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44 protocols using thinprep preservcyt solution

1

Immunofluorescence Staining Protocol

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Anti-MRS antibodies [EPR9873(B)] were obtained from Oncotag (HFTAG201, Suwon, Korea), while the anti-CD3 (2GV6) rabbit monoclonal primary antibody was obtained from Ventana Inc. (790-4341, Arizona, AZ, USA), the Novocastra™ Liquid Mouse monoclonal antibody CD20 from Leica (NCL-L-CD20-L26, Newcastle, UK), the CD14 (5A3B11B5) mouse antibody (sc-58951, Dallas, TX, USA) from Santa Cruz Biotechnology, the human CD45 mouse antibody (MAB1430, Minneapolis, MN, USA) from R&D systems, and the thyroid transcription factor-1 (SPT24) mouse antibody (PA0364, Newcastle, UK) from Leica Biosystems. The anti-Mouse-AF555 (4409), and anti-rabbit-AF (4412) antibodies were obtained from Cell Signaling Technology (Danvers, MA, USA). Molt-4, Daudi, and H460 cells were obtained from the Korean Cell Line Bank (Seoul, Korea). ThinPrep PreservCyt® Solution was obtained from Hologic Inc. (#70097-002, Marlborough, MA, USA) and the Envision Kit and DAB from Dako (#K3468, Carpinteria, CA, USA).
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2

HPV Self-Sampling and Follow-Up Protocol

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Women in the self-sampling subgroup were sent a letter with their HPV test result. Women who were hrHPV-positive by either CLART and/or HC2 also received a scheduled appointment with a gynecologist to have a follow-up specimen collected. Gynecologists were informed about the study and the reason for referral (hrHPV-positive in the self-sampled specimen). Follow-up specimens were collected for Liquid based cytology and HPV testing using ThinPrep® PreservCyt® Solution (Hologic Inc., Marlborough, Massachusetts). Two women preferred to visit their regular physician for cytology without HPV testing. Two women did not attend their scheduled appointment and had no cytology results in the Cytology Register. Follow-up specimens were sent for LBC testing first, after which the remainder of the specimens was then sent for HPV testing as described above. For safety purposes, one woman who was positive for HPV66 and two women with a HPV positivity signal close to the threshold for HPV45 and HPV51 also received a scheduled appointment with a gynecologist. Follow-up specimens for these two women showed normal cytology and HPV-negative results.
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3

Cervical Cell Collection and Preservation

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Exfoliated cervical cells were collected from cervical canals using a cytobrush. The samples were collected in vials containing preservation solutions for HPV DNA testing or in bottles of ThinPrep® PreservCyt® solution (Hologic, Waltham, MA, USA) for cytology examination. The storage conditions of the samples are detailed in our previous study [28 (link),29 (link)].
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4

Comprehensive Screening of Infectious Agents

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HPV was detected using the LINEAR ARRAY HPV Genotyping Test (Roche Diagnostics). This method detects 21 HPV genotypes of high risk (including 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 67, 68, 69, 70, 73 and 82) and 16 HPV genotypes of low risk (6, 11, 40, 42, 54, 55, 61, 62, 64, 71, 72, 81, 83, 84, IS39 and CP6108) in cervical cells from each group preserved in PreservCyt® solution, (ThinPrep® PreservCyt® Solution; Hologic, Inc., Marlborough, MA, USA) according to the manufacturer's protocol. Additionally, anti-CMV, anti-Toxoplasma gondii and anti-Rubella IgG and IgM antibodies were measured in serum using a chemiluminescent microparticle immunoassay (Architect i-1000SR; Abbott Pharmaceutical Co., Ltd.). For the diagnosis of HIV-1/HIV-2 infection, the Architect HIV Ag/Ab Combo assay, a chemiluminescent microparticle immunoassay was utilized (Abbott Pharmaceutical Co., Ltd.). Additionally, serum Hepatitis B surface antigen, anti-HBV and anti-HCV titers were determined via an enzyme immunoassay using the ARCHITECT platform (Abbott Pharmaceutical Co., Ltd.) according to the manufacturer's protocol.
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5

DNA Extraction and Quantification from Cervical Cells

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Cervical cell samples had previously been collected in ThinPrep PreservCyt solution (Hologic, Marlborough, MA) and pelleted before storage −80 °C to retain DNA quality and integrity. Collected samples were stored as both cell material and extracted DNA in a research biobank at Akershus University Hospital. DNA from some samples had to be re-extracted from cell material for this study, and an easyMAG® (Biomérieux, USA) was used for the extraction and the eluate stored in a biobank at −80 °C. The DNA concentration was measured on Qubit® 3.0 Fluorometer (Life Technologies, USA) to ensure optimal DNA quantity in every sample before the PCR reaction.
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6

Cervical HPV DNA Detection Protocol

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The presence of HPV DNA in cervical samples was determined using the Linear Array (LA) assay (Roche Molecular Systems), a commercialized L1 consensus primer‐based PCR method that uses a primer set designated PGMY09/11. The LA test was carried out according to the manufacturer’s recommended protocol. Briefly, exfoliated ecto‐ and endocervical cells were stored in ThinPrep PreservCyt solution (Hologic) until DNA extraction. Total cellular DNA was extracted using a QIAamp MinElute Media kit (Qiagen). Amplicons were subjected to reverse line blot hybridization for detection of 37 individual HPV genotypes (HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 45, 51 to 56, 58, 59, 61, 62, 64, 66 to 73, 81 to 84, and 89). Detection and genotyping of HPV were undertaken at a clinical testing laboratory (SRL, Tokyo, Japan). All of the HPV DNA assays were carried out by individuals who were blinded to the results of the clinical profile for each subject.
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7

HPV Genotyping Using Polymerase Chain Reaction

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Cervical cells were collected using dry swab samples, according to routine procedures, from the cervical canal of all participants and placed in a 20-mL standard test tube filled with ThinPrep PreservCyt solution (Hologic Inc, Waltham, Massachusetts) for HPV DNA testing. For HPV assays, 1 mL of the cell suspension was used for DNA extract and was stored at −20°C. The HPV testing was performed using the polymerase chain reaction-reverse dot blot Yaneng HPV Genotyping Kit (Yaneng Biotech, Shenzhen, China), which is capable of detecting 23 genotypes, including 18 HR-HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, 82, and 83) and 5 low-risk (LR)-HPV types (6, 11, 42, 43, and 81).6 (link)
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8

Cervical Swab Preservation for Analysis

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The sample used in this study was a cervical swab, which was taken by trained health workers using a cytobrush and promptly preserved in a liquid transport medium (ThinPrep PreservCyt Solution®—Hologic, Inc. Malborough, MA, USA). The sample was immediately sent to the Immunology and Biomolecular Laboratory, Clinical Laboratory Department, Faculty of Medicine Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta.
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9

Enrichment of Circulating Tumor Cells

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De-identified blood samples were obtained from newly diagnosed advanced NSCLC patients before treatment with informed consents according to a protocol approved by Institutional Review Board (IRB) at Augusta University. All blood samples were collected into vacutainer tubes (BD, Franklin Lakes, NJ,) containing the anticoagulant K2EDTA and were processed within 3 hours of blood draw. In a typical process, every 1 mL of whole blood was lysed by 10 mL of RBC lysis buffer for 5 minutes at room temperature. WBCs were then collected by spinning down the solution at 800×g for 5 minutes and the pellet was suspended in 1 mL of ferrofluid containing 0.1% (v/v) Pluronic F-68. The sample was then loaded into a 10-mL syringe (BD, Franklin Lakes, NJ,) followed by processing with the FCS device at a flow rate of 6 mL h−1. A stainless-steel sphere (BC Precision, Chattanooga, TN) with a diameter of 1.6 mm was also loaded into a syringe. A magnet was used to gently agitate the sphere to prevent blood cells from settling down every 5–10 minutes. After separation, the FCS device was flushed by PBS or ThinPrep PreservCyt solution (Hologic, Marlborough, MA) at 30 mL h−1 for 20 minutes to remove any cells in outlet reservoir. During the separation, the cells from outlet 6 of a FCS device were directly preserved in ThinPrep PreservCyt solution for further analysis.
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10

Targeted Sequencing Panel for Endometrial Cancer

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Our custom hybrid capture panel covers coding exons and regions prone to mutations of 10,929 genes that had variants in the above WES results or had been reported in the literature of EC [6 (link),7 (link),8 (link),19 (link)]. The list of targeted genes is in Table S2. Oligonucleotide probes were designed by BGI. The probe regions were 4.96 Mb, and the average sequencing depth was 20,000×.
All the samples were profiled by targeted panel sequencing (TPS). Fresh surgical samples (tumor and normal) and PIP-E samples were stored at −80 °C until DNA extraction. PAP-C and SWAB-V samples were preserved in ThinPrep PreservCyt solution at 4 °C (Hologic, Marlborough, MA, USA). After delivery to the laboratory, PAP-C and SWAB-V samples were centrifuged for 5 min at 14,000× g, and the precipitates were used for DNA extraction. DNA extraction, library preparation, and targeted NGS were performed as described above. Raw sequencing data of EC patients were also processed like WES data. Sequencing data from women with risk factors for EC were identified as variants using the HaplotypeCaller module of GATK.
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