Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments

2017 ◽  
Vol 9 (16) ◽  
pp. 13958-13964 ◽  
Author(s):  
Chunmei Li ◽  
Zhilong Yu ◽  
Yusi Fu ◽  
Yuhong Pang ◽  
Yanyi Huang
Keyword(s):  
Copy Number Variation ◽  
Single Cell ◽  
Copy Number ◽  
Genomic Dna ◽  
Dna Fragments ◽  
Number Variation ◽  
Digital Counting

EPCO-28. SINGLE-CELL RNA SEQUENCING IDENTIFIES INTRATUMORAL HETEROGENEITY AND ACTIVATION OF PRO-INVASIVE PATHWAYS IN NON-FUNCTIONING PITUITARY ADENOMAS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi8-vi8
Author(s):  
Saket Jain ◽  
Elaina Wang ◽  
Husam Babikir ◽  
Karin Shamardani ◽  
Aaron Diaz ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Wnt Signaling ◽  
Single Cell ◽  
Rna Sequencing ◽  
Pituitary Adenomas ◽  
Copy Number ◽  
Variation Analysis ◽  
Copy Number Variation Analysis ◽  
Single Cell Rna Sequencing ◽  
Number Variation

Abstract Pituitary adenomas (PA) are one of the most common primary brain tumors and comprise 15% of brain neoplasms. Most PAs are histologically benign but can cause significant morbidity. The genetic profile of PAs is poorly understood. We used single-cell RNA sequencing using the 10X genomic platform to investigate cellular heterogeneity in twelve non-functioning pituitary adenoma samples from nine patients including site-specific (core vs edge) samples from three patients. Our analysis identified discrete clusters of cells associated with activation of specific functional pathways including lipid metabolism, angiogenic, and antigen presentation and processing pathways regardless of location within the tumor. MALT1, a lncRNA associated with increased proliferation and metastasis was ubiquitously expressed amongst these samples. Analysis of the core vs edge samples showed two specific clusters with activated invasion-promoting pathways including PI3k/AKT signaling, Wnt signaling (Wnt6 and FZD4), and epithelial-mesenchymal transition (TGFB1, SMAD1, ZEB1, and SNAI2) in the edge of the tumors. The activated Wnt signaling cascade drove a proinflammatory tumor microenvironment induced by the expression of IL-1, IL-17, and Toll-like receptors (TLR6 and TLR7/8) resulting in suppression of Tregs. Copy number variation analysis using the CONICS-CNV algorithm highlighted distinct chromosomal alterations within our samples that led to insight into clonal variations within each tumor with loss of chromosome 2 an early event in tumorigenesis and gain/loss of chromosome 19 as late events. Mapping the copy number variation analysis with the somatic variant analysis using the Vartrix algorithm identified novel driver mutations within these tumors. These findings help define the molecular fingerprint of pituitary adenomas and provide insights which could be utilized for better management of these tumors.

scholarly journals Analysis of X chromosome genomic DNA sequence copy number variation associated with premature ovarian failure (POF)

2010 ◽  
Vol 25 (8) ◽  
pp. 2139-2150 ◽  
Author(s):  
C. R. Quilter ◽  
A. C. Karcanias ◽  
M. R. Bagga ◽  
S. Duncan ◽  
A. Murray ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Dna Sequence ◽  
X Chromosome ◽  
Premature Ovarian Failure ◽  
Copy Number ◽  
Genomic Dna ◽  
Ovarian Failure ◽  
Number Variation ◽  
Genomic Dna Sequence

scholarly journals Single-cell copy number variation detection

2011 ◽  
Vol 12 (8) ◽  
pp. R80 ◽  
Author(s):  
Jiqiu Cheng ◽  
Evelyne Vanneste ◽  
Peter Konings ◽  
Thierry Voet ◽  
Joris R Vermeesch ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Single Cell ◽  
Copy Number ◽  
Number Variation ◽  
Copy Number Variation Detection

scholarly journals Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

Cell Reports ◽  
2014 ◽  
Vol 8 (5) ◽  
pp. 1280-1289 ◽  
Author(s):  
Xuyu Cai ◽  
Gilad D. Evrony ◽  
Hillel S. Lehmann ◽  
Princess C. Elhosary ◽  
Bhaven K. Mehta ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Human Brain ◽  
Single Cell ◽  
Copy Number ◽  
Genome Wide ◽  
Number Variation ◽  
Cell Genome ◽  
Single Cell Genome

scholarly journals Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

Cell Reports ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. 645 ◽  
Author(s):  
Xuyu Cai ◽  
Gilad D. Evrony ◽  
Hillel S. Lehmann ◽  
Princess C. Elhosary ◽  
Bhaven K. Mehta ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Human Brain ◽  
Single Cell ◽  
Copy Number ◽  
Genome Wide ◽  
Number Variation ◽  
Cell Genome ◽  
Single Cell Genome

scholarly journals scSVAS: CNV clonal visualization online platform for large scale single-cell genomics

2021 ◽  
Author(s):  
Lingxi Chen ◽  
Yuhao Qing ◽  
Ruikang Li ◽  
Chaohui Li ◽  
Hechen Li ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Single Cell ◽  
Real Time ◽  
Copy Number ◽  
Large Scale ◽  
Single Cell Analysis ◽  
Interactive Visualization ◽  
Cell Analysis ◽  
Single Cell Genomics ◽  
Number Variation

The recent advance of single-cell copy number variation analysis plays an essential role in addressing intra-tumor heterogeneity, identifying tumor subgroups, and restoring tumor evolving trajectories at single-cell scale. Pleasant visualization of copy number analysis results boosts productive scientific exploration, validation, and sharing. Several single-cell analysis figures have the effectiveness of visualizations for understanding single-cell genomics in published articles and software packages. However, they almost lack real-time interaction, and it is hard to reproduce them. Moreover, existing tools are time-consuming and memory-intensive when they reach large-scale single-cell throughputs. We present an online visualization platform, scSVAS, for real-time interactive single-cell genomics data visualization. scSVAS is specifically designed for large-scale single-cell analysis. Compared with other tools, scSVAS manifests the most comprehensive functionalities. After uploading the specified input files, scSVAS deploys the online interactive visualization automatically. Users may make scientific discoveries, share interactive visualization, and download high-quality publication-ready figures. scSVAS provides versatile utilities for managing, investigating, sharing, and publishing single-cell copy number variation profiles. We envision this online platform will expedite the biological understanding of cancer clonal evolution in single-cell resolution. All visualizations are publicly hosted at https://sc.deepomics.org.

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