{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:32:06Z","timestamp":1761514326559,"version":"3.37.3"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,2,5]],"date-time":"2019-02-05T00:00:00Z","timestamp":1549324800000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The National Health Services"},{"name":"Gustav V:s Jubilee Foundation"},{"name":"BioCARE"},{"DOI":"10.13039\/501100003173","name":"Crafoord Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003173","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003461","name":"Gunnar Nilsson Cancer Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003461","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004635","name":"Mrs. Berta Kamprad Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004635","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002794","name":"Swedish Cancer Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002794","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The development of multigene classifiers for cancer prognosis, treatment prediction, molecular subtypes or clinicopathological groups has been a cornerstone in transcriptomic analyses of human malignancies for nearly two decades. However, many reported classifiers are critically limited by different preprocessing needs like normalization and data centering. In response, a new breed of classifiers, single sample predictors (SSPs), has emerged. SSPs classify samples in an N-of-1 fashion, relying on, e.g. gene rules comparing expression values within a sample. To date, several methods have been reported, but there is a lack of head-to-head performance comparison for typical cancer classification problems, representing an unmet methodological need in cancer bioinformatics. To resolve this need, we performed an evaluation of two SSPs [k-top-scoring pair classifier (kTSP) and absolute intrinsic molecular subtyping (AIMS)] for two case examples of different magnitude of difficulty in non-small cell lung cancer: gene expression\u2013based classification of (i) tumor histology and (ii) molecular subtype. Through the analysis of ~2000 lung cancer samples for each case example (n\u00a0=\u00a01918 and n\u00a0=\u00a02106, respectively), we compared the performance of the methods for different sample compositions, training data set sizes, gene expression platforms and gene rule selections. Three main conclusions are drawn from the comparisons: both methods are platform independent, they select largely overlapping gene rules associated with actual underlying tumor biology and, for large training data sets, they behave interchangeably performance-wise. While SSPs like AIMS and kTSP offer new possibilities to move gene expression signatures\/predictors closer to a clinical context, they are still importantly limited by the difficultness of the classification problem at hand.<\/jats:p>","DOI":"10.1093\/bib\/bbz008","type":"journal-article","created":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T04:36:55Z","timestamp":1547008615000},"page":"729-740","source":"Crossref","is-referenced-by-count":18,"title":["Performance of gene expression\u2013based single sample predictors for assessment of clinicopathological subgroups and molecular subtypes in cancers: a case comparison study in non-small cell lung cancer"],"prefix":"10.1093","volume":"21","author":[{"given":"Helena","family":"Cirenajwis","sequence":"first","affiliation":[{"name":"Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Lauss","sequence":"additional","affiliation":[{"name":"Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Planck","sequence":"additional","affiliation":[{"name":"Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johan","family":"Vallon-Christersson","sequence":"additional","affiliation":[{"name":"Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5254-5115","authenticated-orcid":false,"given":"Johan","family":"Staaf","sequence":"additional","affiliation":[{"name":"Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,4]]},"reference":[{"key":"2020080709363678800_ref1","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/35021093","article-title":"Molecular portraits of human breast tumours","volume":"406","author":"Perou","year":"2000","journal-title":"Nature"},{"issue":"1","key":"2020080709363678800_ref2","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1093\/jnci\/dju357","article-title":"Absolute assignment of breast cancer intrinsic molecular subtype","volume":"107","author":"Paquet","year":"2015","journal-title":"J Natl 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