Controls for nucleic acid assays
The present invention features a method and kit for isolating microvesicles or extracting microvesicle nucleic acids from a biological sample by using a control particle. The present invention provides control particles that are viruses or virus-like particles, such as bacteriophages, that contain control nucleic acids that can be detected to assess the accuracy, reliability, and efficiency of the microvesicle isolation or nucleic acid extraction steps. The methods described herein may further comprise the analysis of the presence, absence, or level of at least one biomarker associated with a disease or medical condition for diagnosing, prognosing, or monitoring the disease or medical condition.
1. A method comprising:
(a) forming a mixture by adding a known quantity of control particles to a biological sample comprising microvesicles, wherein the control particles are enveloped virus particles, wherein the enveloped virus particles comprise a known copy number of a viral nucleic acid, and wherein the microvesicles comprise nucleic acids;
(b) isolating a fraction comprising the microvesicles and the control particles from the mixture;
(c) extracting nucleic acids from the fraction comprising the microvesicles and the control particles, thereby producing extracted nucleic acids;
(d) measuring the amount of the viral nucleic acid in the extracted nucleic acids of step (c) by quantitative polymerase chain reaction (PCR) using specific primers that hybridize to the viral nucleic acid;
(e) determining the copy number of the viral nucleic acid in the extracted nucleic acids of step (c) by comparing the amount of the viral nucleic acid measured in step (d) to a standard curve generated using known different concentrations of the viral nucleic acid and known different copy numbers of the viral nucleic acid;
(f) determining the amount of the control particles that are present in the fraction from step (b) based on the copy number of the viral nucleic acid in the extracted nucleic acids determined in step (e); and
(g) subjecting the extracted nucleic acids from step (c) to further analysis if the amount of the control particles determined in step (f) is within a predetermined range of values.
2. The method of claim 1 , wherein the biological sample is a bodily fluid sample.
3. The method of claim 2 wherein the bodily fluid sample is urine, blood, cerebrospinal fluid, plasma or serum.
4. The method of claim 1 , wherein the viral nucleic acid comprises RNA or DNA.
5. The method of claim 1 , wherein the enveloped virus particles are mouse hepatitis virus (MHV), transmissible gastroenteritis virus, poliovirus, enterovirus, coxsackievirus, echovirus, hepatitis A virus, hepatitis C virus, encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV), Dengue virus, Yellow Fever Virus, West Nile virus, bovine viral diarrhoea virus (BVDV), eastern equine encephalitis virus, western equine encephalitis virus, rubella virus, human immunodeficiency virus, simian immunodeficiency virus (SW), feline immunodeficiency virus, Marburg virus, Ebola virus, influenza virus, measles virus or rabies virus.
6. The method of claim 1 , wherein the fraction comprising the microvesicles and the control particles is isolated by differential centrifugation, gel permeation chromatography, anion exchange chromatography, a sucrose density gradient, organelle electrophoresis or any combination thereof.
7. The method of claim 1 , wherein the viral nucleic acid is RNA and the quantitative PCR is reverse transcription quantitative PCR.