A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma

被引：11

作者：

Belvedere, Ornella ^{[1
]}

Berri, Stefano ^{[1
]}

Chalkley, Rebecca ^{[1
]}

Conway, Caroline ^{[1
]}

Barbone, Fabio ^{[2
,3
]}

Pisa, Federica ^{[2
,3
]}

MacLennan, Kenneth ^{[1
,4
]}

Daly, Catherine ^{[1
]}

Alsop, Melissa ^{[1
]}

Morgan, Joanne ^{[1
]}

Menis, Jessica ^{[1
]}

Tcherveniakov, Peter ^{[1
,5
]}

Papagiannopoulos, Kostas ^{[1
,5
]}

Rabbitts, Pamela ^{[1
]}

Wood, Henry M. ^{[1
]}

机构：

[1] Univ Leeds, Leeds Inst Mol Med, Leeds LS9 7TF, W Yorkshire, England

[2] Univ Udine, Div Hyg & Epidemiol, Dept Med & Biol Sci, I-33100 Udine, Italy

[3] Univ Hosp Udine, I-33100 Udine, Italy

[4] St James Univ Hosp, Dept Histopathol, Leeds LS9 7TF, W Yorkshire, England

[5] St James Univ Hosp, Dept Thorac Surg, Leeds LS9 7TF, W Yorkshire, England

来源：

GENOMICS | 2012年 / 99卷 / 01期

关键词：

Lung cancer; Copy number; Survival; Next-generation sequencing; ARRAY CGH DATA; NORMALIZATION; DISCOVERY; SURVIVAL;

D O I：

10.1016/j.ygeno.2011.10.006

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Squamous cell carcinoma of the lung is remarkable for the extent to which the same chromosomal abnormalities are detected in individual tumours. We have used next generation sequencing at low coverage to produce high resolution copy number karyograms of a series of 89 non-small cell lung turnouts specifically of the squamous cell subtype. Because this methodology is able to create karyograms from formalin-fixed paraffin-embedded material, we were able to use archival stored samples for which survival data were available and correlate frequently occurring copy number changes with disease outcome. No single region of genomic change showed significant correlation with survival. However, adopting a whole-genome approach, we devised an algorithm that relates to total genomic damage, specifically the relative ratios of copy number states across the genome. This algorithm generated a novel index, which is an independent prognostic indicator in early stage squamous cell carcinoma of the lung. (C) 2011 Elsevier Inc. All rights reserved.

引用

页码：18 / 24

页数：7

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