Friday, November 30, 2018

Nature Genetics Contents: December 2018 Volume 50 Number 12

Nature Genetics

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December 2018 Volume 50, Issue 12

News & Views
Technical Reports
Amendments & Corrections


HLS-CATCH: Cas-9 Assisted Gene Purification

Sage Science's targeted gene isolation technology, HLS-CATCH, integrates genomic DNA extraction with Cas9 digestion to excise large genomic targets (up to 400Kb). Since it does not depend on uniform hybrid-capture of short library fragments, CATCH libraries are easier to design, offer better detection of intragenic CNVs, and enable sequencing of genes that have pseudogenes.

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NGS Target Enrichment

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Winners announced!

We are delighted to announce the first ever winners of the Nature Research Awards for Inspiring Science and Innovating Science, in partnership with The Estée Lauder Companies. Congratulations to both our Award winners!

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Science is social    p1619


Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution    pp1620 - 1623
Thomas O. McDonald, Shaon Chakrabarti & Franziska Michor

Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'    pp1624 - 1626
Benjamin Werner, Marc J. Williams, Chris P. Barnes, Trevor A. Graham & Andrea Sottoriva

Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data    pp1626 - 1628
Abdul Balaparya & Subhajyoti De

Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'    pp1628 - 1630
Marc J. Williams, Benjamin Werner, Timon Heide, Chris P. Barnes, Trevor A. Graham et al.

Neutral tumor evolution?    pp1630 - 1633
Maxime Tarabichi, Iñigo Martincorena, Moritz Gerstung, Armand M. Leroi, Florian Markowetz et al.

Reply to 'Neutral tumor evolution?'    pp1633 - 1637
Timon Heide, Luis Zapata, Marc J. Williams, Benjamin Werner, Giulio Caravagna et al.

Reply to 'No evidence for unknown archaic ancestry in South Asia'    pp1637 - 1639
Mayukh Mondal, Ferran Casals, Partha P. Majumder & Jaume Bertranpetit

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News & Views

Human disease mutations highlight the inhibitory function of TIM-3    pp1640 - 1641
Karen O. Dixon, Madhumita Das & Vijay K. Kuchroo

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Mitochondrial genetic medicine    pp1642 - 1649
Douglas C. Wallace

Mitochondrial variants are important to consider when analyzing the genetics of various metabolic or age-related diseases. These mtDNA variants can influence the penetrance of a phenotype or interact differentially with nuclear DNA variants.


Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome    pp1650 - 1657
Tenzin Gayden, Fernando E. Sepulveda, Dong-Anh Khuong-Quang, Jonathan Pratt, Elvis T. Valera et al.

This study finds germline loss-of-function mutations in HAVCR2, which encodes the immune modulator TIM-3, in individuals with subcutaneous panniculitis-like T cell lymphomas and hemophagocytic lymphohistiocytosis, a life-threatening inflammatory condition.

Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment    pp1658 - 1665
Jillian M. Pattison, Sandra P. Melo, Samantha N. Piekos, Jessica L. Torkelson, Elizaveta Bashkirova et al.

Retinoic acid and BMP4 signaling, together with p63, contribute to dynamic long-range chromatin interactions during keratinocyte differentiation. TP63 decreases chromatin accessibility and promotes H3K27me3 accumulation at enhancers.

Cilia-driven cerebrospinal fluid flow directs expression of urotensin neuropeptides to straighten the vertebrate body axis    pp1666 - 1673
Xiaoli Zhang, Shuo Jia, Zhe Chen, Yan Ling Chong, Haibo Xie et al.

In zebrafish, cilia-driven flow of cerebrospinal fluid transports adrenergic signals that induce urotensin neuropeptides in spinal cord neurons. In turn, these neuropeptides activate their receptor on nearby muscle fibers, straightening the body axis.

Multiple transmissions of de novo mutations in families    pp1674 - 1680
Hákon Jónsson, Patrick Sulem, Gudny A. Arnadottir, Gunnar Pálsson, Hannes P. Eggertsson et al.

Analysis of 1,007 sibling pairs from 251 families identifies 878 de novo mutations shared by siblings at 448 sites. Recurrence probability based on parental somatic mosaicism, sibling sharing, parent of origin, mutation type and genomic position can range from 0.011% to 28.5%.

Meta-analysis of Icelandic and UK data sets identifies missense variants in SMO, IL11, COL11A1 and 13 more new loci associated with osteoarthritis    pp1681 - 1687
Unnur Styrkarsdottir, Sigrun H. Lund, Gudmar Thorleifsson, Florian Zink, Olafur A. Stefansson et al.

Genome-wide association meta-analysis of data sets from Iceland and the UK identifies 16 new risk loci for osteoarthritis, including missense variants in SMO, IL11, and COL11A1.


Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri    pp1688 - 1695
Tammi C. Vesth, Jane L. Nybo, Sebastian Theobald, Jens C. Frisvad, Thomas O. Larsen et al.

De novo assembly of 23 Aspergillus section Nigri and 6 Aspergillus niger genome sequences allows for inter- and intraspecies comparisons and prediction of secondary metabolite gene clusters.

Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia    pp1696 - 1704
Haihua Bai, Xiaosen Guo, Narisu Narisu, Tianming Lan, Qizhu Wu et al.

Whole-genome sequencing of 175 Mongolians representing six tribes highlights population-specific genetic architecture and substantial gene flow among northern Eurasian populations, including derived alleles shared by Mongolians and Finns.

Long noncoding RNA MALAT1 suppresses breast cancer metastasis    pp1705 - 1715
Jongchan Kim, Hai-Long Piao, Beom-Jun Kim, Fan Yao, Zhenbo Han et al.

Targeted inactivation, restoration and overexpression of MALAT1 in multiple in vivo models demonstrate that the lncRNA MALAT1 suppresses breast cancer metastasis through binding and inactivation of the pro-metastatic transcription factor TEAD.

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens    pp1716 - 1727
Michael S. Haney, Christopher J. Bohlen, David W. Morgens, James A. Ousey, Amira A. Barkal et al.

Eight genome-wide CRISPR screens identify genes required for substrate-specific phagocytosis. The study highlights roles for NHLRC2 in filopodia formation, very-long-chain fatty acids in substrate-specific phagocytosis and TM2D3 in uptake of amyloid-β aggregates.

Technical Reports

Distinguishing genetic correlation from causation across 52 diseases and complex traits    pp1728 - 1734
Luke J. O'Connor & Alkes L. Price

This study presents a new latent causal variable (LCV) model that distinguishes between genetic correlation and causation. Applying LCV to genome-wide association summary statistics for 52 traits identified genetically causal effects for 59 pairs of traits.

A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data    pp1735 - 1743
Benjamin J. Ainscough, Erica K. Barnell, Peter Ronning, Katie M. Campbell, Alex H. Wagner et al.

A machine learning approach for refinement of somatic variant calls automates this process and reduces bias stemming from inter-reviewer variability.

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains    pp1744 - 1751
A. Marieke Oudelaar, James O. J. Davies, Lars L. P. Hanssen, Jelena M. Telenius, Ron Schwessinger et al.

Tri-C is a new 3C approach to identify concurrent chromatin interactions at individual alleles. The authors observe specific higher-order structures involving simultaneous interactions between multiple enhancers and promoters, called regulatory hubs.

Amendments & Corrections

Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome    p1752
Daria V. Zhernakova, Trang H. Le, Alexander Kurilshikov, Biljana Atanasovska, Marc Jan Bonder et al.

Author Correction: Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps    p1752
Valentina Iotchkova, Jie Huang, John A Morris, Deepti Jain, Caterina Barbieri et al.

Author Correction: A genome-wide cross-trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases    p1753
Zhaozhong Zhu, Phil H. Lee, Mark D. Chaffin, Wonil Chung, Po-Ru Loh et al.

Author Correction: Public resources aid diabetes gene discovery    p1753
Diana L. Cousminer & Struan F. A. Grant

Author Correction: Distinguishing genetic correlation from causation across 52 diseases and complex traits    p1753
Luke J. O'Connor & Alkes L. Price

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors    p1754
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen et al.

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L    p1754
Jisen Zhang, Xingtan Zhang, Haibao Tang, Qing Zhang, Xiuting Hua et al.

Publisher Correction: Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits    p1755
Evangelos Evangelou, Helen R. Warren, David Mosen-Ansorena, Borbala Mifsud, Raha Pazoki et al.

Focal Point on Vaccine Research

The future of vaccine research may be in Asia - The signs are there in funding levels, and combined with Asian governments' interest in biotechnology, and a highly skilled, highly educated workforce, pharma giants are looking east.
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