The largest database of trusted experimental protocols

Benchmark xt

Manufactured by Roche
Sourced in United States, Switzerland, Azerbaijan, Germany, France, Denmark, United Kingdom, China, Belgium

The BenchMark XT is a fully automated, open-architecture immunohistochemistry (IHC) and in situ hybridization (ISH) system designed for routine and advanced research applications. The system provides consistent, reliable, and high-quality results by automating the entire staining process, from slide preparation to staining, washing, and detection.

Automatically generated - may contain errors

769 protocols using benchmark xt

1

IHC and SISH Analysis of Breast Tumor Markers

Check if the same lab product or an alternative is used in the 5 most similar protocols
Immunohistochemistry (IHC) for ER (1:200, clone 6F11, Bond-Max System, Novocastra, Newcastle upon Tyne, UK), PR (1:800, clone 16, Bond-Max System, Novocastra), HER2 (4B5, BenchMark XT, Ventana, Tucson, AZ, USA), and Ki-67 (1:200, clone MIB-1, Bond-III, Dako, Glostrup, Denmark) was performed on formalin-fixed paraffin-embedded (FFPE) tissue. Silver in situ hybridization (SISH) analysis was performed using INFORM DDISH HER-2 SISH probe kits (BenchMark XT, Ventana) on FFPE tissue. ER and PR were considered positive when at least 1% of tumor cells showed nuclear staining according to the American Society of Clinical Oncology/College of American Pathologists guidelines [9 (link)]. HER2 was considered positive if ≥ 10% of tumor cells showed 3+ staining by IHC or 2+ staining by IHC with amplification using SISH [10 (link)]. The Ki-67 labeling index was determined via automated image analysis. After the Ki-67–stained slide was scanned under × 20 magnification (Ventana iScan), the percentage of positively stained cells was calculated using image analysis software (Ventana Virtuoso, ver. 5.6).
+ Open protocol
+ Expand
2

HER2 Immunostaining and SISH Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Immunohistochemical staining was done by an automatic immunostainer (BenchMark XT, Ventana Medical Systems, Inc., Tucson, AZ, USA) using an anti-HER2/neu antibody (4B5; pre-dilution; Ventana Medical Systems) according to the manufacturer’s guideline. Bright-field dual-color SISH was performed with the automatic SISH stainer (BenchMark XT, Ventana Medical Systems) using INFORM HER2 DNA and INFORM Chromosome 17 (CEP17) probes (Ventana Medical Systems). HER2 status of the FFPE tissues was evaluated with IHC and SISH by an expert pathologist (H.S.L.), as described in the previous study33 (link). According to the DAKO guidelines for scoring HercepTest™ in gastric cancer, IHC scores of 0 and 1+ were considered as HER2 negative, whereas IHC 3+ was considered as HER2 positive. If IHC score is 2+ and SISH score >2.0, it was regarded as HER2 positive34 (link).
+ Open protocol
+ Expand
3

Breast Cancer Biomarker Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols
Preoperative CNB specimen was fixed by 10% formalin for 2 hours. Postoperative SS was serially sectioned into thin slices and fixed by 10% formalin for at least 5 hours. CNB was submitted entirely and SS was submitted at least 2 representative sections of tumor for tissue processing (HistoCore PELORIS 3 Premium Tissue Processing System, Leica Biosystems, IL, USA).
Serial 4-µm-thick paraffin-embedded sections from CNB and SS were stained for ER (SP1, Ventana Medical System, Tucson, AZ, USA), PR (1E2, Ventana Medical System, Tucson, AZ, USA) and HER2/neu (4B5, Ventana Medical Systems) by using an automated immune stainer (BenchMark XT; Ventana Medical System). Silver in situ hybridization was performed using HER2/CEP17 dual-probe (Ventana Medical Systems) through an automated stainer (BenchMark XT; Ventana Medical System).
+ Open protocol
+ Expand
4

Immunohistochemical and DISH Analysis of Breast Cancer Biomarkers

Check if the same lab product or an alternative is used in the 5 most similar protocols
Buffered formalin-fixed paraffin-embedded specimens were cut into 4-μm-thick sections to be prepared for immunohistochemistry for ER, PgR, HER2, and Ki67 as well as dual HER2 in situ hybridization (DISH). The sources of primary antibodies were as follows: ER (1D5, DAKO, Denmark), PgR (PgR636, DAKO, Denmark), HER2 (HercepTest, DAKO, Denmark), and Ki67 (MIB-1, DAKO, Denmark). Immunohistochemistry for ER, PgR, and HER2 was performed manually using the streptavidin-biotin method. In patients with a HER2 score 2+ by immunohistochemistry, amplification of the HER2 gene was evaluated using the dual in situ hybridization (DISH) method with an automated slide processing system (BenchMark® XT, Ventana Medical Systems, Inc., Tucson, Arizona). Furthermore, immunohistochemistry for Ki67 was performed automatically using an automated immunohistochemistry instrument (BenchMark® XT, Ventana Medical Systems, Inc., Tucson, Arizona).
+ Open protocol
+ Expand
5

Immunohistochemical and In Situ Hybridization Assays

Check if the same lab product or an alternative is used in the 5 most similar protocols
Immunohistochemical (IHC) staining was performed on 4-μm tissue sections from paraffin-embedded tissue blocks using the automated staining instrument BenchMark XT and an iVIEW DAB Detection Kit with the PATHWAY ERBB2/HER-2/neu (4B5) antibody (Ventana Medical Systems, Tucson, AZ, USA), according to the manufacturer’s protocol.
Fluorescent in situ hybridization (FISH) was performed on 2-μm tissue sections from paraffin-embedded tissue blocks. Upon xylene deparaffination, antigens were retrieved using TT Mega Milestone (ESBG Scientific, Markham, Ontario, Canada) with CC2 (Cell Conditioning Solution 2, Ventana). Digestion was then performed for 45 min at RT with Pepsin Solution (Kreatech, Inc., Durham, NC, USA). The slides were then washed, dehydrated with ethanol, and air-dried. The PathVysion Kit (PathVysion Her-2 DNA Probe Kit; Abbott, Abbott Park, IL, USA) was then used for in situ hybridization, and DAPI II Counterstain (Abbott) was used for staining nuclei.
Silver in situ hybridization (SISH) was performed on 4-μm tissue sections from paraffin-embedded tissue blocks using an ultraView SISH DNP Detection Kit and INFORM ERBB2/HER2 Dual ISH DNA Probe Cocktail, and an automated IHC/ISH slide-staining system, BenchMark XT (Ventana).
+ Open protocol
+ Expand
6

Immunohistochemical Analysis of HER2 in TURBT

Check if the same lab product or an alternative is used in the 5 most similar protocols
Tissue samples from TURBTs were fixed in 10% neutral formalin solution and embedded in paraffin blocks. Immunohistochemical analysis was performed with the automated system BenchMark XT (Ventana BenchMark XT, Roche, Mannheim, Germany). Deparaffinization was performed with a combination of heat, a mild detergent solution (EZ prep), and spin-mixing. The Optiview DAB IHC Detection Kit, an indirect biotin-free system, was used to detect the primary antigens in paraffin sections. HER2 protein expression was studied with the prediluted VENTANA anti-HER-2 antibody (clone 4B5; Roche). This rabbit monoclonal antibody is directed against the internal domain of HER-2 protein. The staining was membranous, allowing a semi-quantitative detection of HER-2 antigen. Only membrane staining was scored according to the same standard criteria used in breast cancer.4 (link) HER-2 positivity was assessed using the following scoring system:
0: no staining was observed or membrane staining that was incomplete and faint/barely perceptible was found in ≤10% of tumor cells; 1+: incomplete membrane staining that was faint/barely perceptible in >10% of tumor cells (Figure 1); 2+: weak to moderate complete membrane staining was observed in >10% of tumor cells (Figure 2); 3+: circumferential membrane staining that was complete and intense was observed and in >10% of tumor cells (Figure 3).4 (link)
+ Open protocol
+ Expand
7

Immunohistochemical Profiling of Laryngeal Cancer

Check if the same lab product or an alternative is used in the 5 most similar protocols
Formalin-fixed, paraffin-embedded blocks of laryngeal cancer tissue sections were cut at 3-μm thickness. Then the slides were stained in an automated immunostainer (Ventana, Benchmark XT) using primary antibodies of EGFR (CONFIRM anti-Epidermal Growth Factor Receptor (3C6) Primary antibody, Ventana, USA) and Ki-67 (CONFIRM anti-Ki-67 (30-9) Rabbit Monoclonal Primary Antibody, Ventana, USA) according to the manufacturer’s recommended protocol. For MCM-2 (anti-MCM2 rabbit monoclonal antibody (D7611)XP, Cell Signaling Technology, USA), the staining protocol (also using Ventana automated immunostainer, Benchmark XT) was modified by adding Standard CC1 as an antigen retrieval agent and incubating the specimens at 37 °C for 32 min. Distilled water was used as negative control replacing with primary antibodies. Brain, tonsil and colon adenocarcinoma were employed as positive controls of EGFR, Ki-67 and MCM-2, respectively.
+ Open protocol
+ Expand
8

Immunohistochemical and in-situ Hybridization Protocol for Breast Tumor Subtypes

Check if the same lab product or an alternative is used in the 5 most similar protocols
IHC and in-situ hybridisation were performed as described elsewhere39 (link),40 (link). Briefly, the following antibodies were used for IHC staining to determine the subtype: ER (1D5; DAKO, Copenhagen, Denmark), progesterone receptor (PgR; PgR636; DAKO), and HER2 (HercepTest; DAKO). Specimens with a nuclear staining rate ≥1% were considered HR-positive (ER and PgR). HER2 amplification was automatically stained (BenchMark® XT; Ventana Medical Systems, Tucson, Arizona, USA) with dual in-situ hybridisation (DISH; INFORM HER2 Dual ISH DNA Probe Cocktail Assay; Roche, Basel, Switzerland). Patients with ‘HER2 IHC-score 3+’ or ‘HER2 IHC-score 2+ and those positive for HER2 amplification by DISH’ were defined as HER2-positive type. IHC staining for Ki67 (MIB-1, DAKO) was performed automatically using an IHC machine (BenchMark® XT, Ventana Medical Systems, Inc.). The Ki67 labelling index (percentage of positivity) was calculated for approximately 500 cancer cells in hot to warm areas.
Pathological complete response (pCR) to NAC was evaluated in accordance with the guidelines of the Japanese Breast Cancer Society. The details of this evaluation are described elsewhere39 (link). Residual noninvasive cancers or axillary lymph node metastases were not considered while determining the pCR.
+ Open protocol
+ Expand
9

Automated HER2 Immunohistochemistry and SISH

Check if the same lab product or an alternative is used in the 5 most similar protocols
Automatic HER2 immunohistochemical staining was performed on 3-µm slides using PATHWAY anti-HER2/neu (4B5; rabbit monoclonal; pre-dilution; Ventana Medical Systems, Tucson, AZ, USA) antibody and an ultraView Universal DAB kit (Ventana Medical Systems, Tucson, AZ, USA) on an automatic immunostainer (BenchMark XT, Ventana Medical Systems, Tuscon, AZ, USA), following the manufacture’s guidelines. Automatic dual-color SISH of HER2 was performed using an automatic SISH staining device (BenchMark XT, Ventana Medical Systems, Tuscon, AZ, USA), according to the manufacturer’s protocols for INFORM HER2 DNA and INFORM Chromosome 17 (CEP17) probes (Ventana Medical Systems, Tuscon, AZ, USA). Signals from 20 tumor cells were counted and a HER2/CEP17 ratio ≥2.0 was classified as HER2 gene amplification group.
+ Open protocol
+ Expand
10

Immunohistochemical and SISH Analysis of MET

Check if the same lab product or an alternative is used in the 5 most similar protocols
Immunohistochemical staining for MET was performed with anti-total MET (SP44) rabbit monoclonal primary antibodies (Ventana Medical Systems, Tucson, AZ, USA). An automatic immunostainer (BenchMark XT, Ventana Medical Systems) was used according to the manufacturer’s instructions. MET immunostaining was scored with the HercepTest scoring guidelines for GC (DAKO, Glostrup, Denmark): score 0, no membrane staining or membrane staining in <10% of tumor cells; score 1, faint/barely perceptible partial membrane staining in >10% of tumor cells; score 2, weak to moderate staining of the entire membrane in >10% of tumor cells; score 3, strong staining of the entire membrane in >10% of tumor cells (Figure 2).
Dual-color SISH assay was performed with INFORM MET DNA probe and INFORM Chromosome 7 probe (Ventana Medical Systems) on a Ventana BenchMark XT following the manufacturer’s protocols. Signals were enumerated in 40 tumor nuclei per core, and MET gene status was classified into 6 groups using the University of Colorado Cancer Center criteria for epidermal growth factor receptor gene [21] (link) (Figure 2).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!