Whole genome sequencing for lung cancer

Daniels, Marissa, Goh, Felicia, Wright, Casey M., Sriram, Krishna B., Relan, Vandana, Clarke, Belinda E., Duhig, Edwina E., Bowman, Rayleen V., Yang, Ian A. and Fong, Kwun M. (2012) Whole genome sequencing for lung cancer. Journal of Thoracic Disease, 4 2: 155-163. doi:10.3978/j.issn.2072-1439.2012.02.01

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Author Daniels, Marissa
Goh, Felicia
Wright, Casey M.
Sriram, Krishna B.
Relan, Vandana
Clarke, Belinda E.
Duhig, Edwina E.
Bowman, Rayleen V.
Yang, Ian A.
Fong, Kwun M.
Title Whole genome sequencing for lung cancer
Journal name Journal of Thoracic Disease   Check publisher's open access policy
ISSN 2072-1439
Publication date 2012-04
Sub-type Critical review of research, literature review, critical commentary
DOI 10.3978/j.issn.2072-1439.2012.02.01
Volume 4
Issue 2
Start page 155
End page 163
Total pages 9
Place of publication Hong Kong, China
Publisher Pioneer Bioscience Publishing Company
Collection year 2013
Language eng
Abstract Lung cancer is a leading cause of cancer related morbidity and mortality globally, and carries a dismal prognosis. Improved understanding of the biology of cancer is required to improve patient outcomes. Next-generation sequencing (NGS) is a powerful tool for whole genome characterisation, enabling comprehensive examination of somatic mutations that drive oncogenesis. Most NGS methods are based on polymerase chain reaction (PCR) amplification of platform-specific DNA fragment libraries, which are then sequenced. These techniques are well suited to high-throughput sequencing and are able to detect the full spectrum of genomic changes present in cancer. However, they require considerable investments in time, laboratory infrastructure, computational analysis and bioinformatic support. Next-generation sequencing has been applied to studies of the whole genome, exome, transcriptome and epigenome, and is changing the paradigm of lung cancer research and patient care. The results of this new technology will transform current knowledge of oncogenic pathways and provide molecular targets of use in the diagnosis and treatment of cancer. Somatic mutations in lung cancer have already been identified by NGS, and large scale genomic studies are underway. Personalised treatment strategies will improve care for those likely to benefit from available therapies, while sparing others the expense and morbidity of futile intervention. Organisational, computational and bioinformatic challenges of NGS are driving technological advances as well as raising ethical issues relating to informed consent and data release. Differentiation between driver and passenger mutations requires careful interpretation of sequencing data. Challenges in the interpretation of results arise from the types of specimens used for DNA extraction, sample processing techniques and tumour content. Tumour heterogeneity can reduce power to detect mutations implicated in oncogenesis. Next-generation sequencing will facilitate investigation of the biological and clinical implications of such variation. These techniques can now be applied to single cells and free circulating DNA, and possibly in the future to DNA obtained from body fluids and from subpopulations of tumour. As costs reduce, and speed and processing accuracy increase, NGS technology will become increasingly accessible to researchers and clinicians, with the ultimate goal of improving the care of patients with lung cancer
Keyword High-throughput nucleotide sequencing
DNA sequence analysis
Lung neoplasms
Non-small cell lung carcinoma
Small cell lung carcinoma
Q-Index Code CX
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
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