Systems, methods, and apparatus for automated self-contained biological analysis

A method of analyzing a sample, comprising

• placing a sample in a sample collection port in a container assembly, wherein the sample collection port has a bottom opening sealed by a plug member;
• securing a lid assembly to the sample collection port, to close the sample collection port, wherein the lid assembly includes a movable plunger assembly;
• contacting the plug member with the plunger assembly to dislodge the plug member and allow the sample to enter a sample preparation chamber in fluid connection with the bottom opening;
• opening a seal to allow the sample to flow from the sample preparation chamber to a reaction chamber;
• performing a reaction to amplify a biological marker of interest that may be present in the sample;
• and
• detecting the presence of amplified biological marker of interest in the reaction chamber.

A method of detecting a nucleic acid in a sample, comprising:

• providing a receptacle having a plurality of fluidly connected chambers including
• a sample preparation zone,
• an amplification zone,
• one or more sealable ports fluidly connecting the chambers, the sealable ports providing the only access from an exterior of the receptacle to the chambers, and
• introducing the sample into the first chamber via a collection port, wherein the collection port has a bottom opening sealed by a plug member;
• securing a lid assembly to the collection port, to close the collection port, wherein the lid assembly includes a movable plunger assembly;
• contacting the plug member with the plunger to dislodge the plug member and allow the sample to enter a sample preparation chamber in fluid connection with the bottom opening;
• opening a seal to allow the sample to flow from the sample preparation chamber to a reaction chamber;
• sealing the reaction chamber;
• mixing the nucleic acids in the sample with PCR components including primers configured for amplifying one or more targets;
• amplifying the target nucleic acids;
• detecting the fluorescence emission signal from a fluorescent dye in the amplification zone, wherein
• fluorescence is excited by a laser diode,
• emission is detected by a multi-channel spectrometer capable of processing at least 4 spectral channels in parallel in the wavelengths from approximately 350 nm to 1000 nm;
• communicating the fluorescence data to a cloud or local CPU via a mobile phone or other user-controlled device or operating system;
• and
• receiving the analysis result from the cloud or local CPU by a mobile phone or other user-controlled device or operating system.