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  • Genetic-substructure and complex demographic history of South African Bantu speakers
    bioRxiv. Genom. Pub Date : 2020-08-11
    Dhriti Sengupta; Ananyo Choudhury; Cesar Fortes-Lima; Shaun Aron; Gavin Whitelaw; Koen Bostoen; Hilde Gunnink; Natalia Chousou-Polydouri; Peter Delius; Stephen Tollman; F Gomez-Olive Casas; Shane Norris; Felistas Mashinya; Marianne Alberts; Scott Hazelhurst; Carina M Schlebusch; Michéle Ramsay

    South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly

    更新日期:2020-08-11
  • Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes
    bioRxiv. Genom. Pub Date : 2020-08-11
    Dominic Holland; Oleksandr Frei; Rahul Desikan; Chun Chieh Fan; Alexey Shadrin; Olav Smeland; Ole A Andreassen; Anders Dale

    We propose an extended Gaussian mixture model for the distribution of causal effects of common single nucleotide polymorphisms (SNPs) for human complex phenotypes, taking into account linkage disequilibrium (LD) and heterozygosity (H), while also allowing for independent components for small and large effects. Using a precise methodology showing how genome-wide association studies (GWAS) summary statistics

    更新日期:2020-08-11
  • Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories
    bioRxiv. Genom. Pub Date : 2020-08-11
    Sophie G Kellaway; Peter Keane; Benjamin Edginton-White; Regha Kakkad; Ella Kennett; Constanze Bonifer

    Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend upon the class of RUNX1 mutation. The biochemical behaviour of these oncoproteins and their ability to cause unique diseases has been well studied, but the genomic basis of their differential action is unknown. To

    更新日期:2020-08-11
  • Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families
    bioRxiv. Genom. Pub Date : 2020-08-10
    Christopher W. Whelan; Robert E. Handsaker; Giulio Genovese; Seva Kashin; Monkol Lek; Jason Hughes; Joshua McElwee; Michael Lenardo; Daniel MacArthur; Steven A. McCarroll

    Two intriguing forms of genome structural variation (SV) - dispersed duplications, and de novo rearrangements of complex, multi-allelic loci - have long escaped genomic analysis. We describe a new way to find and characterize such variation by utilizing identity-by-descent (IBD) relationships between siblings together with high-precision measurements of segmental copy number. Analyzing whole-genome

    更新日期:2020-08-11
  • Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon.
    bioRxiv. Genom. Pub Date : 2020-08-10
    Michele Wyler; Christoph Stritt; Jean-Claude Walser; Celia Baroux; Anne Carole Roulin

    Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still

    更新日期:2020-08-11
  • Refinement of Genome assemblies of Pigeonpea (Cajanus cajan)
    bioRxiv. Genom. Pub Date : 2020-08-10
    Soma S Marla; Pallavi Mishra; Ranjeet Maurya; Mohar Singh; D P Wankhade; Anil K Gupta; S Rao N; Sanjeev K Singh; Rajesh Kumar

    Recent developments in genome sequencing of several important crops helped to enrich our understanding of basic biology and immensely contributed to crop improvement. However, assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in Next Generation sequencing. Of late multiple draft assemblies are reported for a single genome of an

    更新日期:2020-08-11
  • Integrating linguistics, social structure, and geography to model genetic diversity within India
    bioRxiv. Genom. Pub Date : 2020-08-10
    Aritra Bose; Daniel E. Platt; Laxmi Parida; Peristera Paschou; Petros Drineas

    India represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification. While geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no

    更新日期:2020-08-11
  • Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development
    bioRxiv. Genom. Pub Date : 2020-08-10
    Martin W Breuss; Xiaoxu Yang; Danny Antaki; Johannes C M Schlachetzki; Addison A Lana; Xin Xu; Guoliang Chai; Valentina Stanley; Qiong Song; Traci Fang Newmeyer; An Nguyen; Beibei Cao; Alexander Nott; Jennifer McEvoy-Venneri; Martina P Pasillas; Shareef Nahas; Lucitia Van Der Kraan; Yan Ding; NIMH Brain Somatic Mosaicism Network; Christopher K Glass; Joe G Gleeson

    The structure of the human neocortex underlies species-specific features and is a reflection of intricate developmental programs. Here we analyzed neocortical cellular lineages through a comprehensive assessment of brain somatic mosaicism - which acts as a neutral recorder of lineage history. We employed deep whole genome and variant sequencing in a single postmortem neurotypical human brain across

    更新日期:2020-08-11
  • High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing
    bioRxiv. Genom. Pub Date : 2020-08-10
    Rahul C. Bhoyar; Abhinav Jain; Paras Sehgal; Mohit Kumar Divakar; Disha Sharma; Mohamed Imran; Bani Jolly; Gyan Ranjan; Mercy Rophina; Sumit Sharma; Sanjay Siwach; Kavita Pandhare; Swayamprabha Sahoo; Maheswata Sahoo; Ananya Nayak; Jatindra Nath Mohanty; Jayashankar Das; Sudhir Bhandari; Sandeep K Mathur; Anshul Kumar; Rahul Sahlot; Pallavali Rojarani; Juturu Vijaya Lakshmi; Araveti Surekha; Pulala

    The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput

    更新日期:2020-08-11
  • Early Alpine human occupation backdates westward human migration in Late Glacial Europe
    bioRxiv. Genom. Pub Date : 2020-08-10
    Eugenio Bortolini; Luca Pagani; Gregorio Oxilia; Cosimo Posth; Federica Fontana; Federica Badino; Tina Saupe; Francesco Montinaro; Davide Margaritora; Matteo Romandini; Federico Lugli; Andrea Papini; Marco Boggioni; Nicola Perrini; Antonio Oxilia; Riccardo Aiese Cigliano; Rosa Barcelona; Davide Visentin; Nicolo Fasser; Simona Arrighi; Carla Figus; Giulia Marciani; Sara Silvestrini; Federico Bernardini;

    The end of the Last Glacial Maximum (LGM) in Europe (~16.5 ka ago) set in motion major changes in human culture and population structure. In Southern Europe, Early Epigravettian material culture was replaced by Late Epigravettian art and technology about 18-17 ka ago at the beginning of southern Alpine deglaciation, although available genetic evidence from individuals who lived ~14 ka ago opened up

    更新日期:2020-08-11
  • Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing
    bioRxiv. Genom. Pub Date : 2020-08-10
    Luyi Tian; Jafar S. Jabbari; Rachel Thijssen; Quentin Gouil; Shanika L. Amarasinghe; Hasaru Kariyawasam; Shian Su; Xueyi Dong; Charity W. Law; Alexis Lucattini; Jin D. Chung; Timur Naim; Audrey Chan; Chi Hai Ly; Gordon S. Lynch; James G. Ryall; Casey J.A. Anttila; Hongke Peng; Mary Ann Anderson; Andrew W. Roberts; David C.S. Huang; Michael B. Clark; Matthew E. Ritchie

    Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipeline FLAMES to overcome these issues and perform isoform discovery and quantification, splicing

    更新日期:2020-08-11
  • Susceptibility to gingipains and transcriptomic response to P. gingivalis highlights the ribosome, hypothalamus, and cholinergic neurons
    bioRxiv. Genom. Pub Date : 2020-08-10
    Sejal Patel; Derek Howard; Leon French

    Porphyromonas gingivalis, a keystone species in the development of periodontal disease, is a suspected cause of Alzheimer's disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion proteome-wide. Proteins in the SRP-dependent cotranslational

    更新日期:2020-08-11
  • Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora
    bioRxiv. Genom. Pub Date : 2020-08-10
    Alissa M Williams; Michael W Itgen; Amanda K Broz; Olivia G Carter; Daniel B Sloan

    The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one

    更新日期:2020-08-11
  • Identifying Longevity Associated Genes by Integrating Gene Expression and Curated Annotations
    bioRxiv. Genom. Pub Date : 2020-08-07
    F. William Townes; Kareem Carr; Jeffrey W Miller

    Aging is a complex process with poorly understood genetic mechanisms. Recent studies have sought to classify genes as pro-longevity or anti-longevity using a variety of machine learning algorithms. However, it is not clear which types of features are best for optimizing classification performance and which algorithms are best suited to this task. Further, performance assessments based on held-out test

    更新日期:2020-08-10
  • Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the coffee wilt pathogen Fusarium xylarioide
    bioRxiv. Genom. Pub Date : 2020-08-07
    Lily Peck; Timothy Barraclough; Reuben Nowell; Julie Flood; Matthew Ryan

    Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following an initial 1920s outbreak. After successful management, it later re-emerged reaching two separate epidemics by the 2000s on arabica

    更新日期:2020-08-10
  • Targeted Transcriptome Analysis using Synthetic Long Read Sequencing Uncovers Isoform Reprograming in the Progression of Colon Cancer
    bioRxiv. Genom. Pub Date : 2020-08-07
    Silvia Liu; Indira Wu; Yan-Ping Yu; Michael Balamotis; Bao-Guo Ren; Tuval Ben Yehezkel; Jian-Hua Luo

    Diversity in human gene expression stems, to a large extent, from splicing exons into multiple mRNA isoforms. Characterization of isoforms requires accurate long-read sequencing. However, read lengths, high error rates, low throughput and large input requirements are some of the challenges that remain to be addressed in sequencing technologies. In this study, we used a barcoding-based synthetic long

    更新日期:2020-08-10
  • Multiomics analysis reveals extensive epigenome remodeling during cortical development
    bioRxiv. Genom. Pub Date : 2020-08-07
    Florian Noack; Silvia Vangelisti; Madalena Carido; Faye Chong; Boyan Bonev

    Despite huge advances in stem-cell, single-cell and epigenetic technologies, the precise molecular mechanisms that determine lineage specification remain largely unknown. Applying an integrative multiomics approach, e.g. combining single-cell RNA-seq, single-cell ATAC-seq together with cell-type-specific DNA methylation and 3D genome measurements, we systematically map the regulatory landscape in the

    更新日期:2020-08-10
  • Genome Diversity in Ukraine
    bioRxiv. Genom. Pub Date : 2020-08-07
    Taras K. Oleksyk; Walter W. Wolfsberger; Alexandra Weber; Khrystyna Shchubelka; Olga T. Oleksyk; Olga Levchuk; Alla Patrus; Nelya Lazar; Stephanie O. Castro-Marquez; Patricia Boldyzhar; Alina Urbanovych; Viktoriya Stakhovska; Kateryna Malyar; Svitlana Chervyakova; Olena Podoroha; Natalia Kovalchuk; Yaroslava Hasynets; Juan L. Rodriguez-Flores; Sarah Medley; Fabia Ursula Battistuzzi; Ryan Liu; Yong

    The main goal of this collaborative effort is to provide genome wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented

    更新日期:2020-08-10
  • Multi-omics approach highlights differences between functional RLP classes in Arabidopsis thaliana
    bioRxiv. Genom. Pub Date : 2020-08-07
    Christina E. Steidele; Remco Stam

    The receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others have found to be involved in defence responses. However, functional data is to date, only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function

    更新日期:2020-08-10
  • Genomic evolutionary analysis in R with geaR.
    bioRxiv. Genom. Pub Date : 2020-08-07
    Christopher M Ward; Alastair J Ludington; James Breen; Simon W Baxter

    The analysis and interpretation of datasets generated through sequencing large numbers of individual genomes is becoming commonplace in population and evolutionary genetic studies. Here we introduce geaR, a modular R package for evolutionary analysis of genome-wide genotype data. The package leverages the Genomic Data Structure (GDS) format, which enables memory and time efficient querying of genotype

    更新日期:2020-08-10
  • Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa
    bioRxiv. Genom. Pub Date : 2020-08-07
    Jennifer E Cornick; Patrick Musicha; Chikondi Peno; Ezgi Saeger; Pui-Ying Iroh-Tam; Aisleen Bennett; Neil Kennedy; Nicholas Feasey; Eva Heniz; Amy K Cain

    A suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae in a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes of K. pneumoniae isolated from patients in the hospital over a four-year period were identified. A MDR ST340 clone was implicated as the likely outbreak cause.

    更新日期:2020-08-08
  • Denisovan introgression has shaped the immune system of present-day Papuans
    bioRxiv. Genom. Pub Date : 2020-08-07
    Davide Maria Vespasiani; Guy S. Jacobs; Nicolas Brucato; Murray P. Cox; Irene Gallego Romero

    Modern humans have substantially admixed with multiple archaic hominins. New Guineans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals, whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these events remain poorly understood. Here we investigate the function of archaic alleles of both

    更新日期:2020-08-08
  • Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations
    bioRxiv. Genom. Pub Date : 2020-08-07
    Saif M. Khodary; Ali Mostafa Anwar

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries)

    更新日期:2020-08-08
  • Genome wide efficiency profiling reveals modulation of maintenance and de novo methylation by Tets
    bioRxiv. Genom. Pub Date : 2020-08-07
    Pascal Giehr; Charalampos Kyriakopoulos; Karl Karl Nordström; Abduhlrahman Salhab; Fabian Müller; Ferdinand von Meyenn; Gabriella Ficz; Wolf Reik; Verena Wolf; Jörn Walter

    Background: DNA methylation is an essential epigenetic modification which is set and maintained by DNA methyl transferases (Dnmts) and removed via active and passive mechanisms involving Tet mediated oxidation. While the molecular mechanisms of these enzymes are well studied, their interplay on shaping cell specific methylomes remains less well understood. In our work we model the activities of Tets

    更新日期:2020-08-08
  • Ubiquitous selfish toxin-antidote elements in Caenorhabditis species
    bioRxiv. Genom. Pub Date : 2020-08-07
    Eyal Ben-David; Pinelopi Pliota; Sonya A Widen; Alevtina Koreshova; Tzitziki Lemus-Vergara; Philipp Verpukhovskiy; Sridhar Mandali; Christian Braendle; Alejandro Burga; Leonid Kruglyak

    Toxin-antidote elements (TAs) are selfish genetic dyads that spread in populations by selectively killing non-carriers. TAs are common in prokaryotes, but few examples are known in animals. We discovered five maternal-effect TAs in the nematode Caenorhabditis tropicalis and one in C. briggsae. Unlike previously reported TAs, five of these novel toxins do not kill embryos but instead cause larval arrest

    更新日期:2020-08-08
  • Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin
    bioRxiv. Genom. Pub Date : 2020-08-06
    Elliot Walter Jackson; Roland C Wilhelm; Mitchell R Johnson; Holly L Lutz; Isabelle Danforth; Joseph K Gaydos; Michael H Hart; Ian Hewson Hewson

    A viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association

    更新日期:2020-08-08
  • Modified base-binding EVE and DCD Domains Implicated in the Origins of Programmed Cell Death and the piRNA Pathway
    bioRxiv. Genom. Pub Date : 2020-08-06
    Ryan Bell; Yuri I. Wolf; Eugene V. Koonin

    Background: DNA and RNA of most cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions

    更新日期:2020-08-08
  • The mutational load in natural populations is significantly affected by high primary rates of retroposition
    bioRxiv. Genom. Pub Date : 2020-08-06
    Wenyu Zhang; Chen Xie; Kristian Karsten Ullrich; Yong E. Zhang; Diethard Tautz

    Gene retroposition is known to contribute to patterns of gene evolution and adaptations. However, possible negative effects of gene retroposition remain largely unexplored, since most previous studies have focussed on between-species comparisons where negatively selected copies are mostly not observed, as they are quickly lost from the populations. Here, we show for natural house mouse populations

    更新日期:2020-08-08
  • QTL mapping in an interspecific sorghum population uncovers plasma-membrane intrinsic proteins as key regulators of salinity tolerance
    bioRxiv. Genom. Pub Date : 2020-08-06
    Ashley N Henderson; Rajanikanth Govindarajulu; Jennifer S Hawkins

    Soil salinity impedes crop production via both osmotic and ionic stress and is an intensifying problem affecting lands used to produce agronomically important crops.. Such stress slows plant growth and disrupts normal metabolic processes, resulting in decreased biomass and increased leaf senescence. Therefore, the ability to maintain biomass in response to salt exposure is indicative of tolerant genotypes

    更新日期:2020-08-08
  • Bayesian estimation of cell-type-specific gene expression per bulk sample with prior derived from single-cell data
    bioRxiv. Genom. Pub Date : 2020-08-06
    Jiebiao Wang; Kathryn Roeder; Bernie Devlin

    When assessed over a large number of samples, bulk RNA sequencing provides reliable data for gene expression at the tissue level. Single-cell RNA sequencing (scRNA-seq) deepens those analyses by evaluating gene expression at the cellular level. Both data types lend insights into disease etiology. With current technologies, however, scRNA-seq data are known to be noisy. Moreover, constrained by costs

    更新日期:2020-08-08
  • Photomap of the polythenic chromosomes of Drosophila malerkotliana and in situ mapping of the Hsp83 locus
    bioRxiv. Genom. Pub Date : 2020-08-06
    Pierre Teodosio Felix; José Ferreira dos Santos

    A photomap of the polythenic chromosomes of D. malerkotliana was constructed to facilitate the identification of the chromosomal arms and their sections, in order to allow the identification of the breaking points of inversions and the location of the bands marked by in situ hybridization. The photomap included the six chromosome arms corresponding to pairs I (chromosome X), II and III, excluding pair

    更新日期:2020-08-08
  • Identification of pituitary thyrotrope signature genes and regulatory elements
    bioRxiv. Genom. Pub Date : 2020-08-06
    Alexandre Z Daly; Lindsey A Dudley; Michael T Peel; Stephen A Liebhaber; Stephen CJ Parker; Sally A Camper

    Pituitary thyrotropes are specialized cells that produce thyroid stimulating hormone, a critical factor for growth and maintenance of metabolism. The transcription factors POU1F1 and GATA2 have been implicated in thyrotrope fate and regulation of Tshb transcription, but no transcriptomic or epigenetic analyses of these cells has been undertaken. The goal of this work was to discover key elements that

    更新日期:2020-08-08
  • Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2
    bioRxiv. Genom. Pub Date : 2020-08-06
    Sk. Sarif Hassan; Diksha Attrish; Shinjini Ghosh; Pabitra Pal Choudhury; Bidyut Roy

    One of the most important proteins for COVID-19 pathogenesis in SARS-CoV2 is the ORF3a protein which is the largest accessory protein among others accessory proteins coded by coronavirus genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis and virus release. The coronavirus, SARS-CoV2 is continuously evolving naturally and thereby the encoded proteins

    更新日期:2020-08-08
  • Incorporation of DNA methylation into eQTL mapping in African Americans.
    bioRxiv. Genom. Pub Date : 2020-08-06
    Anmol Singh; Yizhen Zhong; C Sehwan Park; Layan Nahlawi; Cristina Alarcon; Tanima De; Minoli Perera

    Epigenetics is a reversible molecular mechanism that plays a critical role in many developmental, adaptive, and disease processes. DNA methylation has been shown to regulate gene expression and the advent of high throughput technologies has made genome-wide DNA methylation analysis possible. We investigated the effect of DNA methylation in eQTL mapping (methylation-adjusted eQTLs), by incorporating

    更新日期:2020-08-06
  • Dissecting mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage
    bioRxiv. Genom. Pub Date : 2020-08-06
    Xueqing Zou; Gene Ching Chiek Koh; Arjun Scott Nanda; Andrea Degasperi; Katie Urgo; Theodoros Roumeliotis; Chukwuma A Agu; Lucy Side; Glen Brice; Vanesa Perez-Alonso; Daniel Rueda; Cherif Badja; Jamie Young; Celine Gomez; Wendy Bushell; Rebecca Harris; Joyti Choudhary; Josef I. Jiricny; William C Skarnes; Serena Nik-Zainal

    Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. Here, we generate isogenic CRISPR-Cas9 knockouts (Δ) of 43 genes in human induced pluripotent stem cells, culture them in the absence of added DNA damage, and perform whole-genome sequencing of 173 daughter subclones. ΔOGG1, ΔUNG, ΔEXO1, ΔRNF168, ΔMLH1, ΔMSH2, ΔMSH6, ΔPMS1, and ΔPMS2 produce marked mutational

    更新日期:2020-08-06
  • Automatic inference of demographic parameters using Generative Adversarial Networks
    bioRxiv. Genom. Pub Date : 2020-08-06
    Zhanpeng Wang; Jiaping Wang; Michael Kourakos; Nhung Hoang; Hyong Hark Lee; Iain Mathieson; Sara Mathieson

    Population genetics relies heavily on simulated data for validation, inference, and intuition. In particular, since real data is always limited, simulated data is crucial for training machine learning methods. Simulation software can accurately model evolutionary processes, but requires many hand-selected input parameters. As a result, simulated data often fails to mirror the properties of real genetic

    更新日期:2020-08-06
  • Age-related DNA methylation changes are sex-specific: a comprehensive assessment
    bioRxiv. Genom. Pub Date : 2020-08-05
    Igor Yusipov; Maria Giulia Bacalini; Alena Kalyakulina; Mikhail Krivonosov; Chiara Pirazzini; Noémie Gensous; Francesco Ravaioli; Maddalena Milazzo; Maria Vedunova; Giovanni Fiorito; Amedeo Gagliardi; Silvia Polidoro; Paolo Garagnani; Mikhail Ivanchenko; Claudio Franceschi

    In humans, females live longer than males but experience a worse longevity, as genome-wide autosomal DNA methylation differences between males and females have been reported. So far, few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling

    更新日期:2020-08-06
  • Analysis of the potential impact of genomic variants in SARS-CoV-2 genomes from India on molecular diagnostic assays
    bioRxiv. Genom. Pub Date : 2020-08-05
    Abhinav Jain; Mercy Rophina; Saurabh Mahajan; Bhavya Balaji Krishnan; Manasa Sharma; Sreya Mandal; Teresa Fernandez; Sumayra Sultanji; Samatha Mathew; Sridhar Sivasubbu; Vinod Scaria

    An isolated epidemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causing Coronavirus Diseases (C0VID-19) originating in Wuhan, China has now rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of disease

    更新日期:2020-08-06
  • IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation
    bioRxiv. Genom. Pub Date : 2020-08-05
    Fan Zhang; Joseph R. Mears; Lorien Shakib; Jessica I. Beynor; Sara Shanaj; Ilya Korsunsky; Aparna Nathan; Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus; Laura T. Donlin; Soumya Raychaudhuri

    Immunosuppressive and anti-cytokine treatment may have a protective effect for patients with COVID-19. Understanding the immune cell states shared between COVID-19 and other inflammatory diseases with established therapies may help nominate immunomodulatory therapies. Using an integrative strategy, we built a reference by meta-analyzing > 300,000 immune cells from COVID-19 and 5 inflammatory diseases

    更新日期:2020-08-06
  • Analysis of single nucleotide polymorphisms between 2019-nCoV genomes and its impact on codon usage
    bioRxiv. Genom. Pub Date : 2020-08-05
    Suruchi Gupta; Ravail Singh; Prosenjit Paul

    The spread of COVID-19 is a global concern that has taken a toll on entire human health. Researchers across the globe has been working in devising the strategies to combat this dreadful disease. Studies focused on genetic variability helps design effective drugs and vaccines. Considering this, the present study entails the information regarding the genome-wide mutations detected in the 108 SARS CoV-2

    更新日期:2020-08-06
  • Low Quantity single strand CAGE (LQ-ssCAGE) maps regulatory enhancers and promoters
    bioRxiv. Genom. Pub Date : 2020-08-05
    Hazuki Takahashi; Hiromi Nishiyori-Sueki; Jordan A Ramilowski; Masayoshi Itoh; Piero Carninci

    The Cap Analysis of Gene Expression (CAGE) is a powerful method to identify the Transcription Start Sites (TSSs) of capped RNAs while simultaneously measuring transcripts expression level. CAGE allows mapping at single nucleotide resolution at all active promoters and enhancers. Large CAGE datasets have been produced over the years from individual laboratories and consortia, including the Encyclopedia

    更新日期:2020-08-06
  • Controlling the false discovery rate in GWAS with population structure
    bioRxiv. Genom. Pub Date : 2020-08-04
    Matteo Sesia; Stephen Bates; Emmanuel Candès; Jonathan Marchini; Chiara Sabatti

    This paper proposes a novel statistical method to address population structure in genome-wide association studies while controlling the false discovery rate, which overcomes some limitations of existing approaches. Our solution accounts for linkage disequilibrium and diverse ancestries by combining conditional testing via knockoffs with hidden Markov models from state-of-the-art phasing methods. Furthermore

    更新日期:2020-08-05
  • A genomic dating tool for ancient genomes resolves the origins of hundreds of Eurasian genomes
    bioRxiv. Genom. Pub Date : 2020-08-04
    Umberto Esposito; Grace Holland; Ghadeer Alshehab; Ana Maria Dobre; Mehdi Pirooznia; Conrad Brimacombe; Eran Elhaik

    Radiocarbon dating is the gold-standard in archaeology to estimate the age of skeletons, a key to studying their origins. Nearly half of all published ancient human genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we developed the Temporal Population Structure (TPS), the first DNA-based dating method for ancient genomes ranging from the Upper Palaeolithic

    更新日期:2020-08-05
  • Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome
    bioRxiv. Genom. Pub Date : 2020-08-04
    Ruben Van Paemel; Andries De Koker; Christa Caggiano; Annelien Morlion; Pieter Mestdagh; Bram De Wilde; Jo Vandesompele; Katleen De Preter

    Background: The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulfite-based cfDNA methylation profiling. Methods: 15 tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer

    更新日期:2020-08-05
  • Transmission and genetic adaptation of Achromobacter in cystic fibrosis
    bioRxiv. Genom. Pub Date : 2020-08-04
    Migle Gabrielaite; Niels Nørskov-Lauritsen; Finn Cilius Nielsen; Helle Krogh Johansen; Rasmus Lykke Marvig

    Achromobacter species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen has been associated with antibiotic resistance and more severe disease outcomes. Nonetheless, little is known about the extent of transmission and genetic adaptation in Achromobacter infections. We sequenced the genomes of 101 clinical isolates of Achromobacter collected from 51 patients

    更新日期:2020-08-05
  • SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic
    bioRxiv. Genom. Pub Date : 2020-08-04
    Najia K Ghanchi; Kiran I Masood; Asghar Nasir; Waqasuddin Khan; Syed H Abidi; Saba Shahid; Syed F Mahmood; Akbar R Kanji; Safina A Razzak; Zeeshan Ansar; Nazneen Islam; Mohammad B Dharejo; Zahra Hasan; Rumina Hasan

    Objectives: Pakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country. Methods: We performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May. Results: Strains from travelers clustered with those

    更新日期:2020-08-05
  • Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
    bioRxiv. Genom. Pub Date : 2020-08-04
    Rowena A Bull; Thiruni Adikari; Jillian M Hammond; Igor Stevanovski; James M Ferguson; Alicia G Beukers; Zin Naing; Malinna Yeang; Andrey Verich; Hasindu Gamaarachichi; Ki Wook Kim; Fabio Luciani; Sacha Stelzer-Braid; John-Sebastian Eden; William D Rawlinson; Sebastiaan J van Hal; Ira W Deveson

    Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However

    更新日期:2020-08-05
  • Spatial tissue profiling by imaging-free molecular tomography
    bioRxiv. Genom. Pub Date : 2020-08-04
    Halima Hannah Schede; Christian Gabriel Schneider; Johanna Stergiadou; Lars E. Borm; Anurag Ranjak; Tracy M. Yamawaki; Fabrice P.A. David; Peter Lonnerberg; Gilles Laurent; Maria Antonietta Tosches; Simone Codeluppi; Gioele La Manno

    Genomics techniques are currently being adapted to provide spatially resolved omics profiling. However, the adaptation of each new method typically requires the setup of specific detection strategies or specialized instrumentation. A generic approach to spatially resolve different types of high throughput data is missing. Here, we describe an imaging-free framework to localize high throughput readouts

    更新日期:2020-08-05
  • Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs
    bioRxiv. Genom. Pub Date : 2020-08-04
    Mika Sakurai-Yageta; Kazuki Kumada; Chinatsu Gocho; Satoshi Makino; Akira Uruno; Shu Tadaka; Ikuko N Motoike; Masae Kimura; Shin Ito; Akihito Otsuki; Akira Narita; Hisaaki Kudo; Yuichi Aoki; Inaho Danjoh; Jun Yasuda; Hiroshi Kawame; Naoko Minegishi; Seizo Koshiba; Nobuo Fuse; Gen Tamiya; Masayuki Yamamoto; Kengo Kinoshita

    Background: Increasing the power of genome−wide association studies in diverse populations is important for understanding the genetic determinants of disease risks, and large−scale genotype data are collected by genome cohort and biobank projects all over the world. In particular, ethnic−specific SNP arrays are becoming more important because the use of universal SNP arrays has some limitations in

    更新日期:2020-08-05
  • Genome-Wide Screening Reveals CSDE1 as a Novel Regulator of the LDL Receptor
    bioRxiv. Genom. Pub Date : 2020-08-04
    Geoffrey A Smith; Akhil Pampana; Pradeep Natarajan; Kevan Shokat; John S Chorba

    In humans, clearance of LDL cholesterol, which causes atherosclerotic heart disease, is mediated by the hepatic LDL receptor (LDLR). As a result, therapies that upregulate the LDLR are highly effective treatments for atherosclerosis. Since cardiovascular disease remains the leading cause of death in Western countries, we sought to identify regulators of the LDLR beyond the known genetic causes of familial

    更新日期:2020-08-05
  • Dimension reduction and denoising of single-cell RNA sequencing data in the presence of observed confounding variables
    bioRxiv. Genom. Pub Date : 2020-08-04
    Mo Huang; Zhaojun Zhang; Nancy R. Zhang

    Confounding variation, such as batch effects, are a pervasive issue in single-cell RNA sequencing experiments. While methods exist for aligning cells across batches, it is yet unclear how to correct for other types of confounding variation which may be observed at the subject level, such as age and sex, and at the cell level, such as library size and other measures of cell quality. On the specific

    更新日期:2020-08-05
  • Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations
    bioRxiv. Genom. Pub Date : 2020-08-04
    Dhiraj Paul; Kunal Jani; Janesh Kumar; Radha Chauhan; Vasudevan Seshadri; Girdhari Lal; Rajesh Karyakarte; Suvarna Joshi; Murlidhar Tambe; Sourav Sen; Santosh Karade; Kavita Bala Anand; Shelinder Pal Singh Shergill; Rajiv Mohan Gupta; Manoj Kumar Bhat; Arvind Sahu; Yogesh S Shouche

    India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5'UTR

    更新日期:2020-08-05
  • Detection of alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) in association with Bt resistance using RNA-seq and PacBio Iso-Seq
    bioRxiv. Genom. Pub Date : 2020-08-04
    Zixiao Zhao; Christine G Elsik; Bruce E Hibbard; Kent S Shelby

    Alternative splicing increases the transcriptome diversity in eukaryotes. In insects, alternative splicing may causes resistance to pesticides and Bt toxins. The alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) has not been studied. To investigate its alternative splicing pattern and relation to Bt resistance, we carried out single-molecule real-time (SMRT) transcript

    更新日期:2020-08-04
  • Ten Genetic Loci Identified for Milk Yield, Fat, and Protein in Holstein Cattle
    bioRxiv. Genom. Pub Date : 2020-08-04
    Liyuan Liu; Jinghang Zhou; Chunpeng James Chen; Juan Zhang; Wan Wen; Jia Tian; Zhiwu Zhang; Yaling Gu

    High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk production traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production traits in Holstein cattle population from China. These traits included milk yield, protein yield, fat yields;

    更新日期:2020-08-04
  • Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
    bioRxiv. Genom. Pub Date : 2020-08-04
    Marina Athanasouli; Hanh Witte; Christian Weiler; Tobias Loschko; Gabi Eberhardt; Ralf J. Sommer; Christian Rödelsperger

    Background: Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics

    更新日期:2020-08-04
  • A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
    bioRxiv. Genom. Pub Date : 2020-08-03
    Gabriele Flossmann; Christine Wurmser; Hubert Pausch; Amabel Tenghe; Joerg Dodenhoff; Guenther Dahinten; Kay-Uwe Goetz; Ingolf Russ; Hans-Rudolf Fries

    Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of

    更新日期:2020-08-04
  • Allele Frequency Mismatches and Apparent Mismappings in UK Biobank SNP Data
    bioRxiv. Genom. Pub Date : 2020-08-03
    James M Kunert-Graf; Nikita M Sakhanenko; David J Galas

    We report here some anomalies discovered in the minor allele frequencies (MAFs) and some likely mismappings found in our analyses of UK Biobank dataset (UKB) and several other databases. We compared the MAFs present in the UKB to those measured in two other UK studies, ALSPAC and TwinsUK, and found a large set of SNPs for which the UKB MAFs are inconsistent. Additionally, even after accounting for

    更新日期:2020-08-04
  • Esrrb is a cell cycle dependent priming factor balancing between pluripotency and differentiation
    bioRxiv. Genom. Pub Date : 2020-08-03
    Sapir Herchcovici Levi; Lee Arnon; Sharon Feldman; Adi Alajem; Danny Bavli; Xue Sun; Yosef Buganim; Oren Ram

    Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based protocol as a differentiation

    更新日期:2020-08-04
  • Areca catechu-(Betel-nut)-induced whole transcriptome changes associated with diabetes, obesity and metabolic syndrome in a human monocyte cell line
    bioRxiv. Genom. Pub Date : 2020-08-03
    Shirleny Cardosa; William Ogunkolade; Rob Lowe; Emanuel Savage; Charles A Mein; Barbara J Boucher; Graham A Hitman

    Betel-nut consumption is the fourth most common addictive habit globally and there is good evidence to link it with obesity, type 2 diabetes and the metabolic syndrome. We adopted a genome-wide transcriptomic approach in a human monocyte cell line incubated with arecoline and its nitrosated products to identify gene expression changes relevant to obesity, type 2 diabetes and the metabolic syndrome

    更新日期:2020-08-04
  • Nanopore direct RNA sequencing detects differential expression between human cell populations
    bioRxiv. Genom. Pub Date : 2020-08-03
    Josie Gleeson; Tracy A Lane; Paul J Harrison; Wilfried Haerty; Michael B Clark

    Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Therefore, a crucial requirement of RNA sequencing is identifying differential expression. The recent development of long-read direct RNA (dRNA) sequencing has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation

    更新日期:2020-08-04
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