Methods and systems for sample processing and optical pcr

A method for performing PCR, the method comprising:

• providing a system for processing a biological sample, the system comprising:
• a cartridge comprising:
• a sample chamber comprising an inlet configured to receive a biological sample;
• a fluid conduit in communication with the sample chamber, the fluid conduit comprising a trapping site disposed along a length of the fluid conduit, the trapping site having a cross-sectional area larger than an average cross-sectional area of the fluid conduit;
• and
• a plurality of wells disposed on a body of the cartridge, wherein each of the wells are configured to receive one of a plurality of fluids, wherein a portion of the plurality of wells are in fluid communication with the fluid conduit;
• one or more magnetic field sources disposed adjacent the trapping site;
• and
• a PCR device in communication with the cartridge, wherein the PCR device comprising an optical PCR cavity including a light absorbing layer configured for light-to-heat conversion;
• providing a biological sample to the inlet of the sample chamber;
• flowing a lysis buffer from a first well of the plurality of wells to the sample chamber to extract nucleic acids from the biological sample;
• flowing a solid-phase substrate from a second well of the plurality of wells to the sample chamber to produce a sample fluid including extracted nucleic acids bound to the solid-phase substrate;
• flowing the sample fluid from the sample chamber to the fluid conduit;
• applying a magnetic field to trap the solid-phase substrate in the sample fluid in the trapping site of the fluid conduit;
• flowing a wash buffer through the fluid conduit to remove impurities from the solid-phase substrate;
• flowing an immiscible fluid through the fluid conduit to remove residual sample fluid and/or wash buffer;
• flowing an elution buffer through the fluid conduit to elute nucleic acids from the solid-phase substrate;
• transferring the eluted nucleic acids to the optical PCR cavity;
• and
• performing PCR on the eluted nucleic acids in the optical PCR cavity.