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Tracking genetic variants in the biomedical literature using LitVar 2.0 Nat. Genet. (IF 41.307) Pub Date : 2023-06-02 Alexis Allot, Chih-Hsuan Wei, Lon Phan, Timothy Hefferon, Melissa Landrum, Heidi L. Rehm, Zhiyong Lu
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Genetic and biological insights into spontaneous coronary artery dissection Nat. Genet. (IF 41.307) Pub Date : 2023-05-29
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Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation Nat. Genet. (IF 41.307) Pub Date : 2023-05-29 David Adlam, Takiy-Eddine Berrandou, Adrien Georges, Christopher P. Nelson, Eleni Giannoulatou, Joséphine Henry, Lijiang Ma, Montgomery Blencowe, Tamiel N. Turley, Min-Lee Yang, Sandesh Chopade, Chris Finan, Peter S. Braund, Ines Sadeg-Sayoud, Siiri E. Iismaa, Matthew L. Kosel, Xiang Zhou, Stephen E. Hamby, Jenny Cheng, Lu Liu, Ingrid Tarr, David W. M. Muller, Valentina d’Escamard, Annette King, Liam
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The impact of rare protein coding genetic variation on adult cognitive function Nat. Genet. (IF 41.307) Pub Date : 2023-05-25 Chia-Yen Chen, Ruoyu Tian, Tian Ge, Max Lam, Gabriela Sanchez-Andrade, Tarjinder Singh, Lea Urpa, Jimmy Z. Liu, Mark Sanderson, Christine Rowley, Holly Ironfield, Terry Fang, Mark Daly, Aarno Palotie, Ellen A. Tsai, Hailiang Huang, Matthew E. Hurles, Sebastian S. Gerety, Todd Lencz, Heiko Runz
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Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture Nat. Genet. (IF 41.307) Pub Date : 2023-05-25 Linda Kachuri, Angel C. Y. Mak, Donglei Hu, Celeste Eng, Scott Huntsman, Jennifer R. Elhawary, Namrata Gupta, Stacey Gabriel, Shujie Xiao, Kevin L. Keys, Akinyemi Oni-Orisan, José R. Rodríguez-Santana, Michael A. LeNoir, Luisa N. Borrell, Noah A. Zaitlen, L. Keoki Williams, Christopher R. Gignoux, Esteban González Burchard, Elad Ziv
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Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes Nat. Genet. (IF 41.307) Pub Date : 2023-05-25 Gaowei Wang, Joshua Chiou, Chun Zeng, Michael Miller, Ileana Matta, Jee Yun Han, Nikita Kadakia, Mei-Lin Okino, Elisha Beebe, Medhavi Mallick, Joan Camunas-Soler, Theodore dos Santos, Xiao-Qing Dai, Cara Ellis, Yan Hang, Seung K. Kim, Patrick E. MacDonald, Fouad R. Kandeel, Sebastian Preissl, Kyle J. Gaulton, Maike Sander
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Pathogen perception and deception in plant immunity by kinase fusion proteins Nat. Genet. (IF 41.307) Pub Date : 2023-05-22 Tzion Fahima, Gitta Coaker
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An unusual tandem kinase fusion protein confers leaf rust resistance in wheat Nat. Genet. (IF 41.307) Pub Date : 2023-05-22 Yajun Wang, Michael Abrouk, Spyridon Gourdoupis, Dal-Hoe Koo, Miroslava Karafiátová, István Molnár, Kateřina Holušová, Jaroslav Doležel, Naveenkumar Athiyannan, Emile Cavalet-Giorsa, Łukasz Jaremko, Jesse Poland, Simon G. Krattinger
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The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase Nat. Genet. (IF 41.307) Pub Date : 2023-05-22 Guotai Yu, Oadi Matny, Spyridon Gourdoupis, Naganand Rayapuram, Fatimah R. Aljedaani, Yan L. Wang, Thorsten Nürnberger, Ryan Johnson, Emma E. Crean, Isabel M.-L. Saur, Catherine Gardener, Yajuan Yue, Ngonidzashe Kangara, Burkhard Steuernagel, Sadiye Hayta, Mark Smedley, Wendy Harwood, Mehran Patpour, Shuangye Wu, Jesse Poland, Jonathan D. G. Jones, T. Lynne Reuber, Moshe Ronen, Amir Sharon, Matthew
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Including multiracial individuals is crucial for race, ethnicity and ancestry frameworks in genetics and genomics Nat. Genet. (IF 41.307) Pub Date : 2023-05-18 Daphne O. Martschenko, Hannah Wand, Jennifer L. Young, Genevieve L. Wojcik
Current ontologies of race, ethnicity and genetic ancestry rely on categorization, but have limitations — as exemplified by multiracial individuals. We argue that including these individuals will foster inclusion by better capturing complex identities, with equity benefits for the full human population.
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Shared genetics of substance use disorders Nat. Genet. (IF 41.307) Pub Date : 2023-05-12 Kyle Vogan
Genome-wide association studies of substance-use disorders, including problematic tobacco, alcohol, cannabis and opioid use, have provided evidence for a component of genetic liability that is shared across these traits. To explore this shared liability, Hatoum et al. performed multivariate genome-wide association analyses combining datasets for problematic alcohol use, problematic tobacco use, cannabis
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Linking TCL1A to clonal expansions in blood Nat. Genet. (IF 41.307) Pub Date : 2023-05-12 Safia Danovi
Clonal hematopoiesis of indeterminant potential (CHIP) is defined by the acquisition of driver mutations within hematopoietic stem cells (HSCs), that leads to clonal expansions. Factors that determine the extent of clonal expansion in CHIP remain poorly understood. Weinstock et al. developed a method named passenger-approximated clonal expansion rate (PACER) to ascertain clonal fitness. A genome-wide
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Quantifying tRNA abundance by sequencing Nat. Genet. (IF 41.307) Pub Date : 2023-05-12 Wei Li
The abundance and modification profiles of tRNAs are dynamic and contribute to their biological function. The quantification of tRNA abundance and chemical modifications has been challenging using currently available approaches. Lucas et al. developed a nanopore-based, high-throughput sequencing method, named Nano-tRNAseq, that enables accurate measurement of both the abundance and modification dynamics
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Transcription factor affinities in native chromatin Nat. Genet. (IF 41.307) Pub Date : 2023-05-12 Michael Fletcher
Methods such as ChIP–seq and CUT&RUN are used to identify transcription factor-binding sites in the genome, but do not inform on the biochemistry of transcription finding binding — and properties such as affinity and specificity are important for predicting the functional consequences of binding. Neikes et al. address this problem with binding affinities to native chromatin by sequencing (BANC-seq)
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Code deposition is unskippable Nat. Genet. (IF 41.307) Pub Date : 2023-05-12
As computational analysis becomes ever-more ubiquitous for researchers, the deposition of the underlying code is now an expected part of publication. Shortcomings in code sharing can lead to delays in peer review and publication, as well as reproducibility issues that are easily avoided with author preparation.
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CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses Nat. Genet. (IF 41.307) Pub Date : 2023-05-11 Zikun Yang, Chen Wang, Linxi Liu, Atlas Khan, Annie Lee, Badri Vardarajan, Richard Mayeux, Krzysztof Kiryluk, Iuliana Ionita-Laza
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Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk Nat. Genet. (IF 41.307) Pub Date : 2023-05-11 Shohei Kojima, Satoshi Koyama, Mirei Ka, Yuka Saito, Erica H. Parrish, Mikiko Endo, Sadaaki Takata, Misaki Mizukoshi, Keiko Hikino, Atsushi Takeda, Asami F. Gelinas, Steven M. Heaton, Rie Koide, Anselmo J. Kamada, Michiya Noguchi, Michiaki Hamada, Yoichiro Kamatani, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Yukio Nakamura, Kaoru Ito, Chikashi Terao, Yukihide Momozawa, Nicholas F. Parrish
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Clonal evolution during metastatic spread in high-risk neuroblastoma Nat. Genet. (IF 41.307) Pub Date : 2023-05-11 Gunes Gundem, Max F. Levine, Stephen S. Roberts, Irene Y. Cheung, Juan S. Medina-Martínez, Yi Feng, Juan E. Arango-Ossa, Loic Chadoutaud, Mathieu Rita, Georgios Asimomitis, Joe Zhou, Daoqi You, Nancy Bouvier, Barbara Spitzer, David B. Solit, Filemon Dela Cruz, Michael P. LaQuaglia, Brian H. Kushner, Shakeel Modak, Neerav Shukla, Christine A. Iacobuzio-Donahue, Andrew L. Kung, Nai-Kong V. Cheung, Elli
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A systematic analysis of immune escape signals in the primary and metastatic tumor genome Nat. Genet. (IF 41.307) Pub Date : 2023-05-10 Jimmy Van den Eynden
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Genetic immune escape landscape in primary and metastatic cancer Nat. Genet. (IF 41.307) Pub Date : 2023-05-10 Francisco Martínez-Jiménez, Peter Priestley, Charles Shale, Jonathan Baber, Erik Rozemuller, Edwin Cuppen
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Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries Nat. Genet. (IF 41.307) Pub Date : 2023-05-08 Zhanju Liu, Ruize Liu, Han Gao, Seulgi Jung, Xiang Gao, Ruicong Sun, Xiaoming Liu, Yongjae Kim, Ho-Su Lee, Yosuke Kawai, Masao Nagasaki, Junji Umeno, Katsushi Tokunaga, Yoshitaka Kinouchi, Atsushi Masamune, Wenzhao Shi, Chengguo Shen, Zhenglin Guo, Kai Yuan, Shu Zhu, Dalin Li, Jianjun Liu, Tian Ge, Judy Cho, Mark J. Daly, Dermot P. B. McGovern, Byong Duk Ye, Kyuyoung Song, Yoichi Kakuta, Mingsong Li
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Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments Nat. Genet. (IF 41.307) Pub Date : 2023-05-08 Viraat Y. Goel, Miles K. Huseyin, Anders S. Hansen
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Innate immune cell genetic risk factors are linked to COVID-19 severity Nat. Genet. (IF 41.307) Pub Date : 2023-05-05
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Disentangling extrachromosomal circular DNA heterogeneity in single cells with scEC&T-seq Nat. Genet. (IF 41.307) Pub Date : 2023-05-05
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Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing Nat. Genet. (IF 41.307) Pub Date : 2023-05-04 Bin Zhang, Xin Gao
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Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells Nat. Genet. (IF 41.307) Pub Date : 2023-05-04 Rocío Chamorro González, Thomas Conrad, Maja C. Stöber, Robin Xu, Mădălina Giurgiu, Elias Rodriguez-Fos, Katharina Kasack, Lotte Brückner, Eric van Leen, Konstantin Helmsauer, Heathcliff Dorado Garcia, Maria E. Stefanova, King L. Hung, Yi Bei, Karin Schmelz, Marco Lodrini, Stefan Mundlos, Howard Y. Chang, Hedwig E. Deubzer, Sascha Sauer, Angelika Eggert, Johannes H. Schulte, Roland F. Schwarz, Kerstin
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Aberrant splicing prediction across human tissues Nat. Genet. (IF 41.307) Pub Date : 2023-05-04 Nils Wagner, Muhammed H. Çelik, Florian R. Hölzlwimmer, Christian Mertes, Holger Prokisch, Vicente A. Yépez, Julien Gagneur
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Using enormous genealogies to map causal variants in space and time Nat. Genet. (IF 41.307) Pub Date : 2023-05-01 Kelley Harris
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Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits Nat. Genet. (IF 41.307) Pub Date : 2023-05-01 Brian C. Zhang, Arjun Biddanda, Árni Freyr Gunnarsson, Fergus Cooper, Pier Francesco Palamara
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Single duplex DNA sequencing with CODEC detects mutations with high sensitivity Nat. Genet. (IF 41.307) Pub Date : 2023-04-27 Jin H. Bae, Ruolin Liu, Eugenia Roberts, Erica Nguyen, Shervin Tabrizi, Justin Rhoades, Timothy Blewett, Kan Xiong, Gregory Gydush, Douglas Shea, Zhenyi An, Sahil Patel, Ju Cheng, Sainetra Sridhar, Mei Hong Liu, Emilie Lassen, Anne-Bine Skytte, Marta Grońska-Pęski, Jonathan E. Shoag, Gilad D. Evrony, Heather A. Parsons, Erica L. Mayer, G. Mike Makrigiorgos, Todd R. Golub, Viktor A. Adalsteinsson
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Annotating and prioritizing human non-coding variants with RegulomeDB v.2 Nat. Genet. (IF 41.307) Pub Date : 2023-04-25 Shengcheng Dong, Nanxiang Zhao, Emma Spragins, Meenakshi S. Kagda, Mingjie Li, Pedro Assis, Otto Jolanki, Yunhai Luo, J. Michael Cherry, Alan P. Boyle, Benjamin C. Hitz
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Deep learning model improves COPD risk prediction and gene discovery Nat. Genet. (IF 41.307) Pub Date : 2023-04-24
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Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity Nat. Genet. (IF 41.307) Pub Date : 2023-04-24 Ryuya Edahiro, Yuya Shirai, Yusuke Takeshima, Shuhei Sakakibara, Yuta Yamaguchi, Teruaki Murakami, Takayoshi Morita, Yasuhiro Kato, Yu-Chen Liu, Daisuke Motooka, Yoko Naito, Ayako Takuwa, Fuminori Sugihara, Kentaro Tanaka, James B. Wing, Kyuto Sonehara, Yoshihiko Tomofuji, Ho Namkoong, Hiromu Tanaka, Ho Lee, Koichi Fukunaga, Haruhiko Hirata, Yoshito Takeda, Daisuke Okuzaki, Atsushi Kumanogoh, Yukinori
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Machine learning to examine the genetic underpinnings of cardiac fibrosis at scale Nat. Genet. (IF 41.307) Pub Date : 2023-04-20
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Genetics of myocardial interstitial fibrosis in the human heart and association with disease Nat. Genet. (IF 41.307) Pub Date : 2023-04-20 Victor Nauffal, Paolo Di Achille, Marcus D. R. Klarqvist, Jonathan W. Cunningham, Matthew C. Hill, James P. Pirruccello, Lu-Chen Weng, Valerie N. Morrill, Seung Hoan Choi, Shaan Khurshid, Samuel F. Friedman, Mahan Nekoui, Carolina Roselli, Kenney Ng, Anthony A. Philippakis, Puneet Batra, Patrick T. Ellinor, Steven A. Lubitz
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Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models Nat. Genet. (IF 41.307) Pub Date : 2023-04-17 Justin Cosentino, Babak Behsaz, Babak Alipanahi, Zachary R. McCaw, Davin Hill, Tae-Hwi Schwantes-An, Dongbing Lai, Andrew Carroll, Brian D. Hobbs, Michael H. Cho, Cory Y. McLean, Farhad Hormozdiari
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Whole-genome doubling perturbs the 3D genome Nat. Genet. (IF 41.307) Pub Date : 2023-04-13 Michael Fletcher
Whole-genome doubling (WGD) is a cancer hallmark, but its functional consequences during tumorigenesis are unclear. Lambuta et al. chemically induce WGD in three TP53-mutant cell line models and examine its effects on the 3D genome using single-cell and bulk genomic methods including Hi-C. Cells with WGD show a loss of chromatin segregation (LCS) characterized by epigenomic changes (H3K9me3 and CTCF
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Rare disease gene mining Nat. Genet. (IF 41.307) Pub Date : 2023-04-13 Kyle Vogan
Genome sequencing of large collections of individuals with rare diseases is accelerating the discovery of causal genes for monogenic disorders, but extracting robust associations between genotypes and phenotypes remains computationally and statistically challenging. To address this, Greene et al. developed a relational database framework called ‘Rareservoir’ that enables a more efficient representation
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Redefining teleost phylogeny Nat. Genet. (IF 41.307) Pub Date : 2023-04-13 Tiago Faial
Teleosts or ‘ray-finned’ fish comprise approximately half of all vertebrates. Despite their importance, the phylogeny of teleosts has been difficult to determine and the subject of ongoing debate. Parey et al. generated seven high-quality genome assemblies for species that represent key Elopomorpha (tarpons, eels) orders or families. They analyzed these seven Elopomorpha genomes in detail, along with
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Mutation rates across species Nat. Genet. (IF 41.307) Pub Date : 2023-04-13 Safia Danovi
The germline mutation rate (GMR) works hand in glove with genome evolution. GMRs differ significantly across species but understanding the underpinnings of this variation remains unclear. Bergeron et al. sequenced 151 mother–father–offspring triplets from 68 different vertebrate species. Using a bespoke bioinformatics pipeline to uniformly compute species-specific GMRs, they calculated a 40-fold variation
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The Allis code Nat. Genet. (IF 41.307) Pub Date : 2023-04-13
David Allis (1951–2023) was a leading figure in the field of chromatin biology. He inspired many generations of scientists both through his work and his own personal example as a mentor and colleague. His influential ‘histone code’ theory remains an important guiding principle to study and understand gene regulation.
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Inferring phylogenies from pandemic-scale genome datasets Nat. Genet. (IF 41.307) Pub Date : 2023-04-12
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Maximum likelihood pandemic-scale phylogenetics Nat. Genet. (IF 41.307) Pub Date : 2023-04-10 Nicola De Maio, Prabhav Kalaghatgi, Yatish Turakhia, Russell Corbett-Detig, Bui Quang Minh, Nick Goldman
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Tomato super-pangenome highlights the potential use of wild relatives in tomato breeding Nat. Genet. (IF 41.307) Pub Date : 2023-04-07
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Catching active enhancers via H2B N-terminal acetylation Nat. Genet. (IF 41.307) Pub Date : 2023-04-06 Chang Huang, Kristian Helin
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Precise modulation of transcription factor levels identifies features underlying dosage sensitivity Nat. Genet. (IF 41.307) Pub Date : 2023-04-06 Sahin Naqvi, Seungsoo Kim, Hanne Hoskens, Harold S. Matthews, Richard A. Spritz, Ophir D. Klein, Benedikt Hallgrímsson, Tomek Swigut, Peter Claes, Jonathan K. Pritchard, Joanna Wysocka
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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species Nat. Genet. (IF 41.307) Pub Date : 2023-04-06 Ning Li, Qiang He, Juan Wang, Baike Wang, Jiantao Zhao, Shaoyong Huang, Tao Yang, Yaping Tang, Shengbao Yang, Patiguli Aisimutuola, Ruiqiang Xu, Jiahui Hu, Chunping Jia, Kai Ma, Zhiqiang Li, Fangling Jiang, Jie Gao, Haiyan Lan, Yongfeng Zhou, Xinyan Zhang, Sanwen Huang, Zhangjun Fei, Huan Wang, Hongbo Li, Qinghui Yu
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Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes Nat. Genet. (IF 41.307) Pub Date : 2023-04-06 Takeo Narita, Yoshiki Higashijima, Sinan Kilic, Tim Liebner, Jonas Walter, Chunaram Choudhary
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Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer Nat. Genet. (IF 41.307) Pub Date : 2023-04-06 Arvind Ravi, Matthew D. Hellmann, Monica B. Arniella, Mark Holton, Samuel S. Freeman, Vivek Naranbhai, Chip Stewart, Ignaty Leshchiner, Jaegil Kim, Yo Akiyama, Aaron T. Griffin, Natalie I. Vokes, Mustafa Sakhi, Vashine Kamesan, Hira Rizvi, Biagio Ricciuti, Patrick M. Forde, Valsamo Anagnostou, Jonathan W. Riess, Don L. Gibbons, Nathan A. Pennell, Vamsidhar Velcheti, Subba R. Digumarthy, Mari Mino-Kenudson
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Unexpected heterogeneity in oropharyngeal squamous cell tumors Nat. Genet. (IF 41.307) Pub Date : 2023-04-04 David J. Peace, Evgeny Izumchenko, David Sidransky
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New genetic loci associated with gestational duration show a complex link with birth weight Nat. Genet. (IF 41.307) Pub Date : 2023-04-04
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Chimeric transcripts of transposable elements and genes are a source of tumor-specific antigens Nat. Genet. (IF 41.307) Pub Date : 2023-04-03
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MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner Nat. Genet. (IF 41.307) Pub Date : 2023-04-03 Guojia Xie, Ji-Eun Lee, Anna D. Senft, Young-Kwon Park, Younghoon Jang, Shreeta Chakraborty, Joyce J. Thompson, Kaitlin McKernan, Chengyu Liu, Todd S. Macfarlan, Pedro P. Rocha, Weiqun Peng, Kai Ge
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Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma Nat. Genet. (IF 41.307) Pub Date : 2023-04-03 Sidharth V. Puram, Michael Mints, Ananya Pal, Zongtai Qi, Ashley Reeb, Kyla Gelev, Thomas F. Barrett, Sophie Gerndt, Ping Liu, Anuraag S. Parikh, Salma Ramadan, Travis Law, Edmund A. Mroz, James W. Rocco, Doug Adkins, Wade L. Thorstad, Hiram A. Gay, Li Ding, Randal C. Paniello, Patrik Pipkorn, Ryan S. Jackson, Xiaowei Wang, Angela Mazul, Rebecca Chernock, Jose P. Zevallos, Jessica Silva-Fisher, Itay
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Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion Nat. Genet. (IF 41.307) Pub Date : 2023-04-03 Shu Zhang, Nadine Übelmesser, Mariano Barbieri, Argyris Papantonis
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Genetic effects on the timing of parturition and links to fetal birth weight Nat. Genet. (IF 41.307) Pub Date : 2023-04-03 Pol Solé-Navais, Christopher Flatley, Valgerdur Steinthorsdottir, Marc Vaudel, Julius Juodakis, Jing Chen, Triin Laisk, Abigail L. LaBella, David Westergaard, Jonas Bacelis, Ben Brumpton, Line Skotte, Maria C. Borges, Øyvind Helgeland, Anubha Mahajan, Matthias Wielscher, Frederick Lin, Catherine Briggs, Carol A. Wang, Gunn-Helen Moen, Robin N. Beaumont, Jonathan P. Bradfield, Abin Abraham, Gudmar Thorleifsson
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Nucleotide metabolism regulates human telomere length via telomerase activation Nat. Genet. (IF 41.307) Pub Date : 2023-03-30 Tracy M. Bryan
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Mathematical modeling of neuroblastoma associates evolutionary patterns with outcomes Nat. Genet. (IF 41.307) Pub Date : 2023-03-27 Giulio Caravagna
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Prevalent putative chromatin bivalency and partial resetting of H3K27me3 in plant sperm Nat. Genet. (IF 41.307) Pub Date : 2023-03-27
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Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements Nat. Genet. (IF 41.307) Pub Date : 2023-03-27 Nakul M. Shah, H. Josh Jang, Yonghao Liang, Ju Heon Maeng, Shin-Cheng Tzeng, Angela Wu, Noah L. Basri, Xuan Qu, Changxu Fan, Amy Li, Benjamin Katz, Daofeng Li, Xiaoyun Xing, Bradley S. Evans, Ting Wang