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Trace the Cancer of Unknown Primary Origin and Molecular Subtype Via Machine Learning

44 Pages Posted: 22 Aug 2018 Publication Status: Review Complete

See all articles by William F. Flynn

William F. Flynn

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

Sandeep Namburi

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

Carolyn A. Paisie

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

Honey V. Reddi

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

Sheng Li

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

R. Krishna Murthy Karuturi

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

Joshy George

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

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Abstract

Knowledge of a tumor’s primary site of origin and molecular subtype plays a critical role in the choice of treatment regimen and prognosis. We developed accurate machine learning based predictors of cancer primary site of origin and molecular subtype using gene expression data spanning 33 primary cancer types and molecular subtypes from 11 primary cancer types from The Cancer Genome Atlas (TCGA). Validation using external datasets shows that both primary site and molecular subtype predictors can robustly predict the primary site of origin and molecular subtype from microarray data, metastatic tumor data, and patient-derived xenograft (PDX) data. The predictors are available as open source software, freely available for academic non-commercial use.

Suggested Citation

Flynn, William F. and Namburi, Sandeep and Paisie, Carolyn A. and Reddi, Honey V. and Li, Sheng and Karuturi, R. Krishna Murthy and George, Joshy, Trace the Cancer of Unknown Primary Origin and Molecular Subtype Via Machine Learning (2018). Available at SSRN: https://ssrn.com/abstract=3236490 or http://dx.doi.org/10.2139/ssrn.3236490
This version of the paper has not been formally peer reviewed.

William F. Flynn (Contact Author)

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

10 Discovery Dr
Farmington, CT 06032
United States

Sandeep Namburi

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

10 Discovery Dr
Farmington, CT 06032
United States

Carolyn A. Paisie

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

10 Discovery Dr
Farmington, CT 06032
United States

Honey V. Reddi

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine

10 Discovery Dr
Farmington, CT 06032
United States

Sheng Li

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine ( email )

10 Discovery Dr
Farmington, CT 06032
United States

R. Krishna Murthy Karuturi

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine ( email )

10 Discovery Dr
Farmington, CT 06032
United States

Joshy George

The Jackson Laboratory - Jackson Laboratory for Genomic Medicine ( email )

10 Discovery Dr
Farmington, CT 06032
United States

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