Biology & Nature Biotechnology present: RNA at the Bench & Bedside October 8-10, La Jolla, USA RNA therapeutics is poised to deliver major advances. This conference will discuss the many roles of RNAs and the translation of basic science into new therapies. It will address the opportunities, current status and future of this exciting field. | | | |
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