scholarly journals BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Yi Fu ◽  
Guoqiang Yu ◽  
Douglas A. Levine ◽  
Niya Wang ◽  
Ie-Ming Shih ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Alterations ◽  
Absolute Normalization ◽  
Somatic Copy Number Alterations ◽  
Heterogeneous Tumor

scholarly journals LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

2021 ◽  
Author(s):  
Eszter Lakatos ◽  
Helen Hockings ◽  
Maximilian Mossner ◽  
Michelle Lockley ◽  
Trevor A. Graham
Keyword(s):  
Copy Number ◽  
Evolutionary Dynamics ◽  
Cost Effective ◽  
Copy Number Alterations ◽  
Liquid Biopsies ◽  
Metastatic Lung ◽  
Low Pass ◽  
Somatic Copy Number Alterations

AbstractCell-free DNA (cfDNA) measured via liquid biopsies provides a way for minimally-invasive monitoring of tumour evolutionary dynamics during therapy. Here we present liquidCNA, a method to track subclonal evolution from longitudinally collected cfDNA samples based on somatic copy number alterations (SCNAs). LiquidCNA utilises SCNA profiles derived through cost-effective low-pass whole genome sequencing to automatically and simultaneously genotype and quantify the size of the dominant subclone without requiring prior knowledge of the genetic identity of the emerging clone. We demonstrate the accuracy of liquidCNA in synthetically generated sample sets and in vitro and in silico mixtures of cancer cell lines. Application in vivo in patients with metastatic lung cancer reveals the progressive emergence of a novel tumour sub-population. LiquidCNA is straightforward to use, computationally inexpensive and enables continuous monitoring of subclonal evolution to understand and control therapy-induced resistance.

scholarly journals Molecular profiling and genome-wide analysis based on somatic copy number alterations in advanced colorectal cancers

2017 ◽  
Vol 57 (3) ◽  
pp. 451-461 ◽  
Author(s):  
Tamotsu Sugai ◽  
Yayoi Takahashi ◽  
Makoto Eizuka ◽  
Ryo Sugimoto ◽  
Yasuko Fujita ◽  
...  
Keyword(s):  
Copy Number ◽  
Molecular Profiling ◽  
Colorectal Cancers ◽  
Copy Number Alterations ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Somatic Copy Number Alterations

scholarly journals Impressive response to immunotherapy in a metastatic gastric cancer patient: could somatic copy number alterations help patient selection?

2017 ◽  
Vol 5 (1) ◽  
Author(s):  
Gustavo dos Santos Fernandes ◽  
Daniel da Motta Girardi ◽  
Luiza Dib Batista Bugiato Faria ◽  
João Paulo Giacomini Bernardes ◽  
Renata de Almeida Coudry
Keyword(s):  
Gastric Cancer ◽  
Cancer Patient ◽  
Patient Selection ◽  
Gastric Cancer Patient ◽  
Copy Number ◽  
Metastatic Gastric Cancer ◽  
Copy Number Alterations ◽  
Somatic Copy Number Alterations

scholarly journals Impact of somatic copy number alterations on the glioblastoma miRNome: miR-4484 is a genomically deleted tumour suppressor

2017 ◽  
Vol 11 (8) ◽  
pp. 927-944 ◽  
Author(s):  
Zahid Nawaz ◽  
Vikas Patil ◽  
Sivaarumugam Thinagararjan ◽  
Soumya A. Rao ◽  
Alangar S. Hegde ◽  
...  
Keyword(s):  
Copy Number ◽  
Tumour Suppressor ◽  
Copy Number Alterations ◽  
Somatic Copy Number Alterations
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