The technologies disclosed herein relate to a system and method for transferring markings. The system can include an imaging device for imaging a stained slide and an unstained slide, a display for displaying one or more images of the stained slide and the unstained slide. In various embodiments, the system can include a mechanical stage, such as a scaffold, for positioning or orienting the stained slide with respect to the unstained slide. In various embodiments, the system can be coupled with a first application for aligning the images to enable digital marking of the unstained slide and a second application for digitally marking one or more features and transferring the digital markings into coordinates to be used for further processing, such as for dissection.
Some embodiments presented in this disclosure concern an Automated Tissue Dissection (ATD) System. An ATD system is a one stop, and potentially low-cost, system to perform dissections on a substrate from pathologist digital mark or pen mark on the substrate using non-contact and/or mechanical method to extract a Formalin-Fixed Paraffin-Embedded (FFPE) tissue sample with: (a) only the ROI or ROIs as area to be saved; and (b) remove or decompose nucleic acid content in the region of no interest (RONI) and collect all tissue sample from a standard microscope substrate into a specific container.
A system for automation of sample preparation is disclosed. The system for automation includes a fixture configured to hold a sample and a reader system configured for receiving information pertinent to the sample. In various implementations, the system includes a cutting system configured for removing a portion of the sample. In various implementations, the system includes a cutting system configured for cutting the sample into at least two portions. In various implementations, the system further includes a first bin for collecting a first portion of the at least two portions of the sample. In various implementations, the system also includes a second bin for collecting a second portion of the at least two portions of the sample. In various implementations, the plurality of specimens are arranged linearly along one direction or arranged laterally in a two-dimensional array.
The present disclosure relates to methods of monitoring bladder cancer patients and analyzing patient samples for presence of methylated DNA and optionally particular gene mutations. In some embodiments, analysis results are correlated with clinical outcome measures such as risk of bladder cancer recurrence.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
5.
ALGORITHMS AND METHODS FOR ASSESSING LATE CLINICAL ENDPOINTS IN PROSTATE CANCER
The present disclosure relates to uses of a multiple gene-expression based Genomic Prostate ScoreTM (GPSTM ) algorithm for assessment of various clinical endpoints in prostate cancer patients, such as risks of clinical recurrence (CR), biochemical recurrence (BCR), distant metastasis (Mets), and prostate cancer death (PCD). In some embodiments, GPS result is determined for low and intermediate risk prostate cancer patients in order to assist in determining treatment strategies for those patients.
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
6.
METHODS OF INCORPORATION OF TRANSCRIPT CHROMOSOMAL LOCUS INFORMATION FOR IDENTIFICATION OF BIOMARKERS OF DISEASE RECURRENCE RISK
The present invention provides methods for incorporating transcript chromosomal locus information for identification of biomarkers of disease recurrence risk.
The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The present invention also provides methods of obtaining a quantitative score for a patient with kidney cancer based on measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The genes may be grouped into functional gene subsets for calculating the quantitative score and the gene subsets may be weighted according to their contribution to cancer recurrence.
The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient.
The present invention relates to RNA transcripts, or expression products thereof, associated with breast cancer prognosis. These RNA transcripts, or expression products thereof are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient. The present invention also relates to a novel method of counting sequencing reads.
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
10.
GENE FUSIONS AND ALTERNATIVELY SPLICED JUNCTIONS ASSOCIATED WITH BREAST CANCER
The present invention relates to gene fusions and alternative spliced junctions associated with breast cancer. The present invention also relates to novel methods of identifying gene fusions and alternative spliced junctions in RNA sequencing data. The present invention further relates to predicting prognosis of a breast cancer patient based on the number of gene fusion events.
Methods for predicting the efficacy of a treatment with a platinum-based chemotherapy drug in a patient with cancer are disclosed. The methods generally involve determining an expression level of a gene product that correlates with responsiveness to treatment with a platinum-based chemotherapy drug, which may be oxaliplatin. The cancer may be colorectal cancer.
The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes, or their co-expressed genes, from a biological sample obtained from a prostate cancer patient. The genes may be grouped into functional gene subsets for calculating a quantitative score useful to predict a likelihood of a clinical outcome for a prostate cancer patient.
The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient, The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.
Molecular assays that involve measurement of expression levels of prognostic biomarkers, or co-expressed biomarkers, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likely prognosis for said patient, and likelihood that said patient will have a recurrence of prostate cancer, or to classify the tumor by likelihood of clinical outcome or TMPRSS2 fusion status, are provided herein.
The present disclosure provides gene and gene sets, the expression of which is important in the classification and/or prognosis of cancer, in particular of renal cell carcinoma.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
C40B 40/08 - Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
G06F 17/00 - Digital computing or data processing equipment or methods, specially adapted for specific functions
G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)
The present invention provides methods to determine the prognosis and appropriate treatment for patients diagnosed with cancer, based on the expression levels of one or more biomarkers. More particularly, the invention relates to the identification of genes, or sets of genes, able to distinguish breast cancer patients with a good clinical prognosis from those with a bad clinical prognosis. The invention further provides methods for providing a personalized genomics report for a cancer patient. The inventions also relates to computer systems and software for data analysis using the prognostic and statistical methods disclosed herein.
Algorithm-based molecular assays that involve measurement of expression levels of prognostic and/or predictive genes, or co-expressed genes thereof, from a biological sample obtained from a cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of recurrence of colorectal cancer and/or the likelihood of a beneficial response to chemotherapy for the patient are provided herein. Methods of analysis of gene expression values of prognostic and/or predictive genes, as well as methods of identifying gene expression-tumor region ratios, tumor-associated stromal surface area, and gene cliques, i.e. genes that co-express with a validated biomarker and thus may be substituted for that biomarker in an assay, are also provided.
The present disclosure provides methods for assessing a patient's cancer risk and/or recurrence risk, which methods comprise assaying, in a biological sample obtained from the gastrointestinal (GI) tract of the patient, an expression level of a risk gene. The present disclosure also provides methods involving a cancer risk/recurrence risk sequence, i.e. the V600E mutation of the BRAF gene, which is useful for assessing cancer risk and/or recurrence risk in a patient.
The present invention provides methods and compositions to facilitate determining whether an EGFR-expressing cancer in an individual is an EGFR inhibitor-responsive cancer, as well as methods for determining the likelihood that a patient having an EGFR-expressing cancer will exhibit a beneficial response to an EGFR inhibitor therapy. The methods generally involve determining a normalized expression level of a gene product that correlates with EGFR inhibitor responsiveness.
The present disclosure provides methods and compositions to facilitate prediction of the likelihood of responsiveness of cancer patients to treatment including a taxane and/or a cyclophosphamide.
Gene sets which are useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy, are disclosed. Also disclosed is a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets is accomodated for, and therefore is compatible with the most widely available type of biopsy material.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
G01N 33/48 - Biological material, e.g. blood, urine; Haemocytometers
G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)
22.
GENE EXPRESSION MARKERS OF RECURRENCE RISK IN CANCER PATIENTS AFTER CHEMOTHERAPY
The present invention relates to genes, the expression levels of which are correlated with likelihood of breast cancer recurrence in patients after tumor resection and chemotherapy.
A method of predicting clinical outcome in a subject diagnosed with cancer and treated with chemotherapy comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample comprising cancer cells obtained from the subject.
The invention concerns genes that have been identified as being involved in estrogen metabolism, and are useful as diagnostic, prognostic and/or predictive markers in cancer. In particular, the invention concerns genes the tumor expression levels of which are useful in the diagnosis of cancers associated with estrogen metabolism, and/or in the prognosis of clinical outcome and/or prediction of drug response of such cancers.
A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.
The invention concerns genes and gene sets and methods useful in the prediction of the response of a cancer patient to treatment with an epidermal growth factor receptor (EGFR) inhibitor.
The present invention relates to quantitative molecular indicators that can guide clinical decisions in breast cancer, such as estrogen receptor (ESR1)-positive, lymph node-negative breast cancer. In particular, the invention concerns certain genes, the varied expression of which indicates the likelihood of recurrence of surgically resected breast cancer in patients who are not treated with a therapeutic agent in the adjuvant setting. In addition, the invention concerns the use of quantitative measurement of the expression of certain genes, including the ESR1 gene, that measures as a continuous variable, to determine (a) the likelihood of a beneficial response to the anti-estrogen therapeutic agent, such as tamoxifen; and (b) the potential magnitude of beneficial response to chemotheraphy.
The present invention provides gene expression information useful for predicting whether cancer patients are likely to have a beneficial response to treatment response with chemotherapy.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
G06F 19/20 - for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
A system for measuring data includes a first processor for extracting data curves from an assay. The first processor estimates a Quality Score (QS) based on the shape and variation of an amplification curve. A second processor calculates a threshold cycle (CT) value. The CT value is the fractional cycle number at which the assay signal rises above a threshold. The processor makes a status classification of the amplification curve. A database is provided to store the QS, CT, and classification results.
This invention provides a method for the quantitation and quality assurance of QPCR data. In particular, the invention provides a method for extracting data curves from a QPCR assay, estimating the shape and characteristics of an amplification curve and producing a quality score metric. The invention also provides a robust method for calculating a threshold cycle (CT) value and classifying the status of the QPCR results.
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