Methods and systems for validation of a nucleic acid amplification assay
Systems, methods, and apparatus are provided for external control testing of an assay system.
1. A method of quality control of a multiplexed PCR system using a positive control material comprising the steps of:
providing the positive control material comprising a plurality of positive control sequences corresponding to a plurality of test sequences,
providing an assay device comprising a first reaction chamber provided with a plurality of primers for multiplexed nucleic acid amplification of the plurality of positive control sequences,
wherein each positive control sequence comprises the same forward and reverse primer binding sites as its corresponding test sequence and an engineered sequence between the forward and reverse primer binding sites that is different than its corresponding test sequence,
introducing the positive control material into the assay device, wherein the introducing does not include introducing a test sequence with the positive control material into the assay device,
amplifying the plurality of positive control sequences in the first reaction chamber with the plurality of primers to yield a plurality of positive control amplicons,
detecting the positive control amplicons,
melting each positive control amplicon, and
verifying by melting that each amplified positive control amplicon represents a positive control sequence,
wherein detecting each of the positive control amplicons indicates that the multiplexed PCR system is operating correctly, and
wherein each amplified positive control sequence has a melting temperature that is detectably different and distinct from a melting temperature of its corresponding test sequence as a result of the engineered sequence in each positive control sequence between the forward and reverse primer binding sites, and
wherein each positive control sequence melts in a melt window at a temperature in a range of about 2-10° C. higher or lower than a melt window of its corresponding test sequence.
2. The method of claim 1 , wherein each positive control sequence melts in a melt window at a temperature in a range of about 2-9° C., 2-8° C., 2-7° C., 2-6° C., 2-5° C., 2-4° C., 2-3° C., 3-10° C., 3-9° C., 3-8° C., 3-7° C., 3-6° C., 3-5° C., 3-4° C., 4-10° C., 4-9° C., 4-8° C., 4-7° C., 4-6° C., 4-5° C. or any combination thereof higher or lower than a melt window of its corresponding test sequence.
3. The method of claim 1 , wherein the amplifying step includes simultaneously amplifying from about 10 to about 20, about 10 to about 30, or about 10 to about 40 unique positive control sequences in the assay device, and wherein each of the amplified positive control sequences has a melting temperature that is detectably different and distinct from the other amplified positive control sequences.
4. The method of claim 1 , the assay device further comprising at least a second reaction chamber fluidly connected to the first reaction chamber, the second reaction chamber comprising primer pairs configured for further amplification of each of the positive control sequences, and wherein the method further comprises further amplifying the positive control sequences, wherein the further amplifying step occurs prior to the detecting step.
5. The method of claim 4 , wherein the second reaction chamber includes an array of wells with each well having at least one primer pair therein for further amplification of each of the positive control sequences.
6. The method of claim 1 , wherein detecting the positive control amplicons includes observing a DNA melting signal for each of the positive control amplicons, wherein the DNA melting signal is at the different temperature as compared to the melting temperatures of the test sequences that correspond to each positive control amplicon.
7. A method of quality control of a multiplexed PCR system using a positive control material comprising the steps of:
providing an assay device comprising a first reaction chamber provided with a plurality of primers for multiplexed nucleic acid amplification,
providing a positive control material comprising a plurality of control sequences configured to be amplified by the plurality of primers, wherein each one of the plurality of control sequences comprises a same forward and a same reverse primer binding site as a corresponding test nucleic acid sequence and an engineered sequence between the forward and reverse primer binding sites that is different than the corresponding test nucleic acid sequence, wherein the plurality of control sequences control for amplification of one of more of Anthrax, Leptospirosis, Plague ( Yersinia pestis ), Tularemia, Typhoid fever, Paratyphoid fever, Malaria, Leishmaniasis, Chikungunya fever, Crimean-Congo Hemorrhagic Fever, Dengue fever, Ebola virus, Marburg virus, Lassa fever, West Nile fever, Yellow fever, or Zika fever,
introducing the positive control material into the assay device,
amplifying the plurality of positive control sequences in the first reaction chamber with the plurality of primers to yield a plurality of positive control amplicons, and
detecting the positive control amplicons,
melting each positive control amplicon, and
verifying by melting that each amplified positive control amplicon represents a positive control sequence,
wherein detecting each of the positive control amplicons indicates that the multiplexed PCR system is operating correctly, and
wherein each amplified positive control sequence has a melting temperature that is detectably different and distinct from a melting temperature of each corresponding test sequence as a result of the engineered sequence in each positive control sequence between the forward and reverse primer binding sites.
8. The method of claim 7 , wherein each positive control sequence melts in a melt window at a temperature in a range of about 2-10° C., 2-9° C., 2-8° C., 2-7° C., 2-6° C., 2-5° C., 2-4° C., 2-3° C., 3-10° C., 3-9° C., 3-8° C., 3-7° C., 3-6° C., 3-5° C., 3-4° C., 4-10° C., 4-9° C., 4-8° C., 4-7° C., 4-6° C., 4-5° C. or any combination thereof higher or lower than a melt window of its corresponding test sequence.
9. The method of claim 7 , wherein the amplifying step includes simultaneously amplifying from about 2 to about 10, about 2 to about 20, about 2 to about 30, or about 2 to about 40 unique positive control sequences in the assay device, and wherein each of the amplified positive control sequences has a melting temperature that is detectably different and distinct from the other amplified positive control sequences.
10. The method of claim 7 , the assay device further comprising at least a second reaction chamber fluidly connected to the first reaction chamber, the second reaction chamber comprising primer pairs configured for further amplification of each of the positive control sequences, and wherein the method further comprises further amplifying the positive control sequences, wherein the further amplifying step occurs prior to the detecting step.
11. The method of claim 10 , wherein the second reaction chamber includes an array of wells with each well having at least one primer pair therein for further amplification of each of the positive control sequences.
12. The method of claim 7 , wherein detecting the positive control amplicons includes observing a DNA melting signal for each of the positive control amplicons, wherein the DNA melting signal is at the different temperature as compared to the melting temperatures of the test sequences that correspond to each positive control amplicon.