Tempus Labs, Inc.

Tempus Ai, Inc.

Robert Tell

Eric Lefkofsky

Aly Azeem Khan

Nike Tsiapera Beaubier

Hunter Lane

Denise Lau

Shane Colley

Terri M Driessen

Kevin White

Wei Zhu

Isaiah Simpson

Stephen Bush

Brian Reuter

Kaanan Shah

Hailey B Lefkofsky

Justin David Finkle

Christine Lo

Joshua S K Bell

Catherine Igartua

Ameen Salahudeen

Verónica Sánchez Freire

Yilin Zhang

Hailey Lefkofsky

Christopher Shane Colley

Nike Beaubier

Aarti Venkat

Jerod Parsons

A method and system comprising storing a set of user application programs each requiring an application specific subset of data to perform application processes and generate a respective genomic variant characterization for each of a plurality of patients with cancerous cells and receiving cancer treatment. The method including, obtaining clinical records data including cancer related information, generating genomic sequencing data for the patient's cancerous cells and normal cells, shaping at least a subset of the genomic sequencing data to generate system structured data. Storing the system structured data in a first database, selecting the application specific data from the first database, storing the application specific data in a second database for application program interfacing, receiving the respective genomic variant characterization from the user application program, and storing the genomic variant characterization from the user application program in a third database.

Data based cancer research and treatment systems and methods

A method and system for storing user application programs and micro-service programs, for each of multiple patients that have cancerous cells and receive treatment, includes obtaining clinical records data in original forms, storing it in a semi-structured first database, generating sequencing data for the patient's cancerous and normal cells using a next generation genomic sequencer, storing the sequencing data in the first database, shaping at least some of the first database data to generate system structured data optimized for searching and including clinical record data, storing the structured data in a second database, for each user application program, selecting an application-specific subset of data from the second database and storing it in a structure optimized for application program interfacing in a third database, wherein an orchestration manager operatively connected to one or more micro-service programs receives status messages and initiates a respective micro-service program when program prerequisites are satisfied.

A system, method, and mobile device application are configured to capture, with a mobile device, a document such as a next generation sequencing (NGS) report that includes NGS medical information about a genetically sequenced patient. The method includes receiving, from a mobile device, an image of a medical document comprising NGS medical information of the patient, extracting a first region from the image, extracting NGS medical information of the patient from the first region into a structured dataset, the extracted NGS medical information including at least one RNA expression, correlating a portion of the extracted NGS medical information that includes the at least one RNA expression with summarized medical information from a cohort of patients similar to the patient, and generating, for display on the mobile device, a clinical decision support report comprising the summarized medical information.

Mobile supplementation, extraction, and analysis of health records

A method and system for conducting genomic sequencing, the method comprising storing a set of user application programs wherein each of the programs requires an application specific subset of data, for each of a plurality of patients that have cancerous cells and that receive cancer treatment, obtaining clinical records data in original forms including cancer state information, treatment types and treatment efficacy information, storing the clinical records data in a semi-structured first database, for each patient, using a genomic sequencer to generate genomic sequencing data for the patient's cancerous cells and normal cells, storing the sequencing data in the first database, shaping at least a subset of the first database data to generate system structured data including clinical record data and sequencing data wherein the system structured data is optimized for searching, storing the system structured data in a second database, for each user application program, selecting the application specific subset of data from the second database and storing the application specific subset of data in a structure optimized for application program interfacing in a third database.

Methods, systems, and software are provided for validating a somatic sequence variant in a subject having a cancer condition. Sequence reads are obtained from sequencing cell-free DNA fragments in a liquid biopsy sample of the subject. Sequence reads are aligned to a reference sequence. A variant allele fragment count and locus fragment count are identified for a candidate variant that maps to a locus in the reference sequence. The variant allele fragment count is compared against a dynamic variant count threshold for the locus. The threshold is based on a pre-test odds of a positive variant call for the locus, based on the prevalence of variants in a genomic region including the locus in a cohort of subjects having the cancer condition. The somatic sequence variant in the subject is validated, or rejected, when the variant allele fragment count for the candidate variant satisfies, or does not satisfy, the threshold.

Methods and systems for dynamic variant thresholding in a liquid biopsy assay

Methods, systems, and software are provided for estimating a circulating tumor fraction for a test subject. Sequence reads are obtained from a panel-enriched sequencing reaction, including sequences for a first plurality of cfDNA fragments corresponding to probe sequences and a second plurality of cfDNA fragments not corresponding to probe sequences. Bin-level coverage ratios are determined from the sequences. Segments are formed by grouping adjacent bins based on similar coverage ratios and segment-level coverage ratios are determined based on bin-level coverage ratios for bins in the segment. For each simulated circulating tumor fraction in a plurality of circulating tumor fractions, segments are fitted to an integer copy state by identifying the integer copy state that best matches the segment-level coverage ratio. The circulating tumor fraction for the test subject is determined using error optimization between segment-level coverage ratios and integer copy states across the simulated circulated tumor fractions.

Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing

Methods, systems, and software are provided for validating a copy number variation in a test subject. A first dataset is obtained comprising bin-level sequence ratios, segment-level sequence ratios and segment-level measures of dispersion. Bins representing regions of a human reference genome are determined from sequencing cell-free nucleic acids in a liquid biopsy sample and reference samples. Segments encompass subsets of adjacent bins, where segment-level sequence ratios and measures of dispersion are determined using bin-level sequence ratios. A copy number status annotation for a segment is validated by applying the first dataset to a plurality of filters comprising a measure of central tendency bin-level sequence ratio filter, a confidence filter, and a measure of central tendency-plus-deviation bin-level sequence ratio filter. When a filter is fired, the copy number status annotation of the segment is rejected; and when no filter is fired, the copy number status annotation of the segment is validated.

Methods and systems for refining copy number variation in a liquid biopsy assay

Methods, systems, and software are provided for determining a homologous recombination pathway status of a cancer in a test subject, e.g., to improve cancer treatment predictions and outcomes. In some embodiments, classifiers using one or more of (i) a heterozygosity status for DNA damage repair genes in a cancerous tissue, (ii) a measure of the loss of heterozygosity across the genome of the cancerous tissue, (iii) a measure of variant alleles detected in a second plurality of DNA damage repair genes in the genome of the cancerous tissue, (iv) a measure of variant alleles detected in the second plurality of DNA damage repair genes in the genome of a non-cancerous tissue, and (v) tumor sample purity are provided.

Integrated machine-learning framework to estimate homologous recombination deficiency

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Chicago, IL, United States of America

Robert Tell