Methods, compositions, and devices for rapid analysis of biological markers
Provided herein are devices and methods for rapid analysis of biological samples. In particular, devices and methods described herein can be applied to rapid nucleic acid analysis of solid tissue samples.
1. A method for analyzing a surgical margin of a lumpectomy biopsy sample to detect malignant cells, the method comprising:
a) pressing the lumpectomy sample comprising one or more target nucleic acids against a sample collection unit to generate a cellular imprint of the margin of the lumpectomy sample containing the one or more target nucleic acids; and
b) detecting a presence of the one or more target nucleic acids in the cellular imprint on the sample collection unit by extracting the target nucleic acid from the cells on the sample collection unit and determining an expression level of the target nucleic acid, wherein the one or more target nucleic acids comprises at least one of COL10A1 and MMP11, to determine a cellular expression level of the one or more target nucleic acids; and
c) applying a classifier to the cellular expression level of the one or more target nucleic acids determined in (b), wherein the classifier has been trained using at least COL10A1 and MMP11 as features, wherein the classifier has been trained on expression levels for malignant cells and healthy controls to output a score, wherein the score indicates a positive surgical margin, wherein the positive surgical margin indicates the presence of malignant breast cells.
2. The method of claim 1 , wherein the presence of the one or more target nucleic acids in step b) indicates incomplete removal of the malignant cells from the subject.
3. The method of claim 1 , wherein the surgical margin comprises at least 50% of the surface of a surgical specimen.
4. The method of claim 1 , wherein the method has a false negative rate of less than 20%.
5. The method of claim 1 , wherein the target nucleic acid is selected from the group consisting of RNA, mRNA, spliced RNA, and non-spliced RNA.
6. The method of claim 1 , wherein the malignant cells comprise invasive adenocarcinoma of the breast.
7. The method of claim 1 , wherein pressing the surgical margin comprises a method selected from a touch prep method and a blotting method.
8. The method of claim 1 , wherein the pressing of the surgical margin is performed within a surgical suite, an operation room, a procedure room, an examination room, a hospital, a clinic, a pathology laboratory, a clinical laboratory improvement amendments (CLIA) laboratory, a non-CLIA laboratory, or an ambulatory surgical center.
9. The method of claim 1 , wherein the sample collection unit has a coating that promotes adhesion of the surgical margin to the surface, wherein the coating comprises an agent selected from poly-lysine, poly-ornithine, a collagen, a laminin, a fibronectin, a mucopolysacharride, heparin sulfate, hyaluronidate, chondroitin sulfate, and a hydrogel.
10. The method of claim 1 , wherein the sample collection unit is a slide.
11. The method of claim 1 , wherein extracting the target nucleic acid from the sample collection unit comprises adding a lysing agent to the sample collection unit.
12. The method of claim 1 , wherein the margin is a margin of a surgically resected breast tissue obtained via a lumpectomy procedure.