Foundation Medicine, Inc.

Methods for processing clinico-genotnic data are described. The methods may comprise, for example, receiving, at one or more processors, input data that specifies a plurality of prognostic features for a disease; extracting, using the one or more processors, a first data set comprising data corresponding to the plurality of prognostic features for the disease from a clinico-genomic database; generating, using the one or more processors, a second data set based on the first data set, wherein the second data set comprises data from the first data set, data derived from data in the first data set, or a combination thereof; and storing using the one or more processors, the second data set in a standardized table format. In one or more embodiments, the methods further comprise outputting the second data set in the standardized table format.

Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.

Methods and systems for determining a tumor heterogeneity score based on genomic data for a patient that is predictive of the estimated duration of the patient's response to a selected treatment for a given disease, e.g., a cancer, are described. In some instances, for example, the methods may comprise: receiving genomic data for a subject having a disease, wherein the genomic data indicates the presence of one or more short variants in a sample derived from the subject; determining a plurality of cancer cell fraction (CCF) measures by calculating a CCF measure for each of the one or more short variants; determining a tumor heterogeneity score (THS) based on the plurality of CCF measures; comparing the tumor heterogeneity score to one or more predetermined THS thresholds; and predicting an estimated duration of the subject's response to a therapy for treating the disease based on the comparison.

Methods for identifying disease subgroups are described. The methods may comprise, for example, receiving subject data for a plurality of subjects diagnosed with the disease; creating a plurality of candidate best fit latent class or mixture models by: i) providing an estimate of a number of subgroups; ii) generating a set of models, each model of the set comprising the same estimate of the number of subgroups; iii) selecting a candidate best fit model from the set; and iv) repeating (i)-(iii) at least once using a different estimate of the number of subgroups to obtain a plurality of candidate best fit models; selecting a best fit model from the plurality of candidate best fit models based on a fit statistic; and applying the best fit model to the subject data to identify a number of subgroups for the disease and an associated genomic profile for each subgroup.

Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.

Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.