Sequencing articles within Nature Communications

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  • Article
    | Open Access

    Genetic variants in ionotropic glutamate receptors have been implicated in neurodevelopmental disorders. Here, the authors report heterozygous de novo mutations in the GRIA2 gene in 28 individuals with intellectual disability and neurodevelopmental abnormalities associated with reduced Ca2+ transport and AMPAR currents.”

    • Vincenzo Salpietro
    • , Christine L. Dixon
    •  & Henry Houlden

  • Article
    | Open Access

    Whole-genome sequencing data reveals a large number of variants for testing their associations with phenotypic traits and diseases. Here, the authors develop WGScan, a statistical method for detecting the existence and estimating the locations of the association signal at genome-wide scale.

    • Zihuai He
    • , Bin Xu
    •  & Iuliana Ionita-Laza

  • Article
    | Open Access

    A major bottleneck in using DNA as a data storage medium is the slowness of sequencing. Here the authors decode 1.67 megabytes of information using a portable nanopore platform with an assembly strategy for increased throughput.

    • Randolph Lopez
    • , Yuan-Jyue Chen
    •  & Luis Ceze

  • Article
    | Open Access

    The sinus node generates rhythmic heartbeat but the molecular basis of pacemaking is still under debate. Here, the authors combine quantitative proteomics and single-nucleus transcriptomics to characterize the molecular composition of the sinus node and provide insights into the underpinnings of pacemaking.

    • Nora Linscheid
    • , Sunil Jit R. J. Logantha
    •  & Alicia Lundby

  • Article
    | Open Access

    Single-cell studies in solid tissues remain challenging and have benefited from the development of single-nuclei RNA sequencing strategies. Here Lake et al. apply single-nucleus RNA sequencing to human kidney tissues to provide a comprehensive molecular and cellular atlas of the human kidney, with potential implications for the understanding of kidney physiology and disease.

    • Blue B. Lake
    • , Song Chen
    •  & Sanjay Jain

  • Article
    | Open Access

    The transcriptional signature of embryonic lethality has not been defined. Here, the authors, as part of the Deciphering the Mechanisms of Developmental Disorders programme, define genes causing murine embryonic lethality around E9.5 and identify developmental delay transcriptional signatures.

    • John E. Collins
    • , Richard J. White
    •  & Elisabeth M. Busch-Nentwich

  • Article
    | Open Access

    The dynamics of HIV-1 DNA sequences early after HIV-1 transmission remains poorly characterized. Here, the authors perform a longitudinal evaluation of HIV-1 DNA sequences in subtype C-infected individuals during acute infection, providing a landscape of the nature and evolution of the very early viral genome.

    • Guinevere Q. Lee
    • , Kavidha Reddy
    •  & Mathias Lichterfeld

  • Article
    | Open Access

    Simulated single cell RNA sequencing data is useful for method development and comparison. Here, the authors developed SymSim, a simulator that explicitly models the main factors of variation in single cell data.

    • Xiuwei Zhang
    • , Chenling Xu
    •  & Nir Yosef

  • Article
    | Open Access

    Many causative genes are known for epileptic or developmental and epileptic encephalopathies (EE/DEE) yet a genetic diagnosis cannot be made for many patients. Here, the authors analyse whole exome sequencing data from a Japanese case−control cohort to identify common, rare and ultra-rare coding variants associated with EE/DEE.

    • Atsushi Takata
    • , Mitsuko Nakashima
    •  & Naomichi Matsumoto

  • Article
    | Open Access

    Complete gene expression deconvolution remains a challenging problem. Here, the authors provide a solution based on the recognition that expression levels of cell type specific genes are mutually linear across mixtures and mutually linear gene clusters correspond to cell type-specific signatures.

    • Konstantin Zaitsev
    • , Monika Bambouskova
    •  & Maxim N. Artyomov

  • Article
    | Open Access

    Alignment is an important stage in the analysis of sequencing data. Here, the authors present a fast and accurate alignment approach suitable for long and short reads, and introduce two line sweep-based techniques which can replace the often-used chaining approach.

    • Markus Schmidt
    • , Klaus Heese
    •  & Arne Kutzner

  • Article
    | Open Access

    The increasing accessibility of single cell omics technologies beyond transcriptomics demands parallel advances in analysis. Here, the authors introduce STREAM, a pipeline for reconstruction and visualization of differentiation trajectories from both single-cell RNA-seq and ATAC-seq data.

    • Huidong Chen
    • , Luca Albergante
    •  & Luca Pinello

  • Article
    | Open Access

    D-lactic acidosis typically occurs in the context of short bowel syndrome; excess D-lactate is produced by intestinal bacteria. Here, the authors identify two point mutations in the human lactate dehydrogenase D (LDHD) gene that cause enzymatic loss of function and are associated with elevated plasma D-lactate.

    • Glen R. Monroe
    • , Albertien M. van Eerde
    •  & Judith J. Jans

  • Article
    | Open Access

    Spider silk is widely studied for its structural properties; however, other creatures produce silk that could be of interest. Here, the authors study the properties and structure of Bagworm silk and report it as being extraordinarily strong and tough compared to other known silks.

    • Taiyo Yoshioka
    • , Takuya Tsubota
    •  & Tsunenori Kameda

  • Article
    | Open Access

    Rapid and accurate detection of fusion genes is important in cancer diagnostics. Here, the authors demonstrate that targeted RNA sequencing provides fast, sensitive and quantitative gene fusion detection and overcomes the limitations of approaches currently in clinical use.

    • Erin E. Heyer
    • , Ira W. Deveson
    •  & James Blackburn

  • Article
    | Open Access

    Any DNA sequence can be represented by a chiral partner sequence – an exact copy arranged in reverse nucleotide order. Here, the authors show that chiral DNA sequence pairs share important properties and show the utility of synthetic chiral sequences (sequins) as controls for clinical genomics.

    • Ira W. Deveson
    • , Bindu Swapna Madala
    •  & Tim R. Mercer

  • Article
    | Open Access

    Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

    • Zhenchang Liang
    • , Shengchang Duan
    •  & Yang Dong

  • Article
    | Open Access

    Meiotic crossover (CO) landscape differs inter- and intra-species, as well as between sexes. Here, the authors show that male meiosis produces more COs than female in maize and detect CO maturation inefficiency in some genetic backgrounds, which may help to improve breeding efficiency.

    • Cheng Luo
    • , Xiang Li
    •  & Jianbing Yan

  • Article
    | Open Access

    Infection of a cell with influenza B virus (IBV) often results in cell death and the role of surviving cells in pathogenesis is unclear. Here, Dumm et al. generate a recombinant IBV that activates a host-cell reporter to permanently label infected cells, and show that surviving cells are important to preserve epithelial barrier function.

    • Rebekah E. Dumm
    • , Jessica K. Fiege
    •  & Nicholas S. Heaton

  • Article
    | Open Access

    Here, Depledge et al. use nanopore arrays for direct RNA sequencing to profile the HSV-1 transcriptome in productively infected cells. Sequencing of individual RNAs reveals a highly complex viral transcriptome including mRNAs encoding new viral fusion proteins derived by read-through transcription.

    • Daniel P. Depledge
    • , Kalanghad Puthankalam Srinivas
    •  & Angus C. Wilson

  • Article
    | Open Access

    Host-parasite interactions during the exoerythrocytic stage of Plasmodium infection remains poorly understood. Using dual RNA-Seq, the authors show that human mucosal immunity protein mucin-13 is upregulated during Plasmodium hepatic-stage infection and marks infected cells independent of tested Plasmodium species.

    • Gregory M. LaMonte
    • , Pamela Orjuela-Sanchez
    •  & Elizabeth A. Winzeler

  • Article
    | Open Access

    Multiple morphological abnormalities of the sperm flagella (MMAF) is a cause of male infertility. Here the authors identify homozygous nonsense mutations of the glutamine rich 2 (QRICH2) gene in two MMAF patients from 2 consanguineous families and show using QRICH2 knockout mice that the protein is required for sperm flagellar formation and motility.

    • Ying Shen
    • , Feng Zhang
    •  & Wenming Xu

  • Article
    | Open Access

    Researchers can make use of a variety of computational tools to prioritize genetic variants and predict their pathogenicity. Here, the authors evaluate the performance of six of these tools in three typical biological tasks and find generally low concordance of predictions and experimental confirmation.

    • Li Liu
    • , Maxwell D. Sanderford
    •  & Sudhir Kumar

  • Article
    | Open Access

    Adenine base editors are an important contribution to the genome editing toolbox. Here the authors present EndoV-seq, an endonuclease-based assay for evaluating genomewide off-target effects of base editing.

    • Puping Liang
    • , Xiaowei Xie
    •  & Zhou Songyang

  • Article
    | Open Access

    Chromatin conformation studies are limited by the large amounts of starting material required to perform current protocols. Here the authors present Low-C, a Hi-C method for low amounts of input material and produce Low-C maps from primary B-cells of a diffuse large B-cell lymphoma patient, demonstrating the suitability of Low-C to analyse rare cell populations.

    • Noelia Díaz
    • , Kai Kruse
    •  & Juan M. Vaquerizas

  • Article
    | Open Access

    The diversity and function of microbes inhabiting hydrothermal areas is a topic of active interest in marine microbiology. Here, the authors assemble genomes from Guaymas Basin hydrothermal sediments and describe the metabolic roles of the bacterial community, which includes five new bacterial candidate phyla

    • Nina Dombrowski
    • , Andreas P. Teske
    •  & Brett J. Baker

  • Article
    | Open Access

    The function of the Retinoblastoma (Rb) protein is regulated by its cellular environment. Here, the authors perform single cell RNA-sequencing during Drosophila eye development and identify the impact of an Rbf mutation, which sensitises specific cells to apoptosis by changing metabolism.

    • Majd M. Ariss
    • , Abul B. M. M. K. Islam
    •  & Maxim V. Frolov

  • Article
    | Open Access

    Populations from North-eastern Europe, in particular those speaking Uralic languages, carry additional ancestry in similarity with modern East Asian populations. Here, the authors analyse ancient genomic data from 11 individuals from Finland and Northwest Russia, and identify genomic signals of migrations from Siberia that began at least 3500 years ago.

    • Thiseas C. Lamnidis
    • , Kerttu Majander
    •  & Stephan Schiffels

  • Article
    | Open Access

    Human induced pluripotent stem cell derived cardiomyocytes are a powerful model for cardiogenesis and disease in vitro. Here the authors comprehensively map cardiac differentiation using multiple modalities, including single-cell RNA seq and CyTOF, in cells with a gain  or loss of function in key cardiac transcription factors.

    • Jared M. Churko
    • , Priyanka Garg
    •  & Joseph C. Wu

  • Article
    | Open Access

    Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome.

    • Stéphane Deschamps
    • , Yun Zhang
    •  & Haining Lin

  • Article
    | Open Access

    Rare genetic variants can contribute to complex traits but this contribution is not well understood. Here, the authors analyse deep whole genome sequencing data across 1457 individuals from an isolated Greek population and find association of rare variant burdens with cardiometabolic traits.

    • Arthur Gilly
    • , Daniel Suveges
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Cellular heterogeneity in cancer is complex and difficult to study. Here, the authors introduce Protein-indexed Assay of Transposase Accessible Chromatin (Pi-ATAC), which combines single cell chromatin and proteomic profiling to provide deep insight into the tumor microenvironment, and reveal the role of hypoxia in shaping the regulome of a subset of breast cancer cells in vivo.

    • Xingqi Chen
    • , Ulrike M. Litzenburger
    •  & Howard Y. Chang

  • Article
    | Open Access

    The mechanisms underlying the transition from cardiac hypertrophy to heart failure following pressure overload are incompletely understood. Here the authors identify the gene programs encoding the morphological and functional characteristics of cardiomyocytes during the transition from early hypertrophy to heart failure via single-cell transcriptomics, establishing a key role for p53 signalling.

    • Seitaro Nomura
    • , Masahiro Satoh
    •  & Issei Komuro

  • Article
    | Open Access

    The development of single cell RNA sequencing technologies has been instrumental in advancing our understanding of tissue biology. Here, MacParland et al. performed single cell RNA sequencing of human liver samples, and identify distinct populations of intrahepatic macrophages that may play specific roles in liver disease.

    • Sonya A. MacParland
    • , Jeff C. Liu
    •  & Ian D. McGilvray

  • Article
    | Open Access

    Association between variants in 11 different genes and breast cancer risk has been established and sequencing of these genes is recommended to provide personalized diagnosis, therapy, and surveillance for the high-risk patients and their relatives. Here the authors analyse the frequency of germline pathogenic mutations in these genes specifically in a Japanese population.

    • Yukihide Momozawa
    • , Yusuke Iwasaki
    •  & Michiaki Kubo

  • Article
    | Open Access

    Sharing of whole genome sequencing (WGS) data improves study scale and power, but data from different groups are often incompatible. Here, US genome centers and NIH programs define WGS data processing standards and a flexible validation method, facilitating collaboration in human genetics research.

    • Allison A. Regier
    • , Yossi Farjoun
    •  & Ira M. Hall

  • Article
    | Open Access

    Characterizing the binding selectivity landscape of interacting proteins is crucial in protein engineering. Here the authors use multi-target selective library screening and in silico next-generation sequencing to map the binding landscape of proteins and produce improved proteases inhibitors.

    • Si Naftaly
    • , Itay Cohen
    •  & Niv Papo

  • Article
    | Open Access

    Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.

    • Chongyuan Luo
    • , Angeline Rivkin
    •  & Joseph R. Ecker

  • Article
    | Open Access

    Single-cell chromatin accessibility is a promising means to identify regulatory programs in mixtures of cells. Here the authors describe µ-ATAC-seq, a low-cost method that can generate thousands of accessibility profiles per day.

    • Anja Mezger
    • , Sandy Klemm
    •  & William Greenleaf

  • Article
    | Open Access

    Endocrine progenitors form early in pancreatic development but the diversity of this cell population is unclear. Here, the authors use single cell RNA sequencing of the mouse pancreas at e14.5 and e16.5 to show that endocrine progenitors are temporally distinct and those formed later are more likely to become beta cells

    • Marissa A. Scavuzzo
    • , Matthew C. Hill
    •  & Malgorzata Borowiak

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