title: A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma.
abstract: 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 tumours 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.
authors: Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors: Ornella
authors: O
authors: Belvedere
authors: Stefano
authors: S
authors: Berri
authors: Rebecca
authors: R
authors: Chalkley
authors: Caroline
authors: C
authors: Conway
authors: Fabio
authors: F
authors: Barbone
authors: Federica
authors: F
authors: Pisa
authors: Kenneth
authors: K
authors: MacLennan
authors: Catherine
authors: C
authors: Daly
authors: Melissa
authors: M
authors: Alsop
authors: Joanne
authors: J
authors: Morgan
authors: Jessica
authors: J
authors: Menis
authors: Peter
authors: P
authors: Tcherveniakov
authors: Kostas
authors: K
authors: Papagiannopoulos
authors: Pamela
authors: P
authors: Rabbitts
authors: Henry M
authors: HM
authors: Wood
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000465:Algorithms; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000401:mortality* / Q000601:surgery; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000401:mortality* / Q000601:surgery; D005260:Female; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000401:mortality* / Q000601:surgery; D008297:Male; D008875:Middle Aged; D008957:Models, Genetic; D011379:Prognosis; D017422:Sequence Analysis, DNA; D016019:Survival Analysis