title: Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas.
abstract: Gastrointestinal stromal tumor (GIST) has emerged as a clinically distinct type of sarcoma with frequent overexpression and mutation of the c-Kit oncogene and a favorable response to imatinib mesylate [also known as STI571 (Gleevec)] therapy. However, a significant diagnostic challenge remains in the differentiation of GIST from leiomyosarcomas (LMSs). To improve on the diagnostic evaluation and to complement the immunohistochemical evaluation of these tumors, we performed a whole-genome gene expression study on 68 well characterized tumor samples. Using bioinformatic approaches, we devised a two-gene relative expression classifier that distinguishes between GIST and LMS with an accuracy of 99.3% on the microarray samples and an estimated accuracy of 97.8% on future cases. We validated this classifier by using RT-PCR on 20 samples in the microarray study and on an additional 19 independent samples, with 100% accuracy. Thus, our two-gene relative expression classifier is a highly accurate diagnostic method to distinguish between GIST and LMS and has the potential to be rapidly implemented in a clinical setting. The success of this classifier is likely due to two general traits, namely that the classifier is independent of data normalization and that it uses as simple an approach as possible to achieve this independence to avoid overfitting. We expect that the use of simple marker pairs that exhibit these traits will be of significant clinical use in a variety of contexts.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Price
authors.forename: Jonathan
authors.initials: J
authors.lastname: Trent
authors.forename: Adel K
authors.initials: AK
authors.lastname: El-Naggar
authors.forename: David
authors.initials: D
authors.lastname: Cogdell
authors.forename: Ellen
authors.initials: E
authors.lastname: Taylor
authors.forename: Kelly K
authors.initials: KK
authors.lastname: Hunt
authors.forename: Raphael E
authors.initials: RE
authors.lastname: Pollock
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Ilya
authors.initials: I
authors.lastname: Shmulevich
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D015153:Blotting, Western; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003937:Diagnosis, Differential; D005069:Evaluation Studies as Topic; D046152:Gastrointestinal Stromal Tumors / Q000145:classification / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics / Q000379:methods; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics*; D006801:Humans; D007890:Leiomyosarcoma / Q000145:classification / Q000235:genetics*; D009124:Muscle Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics*; D017346:Protein Serine-Threonine Kinases; D020133:Reverse Transcriptase Polymerase Chain Reaction; D064067:Rho Guanine Nucleotide Exchange Factors
chemical_list: D005819:Genetic Markers; D020662:Guanine Nucleotide Exchange Factors; D009124:Muscle Proteins; D064067:Rho Guanine Nucleotide Exchange Factors; C578224:OBSCN protein, human; D017346:Protein Serine-Threonine Kinases