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https://www.readbyqxmd.com/read/30275930/new-chromosome-counts-and-genome-size-estimates-for-28-species-of-taraxacum-sect-taraxacum
#1
Petra Macháčková, Ľuboš Majeský, Michal Hroneš, Eva Hřibová, Bohumil Trávníček, Radim J Vašut
The species-rich and widespread genus Taraxacum F. H. Wiggers, 1780 (Asteraceae subfamily Cichorioideae) is one of the most taxonomically complex plant genera in the world, mainly due to its combination of different sexual and asexual reproduction strategies. Polyploidy is usually confined to apomictic microspecies, varying from 3x to 6x (rarely 10x). In this study, we focused on Taraxacum sect. Taraxacum (= T.sect.Ruderalia; T.officinale group), i.e., the largest group within the genus. We counted chromosome numbers and measured the DNA content for species sampled in Central Europe, mainly in Czechia...
2018: Comparative Cytogenetics
https://www.readbyqxmd.com/read/30247488/a-universal-snp-and-small-indel-variant-caller-using-deep-neural-networks
#2
Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T Afshar, Sam S Gross, Lizzie Dorfman, Cory Y McLean, Mark A DePristo
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging. Here we show that a deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships between images of read pileups around putative variant and true genotype calls. The approach, called DeepVariant, outperforms existing state-of-the-art tools...
November 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/30228881/comparison-of-clustering-tools-in-r-for-medium-sized-10x-genomics-single-cell-rna-sequencing-data
#3
Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Background: The commercially available 10x Genomics protocol to generate droplet-based single-cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method to use. Methods: Here we use one gold standard 10x Genomics dataset, generated from the mixture of three cell lines, as well as three silver standard 10x Genomics datasets generated from peripheral blood mononuclear cells to examine not only the accuracy but also robustness of a dozen methods...
2018: F1000Research
https://www.readbyqxmd.com/read/30138581/statistical-binning-for-barcoded-reads-improves-downstream-analyses
#4
Ariya Shajii, Ibrahim Numanagić, Christopher Whelan, Bonnie Berger
Sequencing technologies are capturing longer-range genomic information at lower error rates, enabling alignment to genomic regions that are inaccessible with short reads. However, many methods are unable to align reads to much of the genome, recognized as important in disease, and thus report erroneous results in downstream analyses. We introduce EMA, a novel two-tiered statistical binning model for barcoded read alignment, that first probabilistically maps reads to potentially multiple "read clouds" and then within clouds by newly exploiting the non-uniform read densities characteristic of barcoded read sequencing...
August 22, 2018: Cell Systems
https://www.readbyqxmd.com/read/30124856/draft-genome-of-glyptosternon-maculatum-an-endemic-fish-from-tibet-plateau
#5
Haiping Liu, Qiyong Liu, Zhiqiang Chen, Yanchao Liu, Chaowei Zhou, Qiqi Liang, Caixia Ma, Jianshe Zhou, Yingzi Pan, Meiqun Chen, Wangjiu, Wenkai Jiang, Shijun Xiao, Zhenbo Mou
Background: Mechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes)...
September 1, 2018: GigaScience
https://www.readbyqxmd.com/read/30061114/single-cell-rna-seq-analysis-identifies-markers-of-resistance-to-targeted-braf-inhibitors-in-melanoma-cell-populations
#6
Yu-Jui Ho, Naishitha Anaparthy, David Molik, Grinu Mathew, Toby Aicher, Ami Patel, James Hicks, Molly Gale Hammell
Single-cell RNA-seq's (scRNA-seq) unprecedented cellular resolution at a genome-wide scale enables us to address questions about cellular heterogeneity that are inaccessible using methods that average over bulk tissue extracts. However, scRNA-seq data sets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we present a <u>s</u>ingle-cell RNA-seq <u>a</u>nalysis and <u>k</u>lustering <u>e</u>valuation (SAKE), a robust method for scRNA-seq analysis that provides quantitative statistical metrics at each step of the analysis pipeline...
September 2018: Genome Research
https://www.readbyqxmd.com/read/29991676/detection-and-removal-of-barcode-swapping-in-single-cell-rna-seq-data
#7
Jonathan A Griffiths, Arianne C Richard, Karsten Bach, Aaron T L Lun, John C Marioni
Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports...
July 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/29914369/hapdenovo-a-haplotype-based-approach-for-filtering-and-phasing-de-novo-mutations-in-linked-read-sequencing-data
#8
Xin Zhou, Serafim Batzoglou, Arend Sidow, Lu Zhang
BACKGROUND: De novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to understanding disease pathogenicity. However, accurate detection is challenging because of their small number relative to the genome-wide false positives in next generation sequencing (NGS) data. Software such as DeNovoGear and TrioDeNovo have been developed to detect DNMs, but at good sensitivity they still produce many false positive calls. RESULTS: To address this challenge, we develop HAPDeNovo, a program that leverages phasing information from linked read sequencing, to remove false positive DNMs from candidate lists generated by DNM-detection tools...
June 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#9
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29608694/scanpav-a-pipeline-for-extracting-presence-absence-variations-in-genome-pairs
#10
Francesca Giordano, Maximilian R Stammnitz, Elizabeth P Murchison, Zemin Ning
Motivation: The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human and non-human genomes. The ever increasing number of assemblies generated by novel de novo pipelines and strategies demands the development of new software to evaluate assembly quality and completeness. One way to determine the completeness of an assembly is by detecting its Presence-Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in the other one...
March 28, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29491155/copy-number-heterogeneity-large-origin-tandem-repeats-and-interspecies-recombination-in-human-herpesvirus-6a-hhv-6a-and-hhv-6b-reference-strains
#11
Alexander L Greninger, Pavitra Roychoudhury, Negar Makhsous, Derek Hanson, Jill Chase, Gerhard Krueger, Hong Xie, Meei-Li Huang, Lindsay Saunders, Dharam Ablashi, David M Koelle, Linda Cook, Keith R Jerome
Quantitative PCR is a diagnostic pillar for clinical virology testing, and reference materials are necessary for accurate, comparable quantitation between clinical laboratories. Accurate quantitation of human herpesvirus 6A/B (HHV-6A/B) is important for detection of viral reactivation and inherited chromosomally integrated HHV-6A/B in immunocompromised patients. Reference materials in clinical virology commonly consist of laboratory-adapted viral strains that may be affected by the culture process. We performed next-generation sequencing to make relative copy number measurements at single nucleotide resolution of eight candidate HHV-6A and seven HHV-6B reference strains and DNA materials from the HHV-6 Foundation and Advanced Biotechnologies Inc...
May 15, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29360925/recurrent-hyperactive-esr1-fusion-proteins-in-endocrine-therapy-resistant-breast-cancer
#12
R J Hartmaier, S E Trabucco, N Priedigkeit, J H Chung, C A Parachoniak, P Vanden Borre, S Morley, M Rosenzweig, L M Gay, M E Goldberg, J Suh, S M Ali, J Ross, B Leyland-Jones, B Young, C Williams, B Park, M Tsai, B Haley, J Peguero, R D Callahan, I Sachelarie, J Cho, J M Atkinson, A Bahreini, A M Nagle, S L Puhalla, R J Watters, Z Erdogan-Yildirim, L Cao, S Oesterreich, A Mathew, P C Lucas, N E Davidson, A M Brufsky, G M Frampton, P J Stephens, J Chmielecki, A V Lee
Background: Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer. Patients and methods: To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples...
April 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29356894/development-of-thinopyrum-ponticum-specific-molecular-markers-and-fish-probes-based-on-slaf-seq-technology
#13
Liqin Liu, Qiaoling Luo, Wan Teng, Bin Li, Hongwei Li, Yiwen Li, Zhensheng Li, Qi Zheng
Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th...
May 2018: Planta
https://www.readbyqxmd.com/read/29204149/diversity-in-grain-amaranths-and-relatives-distinguished-by-genotyping-by-sequencing-gbs
#14
Xingbo Wu, Matthew W Blair
The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29196497/powerful-inference-with-the-d-statistic-on-low-coverage-whole-genome-data
#15
Samuele Soraggi, Carsten Wiuf, Anders Albrechtsen
The detection of ancient gene flow between human populations is an important issue in population genetics. A common tool for detecting ancient admixture events is the D-statistic. The D-statistic is based on the hypothesis of a genetic relationship that involves four populations, whose correctness is assessed by evaluating specific coincidences of alleles between the groups. When working with high-throughput sequencing data, calling genotypes accurately is not always possible; therefore, the D-statistic currently samples a single base from the reads of one individual per population...
February 2, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29190660/actionable-mutations-in-canine-hemangiosarcoma
#16
Guannan Wang, Ming Wu, Martha A Maloneyhuss, John Wojcik, Amy C Durham, Nicola J Mason, David B Roth
BACKGROUND: Angiosarcomas (AS) are rare in humans, but they are a deadly subtype of soft tissue sarcoma. Discovery sequencing in AS, especially the visceral form, is hampered by the rarity of cases. Most diagnostic material exists as archival formalin fixed, paraffin embedded tissue which serves as a poor source of high quality DNA for genome-wide sequencing. We approached this problem through comparative genomics. We hypothesized that exome sequencing a histologically similar tumor, hemangiosarcoma (HSA), that occurs in approximately 50,000 dogs per year, may lead to the identification of potential oncogenic drivers and druggable targets that could also occur in angiosarcoma...
2017: PloS One
https://www.readbyqxmd.com/read/29186506/identification-of-large-rearrangements-in-cancer-genomes-with-barcode-linked-reads
#17
Li C Xia, John M Bell, Christina Wood-Bouwens, Jiamin J Chen, Nancy R Zhang, Hanlee P Ji
Large genomic rearrangements involve inversions, deletions and other structural changes that span Megabase segments of the human genome. This category of genetic aberration is the cause of many hereditary genetic disorders and contributes to pathogenesis of diseases like cancer. We developed a new algorithm called ZoomX for analysing barcode-linked sequence reads-these sequences can be traced to individual high molecular weight DNA molecules (>50 kb). To generate barcode linked sequence reads, we employ a library preparation technology (10X Genomics) that uses droplets to partition and barcode DNA molecules...
February 28, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29183737/cross-platform-single-cell-analysis-of-kidney-development-shows-stromal-cells-express-gdnf
#18
Bliss Magella, Mike Adam, Andrew S Potter, Meenakshi Venkatasubramanian, Kashish Chetal, Stuart B Hay, Nathan Salomonis, S Steven Potter
The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms...
February 1, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29112732/identifying-structural-variants-using-linked-read-sequencing-data
#19
Rebecca Elyanow, Hsin-Ta Wu, Benjamin J Raphael
Motivation: Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing...
November 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29101320/dense-and-accurate-whole-chromosome-haplotyping-of-individual-genomes
#20
David Porubsky, Shilpa Garg, Ashley D Sanders, Jan O Korbel, Victor Guryev, Peter M Lansdorp, Tobias Marschall
The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing...
November 3, 2017: Nature Communications
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