Real time pcr assay

Manufactured by Abbott

Sourced in United States

The Real-time PCR assay is a laboratory instrument used for the amplification and detection of specific DNA or RNA sequences in a sample. It allows for the quantification of target nucleic acids in real-time during the amplification process.

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Lab products found in correlation

Panther system, by Hologic (2 mentions) Genexpert instrument systems platform, by Cepheid (2 mentions) Architect assay, by Abbott (1 mentions) Enzyme immunoassay, by Abbott (1 mentions) Branched dna assay, by Siemens (1 mentions) Facs lysing solution, by BD (1 mentions) Realtime hcv, by Abbott (1 mentions) Versant hcv rna 3, by Bayer (1 mentions)

8 protocols using real time pcr assay

Comparative Analysis of HCV Genotype 1b

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A total of 49 samples with HCV genotype 1b were included for this study. Among them, 26 patients had chronic HCV infection and 23 had HCV-induced hepatocellular carcinoma. t-tests were performed to evaluate differences between the two groups in demographic profile (age and gender), the quantity of HCV RNA, and biochemical profile (AST, ALT, albumin, platelet, bilirubin, and prothrombin time).
The quantity of HCV RNA was measured using a real-time PCR assay (Abbott Molecular Inc., Abbott Park, IL, USA) following the manufacturer's recommendations. HCV RNA level of all samples was over 1.0 × 10⁴ IU/mL.
The study protocol was reviewed and approved by Asan Medical Center Institutional Review Board, Ethics reference number (2013-0643). According to the policy in our institutional review board, informed consent was waived since the remaining serum samples with which HCV genotyping tests were already completed and reported were utilized in this study, and all the patient information was kept anonymous and minimally used only for the study purpose. The recommendations of the Declaration of Helsinki for biomedical research involving human subjects were followed.

Park C.W., Cho M.C., Hwang K., Ko S.Y., Oh H.B, & Lee H.C. (2014). Comparison of Quasispecies Diversity of HCV between Chronic Hepatitis C and Hepatocellular Carcinoma by Ultradeep Pyrosequencing. BioMed Research International, 2014, 853076.

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Quantifying HBsAg and HBV DNA Levels

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The serum HBsAg levels were quantified by using the Architect assay (Abbott Laboratories, Chicago, IL, USA), which has a lower limit of detection (LLOD) of 0.05 IU/mL. Serum HBV DNA levels were measured using a real-time PCR assay (linear dynamic detection range, 15 IU/mL to 1 × 10⁹ IU/mL; Abbott Laboratories). Serological markers including anti-HBs, HBeAg, and anti-HBe were determined by using enzyme immunoassays (Abbott Laboratories) while resistance mutations were determined by direct sequencing of the reverse transcriptase domain (pol/RT) of the HBV polymerase gene. The HBV genotype was not determined because more than 98% of Korean patients with CHB have the HBV genotype C2 [20 (link)].

An J., Lim Y.S., Kim G.A., Han S.B., Jeong W., Lee D., Shim J.H., Lee H.C, & Lee Y.S. (2017). Telbivudine versus entecavir in patients with undetectable hepatitis B virus DNA: a randomized trial. BMC Gastroenterology, 17, 15.

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Monitoring Hepatitis Viral Markers After Surgery

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Anti-HBV prophylaxis was not given, and the levels of hepatitis B viral markers including serum HBsAg, HBsAb, and HBcAb; and hepatitis C antibody level, were routinely checked prior to surgery, as were antihuman immunodeficiency virus antibody levels, and cytomegalovirus titer and antiviral antibody levels. All patients were managed using a defined protocol. Hepatitis B viral markers including serum HBsAg, HBsAb, HBeAg, and hepatitis B envelop antibody were measured, using electrochemiluminescence immunoassays, at every follow-up visit to our outpatient Department. Such visits were made every month during the first year after surgery; every 2 months from years 2-5 after surgery; and every 3 months thereafter. Serum HBV DNA levels were measured every 6 months after surgery using the branched DNA assay (Siemens Healthcare Diagnostics, Eschborn, Germany; lower limit of detection: 2,000 copies/mL) prior to May 2006 and, thereafter, a highly sensitive real-time PCR assay (Abbott, Chicago, IL, USA; lower limit of detection: 34 copies/mL). If de novo hepatitis B infection developed, patients were treated with antiviral agents such as entecavir, with or without HBIG. Liver function tests (AST and ALT levels), the hepatitis B profile, HBV DNA level, and evaluation of drug-induced HBV mutations, were performed after treatment to evaluate the efficacy of treatment.

Han J.H., Kim D.G., Na G.H., Kim E.Y., Lee S.H., Hong T.H., You Y.K., Choi J.Y, & Yoon S.K. (2015). De novo hepatitis B virus infection developing after liver transplantation using a graft positive for hepatitis B core antibody. Annals of Surgical Treatment and Research, 89(3), 145-150.

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Screening for HIV, Gonorrhea, and Chlamydia

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Finger-stick blood samples received by the CVRL were screened for HIV with the
OraQuick Advance Rapid HIV-1/2 Antibody Test (Reynolds & Muwonga, 2004 (link)), and
pharyngeal swabs, rectal swabs, and urine specimens were screened for gonorrhea
and chlamydia using the Abbott RealTime PCR assay (Gaydos et al., 2010 (link)). Hair samples
received by the HAL were visually inspected to determine whether the quantity of
hair was sufficient to potentially conduct PrEP drug-level testing (i.e., ≥20
fibers), whether the hair was affixed to the aluminum foil with an adhesive
label at the distal end, and whether the hair was properly enclosed in the
aluminum foil to protect it from light. No participant identifiable information
was shared with personnel at either the CVRL or the HAL, and the specimens were
connected to results solely based on unique participant IDs. Results were
returned to study staff at UMSN through password-protected files.

Sharma A., Gandhi M., Sallabank G., Merrill L, & Stephenson R. (2022). Study Evaluating Self-Collected Specimen Return for HIV, Bacterial STI, and Potential Pre-Exposure Prophylaxis Adherence Testing Among Sexual Minority Men in the United States. American Journal of Men's Health, 16(4), 15579883221115591.

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Screening and Treatment of STIs in African Women

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At enrollment, endocervical swabs were screened for Chlamydia trachomatis (CT) and Neisseria gonorrhea (NG). For CT/NG testing, GeneXpert Instrument Systems platform (Cepheid Inc., USA) with the Abbott Real Time PCR assay (Abbott Molecular, USA) were used at South African sites while the Panther System (Hologic Inc., USA) was used at the Kenyan site. Treatment was provided for curable STIs diagnosed syndromically, according to national guidelines, or for CT/NG diagnosed etiologically at enrollment. HSV-2 serology was performed using HerpeSelect ELISA (Focus Diagnostics, USA) at enrollment, and confirmatory testing was performed via Western Blot at the UW. BV was assessed using Nugent scoring criteria^{58 (link)} at the National Institute for Communicable Diseases. Nugent scores 7–10 were considered BV + while scores 4–6 were considered intermediate BV, and scores 0–3 considered BV−. Only symptomatic BV was treated as per national guidelines.

Brown B.P., Feng C., Tanko R.F., Jaumdally S.Z., Bunjun R., Dabee S., Happel A.U., Gasper M., Nyangahu D.D., Onono M., Nair G., Palanee-Phillips T., Scoville C.W., Heller K., Baeten J.M., Bosinger S.E., Burgener A., Passmore J.A., Heffron R, & Jaspan H.B. (2023). Copper intrauterine device increases vaginal concentrations of inflammatory anaerobes and depletes lactobacilli compared to hormonal options in a randomized trial. Nature Communications, 14, 499.

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STI Testing and Detection among Women

Cited 1 time

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Women were tested for C. trachomatis (CT) and N. gonorrhoeae (NG) at baseline using endocervical swabs and treatment was provided upon etiologic diagnosis or when a woman presented with symptoms, according to national guidelines. For CT/NG testing, GeneXpert Instrument Systems platform (Cepheid Inc., US) with the Abbott Real Time PCR assay (Abbott Molecular, US) were used at Wits RHI and Emavundleni sites, while the Panther System (Hologic Inc., US) was used at the KEMRI site [17 (link)]. Nugent scoring (BV negative [Nugent 0–3], intermediate [Nugent 4–6], or positive [Nugent 7–10]) was conducted by the National Institute for Communicable Diseases (NICD) laboratory in Johannesburg, South Africa.

Gupta P.M., Balle C., Tharp G.K., Nelson S.A., Gasper M.A., Brown B., Alisoltani A., Onono M., Palanee-Phillips T., Nair G., Ayele H., Noel-Romas L., Passmore J.A., Burgener A.D., Heffron R., Jaspan H.B, & Bosinger S.E. (2023). Systems analysis reveals differential expression of endocervical genes in African women randomized to DMPA-IM, LNG implant or cu-IUD. Clinical Immunology (Orlando, Fla.), 255, 109750.

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Routine CD4+ T Cell Enumeration and HIV-1 Viral Load Quantification

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Routine blood CD4⁺ T cell counts (cells/μl) were obtained by four-color flow cytometry with human CD45⁺, CD3⁺, CD4⁺ and CD8⁺ cell markers (BD Biosciences), on peripheral whole-blood samples from each patient, in FACS lysing solution (BD Biosciences), according to the manufacturer’s instructions. Plasma HIV-1 viral load (copies/ml of plasma) was quantified by real-time PCR assay (Abbott Molecular Inc., Des Plaines, IL, USA) with a sensitivity of 40 copies/ml of plasma for viral RNA detection.

Lu X., Zhang X., Cheung A.K., Moog C., Xia H., Li Z., Wang R., Ji Y., Xia W., Liu Z., Yuan L., Wang X., Wu H., Zhang T, & Su B. (2022). Abnormal Shift in B Memory Cell Profile Is Associated With the Expansion of Circulating T Follicular Helper Cells via ICOS Signaling During Acute HIV-1 Infection. Frontiers in Immunology, 13, 837921.

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HCV RNA Detection and Genotype Determination

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We used a qualitative real-time polymerase chain reaction (COBAS AMPLICOR Hepatitis C Virus Test, ver. 2.0; Roche, Branchburg, NJ, USA) 14 and a quantification-branched DNA assay (Versant HCV RNA 3.0, Bayer, Tarrytown, New Jersey, USA) or RealTime HCV (Abbott Molecular, Des Plaines IL, USA) 15 to detect serum HCV RNA. The HCV genotypes were determined using the Okamoto method 16 or a real-time PCR assay (Abbott Molecular, Des Plaines IL, USA). Liver histology findings obtained within one year prior to the initiation of antiviral therapy were graded and staged according to the scoring system described by Knodell and Scheuer. 17 The IL28B single nucleotide polymorphism rs8099917 was determined using the method described previously. 18 The treatment efficacy, including RVR at week 4, EVR at week 12 treatment and SVR at 24-week post-treatment follow-up was assessed.

Tsai P.C., Liu T.W., Huang C.F., Yeh M.L., Dai C.Y., Chuang W.L., Huang J.F, & Yu M.L. (2018). A real world cost effectiveness analysis of interferon-based therapy for HCV naïve super-responders. Journal of the Chinese Medical Association : JCMA, 81(8).

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