Image-based surrogate biomarkers for molecular subtypes of
colorectal cancer

J 2017

Image-based surrogate biomarkers for molecular subtypes of colorectal cancer

POPOVICI, Vlad, Eva BUDINSKÁ, Ladislav DUŠEK, Michal KOZUBEK, Fred BOSMAN et. al.

Basic information

Original name

Image-based surrogate biomarkers for molecular subtypes of colorectal cancer

Authors

POPOVICI, Vlad (642 Romania, guarantor, belonging to the institution), Eva BUDINSKÁ (703 Slovakia, belonging to the institution), Ladislav DUŠEK (203 Czech Republic, belonging to the institution), Michal KOZUBEK (203 Czech Republic, belonging to the institution) and Fred BOSMAN (528 Netherlands)

Edition

Bioinformatics, Oxford, Oxford University Press, 2017, 1367-4803

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 5.481

RIV identification code

RIV/00216224:14310/17:00097868

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1093/bioinformatics/btx027

UT WoS

000404054700013

Keywords in English

digital pathology; bioinformatics; molecular subtypes

Abstract

V originále

Motivation: Whole genome expression profiling of large cohorts of different types of cancer led to the identification of distinct molecular subcategories (subtypes) that may partially explain the observed inter-tumoral heterogeneity. This is also the case of colorectal cancer (CRC) where several such categorizations have been proposed. Despite recent developments, the problem of subtype definition and recognition remains open, one of the causes being the intrinsic heterogeneity of each tumor, which is difficult to estimate from gene expression profiles. However, one of the observations of these studies indicates that there may be links between the dominant tumor morphology characteristics and the molecular subtypes. Benefiting from a large collection of CRC samples, comprising both gene expression and histopathology images, we investigated the possibility of building image-based classifiers able to predict the molecular subtypes. We employed deep convolutional neural networks for extracting local descriptors which were then used for constructing a dictionary-based representation of each tumor sample. A set of support vector machine classifiers were trained to solve different binary decision problems, their combined outputs being used to predict one of the five molecular subtypes. Results: A hierarchical decomposition of the multi-class problem was obtained with an overall accuracy of 0.84 (95% CI = 0.79-0.88). The predictions from the image-based classifier showed significant prognostic value similar to their molecular counterparts.

Links

4SGA8736, interní kód MU

Name: Computational framework for joint analysis of histopathology images and gene expression data (Acronym: HIGEX)

Investor: South-Moravian Region, Incoming grants

Citovat

POPOVICI, Vlad, Eva BUDINSKÁ, Ladislav DUŠEK, Michal KOZUBEK and Fred BOSMAN. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 13, p. 2002-2009. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx027.

@article{1392199,
   author = {Popovici, Vlad and Budinská, Eva and Dušek, Ladislav and Kozubek, Michal and Bosman, Fred},
   article_location = {Oxford},
   article_number = {13},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btx027},
   keywords = {digital pathology; bioinformatics; molecular subtypes},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {Image-based surrogate biomarkers for molecular subtypes of colorectal cancer},
   volume = {33},
   year = {2017}
}

TY  - JOUR
ID  - 1392199
AU  - Popovici, Vlad - Budinská, Eva - Dušek, Ladislav - Kozubek, Michal - Bosman, Fred
PY  - 2017
TI  - Image-based surrogate biomarkers for molecular subtypes of colorectal cancer
JF  - Bioinformatics
VL  - 33
IS  - 13
SP  - 2002-2009
EP  - 2002-2009
PB  - Oxford University Press
SN  - 13674803
KW  - digital pathology
KW  - bioinformatics
KW  - molecular subtypes
N2  - Motivation: Whole genome expression profiling of large cohorts of different types of cancer led to the identification of distinct molecular subcategories (subtypes) that may partially explain the observed inter-tumoral heterogeneity. This is also the case of colorectal cancer (CRC) where several such categorizations have been proposed. Despite recent developments, the problem of subtype definition and recognition remains open, one of the causes being the intrinsic heterogeneity of each tumor, which is difficult to estimate from gene expression profiles. However, one of the observations of these studies indicates that there may be links between the dominant tumor morphology characteristics and the molecular subtypes. Benefiting from a large collection of CRC samples, comprising both gene expression and histopathology images, we investigated the possibility of building image-based classifiers able to predict the molecular subtypes. We employed deep convolutional neural networks for extracting local descriptors which were then used for constructing a dictionary-based representation of each tumor sample. A set of support vector machine classifiers were trained to solve different binary decision problems, their combined outputs being used to predict one of the five molecular subtypes. Results: A hierarchical decomposition of the multi-class problem was obtained with an overall accuracy of 0.84 (95% CI = 0.79-0.88). The predictions from the image-based classifier showed significant prognostic value similar to their molecular counterparts.
ER  -

POPOVICI, Vlad, Eva BUDINSKÁ, Ladislav DUŠEK, Michal KOZUBEK and Fred BOSMAN. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. \textit{Bioinformatics}. Oxford: Oxford University Press, 2017, vol.~33, No~13, p.~2002-2009. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx027.

Detailed Information on Publication Record