Friday, August 31, 2018

Nature Genetics Contents: September 2018 Volume 50 Number 9

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Nature Genetics

Can saliva replace blood for DNA analysis?

Saliva is increasingly becoming a standard for
DNA-based sample collection in research and healthcare; but can it replace blood?
DNA quality, functionality and cost all need to be considered.  

Read the report and decide for yourself.

September 2018 Volume 50, Issue 9

News & Views
Amendments & Corrections

Communications Biology: Open for Submissions Communications Biology is a new open access journal that publishes high-quality primary research articles, reviews and commentary representing significant advances and new insights to the field of biology. The journal is now open for submissions.
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GPS for navigating healthcare    p1197



High prevalence of clonal monoallelic expression    pp1198 - 1199
Sébastien Vigneau, Svetlana Vinogradova, Virginia Savova & Alexander Gimelbrant

Reply to ‘High prevalence of clonal monoallelic expression’    pp1199 - 1200
Björn Reinius & Rickard Sandberg

COSMIC-3D provides structural perspectives on cancer genetics for drug discovery    pp1200 - 1202
Harry C. Jubb, Harpreet K. Saini, Marcel L. Verdonk & Simon A. Forbes

Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape    pp1203 - 1204
Lisa G. McFerrin, Michael Zager, Jianan Zhang, Gretchen Krenn, Robert McDermott et al.

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News & Views


Visualizing long-range enhancer–promoter interaction    pp1205 - 1206
Albert Tsai & Justin Crocker

Plant H3K27me3 has finally found its readers    pp1206 - 1208
Kristin Krause & Franziska Turck

Copy number signatures in ovarian cancer    pp1208 - 1209
Sohrab P. Shah

Genetic risks and clinical rewards    pp1210 - 1211
Andrew J. Schork, M. Anthony Schork & Nicholas J. Schork

JOBS of the week
Postdoctoral positions in Neuroepidemiology, Boston Children's Hospital
Boston Children's Hospital / Harvard Medical School
Research Fellow
Dana-Farber Cancer Institute (DFCI)
Research Associate
Imperial College London
Postdoctoral Associate, Functional Genomics
Center for Computational and Integrative Biology, MGH/HMS
Assistant / Associate Professor in Geomicrobiology
University of Waterloo, Canada
More Science jobs from
The Genetics of Neuropathic Pain and its Comorbidities
Bar Harbor, USA
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Communications Biology: Open for Submissions Communications Biology is a new open access journal that publishes high-quality primary research articles, reviews and commentary representing significant advances and new insights to the field of biology. The journal is now open for submissions. Find out more >>



Cancer genetics, precision prevention and a call to action    pp1212 - 1218
Clare Turnbull, Amit Sud & Richard S. Houlston

This proposal calls for the initiation of national population-screening programs to identify carriers of cancer gene mutations for long-term, large-scale analysis of longitudinal clinical data to aid in prevention and early detection of disease.




Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations    pp1219 - 1224
Amit V. Khera, Mark Chaffin, Krishna G. Aragam, Mary E. Haas, Carolina Roselli et al.

Genome-wide polygenic risk scores derived from GWAS data for five common diseases can identify subgroups of the population with risk approaching or exceeding that of a monogenic mutation.


Multi-ethnic genome-wide association study for atrial fibrillation    pp1225 - 1233
Carolina Roselli, Mark D. Chaffin, Lu-Chen Weng, Stefanie Aeschbacher, Gustav Ahlberg et al.

This large, multi-ethnic genome-wide association study identifies 97 loci significantly associated with atrial fibrillation. These loci are enriched for genes involved in cardiac development, electrophysiology, structure and contractile function.


Biobank-driven genomic discovery yields new insight into atrial fibrillation biology    pp1234 - 1239
Jonas B. Nielsen, Rosa B. Thorolfsdottir, Lars G. Fritsche, Wei Zhou, Morten W. Skov et al.

Large-scale association analyses identify 142 independent risk variants for atrial fibrillation. Pathway and functional enrichment analyses suggest that many of the putative risk genes act via cardiac structural remodeling.


Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry    pp1240 - 1246
Adam D. Durbin, Mark W. Zimmerman, Neekesh V. Dharia, Brian J. Abraham, Amanda Balboni Iniguez et al.

This study identifies a set of critical dependency genes in MYCN-amplified neuroblastoma that make up the oncogenic transcriptional regulatory circuitry underlying cell state and tumor survival.


EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis    pp1247 - 1253
Zhenlin Yang, Shuiming Qian, Ray N. Scheid, Li Lu, Xiangsong Chen et al.

EBS, which prevents premature flowering in Arabidopsis, is shown to bind H3K27me3 and H3K4me3 via different domains. Disruption of either EBS–H3K27me3 or EBS–H3K4me3 interaction induces early floral transition.




Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants    pp1254 - 1261


Two BAH-domain-containing proteins (SHL and EBS) form a complex with EMF1, reading and effecting the H3K27me3 mark in Arabidopsis. The BAH-EMF1c complex thus shows PRC1-like functions in higher plants.


Copy number signatures and mutational processes in ovarian carcinoma    pp1262 - 1270
Geoff Macintyre, Teodora E. Goranova, Dilrini De Silva, Darren Ennis, Anna M. Piskorz et al.

The authors identify copy number signatures from shallow whole-genome sequencing of high-grade serous ovarian cancer (HGSOC) cases. HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in genomic aberration.


Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors    pp1271 - 1281
Diana Miao, Claire A. Margolis, Natalie I. Vokes, David Liu, Amaro Taylor-Weiner et al.

Analysis of sequencing data from 249 cancer patients with clinically annotated outcomes to immune checkpoint therapy identifies correlates of treatment response. The results highlight complexity in identifying events that generate an immunoresponsive tumor environment.


The maize W22 genome provides a foundation for functional genomics and transposon biology    pp1282 - 1288
Nathan M. Springer, Sarah N. Anderson, Carson M. Andorf, Kevin R. Ahern, Fang Bai et al.

Sequencing and de novo assembly of the maize W22 reference genome enable accurate placement of Mutator (Mu) and Dissociation (Ds) transposable element insertions, providing a foundation for maize functional genomics and transposon biology.


Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes    pp1289 - 1295
Silong Sun, Yingsi Zhou, Jian Chen, Junpeng Shi, Haiming Zhao et al.

The de novo genome assembly of maize line Mo17 and comparative analysis with other sequenced maize lines show extensive gene-order variations. This study provides insights into maize evolution and has implications for improving maize hybrid lines.


Dynamic interplay between enhancer–promoter topology and gene activity    pp1296 - 1303
Hongtao Chen, Michal Levo, Lev Barinov, Miki Fujioka, James B. Jaynes et al.

The authors use genome editing and live imaging to visualize physical enhancer–promoter interaction and transcription at the single-cell level in Drosophila embryos. They show that sustained proximity of an enhancer to its target is required for transcription.


Relatedness disequilibrium regression estimates heritability without environmental bias    pp1304 - 1310
Alexander I. Young, Michael L. Frigge, Daniel F. Gudbjartsson, Gudmar Thorleifsson, Gyda Bjornsdottir et al.

Relatedness disequilibrium regression is a new method for estimating heritability that removes environmental bias by taking advantage of variation in relatedness due to random Mendelian segregation.


High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability    pp1311 - 1317
Pier Francesco Palamara, Jonathan Terhorst, Yun S. Song & Alkes L. Price

ASMC is a new method to estimate coalescence times using SNP array or sequencing data. When applied to data from the UK Biobank or Genome of the Netherlands, ASMC detects signals of recent positive selection and background selection.


Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits    pp1318 - 1326
Yan Zhang, Guanghao Qi, Ju-Hyun Park & Nilanjan Chatterjee

Analysis of summary statistics from 32 GWAS datasets using a new likelihood-based approach evaluates polygenicity across different traits. Effect-size distributions predict the sample sizes needed to explain the SNP-based heritability of traits.




Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk    pp1327 - 1334
Stephane E. Castel, Alejandra Cervera, Pejman Mohammadi, François Aguet, Ferran Reverter et al.

Analysis of GTEx, cancer and autism data sets shows that cis-regulatory variation can modify the penetrance of coding variants. Deleterious coding variants on regulatory haplotypes resulting in high expression are enriched in disease cohorts and selected against in general populations.


Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies    pp1335 - 1341
Wei Zhou, Jonas B. Nielsen, Lars G. Fritsche, Rounak Dey, Maiken E. Gabrielsen et al.

SAIGE (Scalable and Accurate Implementation of GEneralized mixed model) is a generalized mixed model association test that can efficiently analyze large data sets while controlling for unbalanced case-control ratios and sample relatedness, as shown by applying SAIGE to the UK Biobank data for > 1,400 binary phenotypes.


Amendments & Corrections


Author Correction: Quantification of subclonal selection in cancer from bulk sequencing data    p1342
Marc J. Williams, Benjamin Werner, Timon Heide, Christina Curtis, Chris P. Barnes et al.

Author Correction: Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition    p1342
Kerrin S. Small, Marijana Todorčević, Mete Civelek, Julia S. El-Sayed Moustafa, Xiao Wang et al.

Author Correction: Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis    p1343
Johannes Waage, Marie Standl, John A. Curtin, Leon E. Jessen, Jonathan Thorsen et al.

Publisher Correction: Compartmentalized activities of the pyruvate dehydrogenase complex sustain lipogenesis in prostate cancer    p1343
Jingjing Chen, Ilaria Guccini, Diletta Di Mitri, Daniela Brina, Ajinkya Revandkar et al.

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Tissue-based profiling for confident decisions in immuno-oncology

Learn how standardizing tissue profiling in drug development and trial designs in immuno-oncology will improve decision making.

Thursday 12th September 2018

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