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Cobas ampliprep cobas taqman 96

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The COBAS Ampliprep/COBAS TaqMan 96 is a fully automated system designed for the extraction, amplification, and detection of nucleic acids. It provides a streamlined workflow for molecular diagnostic testing.

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Lab products found in correlation

Architect i2000 detection reagent, by Abbott (3 mentions) Cobas ampliprep cobastaqman 48, by Roche (3 mentions) M2000 system platform, by Abbott (2 mentions) Lysis buffer, by bioMérieux (1 mentions) Architect i2000, by Abbott (1 mentions) Facscount, by BD (1 mentions) Cobas 4800 system, by Roche (1 mentions)

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Cobas TaqMan (73 citations) COBAS AmpliPrep/COBAS TaqMan (63 citations) COBAS AmpliPrep (41 citations) COBAS AmpliPrep/TaqMan (7 citations) TaqMan 96 (2 citations)

12 protocols using cobas ampliprep cobas taqman 96

1

Biochemical, Virological, and Serological Analysis

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The biochemical indicators were tested by Hitachi 7600 automatic biochemical analyzer (Hitachi 7600-11; Hitachi, Tokyo, Japan). Virological indicator was measured by Roche Cobas AmpliPrep/Cobas TaqMan 96 automatic real-time fluorescence quantitative polymerase chain reaction detection (PCR) detection reagent (Roche, Pleasanton, CA, USA; with a lower detection limit of 20IU/ml). Serological indexes were quantitated by Abbott Architect i2000 detection reagent (Abbott Diagnostics, USA).
Xie S., Yang L., Bi X., Deng W., Jiang T., Lin Y., Wang S., Zhang L., Liu R., Chang M., Wu S., Gao Y., Hao H., Shen G., Xu M., Chen X., Hu L., Lu Y., Song R., Xie Y, & Li M. (2022). Cytokine profiles and CD8+ T cells in the occurrence of acute and chronic hepatitis B. Frontiers in Immunology, 13, 1036612.
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2

Quantifying Plasma Viral Loads in SIV/HIV-Infected Macaques

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Macaques: Plasma isolated from EDTA-blood of SIVmac251 infected RM was clarified by centrifugation at 2300 × g for 3 minutes. The clarified plasma (0.1 mL) was then lysed directly in lysis buffer (bioMerieux, Durham, NC, USA). Alternatively, a higher volume of plasma (0.5 to 1 ml) was centrifuged to pellet virus by ultracentrifugation at 49 100 × g for 60 min and the pellet lysed in lysis buffer. Viral RNA load in the lysed samples was quantitated using Real-time NASBA assay as described elsewhere 35 (link). Plasma SIVmac239/251 viral loads were determined as described, with an assay threshold of 30 copies/mL24 (link),25 (link) Plasma isolated from the blood of RT-SHIV infected challenged macaques was analyzed using previously described methods 26 (link) where the lower limit of detection was 5 copies/ml.
Humans: Plasma HIV viral load was measured using the COBAS Ampliprep/COBAS TaqMan 96 (Roche, Branchburg, NJ, USA) with a linearity range of 20-10,000,000 copies/ml or Abbott m2000 system platform with a linearity range of 40-10,000,000 copies/ml. The Abbott platform was used in the first 12 months of the study and the Roche for all subsequent measures. Both platforms were registered on an external quality assurance program provided by the American Pathologists and Virology Quality Assurance from RUSH University Medical Center.
Estes J.D., Kityo C., Ssali F., Swainson L., Makamdop K.N., Del Prete G.Q., Deeks S.G., Luciw P., Chipman J., Beilman G., Hoskuldsson T., Khoruts A., Anderson J., Deleage C., Jasurda J., Schmidt T., Hafertepe M., Callisto S., Pearson H., Reimann T., Schuster J., Schoephoerster J., Southern P., Perkey K., Shang L., Wietgrefe S., Fletcher C.V., Lifson J.D., Douek D.C., McCune J.M., Haase A.T, & Schacker T.W. (2017). Defining Total Body AIDS Virus Burden: Implications for Curative Strategies. Nature medicine, 23(11), 1271-1276.
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3

Quantification of HBV Markers and Liver Function

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Serum HBV-DNA load was quantitated with a Roche CobasAmpliPrep/CobasTaqMan 96 full automatic real-time fluorescence quantitative polymerase chain reaction detection reagent (with a lower limit of 20 U/ml) (Roche, Pleasanton, CA, USA). The levels of HBsAg, anti-HBs, HBeAg, and anti-HBe were measured using an Abbott Architect i2000 detection reagent (Abbott Diagnostics, Abbott Park, IL, USA); the HBsAg dynamic range was 0.05–250.00 U/ml. Samples with HBsAg levels >250 U/ml were automatically re-tested at 1:500 dilution. HBsAg <0.05 U/ml was defined as the disappearance of HBsAg.
The parameters of liver and kidney function, including ALT, aspartate aminotransferase (AST), total bilirubin, albumin, creatinine, and blood urea nitrogen, were measured using a Hitachi 7600 automatic biochemical analyzer (Hitachi 7600-020, Japan).
Li M.H., Lu Y., Zhang L., Wang X.Y., Ran C.P., Hao H.X., Zhang D., Qu X.J., Shen G., Wu S.L., Cao W.H., Qi T.L., Liu R.Y., Hu L.P., Chang M., Hua W.H., Liu S.A., Wan G, & Xie Y. (2018). Association of Cytokines with Alanine Aminotransferase, Hepatitis B Virus Surface Antigen and Hepatitis B Envelope Antigen Levels in Chronic Hepatitis B. Chinese Medical Journal, 131(15), 1813-1818.
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4

Quantifying Plasma HIV Viral Load

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Plasma HIV viral load was measured using the COBAS Ampliprep/COBAS TaqMan 96 (Roche, Branchburg, NJ), with a linearity range of 20–10,000,000 copies/mL, or Abbott m2000 system platform, with a linearity range of 40–10,000,000 copies/mL. The Abbott platform was used in the first 12 months of the study and the Roche for all subsequent measures. Both platforms were registered on an external quality assurance program provided by the American Pathologists and Virology Quality Assurance from RUSH University Medical Center.
Rothenberger M., Nganou-Makamdop K., Kityo C., Ssali F., Chipman J.G., Beilman G.J., Hoskuldsson T., Anderson J., Jasurda J., Schmidt T.E., Calisto S.P., Pearson H., Reimann T., David C., Perkey K., Southern P., Wietgrefe S., Helgeson E., Reilly C., Haase A.T., Douek D.C., Fletcher C.V, & Schacker T.W. (2019). Impact of Integrase Inhibition Compared With Nonnucleoside Inhibition on HIV Reservoirs in Lymphoid Tissues. Journal of Acquired Immune Deficiency Syndromes (1999), 81(3), 355-360.
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5

Comprehensive Hepatitis B Biomarker Evaluation

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The parameters of liver and kidney functions, including ALT, aspartate aminotransferase, total bilirubin, albumin, creatinine, and blood urea nitrogen, were measured by Hitachi 7600 automatic biochemical analyzer (Hitachi 7600-11; Hitachi, Tokyo, Japan). Serum HBV DNA was quantitated using a Roche CobasAmpliPrep/CobasTaqMan 96 real-time fluorescence quantitative polymerase chain reaction detection reagent (with a lower limit of 20 U/ml; Roche, Pleasanton, CA, USA). The levels of HBsAg, anti-HBs, HBeAg, and anti-HBe were tested using an Abbott Architect i2000 detection reagent (Abbott Diagnostics, Abbott Park, IL, USA); the HBsAg dynamic range was 0.05–250.00 U/ml. Samples with HBsAg levels >250.00 U/ml were automatically re-tested at 1:500 dilution. HBsAg negative was defined as <0.05 U/ml.
Li M.H., Zhang L., Zhang D., Cao W.H., Qi T.L., Hao H.X., Wang X.Y., Ran C.P., Qu X.J., Liu S.A., Lu Y., Shen G., Wu S.L., Chang M., Liu R.Y., Hu L.P., Hua W.H., Wan G., Cheng J, & Xie Y. (2018). Plasmacytoid Dendritic Cell Function and Cytokine Network Profiles in Patients with Acute or Chronic Hepatitis B Virus Infection. Chinese Medical Journal, 131(1), 43-49.
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6

Plasma HIV Viral Load Measurement

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plasma HIV viral load was measured using the COBAS Ampliprep/COBAS TaqMan 96 (Roche, Branchburg, NJ, USA) with a linearity range of 20-10,000,000 copies/ml or Abbott m2000 system platform with a linearity range of 40-10,000,000 copies/ml. The Abbott platform was used in the first 12 months of the study and the Roche for all subsequent measures. Both platforms were registered on an external quality assurance program provided by the American Pathologists and Virology Quality Assurance from RUSH University Medical Center.
Rothenberger M., Nganou-Makamdop K., Kityo C., Ssali F., Chipman J.G., Beilman G.J., Hoskuldsson T., Anderson J., Jasurda J., Schmidt T.E., Calisto S.P., Pearson H., Reimann T., David C., Perkey K., Southern P., Wietgrefe S., Helgeson E., Reilly C., Haase A.T., Douek D.C., Fletcher C.V, & Schacker T.W. (2019). Impact of Integrase Inhibition Compared With Nonnucleoside Inhibition on HIV Reservoirs in Lymphoid Tissues. Journal of Acquired Immune Deficiency Syndromes (1999), 81(3), 355-360.
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7

Quantification of HIV Viral Load

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HIV viral load was measured in plasma using the COBAS Ampliprep/COBAS TaqMan 96 (Roche) with a linearity range of 20–10,000,000 copies/ml or Abbott m2000 system platform with a linearity range of 40–10,000,000 copies/ml (respective lower limits of quantitation 20 and 40 copies/ml). The Abbott platform was used in the first 12 months of the study and the Roche for subsequent measures. Both platforms were registered on an external quality assurance program provided by the American Pathologists and Virology Quality Assurance from RUSH University Medical Center. Blood CD4 and CD8 T cells counts were measured by flow cytometry using FACSCount™ (Becton Dickinson).
Nganou-Makamdop K., Talla A., Sharma A.A., Darko S., Ransier A., Laboune F., Chipman J.G., Beilman G.J., Hoskuldsson T., Fourati S., Schmidt T.E., Arumugam S., Lima N.S., Moon D., Callisto S., Schoephoerster J., Tomalka J., Mugyenyi P., Ssali F., Muloma P., Ssengendo P., Leda A.R., Cheu R.K., Flynn J.K., Morou A., Brunet-Ratnasingham E., Rodriguez B., Lederman M.M., Kaufmann D.E., Klatt N.R., Kityo C., Brenchley J.M., Schacker T.W., Sekaly R.P, & Douek D.C. (2021). Translocated microbiome composition determines immunological outcome in treated HIV infection. Cell, 184(15), 3899-3914.e16.
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8

Quantitative Assessment of HBV Markers

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Serum HBV DNA levels were measured by PCR quantitation with the Roche Cobas AmpliPrep/Cobas TaqMan96 and full automatic real-time fluorescent quantitative PCR detection reagent (Roche, Pleasanton, CA, USA), at the range of 20-108 IU/mL. Serum HBsAg/anti-HB and HBeAg/anti-HBeAb levels were measured with the Abbott Architect i2000 Detection Reagent (Abbott Diagnostics, Abbott Park, IL, USA). The ALT levels were measured with the Hitachi 7600 full-automatic biochemical analyzer (Hitachi, Japan) with the upper limit of normal values of 40 U/L. All the tests were performed at the Clinical Laboratory Center of Beijing Ditan Hospital Affiliated to Capital Medical University in China.
Cao W., Li M., Zhang L., Lu Y., Wu S., Shen G., Chang M., Liu R., Gao Y., Hao H., Hu L., Yi W., Pan C.Q, & Xie Y. (2021). The Characteristics of Natural Killer Cells in Chronic Hepatitis B Patients Who Received PEGylated-Interferon versus Entecavir Therapy. BioMed Research International, 2021, 2178143.
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9

Viral Load Testing in Zambia

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Viral load testing is currently centralized at 18 laboratories across Zambia. Current equipment being used includes the Roche Cobas®Ampliprep/Cobas®TaqMan 48 and the Roche Cobas®Ampliprep/Cobas®TaqMan 96 (Roche Molecular Diagnostics, Branchburg, US). POC and near-POC equipment for viral load testing has not yet been approved for use in Zambia. For this analysis, we assumed procurement and use of the GeneXpert® Omni molecular diagnostic system, though not yet launched (Cepheid Inc. Sunnyvale CA, USA), as an example of a low output device. It has been designed for low output resource-limited settings, weighs only 1kg, has an integrated rechargeable battery providing 4 hours of power supply and a supplemental rechargeable battery supply with up to 12 hours of battery life, and has a weekly viral load capacity of approximately 30 tests. Tests are performed on plasma samples. Mini centrifuges were allocated to each POC instrument for centrifuging plasma samples prior to testing.
Girdwood S.J., Nichols B.E., Moyo C., Crompton T., Chimhamhiwa D, & Rosen S. (2019). Optimizing viral load testing access for the last mile: Geospatial cost model for point of care instrument placement. PLoS ONE, 14(8), e0221586.
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10

Decentralized HIV Viral Load Testing

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VL testing is currently centralized at 19 laboratories across Zambia. Equipment currently utilized includes the Roche Cobas Ampliprep/Cobas TaqMan 48 and the Roche Cobas Ampliprep/Cobas TaqMan 96 (CAP/CTM), and the Cobas 4800 system (Cobas) (Roche Molecular Diagnostics, Branchburg, New Jersey). For this analysis, we explored the use of the recently launched Roche PSC on both the CAP/CTM and Cobas as an alternative to DBS on the CAP/CTM. The sensitivity and specificity of PSC was applied to the respective volumes of CAP/CTM and Cobas expected by the sample transport system: 42% on CAP/CTM in the partial adoption scenario, and 61% on CAP/CTM in the full adoption scenario. We assume that DBS sample preparation on CAP/CTM will be done using the free virus elution protocol, given its higher sensitivity and specificity compared to the specimen preextraction reagent sample preparation methodology [5 , 10 (link), 11 (link)].
Nichols B.E., Girdwood S.J., Shibemba A., Sikota S., Gill C.J., Mwananyanda L., Noble L., Stewart-Isherwood L., Scott L., Carmona S., Rosen S, & Stevens W. (2019). Cost and Impact of Dried Blood Spot Versus Plasma Separation Card for Scale-up of Viral Load Testing in Resource-limited Settings. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 70(6), 1014-1020.
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