This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

RNA from a biological fluid is stabilized during isolation and/or storage using DNA. In especially preferred aspects, the RNA is cfRNA and/or ctRNA, and the biological fluid is blood.

This invention provides nucleoside polyphosphate analogues each of which comprises a tag comprising a plurality of Raman-scattering moieties; compounds comprising said nucleoside polyphosphate analogs. This invention also provides nucleotide polymerases with one or more attached and/or conjugated noble metal nanoparticles, wherein the noble metal nanoparticles are surface-enhanced Raman spectroscopy (SERS) substrates thereby creating a region of enhanced sensitivity for surface enhanced Raman spectroscopy (SERS) within or adjacent to the polymerase. This invention also provides a surface with regions of enhanced sensitivity for surface enhanced Raman spectroscopy comprising interspersed rough or nanostructured noble metal surface. This invention also provides methods for determining the sequence of a single stranded DNA or RNA polynucleotide using one or more of nucleoside polyphosphate analogues, polymerase with noble metal nanoparticles, and surface with noble metal.

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

RNA from a biological fluid is stabilized during isolation and/or storage using DNA. In especially preferred aspects, the RNA is cfRNA and/or ctRNA, and the biological fluid is blood.

The disclosure provides population and non-population-based classifiers to categorize patients and cancers. The population-based classifiers disclosed integrate signatures, i.e., global scores related to the expression of genes in particular gene panels. The non-population-based classifiers are generated using machine-learning techniques (e.g., regression, random forests, or ANN). Each type of classifier stratifies patients and cancers according to tumor microenvironments (TME) as biomarker-positive or biomarker-negative, and treatment decisions are then guided by the presence/absence of a particular TME. Also provided are methods for treating a subject, e.g., a human subject, afflicted with cancer comprising administering a particular therapy depending on the classification of the cancer's TME according to the disclosed classifiers. Also provided are personalized treatments that can be administered to a subject having a cancer classified into a particular TME, and gene panels that can be used for identifying a human subject afflicted with a cancer suitable for treatment with a particular therapeutic agent.

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

An automatic analyzer including a function for operating control materials and its operation method are provided. The analyzer is configured to start sampling by giving priority to an entirety of control materials corresponding to all assay items required for measurement. The analyzer is also configured to automatically start sampling of a patient specimen based on a preliminarily set sampling timing after completion of sampling of the entirety of control materials. The analyzer is also configured to stop, when an abnormality is present in a measurement result of at least any one of control materials in the group of control materials, sampling of a patient specimen corresponding to a control material in which the abnormality is found, and notify a tester of the abnormality.

The present disclosure relates to methods of identifying patients that may be responsive to mitochondrial inhibitor therapies to target and eradicate cancer stem cells. Also described are diagnostic kits that may be used to identify patients responsive to mitochondrial inhibitor therapies.