NDLI: An Integrated Inspection of the Somatic Mutations in a Lung Squamous Cell Carcinoma Using Next-Generation Sequencing

Content Provider	PubMed Central
Author	Stead, Lucy F. Egan, Philip Devery, Aoife Conway, Caroline Daly, Catherine Berri, Stefano Wood, Henry Belvedere, Ornella Papagiannopoulos, Kostas Ryan, Anderson Rabbitts, Pamela
Editor	Deb, Sumitra
Copyright Year	2013
Abstract	Squamous cell carcinoma (SCC) of the lung kills over 350,000 people annually worldwide, and is the main lung cancer histotype with no targeted treatments. High-coverage whole-genome sequencing of the other main subtypes, small-cell and adenocarcinoma, gave insights into carcinogenic mechanisms and disease etiology. The genomic complexity within the lung SCC subtype, as revealed by The Cancer Genome Atlas, means this subtype is likely to benefit from a more integrated approach in which the transcriptional consequences of somatic mutations are simultaneously inspected. Here we present such an approach: the integrated analysis of deep sequencing data from both the whole genome and whole transcriptome (coding and non-coding) of LUDLU-1, a SCC lung cell line. Our results show that LUDLU-1 lacks the mutational signature that has been previously associated with tobacco exposure in other lung cancer subtypes, and suggests that DNA-repair efficiency is adversely affected; LUDLU-1 contains somatic mutations in TP53 and BRCA2, allelic imbalance in the expression of two cancer-associated BRCA1 germline polymorphisms and reduced transcription of a potentially endogenous PARP2 inhibitor. Functional assays were performed and compared with a control lung cancer cell line. LUDLU-1 did not exhibit radiosensitisation or an increase in sensitivity to PARP inhibitors. However, LUDLU-1 did exhibit small but significant differences with respect to cisplatin sensitivity. Our research shows how integrated analyses of high-throughput data can generate hypotheses to be tested in the lab.
Related Links	http://dx.doi.org/10.1371/journal.pone.0078823
Starting Page	78823
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	11
Volume Number	8
Language	English
Publisher	Public Library of Science
Publisher Date	2013-11-11
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Targeted next-generation sequencing of 50 cancer-related genes in Japanese patients with oral squamous cell carcinoma

Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma

Next-generation sequencing revealed synchronous double primary lung squamous carcinoma: a case report

Germline and somatic variants in ovarian carcinoma: A next-generation sequencing (NGS) analysis

Empyema caused by Fusobacterium nucleatum with squamous cell carcinoma of the lung: a case report and literature review

Diagnosis of lung squamous cell carcinoma based on metagenomic Next-Generation Sequencing

Mutational Landscape of DDR2 Gene in Lung Squamous Cell Carcinoma Using Next-generation Sequencing

Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma

Next Generation Sequencing and Genetic Alterations in Squamous Cell Lung Carcinoma: Where Are We Today?

An Integrated Inspection of the Somatic Mutations in a Lung Squamous Cell Carcinoma Using Next-Generation Sequencing

Similar Documents

Targeted next-generation sequencing of 50 cancer-related genes in Japanese patients with oral squamous cell carcinoma

Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma

Next-generation sequencing revealed synchronous double primary lung squamous carcinoma: a case report

Germline and somatic variants in ovarian carcinoma: A next-generation sequencing (NGS) analysis

Empyema caused by Fusobacterium nucleatum with squamous cell carcinoma of the lung: a case report and literature review

Diagnosis of lung squamous cell carcinoma based on metagenomic Next-Generation Sequencing

Mutational Landscape of DDR2 Gene in Lung Squamous Cell Carcinoma Using Next-generation Sequencing

Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma

Next Generation Sequencing and Genetic Alterations in Squamous Cell Lung Carcinoma: Where Are We Today?

An Integrated Inspection of the Somatic Mutations in a Lung Squamous Cell Carcinoma Using Next-Generation Sequencing