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https://www.readbyqxmd.com/read/30061114/single-cell-rna-seq-analysis-identifies-markers-of-resistance-to-targeted-braf-inhibitors-in-melanoma-cell-populations
#1
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 datasets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we present SAKE (Single-cell RNA-seq Analysis and Klustering Evaluation): a robust method for scRNA-seq analysis that provides quantitative statistical metrics at each step of the scRNA-seq analysis pipeline...
July 30, 2018: Genome Research
https://www.readbyqxmd.com/read/29991676/detection-and-removal-of-barcode-swapping-in-single-cell-rna-seq-data
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/29093801/chromosomal-constitutions-of-five-wheat-elytrigia-elongata-partial-amphiploids-as-revealed-by-gish-multicolor-gish-and-fish
#16
Fang He, Yuhai Wang, Yinguang Bao, Yingxue Ma, Xin Wang, Xingfeng Li, Honggang Wang
A combination of meiotic pairing analysis and in situ hybridization (genomic in situ hybridization [GISH], multicolor GISH [mcGISH] and fluorescence in situ hybridization [FISH]) of five Triticum aestivum (Linnaeus, 1753) - Elytrigia elongata (Podpěra, 1902) (2n = 10x = 70) amphiploids was employed to investigate the genomic constitution and relationships between wheat and alien chromosomes. GISH, multicolor GISH and FISH patterns of mitotic chromosomes indicate that the genomic constitution of the five partial amphiploids (XY693, XY7430, SN19, SN20 and SN122) are 14A + 12B + 14D + 8Js + 8J, 12A + 16B + 14D + 2St + 8Js + 2J + 2 W-E, 14A + 14B + 14D + 4St + 8Js, 14A + 14B + 14D + 2St + 10Js + 2J, and 14A + 14B + 14D + 2St + 8Js + 4J, respectively...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29069293/arcs-scaffolding-genome-drafts-with-linked-reads
#17
Sarah Yeo, Lauren Coombe, René L Warren, Justin Chu, Inanç Birol
Motivation: Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA-a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics. Results: Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies...
March 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29045639/a-new-perspective-on-polyploid-fragaria-strawberry-genome-composition-based-on-large-scale-multi-locus-phylogenetic-analysis
#18
Yilong Yang, Thomas M Davis
The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform...
December 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28759728/molecular-cytogenetic-identification-of-a-wheat-thinopyrum-ponticum-substitution-line-with-stripe-rust-resistance
#19
Chen Zhu, Yanzhen Wang, Chunhuan Chen, Changyou Wang, Aicen Zhang, Nana Peng, Yajuan Wang, Hong Zhang, Xinlun Liu, Wanquan Ji
Thinopyrum ponticum (Th. ponticum) (2n = 10x = 70) is an important breeding material with excellent resistance and stress tolerance. In this study, we characterized the derivative line CH1113-B13-1-1-2-1 (CH1113-B13) through cytological, morphological, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), expressed sequence tag (EST), and PCR-based landmark unique gene (PLUG) marker analysis. The GISH analysis revealed that CH1113-B13 contained 20 pairs of common wheat chromosomes and one pair of JSt genomic chromosomes...
October 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28714986/genome-wide-reconstruction-of-complex-structural-variants-using-read-clouds
#20
Noah Spies, Ziming Weng, Alex Bishara, Jennifer McDaniel, David Catoe, Justin M Zook, Marc Salit, Robert B West, Serafim Batzoglou, Arend Sidow
In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets...
September 2017: Nature Methods
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