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US 2019/0293525 A1Published application
System and method for sample processing
AssigneeVentana Medical Systems, Inc.
InventorsDaniel BAUER, David CHAFIN, Michael OTTER
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Abstract
A method is disclosed that permits calculation of reagent concentrations (in SI units) over time and space within a tissue sample as the sample is immersed in the reagent and the reagent diffuses into the tissue sample. The disclosed method has yielded the surprising result that once a formaldehyde concentration at all points within a tissue sample exceeds about 90 mM during a cold step of a cold+hot fixation protocol, the hot step of the fixation protocol can be commenced to provide reliable detection of molecular targets and preservation of tissue morphology in downstream analyses.
Claims20
A method for determining a reagent concentration comprising:
- immersing the sample in the reagent;
- obtaining an experimental time-of-flight versus time for the sample immersed in the reagent;
- providing a plurality of candidate diffusivity constants;
- simulating a spatial dependence of diffusion into the sample to generate a model time-of-flight versus time over a plurality of time points, wherein the simulation is conducted for each of the candidate diffusivity constants;
- comparing the model time-of-flight versus time with the experimental time-of-flight versus time to obtain an error function, wherein a minimum of the error function yields a diffusivity constant for the sample;
- providing a plurality of candidate tissue porosities;
- simulating a spatial dependence of diffusion into the sample to generate a model time-of-flight versus time over a plurality of time points, wherein the simulation is conducted for each of the candidate porosities;
- comparing the model time-of-flight with the experimental time-of-flight to obtain a second error function, wherein a minimum of the error function yields a porosity of the sample;
- and
- calculating a concentration of the reagent at one or more particular spatial points within the sample at a particular time using the diffusivity constant for the sample and the porosity of the sample.
7 more elements
A method for fixing a tissue sample, comprising:
- immersing the tissue sample in a cold formalin solution until a point at the center of the tissue sample is determined to have a formaldehyde concentration of at least 90 mM, and
- contacting the tissue sample with a hot formalin solution once formaldehyde concentration at the point at the center of the tissue sample is determined to be above 90 mM for a time sufficient to form cross-links, thereby fixing the tissue sample.
A system, comprising:
- an acoustic monitoring device that detects acoustic waves that have traveled through a tissue sample;
- one or more processors communicatively coupled to the acoustic monitoring device, wherein the one or more processors are configured to evaluate a speed of the acoustic waves based on a time-of-flight;
- one or more memories communicatively coupled to the one or more processors, the one or more memories having stored thereon instructions, which when executed cause the processor to perform operations comprising:
- setting a range of candidate diffusivity constants for the tissue sample;
- simulating a spatial dependence of a reagent within the tissue sample for a plurality of time points and for a first of candidate diffusivity points;
- determining a modeled time-of-flight based on the spatial dependence;
- repeating the spatial dependence simulation for each of the plurality of diffusivity constants;
- determining an error between the modeled-time-of-flight for the plurality of diffusivity constants versus an experimental time-of-flight for the tissue sample, wherein a minimum of an error function based on the error yields a diffusivity constant for the tissue sample;
- setting a range of candidate porosities for the tissue sample that includes a plurality of candidate porosities;
- determining a second modeled time-of-flight based on the diffusivity constant of the sample and a first of the plurality of candidate porosities, and determining a second error between the experimental time-of-flight and the second modeled time-of-flight;
- repeating the determination of the second modeled time-of-flight for others of the plurality of candidate porosities and their corresponding second errors, wherein a minimum of the error identifies the porosity of the sample;
- and calculating a spatial dependence of reagent concentration within the sample at a particular time from the identified diffusivity constant and the identified porosity of the sample.
9 more elements
Dependencies are inferred from the claim text.