Thursday, May 3, 2018

Nature Genetics Contents: May 2018 Volume 50 Number 5

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TABLE OF CONTENTS

May 2018 Volume 50, Issue 5

Editorial
Correspondence
News & Views
Letters
Articles
Analysis
Technical Reports
Amendments & Corrections
 
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Editorial

 

Straws in a haystack    p631
doi:10.1038/s41588-018-0125-9

Correspondence

 

No evidence for unknown archaic ancestry in South Asia    pp632 - 633
Pontus Skoglund, Swapan Mallick, Nick Patterson & David Reich
doi:10.1038/s41588-018-0097-9

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News & Views

 

Expanding the toolbox for 3D genomics    pp634 - 635
Ralph Stadhouders
doi:10.1038/s41588-018-0112-1

Sizing up whole-genome sequencing studies of common diseases    pp635 - 637
Naomi R. Wray & Jacob Gratten
doi:10.1038/s41588-018-0113-0

 
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Letters

 

Telobox motifs recruit CLF/SWN-PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis    pp638 - 644
Yue Zhou, Yuejun Wang, Kristin Krause, Tingting Yang, Joram A. Dongus et al.
doi:10.1038/s41588-018-0109-9

This study provides genome-wide evidence of PRC2 recruitment by telomere-repeat-binding factors (TRBs) through telobox-related motifs in Arabidopsis. Telobox-related motifs recruit PRC2 through the interaction between TRBs and CLF/SWN.

 

The long tail of oncogenic drivers in prostate cancer    pp645 - 651
Joshua Armenia, Stephanie A. M. Wankowicz, David Liu, Jianjiong Gao, Ritika Kundra et al.
doi:10.1038/s41588-018-0078-z

Meta-analysis of exome sequencing data identifies new recurrently mutated driver genes for prostate cancer. Comparison of primary and metastatic tumors further identifies genomic markers for advanced prostate cancer that may inform risk stratification.

 

Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability    pp652 - 656
Pirro G. Hysi, Ana M. Valdes, Fan Liu, Nicholas A. Furlotte, David M. Evans et al.
doi:10.1038/s41588-018-0100-5

Genome-wide meta-analysis identifies >100 loci associated with hair color variation in humans of European ancestry. These loci explain a large portion of the heritability of this trait & provide insights into pathways regulating hair pigmentation.

 

Deconvolution of seed and RNA-binding protein crosstalk in RNAi-based functional genomics    pp657 - 661

doi:10.1038/s41588-018-0104-1

This study presents evidence that siRNAs or miRNAs with seed sequences that overlap RBP motifs have extended biological effects by perturbing RBP activity. Seed-to-RBP crosstalk contributes to off-target activity and growth phenotype modulation.

 

Polymer physics predicts the effects of structural variants on chromatin architecture    pp662 - 667
Simona Bianco, Darío G. Lupiáñez, Andrea M. Chiariello, Carlo Annunziatella, Katerina Kraft et al.
doi:10.1038/s41588-018-0098-8

The authors present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR correctly predicts ectopic contacts induced by pathogenic SVs at the mouse Epha4 locus.

 

Articles

 

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression    pp668 - 681
Naomi R. Wray, Stephan Ripke, Manuel Mattheisen, Maciej Trzaskowski, Enda M. Byrne et al.
doi:10.1038/s41588-018-0090-3

A genome-wide association meta-analysis of individuals with clinically assessed or self-reported depression identifies 44 independent risk loci. Comparisons with other psychiatric disorders and candidate gene analyses provide new insights into major depressive disorder.

 

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets    pp682 - 692
David C. Wedge, Gunes Gundem, Thomas Mitchell, Dan J. Woodcock, Inigo Martincorena et al.
doi:10.1038/s41588-018-0086-z

Joint analysis of new and previously published sequencing data for primary and metastatic prostate cancers identifies new candidate driver mutations and provides insights into disease progression and potential drug targets.

 

Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases    pp693 - 698
Marie Verbanck, Chia-Yen Chen, Benjamin Neale & Ron Do
doi:10.1038/s41588-018-0099-7

The MR-PRESSO test detects and corrects horizontal pleiotropy in multi-instrument Mendelian randomization (MR) analyses. Applying the MR-PRESSO test to 4,250 MR tests of complex traits and diseases finds horizontal pleiotropy in?>48% of causal relationships.

 

Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity    pp699 - 707
John B. Harley, Xiaoting Chen, Mario Pujato, Daniel Miller, Avery Maddox et al.
doi:10.1038/s41588-018-0102-3

Linking transcription factors with disease loci implicates EBNA2, encoded by Epstein-Barr virus, in autoimmune diseases. Applying the method more widely identifies associations for hundreds of transcription factors, illuminating disease mechanisms.

 

Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma    pp708 - 717
Ana C. deCarvalho, Hoon Kim, Laila M. Poisson, Mary E. Winn, Claudius Mueller et al.
doi:10.1038/s41588-018-0105-0

Analysis of glioblastoma samples and derived neurospheres and xenografts shows that chromosomal and extrachromosomal alterations often display divergent inheritance patterns during cell culture and xenografting.

 

Analysis

 

Inferring parsimonious migration histories for metastatic cancers    pp718 - 726
Mohammed El-Kebir, Gryte Satas & Benjamin J. Raphael
doi:10.1038/s41588-018-0106-z

MACHINA is an algorithm that analyzes metastatic cancer sequence data to simultaneously infer clone trees and migration histories. Analysis of different metastatic cancer datasets provides more evidence for simple, rather than complex, migration patterns.

 

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder    pp727 - 736
Donna M. Werling, Harrison Brand, Joon-Yong An, Matthew R. Stone, Lingxue Zhu et al.
doi:10.1038/s41588-018-0107-y

This study presents a framework to evaluate rare and de novo variation from whole-genome sequencing (WGS). The work suggests that robust results from WGS studies will require large cohorts and strategies that consider the substantial multiple-testing burden.

 

Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits    pp737 - 745
Luke M. Evans, Rasool Tahmasbi, Scott I. Vrieze, Gonçalo R. Abecasis, Sayantan Das et al.
doi:10.1038/s41588-018-0108-x

This analysis compares methods for estimating the heritability and genetic architecture of complex traits using whole-genome data. The results provide guidance for best practices and proper interpretation of published heritability estimates.

 

Signatures of negative selection in the genetic architecture of human complex traits    pp746 - 753
Jian Zeng, Ronald de Vlaming, Yang Wu, Matthew R. Robinson, Luke R. Lloyd-Jones et al.
doi:10.1038/s41588-018-0101-4

BayesS estimates SNP-based heritability, polygenicity, and the relationship between effect size and minor allele frequency using genome-wide SNP data. Applying BayesS to UK Biobank data identifies signatures of natural selection for 23 complex traits.

 

Technical Reports

 

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture    pp754 - 763
Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal et al.
doi:10.1038/s41588-018-0111-2

DLO Hi-C is a new method to investigate the 3D genome. It requires only two rounds of digestion and ligation and removes non-ligated DNA in a cost-effective step by purifying specific linker-ligated DNA fragments.

 

Amendments & Corrections

 

Author Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells    p764
Nipun Verma, Heng Pan, Louis C. Doré, Abhijit Shukla, Qing V. Li et al.
doi:10.1038/s41588-017-0025-4

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis    p764
Francesc Coll, Jody Phelan, Grant A. Hill-Cawthorne, Mridul B. Nair, Kim Mallard et al.
doi:10.1038/s41588-018-0074-3

Publisher Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells    p764
Nipun Verma, Heng Pan, Louis C. Doré, Abhijit Shukla, Qing V. Li et al.
doi:10.1038/s41588-017-0024-5

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity    pp765 - 766
Valérie Turcot, Yingchang Lu, Heather M. Highland, Claudia Schurmann, Anne E. Justice et al.
doi:10.1038/s41588-018-0050-y

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity    pp766 - 767
Valérie Turcot, Yingchang Lu, Heather M. Highland, Claudia Schurmann, Anne E. Justice et al.
doi:10.1038/s41588-018-0082-3

Publisher Correction: BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange-like syndrome    p767
Gabrielle Olley, Morad Ansari, Hemant Bengani, Graeme R. Grimes, James Rhodes et al.
doi:10.1038/s41588-018-0069-0

Publisher Correction: Embryonic defects induced by maternal obesity in mice derive from Stella insufficiency in oocytes    p768
Longsen Han, Chao Ren, Ling Li, Xiaoyan Li, Juan Ge et al.
doi:10.1038/s41588-018-0077-0

Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution    p768
Jeramiah J. Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C. Keinath et al.
doi:10.1038/s41588-018-0075-2

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