Identification of breast cancer prognosis markers using integrative sparse boosting.

Methods of Information in Medicine
Shuangge MaN Yi

Abstract

In breast cancer research, it is important to identify genomic markers associated with prognosis. Multiple microarray gene expression profiling studies have been conducted, searching for prognosis markers. Genomic markers identified from the analysis of single datasets often suffer a lack of reproducibility because of small sample sizes. Integrative analysis of data from multiple independent studies has a larger sample size and may provide a cost-effective solution. We collect four breast cancer prognosis studies with gene expression measurements. An accelerated failure time (AFT) model with an unknown error distribution is adopted to describe survival. An integrative sparse boosting approach is employed for marker selection. The proposed model and boosting approach can effectively accommodate heterogeneity across multiple studies and identify genes with consistent effects. Simulation study shows that the proposed approach outperforms alternatives including meta-analysis and intensity approaches by identifying the majority or all of the true positives, while having a low false positive rate. In the analysis of breast cancer data, 44 genes are identified as associated with prognosis. Many of the identified genes have been previo...Continue Reading

References

Sep 13, 2001·Proceedings of the National Academy of Sciences of the United States of America·T SørlieA L Børresen-Dale
Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
May 16, 2003·Lancet·Erich HuangAndrew T Huang
Jun 13, 2003·Bioinformatics·Marcel Dettling, Peter Bühlmann
Aug 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Christos SotiriouEdison T Liu
Jun 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Daniel R RhodesArul M Chinnaiyan
Jun 23, 2004·Annals of the New York Academy of Sciences·Daniel R Rhodes, Arul M Chinnaiyan
Oct 7, 2004·Bioinformatics·Marcel Dettling
Feb 16, 2006·Journal of the National Cancer Institute·Christos SotiriouMauro Delorenzi
Jul 28, 2007·Molecular & Cellular Proteomics : MCP·Vathany Kulasingam, Eleftherios P Diamandis
Nov 28, 2007·Annual Review of Pathology·Maggie C U CheangTorsten O Nielsen
Jun 10, 2008·BMC Bioinformatics·Matthias Schmid, Torsten Hothorn
Aug 25, 2009·The American Journal of Pathology·Lyndsey A EmeryCarol L Rosenberg
Feb 4, 2010·Briefings in Bioinformatics·Shuangge MaBen-Chang Shia
Sep 3, 2010·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Fangyi GuPeter Kraft
Nov 3, 2011·Biostatistics·Yuan HuangShuangge Ma
Nov 23, 2011·Statistics in Medicine·Shuangge MaKuangnan Fang

❮ Previous
Next ❯

Citations

Sep 7, 2012·Genetics Research·Shuangge MaKuangnan Fang
Jan 16, 2015·Applied Clinical Informatics·R Haux, C U Lehmann
Aug 13, 2014·Methods of Information in Medicine·A MayrM Schmid
Nov 25, 2014·Pathology Oncology Research : POR·Seyedmehdi NourashrafeddinMohammad Nouri
Jun 30, 2016·Journal of Ultrasound in Medicine : Official Journal of the American Institute of Ultrasound in Medicine·Florian FaschingbauerAndreas Mayr

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.