Benchmark ultra platform

Manufactured by Roche

Sourced in United States

The Benchmark Ultra platform is a laboratory equipment product designed for automated nucleic acid extraction and purification. It features a modular design and can be configured to handle a wide range of sample types and volumes. The platform is capable of processing multiple samples simultaneously, optimizing laboratory workflow efficiency.

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Lab products found in correlation

Optiview dab detection kit, by Roche (6 mentions) Iview dab detection kit, by Roche (4 mentions) Sp263, by Roche (2 mentions) Iviewblue detection kit, by Roche (2 mentions) Inform eber probe, by Roche (2 mentions) Optiview dab ihc detection kit, by Roche (2 mentions) Optiview amplification kit, by Roche (2 mentions) 22c3 pharmdx, by Agilent Technologies (1 mentions) Confirm anti er sp1, by Roche (1 mentions) Refine detection kit, by Leica (1 mentions) Optiview dab detection system, by Roche (1 mentions) Cytospin centrifuge, by Thermo Fisher Scientific (1 mentions) E1l3n, by Cell Signaling Technology (1 mentions) Anti human c erbb 2 a0485 polyclonal antibody, by Agilent Technologies (1 mentions) Inform her2 dual ish dna probe cocktail, by Roche (1 mentions) Cintec histology kit, by Roche (1 mentions) Epr17341, by Roche (1 mentions) Cintec p16 kit, by Roche (1 mentions) Clone e6h4, by Roche (1 mentions) Ultraview detection kit, by Roche (1 mentions)

Close spelling variants of this product

Benchmark Ultra (524 citations) Ventana Benchmark Ultra platform (29 citations) Benchmark platform (10 citations) BenchMark ULTRA IHC/ISH Automatic staining platform (3 citations) Benchmark Ultra Staining platform (3 citations) BenchMark ULTRA automated staining platform (2 citations) BenchMark ULTRA IHC/ISH staining platform (2 citations)

51 protocols using benchmark ultra platform

Evaluation of HER2 Expression and Amplification

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To detect both WTHER2 and d16HER2 isoform expression, we used the anti-human c-erbB-2 A0485 polyclonal antibody (dilution 1:500; Dako) on 3-μm FFPE sections. IHC was performed using a BenchMark Ultra Platform (Ventana Medical Systems, Tucson, AZ) with the Optiview DAB Detection Kit (Ventana Medical Systems). HER2 immunoreactivity in breast and gastric carcinomas was scored as 0, 1+, 2+, 3+ according to international guidelines systems^{34 ,37 (link),38 (link)}. HER2 immunoreactivity in colon carcinomas was evaluated according to guidelines for gastric carcinomas.
Dual color silver in situ hybridization (DC-SISH) was performed on a BenchMark Ultra Platform (Ventana Medical Systems) according to the manufacturer’s protocol. The gene status was assessed on 3-μm FFPE sections using the INFORM HER2 Dual ISH DNA Probe Cocktail (Ventana Medical Systems). HER2 gene amplification was evaluated according to previously described scoring systems^{35 (link),37 (link),38 (link)}. Briefly, HER2 gene amplification was defined as positive when HER2/CEP17 ratio was >2 or when HER2 gene copy number was of >6 for breast carcinomas or of >6 for gastric and colon carcinomas.
Scoring systems for HER2 protein expression and gene amplification evaluations were applied for clinical samples, cell lines and PDX.

Volpi C.C., Pietrantonio F., Gloghini A., Fucà G., Giordano S., Corso S., Pruneri G., Antista M., Cremolini C., Fasano E., Saggio S., Faraci S., Di Bartolomeo M., de Braud F., Di Nicola M., Tagliabue E., Pupa S.M, & Castagnoli L. (2019). The landscape of d16HER2 splice variant expression across HER2-positive cancers. Scientific Reports, 9, 3545.

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Immunohistochemical Staining for PD-L1

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PD-L1 was stained immunohistochemically using the antibody clone 22C3 pharm Dx (Dako Omnis, 1:30 dilution) on the automated BenchMark Ultra platform (Roche Diagnostics) with positive controls of the spleen, tonsil, and placenta as part of a multi-tissue control. Scoring was conducted by board-certified and trained pathologists [42 (link)].

Schatz S., Falk M., Jóri B., Ramdani H.O., Schmidt S., Willing E.M., Menon R., Groen H.J., Diehl L., Kröger M., Wesseler C., Griesinger F., Hoffknecht P., Tiemann M, & Heukamp L.C. (2020). Integration of Tumor Mutation Burden and PD-L1 Testing in Routine Laboratory Diagnostics in Non-Small Cell Lung Cancer. Cancers, 12(6), 1685.

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Standardized ER Assessment of Liver Metastases

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According to standard clinical care procedures, all ultrasound-guided percutaneous 18G core needle liver biopsies were performed by experienced abdominal radiologists. ER status of the liver metastasis was determined by staining the formalin-fixed paraffin-embedded liver biopsies using the CONFIRM anti-ER (SP1, Roche) on an automated Benchmark Ultra platform (Roche). Metastases were deemed ER+ if ≥10% of the tumor cells showed nuclear staining, according to Dutch guidelines. The immunohistochemical evaluation of the ER status was used as the reference standard.

Boers J., Loudini N., de Haas R.J., Willemsen A.T., van der Vegt B., de Vries E.G., Hospers G.A., Schröder C.P., Glaudemans A.W, & de Vries E.F. (2021). Analyzing the Estrogen Receptor Status of Liver Metastases with [18F]-FES-PET in Patients with Breast Cancer. Diagnostics, 11(11), 2019.

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Immunohistochemical Assessment of SMARCA Proteins

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Immunohistochemical assessment of BRG1 (SMARCA4) was performed using a Leica Bond-3 automate stainer platform (Leica, Buffalo Grove, IL). In brief, following heat-based antigen retrieval, tissue sections were incubated for 30 min with the monoclonal antibody clone G7 for BRG1 (Santa Cruz, Dallas, Texas) at a 1:250 dilution or the monoclonal antibody clone D9E8B for BRM (SMARCA2; Cell Signaling) at a 1:1000 for 30 min for 30 min. The primary antibodies were detected using the Refine Detection kit (Leica). SMARCA4/SMARCA2-deficient tumors and normal breast tissue/lymphocytes were used as controls. INI1 (SMARCB1) immunohistochemistry was performed using a BenchMark ULTRA platform (Roche, Basel, Switzerland), following antigen retrieval with a cell conditioning solution (CC1, Roche). Tissue sections were incubated with the monoclonal antibody clone 25/BAF47 for INI1 (BD Biosciences, San Jose, California) at a 1:200 dilution and detected using the OptiView DAB detection system (Roche). INI1-deficient tumors and normal breast tissue served as controls.
We classified tumors as having retained, loss or mosaic expression (i.e., partial loss observed in a subset of cells and diminished staining intensity) of proteins encoded by SMARC genes as previously described [18 (link), 19 (link), 28 (link)].

Schwartz C.J., Pareja F., da Silva E.M., Selenica P., Ross D.S., Weigelt B., Brogi E., Reis-Filho J.S, & Wen H.Y. (2021). Histologic and genomic features of breast cancers with alterations affecting the SWI/SNF (SMARC) genes. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 34(10), 1850-1859.

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Quantifying Ki-67 Expression in Cells

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Following 24 h after DHRS7 siRNA transfection, cells were detached, diluted to 10,000 cells in 100 μL, and placed onto a Superfrost™ microscope slide using a Cytospin™ centrifuge (Thermo Scientific). The slides were fixed in delaune for 2 min and then left to dry at room temperature for 5 min. Ki-67 staining was performed with a BenchMark Ultra platform automated immunohistochemistry/in situ hybridization (IHC/ISH) staining system (Roche, Rotkreuz, Switzerland). Ki-67 index was determined by ascertaining the percentage of Ki-67 positively stained cells in five fields scanned at 20× magnifications using ImageJ software (http://imagej.nih.gov/ij/).

Seibert J.K., Quagliata L., Quintavalle C., Hammond T.G., Terracciano L, & Odermatt A. (2015). A role for the dehydrogenase DHRS7 (SDR34C1) in prostate cancer. Cancer Medicine, 4(11), 1717-1729.

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Immunohistochemical Analysis of TARC

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A lymph node biopsy was done at baseline, i.e., before start of BV-DHAP. For n = 21 patients for whom insufficient material was available for additional IHC staining, the primary diagnostic biopsy was used. Central pathology review was performed by two experienced hemato-pathologists (AD, DdJ). All cases were stained for TARC in an automated setting. Paraffin tissue sections (3 µm) were incubated with polyclonal goat-anti-human TARC antibody (1:800 R&D Systems, Minneapolis, MN) on the automated Benchmark ULTRA platform (Ultra CC1, 52 min, Roche, Ventana Medical Systems). For each TARC stain, a section of cHL tissue was applied on the same slide as an external positive control. Intensity of TARC staining (i.e., negative, weak, positive) was scored by an experienced hemato-pathologist (AD), blinded for patient outcome. Positive TARC staining was defined as cytoplasmic staining visible at a magnification of ×20 or less, weak staining was defined as cytoplasmic staining only discernable at higher magnification (×200).

Driessen J., Kersten M.J., Visser L., van den Berg A., Tonino S.H., Zijlstra J.M., Lugtenburg P.J., Morschhauser F., Hutchings M., Amorim S., Gastinne T., Nijland M., Zwezerijnen G.J.C., Boellaard R., de Vet H.C.W., Arens A.I.J., Valkema R., Liu R.D.K., Drees E.E.E., de Jong D., Plattel W.J, & Diepstra A. (2022). Prognostic value of TARC and quantitative PET parameters in relapsed or refractory Hodgkin lymphoma patients treated with brentuximab vedotin and DHAP. Leukemia, 36(12).

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Evaluating Immune Profiles in Rectal Cancer

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Sections of archival formalin-fixed paraffin-embedded (FFPE) tissues from 50 patients with rectal cancer (untreated endoscopy biopsy samples at diagnosis and paired posttreatment surgical samples) were analyzed by IHC for CD73, CD8, and Pan-cytokeratin using the Ventana Benchmark Ultra platform (PR_PATMO_0010) as described previously and in the Supplementary Data (25 (link)). A total of 7 samples did not show residual tumor post-chemoradiation and were excluded from the analysis.

Wurm M., Schaaf O., Reutner K., Ganesan R., Mostböck S., Pelster C., Böttcher J., de Andrade Pereira B., Taubert C., Alt I., Serna G., Auguste A., Stadermann K.B., Delic D., Han F., Capdevila J., Nuciforo P.G., Kroe-Barrett R., Adam P.J., Vogt A.B, & Hofmann I. (2021). A Novel Antagonistic CD73 Antibody for Inhibition of the Immunosuppressive Adenosine Pathway. Molecular Cancer Therapeutics, 20(11), 2250-2261.

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Mismatch Repair Protein Expression

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Mismatch repair gene deletion was determined according to the absence of protein expression for any one of several genes, including hMLH1, hMSH2, hMSH6, and hPMS2. IHC was performed using the fully automated BenchMark ULTRA platform (Ventana Medical Systems, Inc., Tucson, AZ, United States). Normal tissues adjacent to the tumor or lymphocytes in the stroma served as internal positive controls. Each result was confirmed by at least two experienced pathologists.

Xu Y., Li C., Zhang Y., Guo T., Zhu C., Xu Y, & Liu F. (2020). Comparison Between Familial Colorectal Cancer Type X and Lynch Syndrome: Molecular, Clinical, and Pathological Characteristics and Pedigrees. Frontiers in Oncology, 10, 1603.

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Standardized IHC Protocol for Human Tissues

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Example 2

IHC protocol on human tissues: Standard ultraView Universal DAB Detection Kit protocol is used on human tissues (skin, skin squamous cell carcinoma, cervix, and esophagus) using BenchMark Ultra platform (Ventana Medical System). Briefly, selects StdCC1 cell conditioning for antigen retrieval, dilutes anti-C4.4a antibody clone SP245 (a S20H1L1 clone) at 1:400 (3 μg/ml) in antibody diluent (Catalog Number 251-018, Ventana), incubates the primary antibody for 16 min at room temperature, selects standard ultraView Universal DAB Detection protocol. Lastly, target antigen is detected using DAB, followed with hematoxylin counterstaining for 1 minute. See FIG. 2A, FIG. 2B.

As used herein, the term “about” refers to plus or minus 10% of the referenced number.

The abbreviation “aa” means “amino acid”.

The disclosures of the following documents are incorporated in their entirety by reference herein: WO2014183119; US20120295803; US20130066055; WO2011158883; US20120321619; EP1220919.

Various modifications of the invention, in addition to those described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. Each reference cited in the present application is incorporated herein by reference in its entirety.

US10948493B2. Antibodies, compositions, and immunohistochemistry methods for detecting C4.4a (2021-03-16). Ventana Medical Systems, Inc. [US]. Inventors: Fernando Jose Rebelo do Couto [US], Zhiming Liao [US], Yifei Zhu [US].

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PD-L1 Immunohistochemistry for Cancer

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Immunohistochemistry was performed using the following monoclonal antibodies against PD‐L1: 22C3 (Dako, Glostrup, Denmark), E1L3N (Cell Signaling Technology, Danvers, MA, USA), and SP263 (Ventana, Tucson, AZ, USA). Staining with clone 22C3 was performed with the corresponding Dako pharmDx assay. Staining with clone SP263 on the Ventana Benchmark Ultra platform was performed with the SP263 Ventana assay. In this study, a score of 50% was defined as “PD‐L1‐high” and a score of less than 50% or equal to 50% as “PD‐L1‐low”. Details of PD‐L1 immunohistochemistry profiles are described in Table S1.

Heo J.Y., Park C., Keam B., Ock C., Kim M., Kim T.M., Kim D., Kim S.H., Kim Y.J., Lee J.S, & Heo D.S. (2019). The efficacy of immune checkpoint inhibitors in anaplastic lymphoma kinase‐positive non‐small cell lung cancer. Thoracic Cancer, 10(11), 2117-2123.

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