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Somatic mutation landscapes at single-molecule resolution
NanoSeq is used to detect mutations in single DNA molecules and analyses show that mutational processes that are independent of cell division are important contributors to somatic mutagenesis.
- Federico Abascal
- , Luke M. R. Harvey
- & Iñigo Martincorena
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News |
Why US coronavirus tracking can’t keep up with concerning variants
The country has an enormous virus-sequencing capacity, but funding and coordination roadblocks are holding it back.
- Amy Maxmen
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Article
| Open AccessSequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.
- Daniel Taliun
- , Daniel N. Harris
- & Gonçalo R. Abecasis
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Article |
The kinetic landscape of an RNA-binding protein in cells
Time-resolved RNA–protein cross-linking with a pulsed femtosecond ultraviolet laser, followed by immunoprecipitation and high-throughput sequencing, enables the determination of binding and dissociation kinetics of the RNA-binding protein DAZL within cells.
- Deepak Sharma
- , Leah L. Zagore
- & Eckhard Jankowsky
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Article |
A map of cis-regulatory elements and 3D genome structures in zebrafish
A comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish (Danio rerio) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development.
- Hongbo Yang
- , Yu Luan
- & Feng Yue
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Article |
High-depth African genomes inform human migration and health
Whole-genome sequencing analyses of African populations provide insights into continental migration, gene flow and the response to human disease, highlighting the importance of including diverse populations in genomic analyses to understand human ancestry and improve health.
- Ananyo Choudhury
- , Shaun Aron
- & Neil A. Hanchard
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Article |
The landscape of RNA Pol II binding reveals a stepwise transition during ZGA
Binding of RNA polymerase II during zygotic genome activation in mouse embryos is determined using the newly developed method Stacc–seq.
- Bofeng Liu
- , Qianhua Xu
- & Wei Xie
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Article |
Single-cell mutation analysis of clonal evolution in myeloid malignancies
The evolution of myeloid malignancies is investigated using combined single-cell sequencing and immunophenotypic analysis.
- Linde A. Miles
- , Robert L. Bowman
- & Ross L. Levine
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Article
| Open AccessExome sequencing and characterization of 49,960 individuals in the UK Biobank
Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
- Cristopher V. Van Hout
- , Ioanna Tachmazidou
- & Aris Baras
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Matters Arising |
APP gene copy number changes reflect exogenous contamination
- Junho Kim
- , Boxun Zhao
- & Eunjung Alice Lee
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Article |
Position-specific oxidation of miR-1 encodes cardiac hypertrophy
The 8-oxoguanine modification of the microRNA miR-1 results in redirected recognition and silencing of target genes and leads to cardiac hypertrophy in mice.
- Heeyoung Seok
- , Haejeong Lee
- & Sung Wook Chi
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Article
| Open AccessTelomere-to-telomere assembly of a complete human X chromosome
High-coverage, ultra-long-read nanopore sequencing is used to create a new human genome assembly that improves on the coverage and accuracy of the current reference (GRCh38) and includes the gap-free, telomere-to-telomere sequence of the X chromosome.
- Karen H. Miga
- , Sergey Koren
- & Adam M. Phillippy
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Article |
Physiological blood–brain transport is impaired with age by a shift in transcytosis
Tagging and tracking the blood plasma proteome as a discovery tool reveals widespread endogenous transport of proteins into the healthy brain and the pharmacologically modifiable mechanisms by which the brain endothelium regulates this process with age.
- Andrew C. Yang
- , Marc Y. Stevens
- & Tony Wyss-Coray
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Article |
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping
A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.
- Aldema Sas-Chen
- , Justin M. Thomas
- & Schraga Schwartz
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Article |
Insights into variation in meiosis from 31,228 human sperm genomes
Thousands of sperm genomes have been analysed with a new method called Sperm-seq, revealing interconnected meiotic variation at the single-cell and person-to-person levels, and suggesting chromosome compaction as a way to explain the relationships between diverse recombination phenotypes.
- Avery Davis Bell
- , Curtis J. Mello
- & Steven A. McCarroll
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Article |
RIC-seq for global in situ profiling of RNA–RNA spatial interactions
RNA in situ conformation sequencing (RIC-seq) enables the generation of three-dimensional interaction maps of RNA in cells, which sheds light on the interactions and regulatory functions of RNA.
- Zhaokui Cai
- , Changchang Cao
- & Yuanchao Xue
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Article |
Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids
Single-cell RNA sequencing and spatial transcriptomics reveal that the somitogenesis clock is active in mouse gastruloids, which can be induced to generate somites with the correct rostral–caudal patterning.
- Susanne C. van den Brink
- , Anna Alemany
- & Alexander van Oudenaarden
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News |
Controversial ‘gay gene’ app provokes fears of a genetic Wild West
Debate highlights broader concerns about tools that use the results of direct-to-consumer genetic testing.
- Amy Maxmen
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Article |
Decoding human fetal liver haematopoiesis
Single-cell transcriptomic profiling of fetal liver, skin, kidney and yolk sac reveals the differentiation trajectories of human haematopoietic stem cells and multipotent progenitors, which are validated to produce an integrated map of fetal liver haematopoiesis.
- Dorin-Mirel Popescu
- , Rachel A. Botting
- & Muzlifah Haniffa
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Letter |
Genome architecture and stability in the Saccharomyces cerevisiae knockout collection
Whole-genome sequencing of the strains of the Saccharomyces cerevisiae gene-knockout collection reveals the effects of the deletion of non-essential genes on genome stability.
- Fabio Puddu
- , Mareike Herzog
- & Stephen P. Jackson
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Letter |
Molecular architecture of lineage allocation and tissue organization in early mouse embryo
Spatially resolved transcriptomes of cell populations at defined positions in the early mouse embryo reveal molecular bases of lineage specification and tissue patterning.
- Guangdun Peng
- , Shengbao Suo
- & Naihe Jing
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Article |
Exome sequencing of Finnish isolates enhances rare-variant association power
Exome-wide sequencing studies of populations in Finland identified 26 deleterious alleles associated with 64 quantitative traits that are clinically relevant to cardiovascular and metabolic diseases.
- Adam E. Locke
- , Karyn Meltz Steinberg
- & Nelson B. Freimer
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Letter |
Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects
Single-cell RNA-sequencing analysis reveals functions of lineage-specifying transcription factors underlying congenital defects in heart development.
- T. Yvanka de Soysa
- , Sanjeev S. Ranade
- & Deepak Srivastava
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Letter |
scSLAM-seq reveals core features of transcription dynamics in single cells
A technique known as scSLAM-seq that combines single-cell RNA sequencing with metabolic RNA labelling and nucleoside conversion is used to study the onset of cytomegalovirus infection in single mouse fibroblasts.
- Florian Erhard
- , Marisa A. P. Baptista
- & Lars Dölken
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Letter |
Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America
DNA analysis of ancient individuals and modern populations suggests that the population history of North America can be explained by the admixture of two ancestral lineages—Palaeo-Eskimos and First Peoples.
- Pavel Flegontov
- , N. Ezgi Altınışık
- & Stephan Schiffels
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Article
| Open AccessExome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls
Exome-sequencing analyses of a large cohort of patients with type 2 diabetes and control individuals without diabetes from five ancestries are used to identify gene-level associations of rare variants that are associated with type 2 diabetes.
- Jason Flannick
- , Josep M. Mercader
- & Michael Boehnke
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Article |
Charting cellular identity during human in vitro β-cell differentiation
Single-cell transcriptional profiling of in vitro human pancreatic β-cell differentiation reveals progenitor and terminal fates, produces a detailed time course of endocrine induction and underpins a lineage model.
- Adrian Veres
- , Aubrey L. Faust
- & Douglas A. Melton
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Article |
Single-cell mapping of lineage and identity in direct reprogramming
Combinatorial tagging of single cells using expressed DNA barcodes, delivered by a lentiviral vector, is used to track individual cells and reconstruct their lineages and trajectories during cell fate reprogramming.
- Brent A. Biddy
- , Wenjun Kong
- & Samantha A. Morris
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Letter
| Open AccessGenome organization and DNA accessibility control antigenic variation in trypanosomes
Long-read sequencing allows the assembly of antigen-gene arrays in Trypanosoma brucei and, coupled with deletion experiments, demonstrates that histone variants act as a molecular link between genome architecture, chromatin conformation and antigen variation.
- Laura S. M. Müller
- , Raúl O. Cosentino
- & T. Nicolai Siegel
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Article |
The genetic basis and cell of origin of mixed phenotype acute leukaemia
A large-scale genomics study shows that the cell of origin and founding mutations determine disease subtype and lead to the expression of multiple haematopoietic lineage-defining antigens in mixed phenotype acute leukaemia.
- Thomas B. Alexander
- , Zhaohui Gu
- & Charles G. Mullighan
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Letter
| Open AccessGenome sequence of the progenitor of wheat A subgenome Triticum urartu
The genome sequence of Triticum urartu, the progenitor of the A subgenome of hexaploid wheat, provides insight into genome duplication during grass evolution.
- Hong-Qing Ling
- , Bin Ma
- & Chengzhi Liang
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Letter |
Reconstructing the genetic history of late Neanderthals
Genetic similarity among late Neanderthals is predicted well by their geographical location, and although some of these Neanderthals were contemporaneous with early modern humans, their genomes show no evidence of recent gene flow from modern humans.
- Mateja Hajdinjak
- , Qiaomei Fu
- & Janet Kelso
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Letter
| Open AccessSooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Whole-genome sequencing and comparative genomic analysis of immune-related genes of Cercocebus atys and Macaca mulatta identify candidate genes, such as ICAM2 and TLR4, that may explain the AIDS resistance of C. atys.
- David Palesch
- , Steven E. Bosinger
- & Guido Silvestri
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Letter |
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
An Ancient Beringian population from Late Pleistocene Alaska and the ancestors of other Native American groups descended from a single founding population that diversified around twenty thousand years ago.
- J. Víctor Moreno-Mayar
- , Ben A. Potter
- & Eske Willerslev
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Letter |
Genetic diversity of the African malaria vector Anopheles gambiae
Genome sequencing analyses from 765 specimens of Anopheles gambiae and Anopheles coluzzii from 15 locations across Africa characterize patterns of gene flow and variations in population size, and provide a resource for studying the evolution of natural malaria vector populations.
- Alistair Miles
- , Nicholas J. Harding
- & Dominic P. Kwiatkowski
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Letter
| Open AccessThe impact of rare variation on gene expression across tissues
The authors show that rare genetic variants contribute to large gene expression changes across diverse human tissues and provide an integrative method for interpretation of rare variants in individual genomes.
- Xin Li
- , Yungil Kim
- & Stephen B. Montgomery
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Review Article |
DNA sequencing at 40: past, present and future
The history and future potential of DNA sequencing, including the development of the underlying technologies and the expansion of its areas of application, are reviewed.
- Jay Shendure
- , Shankar Balasubramanian
- & Robert H. Waterston
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Letter
| Open AccessSequencing and de novo assembly of 150 genomes from Denmark as a population reference
A report of high-depth, short-read sequencing and de novo assemblies for 150 individuals from 50 parent–offspring trios as part of establishing a population reference genome for the GenomeDenmark project.
- Lasse Maretty
- , Jacob Malte Jensen
- & Mikkel Heide Schierup
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Letter |
Zika virus evolution and spread in the Americas
One hundred and ten Zika virus genomes from ten countries and territories involved in the Zika virus epidemic reveal rapid expansion of the epidemic within Brazil and multiple introductions to other regions.
- Hayden C. Metsky
- , Christian B. Matranga
- & Pardis C. Sabeti
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Article
| Open AccessA chromosome conformation capture ordered sequence of the barley genome
The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare.
- Martin Mascher
- , Heidrun Gundlach
- & Nils Stein
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Letter |
Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism
Gene expression analysis in brain tissue from individuals with and without autism spectrum disorder (ASD) suggests that the transcription factor SOX5 contributes to an ASD-associated reduction in transcriptional differences between brain areas and indicates that common transcriptomic changes occur in different forms of ASD.
- Neelroop N. Parikshak
- , Vivek Swarup
- & Daniel H. Geschwind
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Letter |
Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in C. elegans
Precursor mRNA splicing homeostasis is a biomarker and predictor of life expectancy in Caenorhabditis elegans and defects in global pre-mRNA splicing associated with age are reduced by dietary restriction via splicing factor 1.
- Caroline Heintz
- , Thomas K. Doktor
- & William B. Mair
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Spotlight |
Spotlight on Genetics
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Letter |
Global profiling of SRP interaction with nascent polypeptides
Here, the selection of substrates by the protein–RNA complex known as the signal recognition particle (SRP) is investigated in the bacterium Escherichia coli, revealing that the SRP has a strong preference for hydrophobic transmembrane domains of inner membrane proteins.
- Daniela Schibich
- , Felix Gloge
- & Günter Kramer
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Letter |
Dynamics of ribosome scanning and recycling revealed by translation complex profiling
A translation complex sequencing approach has been developed enabling intermediates of all mRNA-associated processes of translation to be isolated and localized across the transcriptome; the results support longstanding models of initiation and termination and offer new mechanistic insights.
- Stuart K. Archer
- , Nikolay E. Shirokikh
- & Thomas Preiss
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Article |
The genetic architecture of type 2 diabetes
Sequencing data from two large-scale studies show that most of the genetic variation influencing the risk of type 2 diabetes involves common alleles and is found in regions previously identified by genome-wide association studies, clarifying the genetic architecture of this disease.
- Christian Fuchsberger
- , Jason Flannick
- & Mark I. McCarthy
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Article |
DNA methylation on N6-adenine in mammalian embryonic stem cells
The prevalence of N6-adenine DNA methylation in mammals was previously unknown; this study reveals that N6-methyladenine can be found in mouse embryonic stem cells, especially at subfamilies of young (<1.5 million years old) LINE-1 transposons.
- Tao P. Wu
- , Tao Wang
- & Andrew Z. Xiao
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Letter |
Tumour-specific proline vulnerability uncovered by differential ribosome codon reading
Tumours can require certain amino acids for their proliferation, and the diricore method described here helps to identify such restrictive amino acids; using this method in kidney cancer tissue and breast carcinoma cells, the authors observe an association between proline deficiency and upregulation of PYCR1, an enzyme required for proline synthesis.
- Fabricio Loayza-Puch
- , Koos Rooijers
- & Reuven Agami
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Letter |
Real-time, portable genome sequencing for Ebola surveillance
A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection.
- Joshua Quick
- , Nicholas J. Loman
- & Miles W. Carroll