Applications of Very Low-Coverage Sequencing in Cancer Genomics: Copy Number, Virus Detection and Survival

Chapter

Abstract

Since the advent of next-generation sequencing technology, much technological progress has been directed to increasing the depth of sequence coverage, either by improvements in chemistry or hardware to ever-increasing read numbers and lengths or by targeted capture of specific regions.

However there have also been developments in using lower-depth sequencing, mostly by utilising the aligned position of each read. Counting the frequency of aligned reads across the genome allows genomic copy number patterns to be measured. This technique has been shown to work using small amounts of DNA from fixed pathology archive samples and is amenable to high levels of multiplexing. A slight modification also allows viral infection in HPV-positive tumours to be detected, genotyped and quantified. Analysis of a number of tumours has allowed a sophisticated normalisation method to be developed which takes into account the amount of normal cells infiltrating a tumour sample and any tumour aneuploidy. This enables a more accurate definition of genomic gain and loss. This normalisation was applied to a cohort of early stage lung squamous cell carcinomas. No individual regions of gain or loss were associated with known clinical features such as stage, grade or length of survival; however, a pan-genomic index was developed which was linked to survival. This index is based on the total amount of genomic gain and loss seen in a tumour and the level of within-tumour heterogeneity, with loss and heterogeneity being linked to poorer survival.

Keywords

Copy number Next-generation sequencing Lung cancer Survival Heterogeneity 

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Leeds Institute of Molecular MedicineUniversity of LeedsLeedsUK

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