Abstract: Methods for determining a cancer composition of a subject are provided that include generating machine-learning models configured to identify cell types based on respective cell-type RNA expression profiles, and using the models to determine the cancer composition of the subject.

Abstract: A system and method that receive a distance matrix for multiple patients and a patient of interest, assign a radial distance value between the patient of interest and the other patients based on the distance matrix value for each of the multiple patients, generate an angular distance value between the multiple patients based at least in part on a measure of similarity between each patient, and minimize a cost function based at least in part on the angular distance value between each patient and each other patient. Minimizing the cost function may include calculating a patient contribution to the cost function for a plurality of angular distance values and selecting the angular distance value with the smallest patient contribution. The processor also may be configured to generate and display a radar plot based on the assigned radial distance value and generated angular distance value of each patient.

Abstract: In one aspect, the present disclosure provides a method for labeling one or more medications concurrently administered to a patient as a line of therapy. The method includes identifying medical records of the patient from a plurality of digital records, creating, from the subset of medical records, a plurality of treatment intervals including at least one medication administered to the patient and a time interval, associating medications of the one or more treatments with a respective treatment interval when the administration of the medication falls within the time interval, refining the time interval of a respective treatment interval when a treatment of the one or more treatments falls outside the time interval but within an extension period, identifying one or more potential lines of therapy from the plurality of treatment intervals, and labeling the potential line of therapy having the highest maximum likelihood estimation as the line of therapy.

Abstract: The present disclosure provides methods for manufacturing nucleic acid probes for genotyping by sequencing, methods for genotyping a DNA sample by sequencing using a set of nucleic acid probes, and systems for carrying out such methods.

Abstract: In one aspect, the present disclosure provides a method for labeling one or more medications concurrently administered to a patient as a line of therapy. The method includes identifying medical records of the patient from a plurality of digital records, creating, from the subset of medical records, a plurality of treatment intervals including at least one medication administered to the patient and a time interval, associating medications of the one or more treatments with a respective treatment interval when the administration of the medication falls within the time interval, refining the time interval of a respective treatment interval when a treatment of the one or more treatments falls outside the time interval but within an extension period, identifying one or more potential lines of therapy from the plurality of treatment intervals, and labeling the potential line of therapy having the highest maximum likelihood estimation as the line of therapy.

Abstract: Methods for determining a cancer composition of a subject are provided that include generating machine-learning models configured to identify cell types based on respective cell-type RNA expression profiles, and using the models to determine the cancer composition of the subject.

Abstract: In one aspect, the present disclosure provides a method for labeling one or more medications concurrently administered to a patient as a line of therapy. The method includes identifying medical records of the patient from a plurality of digital records, creating, from the subset of medical records, a plurality of treatment intervals including at least one medication administered to the patient and a time interval, associating medications of the one or more treatments with a respective treatment interval when the administration of the medication falls within the time interval, refining the time interval of a respective treatment interval when a treatment of the one or more treatments falls outside the time interval but within an extension period, identifying one or more potential lines of therapy from the plurality of treatment intervals, and labeling the potential line of therapy having the highest maximum likelihood estimation as the line of therapy.

Abstract: A platform for transcriptome deconvolution of gene expression data is provided and may be used in assessing metastatic cancer samples. The deconvolution is performed using an unsupervised clustering technique, such as grade of membership, that allows for samples to be assigned to multiple clusters during a training process. A deconvolution gene expression model is generated as a result and is used for accurate assess of metastases in subsequent samples.

Abstract: A system and method that receive a distance matrix for multiple patients and a patient of interest, assign a radial distance value between the patient of interest and the other patients based on the distance matrix value for each of the multiple patients, generate an angular distance value between the multiple patients based at least in part on a measure of similarity between each patient, and minimize a cost function based at least in part on the angular distance value between each patient and each other patient. Minimizing the cost function may include calculating a patient contribution to the cost function for a plurality of angular distance values and selecting the angular distance value with the smallest patient contribution. The processor also may be configured to generate and display a radar plot based on the assigned radial distance value and generated angular distance value of each patient.