Low-cost and clinically applicable copy number profiling using repeat DNA
Abujudeh S., Zeki SS., van Lanschot MCV., Pusung M., Weaver JMJ., Li X., Noorani A., Metz AJ., Bornschein J., Bower L., Miremadi A., Fitzgerald RC., Morrissey ER., Lynch AG., Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS)Consortium None., Fitzgerald R., Noorani A., Edwards PAW., Grehan N., Nutzinger B., Hughes C., Fidziukiewicz E., Bornschein J., MacRae S., Crawte J., Northrop A., Contino G., Li X., la Rue RD., O’Donovan M., Miremadi A., Malhotra S., Tripathi M., Tavaré S., Lynch A., Eldridge M., Secrier M., Bower L., Devonshire G., Perner J., Jammula S., Davies J., Crichton C., Carroll N., Safranek P., Hindmarsh A., Sujendran V., Hayes S., Ang Y., Preston S., Oakes S., Bagwan I., Save V., Skipworth RJE., Hupp T., O’Neill R., Tucker O., Beggs A., Taniere P., Puig S., Underwood T., Noble F., Owsley J., Barr H., Shepherd N., Old O., Lagergren J., Gossage J., Davies A., Chang F., Zylstra J., Mahadeva U., Goh V., Ciccarelli F., Sanders G., Berrisford R., Harden C., Lewis M., Cheong E., Kumar B., Parsons S., Soomro I., Kaye P., Saunders J., Lovat L., Haidry R., Igali L., Scott M., Sothi S., Suortamo S., Lishman S., Hanna G., Peters C., Grabowska A., Turkington R.
Large-scale cancer genome studies suggest that tumors are driven by somatic copy number alterations (SCNAs) or single-nucleotide variants (SNVs). Due to the low-cost, the clinical use of genomics assays is biased towards targeted gene panels, which identify SNVs. There is a need for a comparably low-cost and simple assay for high-resolution SCNA profiling. Here we present our method, conliga, which infers SCNA profiles from a low-cost and simple assay.