Genetics & Heredity

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Editorial Material Ecology

The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, Jose A. Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklos Balint

Summary: Progress in genome sequencing has enabled the generation of large-scale reference genomes, representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, allowing comprehensive analyses in population and functional genomics, and are expected to revolutionize conservation genomics.

TRENDS IN ECOLOGY & EVOLUTION (2022)

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Article Genetics & Heredity

Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis

Siddhartha P. Kar, Pedro M. Quiros, Muxin Gu, Tao Jiang, Jonathan Mitchell, Ryan Langdon, Vivek Iyer, Clea Barcena, M. S. Vijayabaskar, Margarete A. Fabre, Paul Carter, Slave Petrovski, Stephen Burgess, George S. Vassiliou

Summary: This study analyzes genetic data to understand the genetic predisposition and causal links of clonal hematopoiesis (CH) in a large population. It identifies new genetic loci associated with CH, subtype-specific associations, and causal relationships between CH and other traits.

NATURE GENETICS (2022)

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Article Evolutionary Biology

Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination

Spyros Lytras, Joseph Hughes, Darren Martin, Phillip Swanepoel, Arne de Klerk, Rentia Lourens, Sergei L. Kosakovsky Pond, Wei Xia, Xiaowei Jiang, David L. Robertson

Summary: The study suggests that horseshoe bats in southern China and Southeast Asia are likely the reservoir species for the proximal animal ancestor of SARS-CoV-2. The research also reveals recent geographic movement and cocirculation of these viruses' ancestors. However, a direct proximal ancestor to SARS-CoV-2 has not been sampled yet, highlighting the need for more wildlife sampling to determine the exact origins, intermediate species involved in transmission, and the diversity of related sarbecoviruses that pose a high risk for future spillovers.

GENOME BIOLOGY AND EVOLUTION (2022)

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Article Genetics & Heredity

Resveratrol protects against myocardial ischemia-reperfusion injury via attenuating ferroptosis

Ting Li, Ying Tan, Shao Ouyang, Jin He, Lingling Liu

Summary: Res has been shown to protect against myocardial I/R injury by reducing oxidative stress and inhibiting ferroptosis, potentially through the regulation of USP19-Beclin1 autophagy.

GENE (2022)

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Review Biotechnology & Applied Microbiology

Statistics or biology: the zero-inflation controversy about scRNA-seq data

Ruochen Jiang, Tianyi Sun, Dongyuan Song, Jingyi Jessica Li

Summary: Researchers have differing views on the interpretation of zeros in single-cell RNA-seq data, with some considering them as biological signals while others see them as missing data; factors contributing to biological and non-biological zeros were discussed, as well as their impact on data analysis; emphasis was placed on the importance of transparent analysis.

GENOME BIOLOGY (2022)

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Article Biotechnology & Applied Microbiology

Lyophilization provides long-term stability for a lipid nanoparticle-formulated , nucleoside-modified mRNA vaccine

Hiromi Muramatsu, Kieu Lam, Csaba Bajusz, Dorottya Laczko, Katalin Kariko, Petra Schreiner, Alan Martin, Peter Lutwyche, James Heyes, Norbert Pardi

Summary: Research demonstrates that nucleoside-modified mRNA-LNP vaccines can be lyophilized and maintain their physicochemical properties after storage at room temperature for 12 weeks or at 4℃ for at least 24 weeks. Comparative studies also show that lyophilized mRNA-LNP vaccines maintain high expression and immunogenicity even after storage.

MOLECULAR THERAPY (2022)

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Review Plant Sciences

Developing drought-smart, ready-to-grow future crops

Ali Raza, Muhammad Salman Mubarik, Rahat Sharif, Madiha Habib, Warda Jabeen, Chong Zhang, Hua Chen, Zhong-Hua Chen, Kadambot H. M. Siddique, Weijian Zhuang, Rajeev K. Varshney

Summary: Breeding crop plants with increased yield potential and improved tolerance to drought stress is crucial for global food security. Understanding the physiological, biochemical, molecular, and ecological mechanisms associated with drought stress is essential. Suboptimal water sources negatively impact crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. Mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods can help control the detrimental effects of drought stress and develop drought-smart cultivars.

PLANT GENOME (2023)

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Article Genetics & Heredity

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

William L. Hwang, Karthik A. Jagadeesh, Jimmy A. Guo, Hannah Hoffman, Payman Yadollahpour, Jason W. Reeves, Rahul Mohan, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Orr Ashenberg, Samouil L. Farhi, Denis Schapiro, Prajan Divakar, Eric Miller, Daniel R. Zollinger, George Eng, Jason M. Schenkel, Jennifer Su, Carina Shiau, Patrick Yu, William A. Freed-Pastor, Domenic Abbondanza, Arnav Mehta, Joshua Gould, Conner Lambden, Caroline B. M. Porter, Alexander Tsankov, Danielle Dionne, Julia Waldman, Michael S. Cuoco, Lan Nguyen, Toni Delorey, Devan Phillips, Jaimie L. Barth, Marina Kem, Clifton Rodrigues, Debora Ciprani, Jorge Roldan, Piotr Zelga, Vjola Jorgji, Jonathan H. Chen, Zackery Ely, Daniel Zhao, Kit Fuhrman, Robin Fropf, Joseph M. Beechem, Jay S. Loeffler, David P. Ryan, Colin D. Weekes, Cristina R. Ferrone, Motaz Qadan, Martin J. Aryee, Rakesh K. Jain, Donna S. Neuberg, Jennifer Y. Wo, Theodore S. Hong, Ramnik Xavier, Andrew J. Aguirre, Orit Rozenblatt-Rosen, Mari Mino-Kenudson, Carlos Fernandez-del Castillo, Andrew S. Liss, David T. Ting, Tyler Jacks, Aviv Regev

Summary: This study provides a high-resolution molecular landscape of pancreatic ductal adenocarcinoma (PDAC) using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling. It identifies recurrent expression programs in malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program associated with poor prognosis. The study also reveals three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes. This refined molecular and cellular classification can guide clinical trials and therapeutic targeting for specific cellular phenotypes and multicellular interactions.

NATURE GENETICS (2022)

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Article Genetics & Heredity

ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG)

David T. Miller, Kristy Lee, Noura S. Abul-Husn, Laura M. Amendla, Kyle Brothers, Wendy K. Chung, Michael H. Gollob, Adam S. Gordon, Steven M. Harrison, Ray E. Hershberger, Teri E. Klein, Carolyn Sue Richards, Douglas R. Stewart, Christa Lese Martin

Summary: This statement serves as an educational resource for medical geneticists and clinicians, providing guidance for quality medical services. Clinicians are advised to use their professional judgment and document their reasons for specific procedures or tests. They should also be aware of the adoption date of this statement and consider potential intellectual property restrictions.

GENETICS IN MEDICINE (2022)

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Article Biotechnology & Applied Microbiology

Comparison and evaluation of statistical error models for scRNA-seq

Saket Choudhary, Rahul Satija

Summary: This study analyzes 59 scRNA-seq datasets to evaluate the performance of different error models in modeling variation in scRNA-seq data. The results show clear evidence of overdispersion for genes with sufficient sequencing depth, necessitating the use of a negative binomial model. The degree of overdispersion varies widely across datasets, systems, and gene abundances.

GENOME BIOLOGY (2022)

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Article Genetics & Heredity

Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease

Julie E. Horowitz, Jack A. Kosmicki, Amy Damask, Deepika Sharma, Genevieve H. L. Roberts, Anne E. Justice, Nilanjana Banerjee, Marie Coignet, Ashish Yadav, Joseph B. Leader, Anthony Marcketta, Danny S. Park, Rouel Lanche, Evan Maxwell, Spencer C. Knight, Xiaodong Bai, Harendra Guturu, Dylan Sun, Asher Baltzell, Fabricio S. P. Kury, Joshua D. Backman, Ahna R. Girshick, Colm O'Dushlaine, Shannon R. McCurdy, Raghavendran Partha, Adam J. Mansfield, David A. Turissini, Alexander H. Li, Miao Zhang, Joelle Mbatchou, Kyoko Watanabe, Lauren Gurski, Shane E. McCarthy, Hyun M. Kang, Lee Dobbyn, Eli Stahl, Anurag Verma, Giorgio Sirugo, Marylyn D. Ritchie, Marcus Jones, Suganthi Balasubramanian, Katherine Siminovitch, William J. Salerno, Alan R. Shuldiner, Daniel J. Rader, Tooraj Mirshahi, Adam E. Locke, Jonathan Marchini, John D. Overton, David J. Carey, Lukas Habegger, Michael N. Cantor, Kristin A. Rand, Eurie L. Hong, Jeffrey G. Reid, Catherine A. Ball, Aris Baras, Goncalo R. Abecasis, Manuel A. R. Ferreira

Summary: A variant that downregulates ACE2 expression is found to reduce the risk of SARS-CoV-2 infection. Associations of previously reported risk variants are replicated, and certain variants are associated with worse outcomes in individuals infected with the virus. A genetic risk score improves the prediction of disease severity.

NATURE GENETICS (2022)

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Article Genetics & Heredity

Portability of 245 polygenic scores when derived from the UK Biobank and applied to 9 ancestry groups from the same cohort

Florian Prive, Hugues Aschard, Shai Carmi, Lasse Folkersen, Clive Hoggart, Paul F. O'Reilly, Bjarni J. Vilhjalmsson

Summary: This study examines the portability of polygenic scores (PGSs) between ancestries and finds a significant reduction in portability when PGSs trained using Northwestern European individuals are applied to other ancestry groups.

AMERICAN JOURNAL OF HUMAN GENETICS (2022)

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Review Genetics & Heredity

A guide for the diagnosis of rare and undiagnosed disease: beyond the exome

Shruti Marwaha, Joshua W. Knowles, Euan A. Ashley

Summary: Rare diseases affect hundreds of millions of people worldwide, with traditional diagnostic techniques often failing to provide accurate diagnoses. New technologies such as whole genome sequencing and transcriptomics offer additional benefits in diagnosing undiagnosed patients. This review discusses the potential of these technologies, as well as computational methods and automation in genomic analysis.

GENOME MEDICINE (2022)

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Review Genetics & Heredity

Alternative splicing as a source of phenotypic diversity

Charlotte J. Wright, Christopher W. J. Smith, Chris D. Jiggins

Summary: This article discusses how alternative splicing generates phenotypic diversity and contributes to adaptation and species divergence. Comparisons of splicing profiles between closely related species using new technologies have helped in understanding the evolution of alternative splicing.

NATURE REVIEWS GENETICS (2022)

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Review Genetics & Heredity

Gut microbiota in patients with obesity and metabolic disorders - a systematic review

Zhilu Xu, Wei Jiang, Wenli Huang, Yu Lin, Francis K. L. Chan, Siew C. Ng

Summary: This study identified specific bacteria associated with obesity and metabolic disorders in both western and eastern populations. Mechanistic studies are required to determine whether these microbes are a cause or a product of obesity and metabolic disorders.

GENES AND NUTRITION (2022)

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Article Ecology

Seed germination and vigor: ensuring crop sustainability in a changing climate

Reagan C. Reed, Kent J. Bradford, Imtiyaz Khanday

Summary: Maintaining a steady food supply for the increasing world population will require high-yielding crop plants that can thrive under changing conditions. Seed vigor plays a crucial role in the successful establishment of plants, and climate change, including warming trends and temperature variability, can affect seed germination and growth.

HEREDITY (2022)

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Review Genetics & Heredity

Biological roles of adenine methylation in RNA

Konstantinos Boulias, Eric Lieberman Greer

Summary: Boulias and Greer review the functions of N-6-methyladenosine (m(6)A) in RNA, covering its impact on RNA substrates, chromatin architecture, gene expression regulation, genome stability, as well as its roles in stem-cell differentiation, neurogenesis, and immunity.

NATURE REVIEWS GENETICS (2023)

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Article Biotechnology & Applied Microbiology

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

Ping Lin, Kailiang Wang, Yupeng Wang, Zhikang Hu, Chao Yan, Hu Huang, Xianjin Ma, Yongqing Cao, Wei Long, Weixin Liu, Xinlei Li, Zhengqi Fan, Jiyuan Li, Ning Ye, Huadong Ren, Xiaohua Yao, Hengfu Yin

Summary: This study establishes a chromosome-scale reference genome for oil-Camellia plants and reveals the genetic and genomic basis of oil-Camellia domestication. Artificial selection of genes involved in oil biosynthesis and phytohormone pathways contributes to improving the yield and quality of seed oil in oil-Camellia.

GENOME BIOLOGY (2022)

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Review Biotechnology & Applied Microbiology

COVID-19 mRNA vaccines: Platforms and current developments

Gabor Tamas Szabo, Azita Josefine Mahiny, Irena Vlatkovic

Summary: Since the discovery of the advantages of mRNA vaccines nearly 30 years ago, significant progress has been made in this field. The development of COVID-19 vaccines using mRNA technology has achieved unprecedented success globally, demonstrating the safety and effectiveness of mRNA vaccines in combating COVID-19 and highlighting their potential for other infectious diseases and medical conditions.

MOLECULAR THERAPY (2022)

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Article Genetics & Heredity

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Laurence J. Howe, Michel G. Nivard, Tim T. Morris, Ailin F. Hansen, Humaira Rasheed, Yoonsu Cho, Geetha Chittoor, Rafael Ahlskog, Penelope A. Lind, Teemu Palviainen, Matthijs D. van der Zee, Rosa Cheesman, Massimo Mangino, Yunzhang Wang, Shuai Li, Lucija Klaric, Scott M. Ratliff, Lawrence F. Bielak, Marianne Nygaard, Alexandros Giannelis, Emily A. Willoughby, Chandra A. Reynolds, Jared V. Balbona, Ole A. Andreassen, Helga Ask, Aris Baras, Christopher R. Bauer, Dorret I. Boomsma, Archie Campbell, Harry Campbell, Zhengming Chen, Paraskevi Christofidou, Elizabeth Corfield, Christina C. Dahm, Deepika R. Dokuru, Luke M. Evans, Eco J. C. de Geus, Sudheer Giddaluru, Scott D. Gordon, K. Paige Harden, W. David Hill, Amanda Hughes, Shona M. Kerr, Yongkang Kim, Hyeokmoon Kweon, Antti Latvala, Deborah A. Lawlor, Liming Li, Kuang Lin, Per Magnus, Patrik K. E. Magnusson, Travis T. Mallard, Pekka Martikainen, Melinda C. Mills, Pal Rasmus Njolstad, John D. Overton, Nancy L. Pedersen, David J. Porteous, Jeffrey Reid, Karri Silventoinen, Melissa C. Southey, Camilla Stoltenberg, Elliot M. Tucker-Drob, Margaret J. Wright, Hyeokmoon Kweon, John K. Hewitt, Matthew C. Keller, Michael C. Stallings, James J. Lee, Kaare Christensen, Sharon L. R. Kardia, Patricia A. Peyser, Jennifer A. Smith, James F. Wilson, John L. Hopper, Sara Hagg, Tim D. Spector, Jean-Baptiste Pingault, Robert Plomin, Alexandra Havdahl, Meike Bartels, Nicholas G. Martin, Sven Oskarsson, Anne E. Justice, Iona Y. Millwood, Kristian Hveem, Oyvind Naess, Cristen J. Willer, Bjorn Olav Asvold, Philipp D. Koellinger, Jaakko Kaprio, Sarah E. Medland, Robin G. Walters, Daniel J. Benjamin, Patrick Turley, David M. Evans, George Davey Smith, Caroline Hayward, Ben Brumpton, Gibran Hemani, Neil M. Davies

Summary: Estimates from genome-wide association studies (GWAS) can be influenced by inherited variation, population stratification, and indirect genetic effects. This study combines data from 178,086 siblings to generate population and within-family GWAS estimates for 25 phenotypes. The within-family estimates are smaller than population estimates for certain phenotypes and show differences in genetic correlations and Mendelian randomization analyses.

NATURE GENETICS (2022)

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