Sequencing articles within Nature Communications

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  • Article
    | Open Access

    Association analyses that capture rare and noncoding variants in whole genome sequencing data are limited by factors like statistical power. Here, the authors present KnockoffScreen, a statistical method using the knockoff framework to detect, localise and prioritise rare and common risk variants at genome-wide scale.

    • Zihuai He
    • , Linxi Liu
    •  & Iuliana Ionita-Laza

  • Article
    | Open Access

    Combining scRNA-seq with spatial information to enable the reconstruction of spatially-resolved cell atlases is challenging for rare cell types. Here the authors present ClumpSeq, an approach for sequencing small clumps of tissue attached cells, and apply it to establish spatial atlases for all secretory cell types in the small intestine.

    • Rita Manco
    • , Inna Averbukh
    •  & Shalev Itzkovitz

  • Article
    | Open Access

    Cellular genetic heterogeneity is common across biological conditions, yet application of long-read sequencing to this subject is limited by error rates. Here, the authors present iGDA, a tool for detection and phasing of minor variants from long-read sequencing data, allowing accurate reconstruction of haplotypes.

    • Zhixing Feng
    • , Jose C. Clemente
    •  & Eric E. Schadt

  • Article
    | Open Access

    Osteocytes are the master regulatory cells within the skeleton. Here, the authors map the transcriptome of osteocytes from diverse skeletal sites, ages and between sexes and identify an osteocyte transcriptome signature associated with rare skeletal disorders and common complex skeletal diseases.

    • Scott E. Youlten
    • , John P. Kemp
    •  & Peter I. Croucher

  • Article
    | Open Access

    The proximity extension assay (PEA) is a popular tool to measure plasma protein levels. Here, the authors extend the proteome coverage of PEA by combining it with next-generation sequencing, enabling the analysis of nearly 1500 proteins from minute amounts of plasma.

    • Wen Zhong
    • , Fredrik Edfors
    •  & Mathias Uhlén

  • Article
    | Open Access

    Alterations in metabolism and amino acid usage are common in cancer cells. Here, the authors show in prostate cancer cells that arginine globally upregulates nuclear-encoded oxidative phosphorylation genes by altering histone acetylation and retaining TEAD4 in the nucleus to transactivate genes.

    • Chia-Lin Chen
    • , Sheng-Chieh Hsu
    •  & Hsing-Jien Kung

  • Article
    | Open Access

    Clostridioides difficile infection (CDI) is the most common cause of antibiotic-associated diarrhoea (AAD); however, markers predictive of CDI or AAD development are as yet lacking. Here, to identify markers predictive of CDI, the authors profile the intestinal microbiota of 945 hospitalised patients from 34 hospitals in 6 different European countries and show distinct microbiota enriched in Enterococcus and depleted of Ruminococcus, Blautia, Prevotella and Bifidobacterium compared to non-CDI patients.

    • Matilda Berkell
    • , Mohamed Mysara
    •  & Odile Launay

  • Article
    | Open Access

    Circulating tumour DNA (ctDNA) represents a non-invasive option to monitor cancer progression. Here, the authors perform deep sequencing of plasma cell-free DNA, and find that nucleosome-dependent cfDNA degradation at 6 specific regulatory regions is predictive of ctDNA burden.

    • Guanhua Zhu
    • , Yu A. Guo
    •  & Anders J. Skanderup

  • Article
    | Open Access

    Variable number tandem repeats (VNTRs) are implicated in human diseases yet have been difficult to analyse computationally. Here, the authors describe a neural network method, adVNTR-NN, that allows rapid and accurate genotyping of VNTRs from large whole genome sequencing datasets.

    • Mehrdad Bakhtiari
    • , Jonghun Park
    •  & Vineet Bafna

  • Article
    | Open Access

    Our understanding on the humoral immunity induced by SARS-CoV-2 is still lacking. Here the authors analyze B cell responses at the single cell level to find that, in severe COVID-19 patients, plasmablasts shift from IFN to TGFβ instruction to produce IgA antibodies that are not specific to dominant SARS-CoV-2 antigens.

    • Marta Ferreira-Gomes
    • , Andrey Kruglov
    •  & Mir-Farzin Mashreghi

  • Article
    | Open Access

    It is unclear how changes in gene expression are induced by changes in oxygen levels during late lung development. Here, the authors provide data from MULTI-seq scRNAseq in mice showing exposure to higher oxygen levels affects cell fates, especially for alveolarisation, and define gene/cell signatures of impaired lung development under hyperoxia.

    • Maria Hurskainen
    • , Ivana Mižíková
    •  & Bernard Thébaud

  • Article
    | Open Access

    How transposable elements (TE) contribute to cell fate changes is unclear. Here, the authors generate a pipeline to quantify TE expression from single cell data. They show the dynamic expression of TEs from gastrulation to somatic cell reprogramming and human disease

    • Jiangping He
    • , Isaac A. Babarinde
    •  & Jiekai Chen

  • Article
    | Open Access

    The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.

    • Joseph H. Collins
    • , Kevin W. Keating
    •  & Eric M. Young

  • Article
    | Open Access

    Single cell analysis of transposase-accessible chromatin is deepening our understanding on the origins of cellular diversity, yet methods are limited by data sparsity. Here, the authors introduce SnapATAC, a pipeline to resolve cellular heterogeneity and reveal candidate regulatory elements across different cell populations.

    • Rongxin Fang
    • , Sebastian Preissl
    •  & Bing Ren

  • Article
    | Open Access

    Erasure of DNA methylation from the parental genomes is critical to reset the methylome of differentiated gametes to pluripotent cells in the blastocyst. Here, the authors present a high-throughput single-cell method that enables strand-specific quantification of DNA methylation and identify distinct modes of DNA demethylation dynamics during early mammalian development.

    • Maya Sen
    • , Dylan Mooijman
    •  & Alexander van Oudenaarden

  • Article
    | Open Access

    Exolytic heparinases are needed for sequencing of heparin and heparan sulfate (HP), but have not yet been reported. Here, the authors identify exolytic heparinases from different bacteria and show that the heparinases preferentially digest HP, determine the crystal structure of the exoheparinase BlexoHep and perform sequencing of HP octasaccharides using the enzyme.

    • Qingdong Zhang
    • , Hai-Yan Cao
    •  & Fuchuan Li

  • Article
    | Open Access

    Dietary changes can impact the microbial constitution of the gastrointestinal tract and modulate the local immune response. Here, the authors show supplementation using lysates of Methylococcus capsulatus Bath result in changes to the microbiota, modulate Treg populations and metabolic read outs in a dietary control murine model.

    • Benjamin A. H. Jensen
    • , Jacob B. Holm
    •  & Tor E. Lea

  • Article
    | Open Access

    Bulk and single-cell transcriptomic data can be a source of novel insights into how cells interact with each other. Here the authors develop ICELLNET, a global, biologically validated, and easy-to-use framework to dissect cell communication from individual or multiple cell-based transcriptomic profiles.

    • Floriane Noël
    • , Lucile Massenet-Regad
    •  & Vassili Soumelis

  • Article
    | Open Access

    Accurate analysis of single-cell RNA sequencing (scRNA-seq) data is affected by issues including technical noise and high dropout rate. Here, the authors develop a hierarchical autoencoder, scDHA, which outperforms existing methods in scRNA-seq analyses such as cell segregation and classification.

    • Duc Tran
    • , Hung Nguyen
    •  & Tin Nguyen

  • Article
    | Open Access

    Sex chromosome gene content and expression is unusual. Here the authors use single cell RNA-Seq on Drosophila larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, while genes on the single Y chromosome become maximally active in primary spermatocytes.

    • Sharvani Mahadevaraju
    • , Justin M. Fear
    •  & Brian Oliver

  • Article
    | Open Access

    Single cell genomics uses cells from the same individual, or pseudoreplicates, that can introduce biases and inflate type I error rates. Here the authors apply generalized linear mixed models with a random effect for individual, to properly account for both zero inflation and the correlation structure among cells within an individual.

    • Kip D. Zimmerman
    • , Mark A. Espeland
    •  & Carl D. Langefeld

  • Article
    | Open Access

    Endothelial cells play a critical role in the adaptation of tissues to injury and show a remarkable plasticity. Here the authors show, using single cell sequencing, that endothelial cells acquire a transient mesenchymal state associated with metabolic adaptation after myocardial infarction.

    • Lukas S. Tombor
    • , David John
    •  & Stefanie Dimmeler

  • Article
    | Open Access

    Brain myelinating oligodendrocytes are rare and difficult to isolate, which has limited data on their development. Here the authors develop a reporter for scalable purification of human pluripotent stem cell derived oligodendrocyte lineage cells, and use this to map differentiation using single cell RNA-sequencing,

    • Xitiz Chamling
    • , Alyssa Kallman
    •  & Donald J. Zack

  • Article
    | Open Access

    Sequencing and mapping of long repetitive regions can be challenging due to technical difficulties in sequencing and assembly of the sequence data. Here authors report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe to reveal highly polymorphic and hot spots for genome variation features.

    • Yusuke Oizumi
    • , Takuto Kaji
    •  & Junko Kanoh

  • Article
    | Open Access

    Single-cell RNA-seq offers the opportunity to improve efficacy of T-cell based immunotherapy. Here the authors develop a plate-based method for cytotoxic T cell profiling. It captures a higher number of transcripts and detects gene with increased dynamic range in comparison to droplet-based methods.

    • Kristiyan Kanev
    • , Patrick Roelli
    •  & Dietmar Zehn

  • Article
    | Open Access

    Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.

    • Mathieu Quinodoz
    • , Virginie G. Peter
    •  & Carlo Rivolta

  • Article
    | Open Access

    Aberrant splicing is a major contributor to rare disease, but detection accuracy using current methods is limited. Here, the authors develop an algorithm that detects aberrant splicing and intron retention events from RNA-seq data and apply it to diagnosis in mitochondrial disease.

    • Christian Mertes
    • , Ines F. Scheller
    •  & Julien Gagneur

  • Article
    | Open Access

    Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. Here the authors demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation.

    • Yapeng Li
    • , Junfeng Gao
    •  & Hua Huang

  • Article
    | Open Access

    Accurate prediction of variant pathogenicity is essential to understanding genetic risks in disease. Here, the authors present a deep neural network method for prediction of missense variant pathogenicity, MVP, and demonstrate its utility in prioritizing de novo variants contributing to developmental disorders.

    • Hongjian Qi
    • , Haicang Zhang
    •  & Yufeng Shen

  • Article
    | Open Access

    The tumor suppressor p53 is a master regulator of cellular stress response pathways, including cell cycle arrest and apoptosis. Here, the authors identify molecular mechanisms of p53 binding to high- and low-affinity p53 response elements in the genome, linked to cell cycle arrest and pro-apoptotic genes, respectively.

    • Marina Farkas
    • , Hideharu Hashimoto
    •  & Steven B. McMahon

  • Article
    | Open Access

    Circular RNAs have been identified using short-read RNA sequencing. Here, the authors report isoCirc, a long-read sequencing method to characterize full-length circRNA isoforms and generate a catalogue of full-length circRNA isoforms in 12 human tissues and one human cell line.

    • Ruijiao Xin
    • , Yan Gao
    •  & Yi Xing

  • Article
    | Open Access

    The intact proviral DNA assay quantifies the genomically intact HIV reservoir, but assay failure due to HIV-1 polymorphism has been observed. Here, the authors report a 28% failure rate in a cohort of people with HIV-1, and note within-host HIV-1 diversity as a further challenge to IPDA accuracy.

    • Natalie N. Kinloch
    • , Yanqin Ren
    •  & R. Brad Jones

  • Article
    | Open Access

    The detection of aberrations in circulating tumour DNA represents a non-invasive method to survey the oncogenes and tumour suppressors that are modified within a patient’s cancer. Here, the authors analysed more than 10,000 patients using a targeted sequencing panel and report on the frequencies of the mutations that they found.

    • Yongliang Zhang
    • , Yu Yao
    •  & Qiang Zeng

  • Article
    | Open Access

    Gene flow is classically thought to impede local adaptation via parallel evolution. However, a genomic study on Hawaiian crickets from different island populations finds evidence of parallel adaptation to the same lethal parasitoid in spite of strong ongoing gene flow.

    • Xiao Zhang
    • , Jack G. Rayner
    •  & Nathan W. Bailey

  • Article
    | Open Access

    The human proteome represents a crucial link between complex disease and genetic/environmental factors. Here, the authors investigate 257 cardiometabolic-relevant protein biomarkers in whole genome sequencing data from 1328 individuals, revealing the genetic architecture underlying biomarker variation.

    • Arthur Gilly
    • , Young-Chan Park
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Nanopore sequencing (ONT) has been used in SARS-CoV-2 studies, however adoption of ONT for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. Here, the authors perform a comprehensive evaluation of ONT analytical performance on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls.

    • Rowena A. Bull
    • , Thiruni N. Adikari
    •  & Ira W. Deveson

  • Article
    | Open Access

    Chromatin structure and topology play important roles in the regulation of gene expression. Here the authors study the spatio-temporal re-organization of promoter-enhancer interactions in pluripotent ES and skeletal muscle stem cells and the corresponding impact on gene expression as a consequence of myogenic commitment and differentiation.

    • Nan Zhang
    • , Julen Mendieta-Esteban
    •  & Brian David Dynlacht

  • Article
    | Open Access

    The success of protein evolution is dependent on the sequence context mutations are introduced into. Here the authors present UMIC-seq that allows consensus generation for closely related genes by using unique molecular identifiers linked to gene variants.

    • Paul Jannis Zurek
    • , Philipp Knyphausen
    •  & Florian Hollfelder

  • Article
    | Open Access

    Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.

    • Sonia Brockway
    • , Geng Wang
    •  & Marc L. Mendillo

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