Thursday, August 2, 2018

Nature Genetics Contents: August 2018 Volume 50 Number 8

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Nature Genetics

Read the latest science news from A*STAR, the Agency for Science, Technology and Research, Singapore's leading research organization

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Mutations: Pinpointing cancer drivers 
Genetics: Mutation linked to rare skin disease 
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August 2018 Volume 50, Issue 8

Amendments & Corrections
Focus on Autoimmune Disease from Nature Immunology

A series of Reviews specially commissioned by Nature Immunology discuss the genetic, environmental, microbial and cellular factors underpinning autoimmune disease as well as highlight avenues for therapeutic intervention. 

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DNA methylation haplotypes as cancer markers    pp1062 - 1063
Cathal Seoighe, Nick J. Tosh & John M. Greally

Reply to ‘DNA methylation haplotypes as cancer markers’    pp1063 - 1066
Dinh Diep & Kun Zhang

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Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma    pp1067 - 1071
Stuart MacGregor, Jue-Sheng Ong, Jiyuan An, Xikun Han, Tiger Zhou et al.

A combined analysis of participants from the UK Biobank and the International Glaucoma Genetic Consortium identifies 85 new loci for intraocular pressure (IOP). Pathway analysis uncovers new pathways associated with both IOP and glaucoma.


Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis    pp1072 - 1080
Johannes Waage, Marie Standl, John A. Curtin, Leon E. Jessen, Jonathan Thorsen et al.

Genome-wide association analyses identify new risk loci for allergic rhinitis and for sensitization to inhalant allergens. The associated regions implicate immune-related pathways, including innate and adaptive IgE-related mechanisms.


Common variation near IRF6 is associated with IFN-β-induced liver injury in multiple sclerosis    pp1081 - 1085
Kaarina Kowalec, Galen E. B. Wright, Britt I. Drögemöller, Folefac Aminkeng, Amit P. Bhavsar et al.

A genome-wide study identifies common variation near IRF6 associated with liver injury induced by IFN-β in individuals treated for multiple sclerosis. The risk locus is associated with differential expression of IRF6 and may help guide safer use of this biologic.


Krebs-cycle-deficient hereditary cancer syndromes are defined by defects in homologous-recombination DNA repair    pp1086 - 1092
Parker L. Sulkowski, Ranjini K. Sundaram, Sebastian Oeck, Christopher D. Corso, Yanfeng Liu et al.

High levels of fumarate or succinate suppress the homologous-recombination DNA-repair pathway in cancer cells that are deficient for FH or SDH, respectively. These tumor cells are vulnerable to PARP inhibitors.


Biallelic loss of human CTNNA2, encoding αN-catenin, leads to ARP2/3 complex overactivity and disordered cortical neuronal migration    pp1093 - 1101
Ashleigh E. Schaffer, Martin W. Breuss, Ahmet Okay Caglayan, Nouriya Al-Sanaa, Hind Y. Al-Abdulwahed et al.

Biallelic truncating mutations in CTNNA2, encoding αN-catenin, cause a new pachygyria syndrome associated with actin regulation and ARP2 and ARP3 repression in neurons.


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Adaptation and conservation insights from the koala genome    pp1102 - 1111
Rebecca N. Johnson, Denis O’Meally, Zhiliang Chen, Graham J. Etherington, Simon Y. W. Ho et al.

The assembly of the genome of the koala provides insights into its adaptive biology and identifies gene expansions that contribute to its ability to detoxify eucalyptus-derived compounds and perceive plant secondary metabolites.


Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals    pp1112 - 1121
James J. Lee, Robbee Wedow, Aysu Okbay, Edward Kong, Omeed Maghzian et al.

Gene discovery and polygenic predictions from a genome-wide association study of educational attainment in 1.1 million individuals.


Type 2 diabetes risk alleles in PAM impact insulin release from human pancreatic β-cells    pp1122 - 1131
Soren K. Thomsen, Anne Raimondo, Benoit Hastoy, Shahana Sengupta, Xiao-Qing Dai et al.

Coding variants in peptidylglycine α-amidating monooxygenase (PAM) associated with type 2 diabetes risk negatively impact overall PAM activity via defects in expression and catalytic function, resulting in reduced insulin content and altered dynamics of insulin secretion.


CRISPR–Cas9 genome editing in human cells occurs via the Fanconi anemia pathway    pp1132 - 1139
Chris D. Richardson, Katelynn R. Kazane, Sharon J. Feng, Elena Zelin, Nicholas L. Bray et al.

A coupled knockdown-editing screen shows that CRISPR–Cas9 editing in human cells requires the Fanconi anemia pathway, which acts by diverting double-strand break repair away from non-homologous end joining toward single-strand template repair.


Genetic determinants of co-accessible chromatin regions in activated T cells across humans    pp1140 - 1150
Rachel E. Gate, Christine S. Cheng, Aviva P. Aiden, Atsede Siba, Marcin Tabaka et al.

Analysis of ATAC-seq and RNA-seq data from stimulated T cells identifies genetic variants that disrupt transcription factor binding sites within ATAC-seq peaks. ATAC quantitative trait loci (ATAC-QTLs) are enriched for autoimmune disease-associated variants.


Enhancer hubs and loop collisions identified from single-allele topologies    pp1151 - 1160
Amin Allahyar, Carlo Vermeulen, Britta A. M. Bouwman, Peter H. L. Krijger, Marjon J. A. M. Verstegen et al.

Multi-contact 4C (MC-4C) sequencing analyzes multi-way conformations of individual alleles. MC-4C identifies the β-globin superenhancer as a hub that can accommodate two genes simultaneously and shows that CTCF-anchored loops collide in WAPL-depleted cells.


Predicting the clinical impact of human mutation with deep neural networks    pp1161 - 1170
Laksshman Sundaram, Hong Gao, Samskruthi Reddy Padigepati, Jeremy F. McRae, Yanjun Li et al.

Using common variants in six non-human primate species, the authors train a deep neural network that identifies pathogenic mutations in patients with rare disease with 88% accuracy and enables the discovery of 14 new candidate genes in intellectual disability.


Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk    pp1171 - 1179
Jian Zhou, Chandra L. Theesfeld, Kevin Yao, Kathleen M. Chen, Aaron K. Wong et al.

ExPecto is a deep learning–based framework that can predict the tissue-specific transcriptional effects of mutations on the basis of DNA sequence alone. ExPecto can prioritize causal variants from GWAS loci and be used to predict the disease risk of a variant.


High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction    pp1180 - 1188
Gang Li, Marta Martínez-Bonet, Di Wu, Yu Yang, Jing Cui et al.

A high-throughput method for functional SNP identification uses enzymatic restriction to detect altered regulatory protein binding and identifies 148 candidate fSNPs associated with juvenile idiopathic arthritis, including two that regulate STAT4 via the regulatory proteins SATB2 and H1.2.




Genome doubling shapes the evolution and prognosis of advanced cancers    pp1189 - 1195
Craig M. Bielski, Ahmet Zehir, Alexander V. Penson, Mark T. A. Donoghue, Walid Chatila et al.

The authors identify whole-genome doubling (WGD) in 30% of ~10,000 sequenced tumors from patients with advanced cancer. WGD correlates with increased risk of death across cancer types.


Amendments & Corrections


Author Correction: Reduced mutation rate in exons due to differential mismatch repair    p1196
Joan Frigola, Radhakrishnan Sabarinathan, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez et al.

Publisher Correction: Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases    p1196
Marie Verbanck, Chia-Yen Chen, Benjamin Neale & Ron Do

Publisher Correction: Eggs sense high-fat diet    p1196
Harry G. Leitch & Petra Hajkova

Publisher Correction: Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice    p1196
Qiang Zhao, Qi Feng, Hengyun Lu, Yan Li, Ahong Wang et al.

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