Claudio Lottaz and Rainer Spang
Molecular Decomposition of Complex Clinical Phenotypes using Biologically Structured Analysis of Microarray Data

Examples for StAM's Predictive Use

The analyses linked on this page are generated after splitting the data into training and test sets. We illustrate here, how StAM can be used for stratification of complex phenotypes. Thereby, new patients (our test samples) are attributed to disease sub-entities according to absence or presence of molecular symptoms.

Duke Breast Cancer Study

Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT. 
Gene expression predictors of breast cancer outcomes.
Lancet. 2003 May 10;361(9369):1590-6.

• Risk assessment: high risk vs. low risk
• Recurrence: recurrance vs. non-recurred

Harvard Lung Cancer Study

Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M.
Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13790-5. Epub 2001 Nov 13.

• Adeno carcinomas vs. various lung tissues 
• Adeno carcinomas vs. normal lung tissue
• Carcinoid:vs. various lung tissues
• Normal lung tissue vs. various lung cancers
• Squamous vs. various lung tissues
• Squamous vs. normal lung tissue

St. Jude  Leukemia Study

Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm FG, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui CH, Evans WE, Naeve C, Wong L, Downing JR. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling.
Cancer Cell. 2002 Mar;1(2):133-43.

• BCR-ABL translocation
• E2A-PBS1 translocation
• MLL rearrangements
• TEL-AML1 translocation
• Hyperdiploidity
• T-ALL