Next-generation sequencing: advances and applications in cancer diagnosis

S Serratì, S De Summa, B Pilato, D Petriella… - OncoTargets and …, 2016 - Taylor & Francis
Technological advances have led to the introduction of next-generation sequencing (NGS)
platforms in cancer investigation. NGS allows massive parallel sequencing that affords …

Whole-genome CNV analysis: advances in computational approaches

M Pirooznia, FS Goes, PP Zandi - Frontiers in genetics, 2015 - frontiersin.org
Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a
significant contribution to human diversity and also play an important role in disease …

An evaluation of copy number variation detection tools from whole‐exome sequencing data

R Tan, Y Wang, SE Kleinstein, Y Liu, X Zhu… - Human …, 2014 - Wiley Online Library
Copy number variation (CNV) has been found to play an important role in human disease.
Next‐generation sequencing technology, including whole‐genome sequencing (WGS) and …

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data

F Zare, M Dow, N Monteleone, A Hosny, S Nabavi - BMC bioinformatics, 2017 - Springer
Background Recently copy number variation (CNV) has gained considerable interest as a
type of genomic/genetic variation that plays an important role in disease susceptibility …

Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics

Z Zhong, J Hou, Z Yao, L Dong, F Liu, J Yue… - Nature …, 2024 - nature.com
Single-cell and spatial transcriptome sequencing, two recently optimized transcriptome
sequencing methods, are increasingly used to study cancer and related diseases. Cell …

Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

ÍF do Valle, E Giampieri, G Simonetti, A Padella… - BMC …, 2016 - Springer
Background Detecting somatic mutations in whole exome sequencing data of cancer
samples has become a popular approach for profiling cancer development, progression and …

[HTML][HTML] Assessing copy number alterations in targeted, amplicon-based next-generation sequencing data

C Grasso, T Butler, K Rhodes, M Quist, TL Neff… - The Journal of Molecular …, 2015 - Elsevier
Changes in gene copy number are important in the setting of precision medicine. Recent
studies have established that copy number alterations (CNAs) can be detected in …

Sequencing structural variants in cancer for precision therapeutics

G Macintyre, B Ylstra, JD Brenton - Trends in Genetics, 2016 - cell.com
The identification of mutations that guide therapy selection for patients with cancer is now
routine in many clinical centres. The majority of assays used for solid tumour profiling use …

Next-generation sequencing informatics: challenges and strategies for implementation in a clinical environment

S Roy, WA LaFramboise… - … of pathology & …, 2016 - meridian.allenpress.com
Context.—Next-generation sequencing (NGS) is revolutionizing the discipline of laboratory
medicine, with a deep and direct impact on patient care. Although it empowers clinical …

[HTML][HTML] Application of plasma genotyping technologies in non–small cell lung cancer: a practical review

AG Sacher, KM Komatsubara, GR Oxnard - Journal of Thoracic Oncology, 2017 - Elsevier
The rational treatment of metastatic NSCLC hinges on the timely detection of potentially
targetable genomic alterations to guide therapy. Recent advances in highly sensitive …