Copy number variation analysis increases the diagnostic yield of NGS studies in muscle disease patients

2017 ◽  
Vol 27 ◽  
pp. S193-S194
Author(s):  
S. Valipakka ◽  
M. Savarese ◽  
M. Johari ◽  
L. Sagath ◽  
M. Arumilli ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Diagnostic Yield ◽  
Muscle Disease ◽  
Variation Analysis ◽  
Copy Number Variation Analysis ◽  
Number Variation

scholarly journals Validation of copy number variation analysis for next-generation sequencing diagnostics

2017 ◽  
Vol 25 (6) ◽  
pp. 719-724 ◽  
Author(s):  
Jamie M Ellingford ◽  
Christopher Campbell ◽  
Stephanie Barton ◽  
Sanjeev Bhaskar ◽  
Saurabh Gupta ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Copy Number ◽  
Variation Analysis ◽  
Next Generation ◽  
Copy Number Variation Analysis ◽  
Number Variation ◽  
Generation Sequencing

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.

Germline copy number variation analysis in Finnish families with hereditary prostate cancer

The Prostate ◽  
2015 ◽  
Vol 76 (3) ◽  
pp. 316-324 ◽  
Author(s):  
Virpi H. Laitinen ◽  
Oyediran Akinrinade ◽  
Tommi Rantapero ◽  
Teuvo L.J. Tammela ◽  
Tiina Wahlfors ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Variation Analysis ◽  
Hereditary Prostate Cancer ◽  
Copy Number Variation Analysis ◽  
Number Variation

scholarly journals Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays

2010 ◽  
Vol 38 (10) ◽  
pp. 3275-3286 ◽  
Author(s):  
Derek A. Oldridge ◽  
Samprit Banerjee ◽  
Sunita R. Setlur ◽  
Andrea Sboner ◽  
Francesca Demichelis
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Short Sequence ◽  
Variation Analysis ◽  
Oligonucleotide Arrays ◽  
Copy Number Variation Analysis ◽  
Genome Wide ◽  
Number Variation
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