Genomic heterogeneity as a barrier to precision medicine in gastroesophageal adenocarcinoma

E Pectasides, MD Stachler, S Derks, Y Liu, S Maron… - Cancer discovery, 2018 - AACR
Gastroesophageal adenocarcinoma (GEA) is a lethal disease where targeted therapies,
even when guided by genomic biomarkers, have had limited efficacy. A potential reason for …

Paired exome analysis of Barrett's esophagus and adenocarcinoma

MD Stachler, A Taylor-Weiner, S Peng, A McKenna… - Nature …, 2015 - nature.com
Barrett's esophagus is thought to progress to esophageal adenocarcinoma (EAC) through a
stepwise progression with loss of CDKN2A followed by TP53 inactivation and aneuploidy …

[HTML][HTML] Integrative genomic and transcriptomic analysis of leiomyosarcoma

P Chudasama, SS Mughal, MA Sanders… - Nature …, 2018 - nature.com
Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic
options. The mechanisms underlying LMS development, including clinically actionable …

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

Nature genetics, 2012 - nature.com
Burkitt lymphoma is a mature aggressive B-cell lymphoma derived from germinal center B
cells. Its cytogenetic hallmark is the Burkitt translocation t (8; 14)(q24; q32) and its variants …

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

H Kim, S Zheng, SS Amini, SM Virk… - Genome …, 2015 - genome.cshlp.org
Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional
therapy. A small residual population of cells escapes surgery and chemoradiation, resulting …

[HTML][HTML] Genomic alterations driving precancerous to cancerous lesions in esophageal cancer development

J Chang, X Zhao, Y Wang, T Liu, C Zhong, Y Lao… - Cancer Cell, 2023 - cell.com
Esophageal squamous cell carcinoma (ESCC) develops through a series of increasingly
abnormal precancerous lesions. Previous studies have revealed the striking differences …

A survey of computational tools to analyze and interpret whole exome sequencing data

JD Hintzsche, WA Robinson… - International journal of …, 2016 - Wiley Online Library
Whole Exome Sequencing (WES) is the application of the next‐generation technology to
determine the variations in the exome and is becoming a standard approach in studying …

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations

J Jabs, FM Zickgraf, J Park, S Wagner… - Molecular systems …, 2017 - embopress.org
Cancer drug screening in patient‐derived cells holds great promise for personalized
oncology and drug discovery but lacks standardization. Whether cells are cultured as …

[HTML][HTML] Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer

N Ishaque, ML Abba, C Hauser, N Patil… - Nature …, 2018 - nature.com
Incomplete understanding of the metastatic process hinders personalized therapy. Here we
report the most comprehensive whole-genome study of colorectal metastases vs. matched …

[HTML][HTML] Evolution from adherent to suspension: systems biology of HEK293 cell line development

M Malm, R Saghaleyni, M Lundqvist, M Giudici… - Scientific reports, 2020 - nature.com
The need for new safe and efficacious therapies has led to an increased focus on biologics
produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for …