Classification of unknown primary tumors with a data-driven method based on a large microarray reference database

Kalle A Ojala; Sami K Kilpinen; Olli P Kallioniemi

doi:10.1186/gm279

Classification of unknown primary tumors with a data-driven method based on a large microarray reference database

Genome Med. 2011 Oct 17;3(9):63. doi: 10.1186/gm279.

Authors

Kalle A Ojala¹, Sami K Kilpinen, Olli P Kallioniemi

Affiliation

¹ Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 00140 Helsinki, Finland. olli.kallioniemi@fimm.fi.

PMID: 21955394
PMCID: PMC3239238
DOI: 10.1186/gm279

Abstract

We present a new method to analyze cancer of unknown primary origin (CUP) samples. Our method achieves good results with classification accuracy (88% leave-one-out cross validation for primary tumors from 56 categories, 78% for CUP samples), and can also be used to study CUP samples on a gene-by-gene basis. It is not tied to any a priori defined gene set as many previous methods, and is adaptable to emerging new information.