CIRI is a risk model from the Alizadeh Lab and the Diehn Lab developed by Kurtz, Esfahani, Scherer, et al. for integrating diverse prognostic markers in cancer to produce a unified prediction of risk. CIRI incorporates serial information obtained throughout a patient’s course to provide a personalized estimate of risk over time.
Lung-CLiP is a novel approach from the Alizadeh Lab and the Diehn Lab developed by Chabon, Hamilton, Kurtz, Shahrokh, et al. for noninvasive early NSCLC detection that integrates improved sequencing library preparation and machine learning to predict the presence of tumor-derived cfDNA in a blood sample.
iDES is a general framework from the Alizadeh Lab and the Diehn Lab for error suppression in high throughput sequencing data. A key advance within iDES is the use of computational “background polishing” to model and eliminate stereotypical sequencing artifacts. Background polishing can deliver performance gains that match, and often surpass, molecular barcoding alone. Applied together, the two techniques can improve analytical sensitivity by ~15-fold.
FACTERA is a tool from the Alizadeh Lab and the Diehn Lab for practical and robust de novo enumeration of genomic fusions and breakpoints from paired-end targeted (or genome-wide) sequencing data. FACTERA has minimal external dependencies, works directly on a preexisting BAM alignment file, and produces easily interpretable output.
Two Gene Score (TGS) calculator to determine prognosis in Diffuse Large B-cell Lymphoma (DLBCL) using the Two Gene Score (TGS) and the International Prognostic Index (IPI). Measurement of a single gene expressed by tumor cells (LMO2) and a single gene expressed by the immune microenvironment (TNFRSF9) powerfully predicts overall survival in patients with DLBCL. This simple test can be used to select patients of different risk groups for clinical trials.
SOURCE (legacy website) is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports. It was moved to Princeton University, and the supporting database was last updated on June 10, 2015.