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Cytoscan™ Assay Automated Workflow Site Preparation Guide—Applied Biosystems™ NIMBUS™ Instrument 3 Contents

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Cytoscan™ Assay Automated Workflow Site Preparation Guide—Applied Biosystems™ NIMBUS™ Instrument 3 Contents CytoScan™ Assay Automated Workflow on Applied Biosystems™ NIMBUS™ SITE PREPARATION GUIDE for 25 or 49 Samples Catalog Numbers 901808, 901833, and 901858 Publication Number 703142 Revision 3 For Research Use Only. Not for use in diagnostic procedures. Manufacturer: Products: Affymetrix Pte Ltd CytoScan™ Arrays 7 Gul Circle #2M-01 Keppel Logistics Building Singapore 629563 Manufacturer: Products: Thermo Fisher Scientific Baltics UAB CytoScan™ Reagent Kit V.A. Graiciuno 8, LT-02241 Vilnius, Lithuania The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, Thermo Fisher Scientific AND/OR ITS AFFILIATE(S) will NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT. Revision history: Pub. No. 703142 Revision Date Description 3 06 September 2018 Updated to the current document template, with associated updates to trademarks, logos, licensing, and warranty. Updated to include improved fragmentation protocol and reagents. 2 04 April 2013 Baseline for revision history. Important Licensing Information This product may be covered by one or more Limited Use Label Licenses. By use of this product, you accept the terms and conditions of all applicable Limited Use Label Licenses. Corporate entity Life Technologies | Carlsbad, CA 92008 USA | Toll Free in USA 1 800 955 6288 TRADEMARKS All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Kimwipes is a trademark and brand of Kimberly-Clark Worldwide, Inc. Costar is a registered trademark of Corning, Inc. Hard-Shell is a registered trademark of Bio- Rad Laboratories, Inc. Microsoft and Excel are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. Tygon is a registered trademark of Saint-Gobain Performance Plastics. Clontech and Titanium are trademarks of Clontech Laboratories, Inc. Bioanalyzer is a trademark of Agilent Technologies, Inc. Tough-Spots is a registered trademark of Diversified Biotech, Inc. Gentra and Puregene are registered trademarks of QIAGEN. GeneMate is a trademark and brand of BioExpress, LLC. ©2018 Thermo Fisher Scientific Inc. All rights reserved. Contents CHAPTER 1 Introduction. 5 About CytoScan™ Automated Target Preparation Solution on the NIMBUS™ Instrument . 5 CHAPTER 2 Safety precautions and hazards . 6 General precautions . 6 Operating the instrument . 6 Method programming . 6 Biohazard precautions . 7 Computer precautions . 7 Electrical Safety precautions . 7 Safety . 8 Pinch Points–Keep Hands Clear! . 10 CHAPTER 3 Pre-installation and site preparation . 11 Pre-installation information . 11 Site selection . 11 O-ring care . 13 Inventory of components and warranty registration . 13 Preparing the computer . 13 Preparing the power requirements . 13 Hamilton equipment, software, and labware . 14 Operation specifications for NIMBUS™ Instrument and devices . 14 Equipment. 15 Set up CytoScan™ Assay-specific deck . 16 Secure the pedestals, thermoshake, and CPAC to the deck . 16 Assembling the trash chute . 24 Setting up the Thermoshake. 27 Assembling the CPAC tube adapter and cover . 29 Placing the reagent template onto the CPAC device . 31 CytoScan™ Reagent Template . 32 Related Hamilton documentation . 32 Laboratory setup and recommendations . 33 CytoScan™ Assay Automated Workflow Site Preparation Guide—Applied Biosystems™ NIMBUS™ Instrument 3 Contents Configuration 1—two separate rooms . 33 Configuration 2—one room . 36 Contamination prevention . 39 Equipment and calibration . 39 Reagent handling and storage . 40 Laboratory workflow . 41 Thermal cyclers, 96-well plate, and adhesive seals . 41 Hybridization oven . 42 Reagents, equipment, and consumables . 43 Equipment, software, and arrays required . 43 Reagents required . 45 Consumables required . 46 Optional equipment from Thermo Fisher Scientific . 47 Equipment required from other suppliers. 48 4 CytoScan™ Assay Automated Workflow Site Preparation Guide—Applied Biosystems™ NIMBUS™ Instrument 1 Introduction About CytoScan™ Automated Target Preparation Solution on the NIMBUS™ Instrument IMPORTANT! The CytoScan™ Automated Target Preparation Assay protocol is optimized for processing from 25 or 49 samples at a time using the Applied Biosystems™ NIMBUS™ Target Preparation Instrument to obtain whole genome copy number and SNP information from Applied Biosystems™ CytoScan™ Arrays. Only the post-PCR steps from PCR purification to adding hybridization master mix are automated. This protocol is not intended for genome-wide association studies. Cytogenetics research studies are performed to identify structural changes in DNA, such as copy number changes (CNV), loss of heterozygosity (LOH), and mosaicism. Individuals typically have two copies of the genome in each of their cells: one inherited from the mother and one inherited from the father. Chromosomal abnormalities, such as the ones listed below, are common in several disease states: • Deletions–When one or both copies of a particular chromosome region are lost. • Gains–When a chromosome or chromosomal region is duplicated or multiplied. • Uniparental Disomies (UPDs)–When two copies of a chromosome or chromosomal region are present, but both have been inherited from a single parent. Traditional cytogenetics techniques, such as karyotyping and fluorescent in situ hybridization (FISH) have been used to study chromosomal abnormalities for decades. However, karyotyping only detects abnormalities at low resolutions (larger than ~5 Mb), and FISH is a more focused and targeted approach without the benefit of genome-wide analysis. Further, these techniques are limited to only providing copy number information so that UPDs cannot be identified. Together, CytoScan™ Arrays and CytoScan™ Assay Automated Workflow, along with the Command Console and Chromosome Analysis Suite software, enable you to perform high-resolution genome-wide DNA copy number analysis. The Thermo Fisher Scientific solution for cytogenetics research also provides genotyping information with over 750,000 SNPs, enabling detection of loss of heterozygosity (LOH), which can be used to detect UPDs. The combined high resolution DNA copy number data and the ability to detect gains, losses, mosaicism, and LOH on a single array makes the CytoScan™ Solution a great tool for next generation cytogenetics research studies. CytoScan™ Assay Automated Workflow Site Preparation Guide—Applied Biosystems™ NIMBUS™ Instrument 5 2 Safety precautions and hazards General precautions . 6 Computer precautions . 7 Electrical Safety precautions . 7 Safety . 8 Pinch Points–Keep Hands Clear! . 10 General precautions Applied Biosystems™ CytoScan™ Assay Kit as well as Applied Biosystems™ CytoScan™ Arrays are for research use only. All blood and other potentially infectious materials should be handled as if capable of transmitting infection and disposed of with proper precautions in accordance with federal, state, and local regulations. Some components required for this assay may pose significant health risks. Follow prudent laboratory practices when handling and disposing of carcinogens and toxins. Refer to the manufacturer’s Safety Data Sheet for additional information. Wear appropriate personal protective equipment when performing this assay. At a minimum, safety glasses and chemical resistant gloves should be worn. Operating the Good Laboratory Practices (GLP) must be observed when using Applied Biosystems™ instrument NIMBUS™ Target Preparation Instrument. Wear suitable protective clothing, safety glasses, and protective gloves, particularly when dealing with an instrument malfunction where the risk of contamination from spilled liquids exists. During operation of the NIMBUS Instrument, stand clear of any moving parts or the working deck of the instrument. In general, never lean over the NIMBUS Instrument when working with it. Method Perform test runs with tap water first and then with the final liquids prior to routine programming use, first perform test runs with tap water and then with the final liquids. Test all the liquid classes that will be used. A newly programmed test method must first be run on the NIMBUS Instrument with the final liquids prior to validation of the method and routine use. The method programmer should supervise this run. Before using any newly created or modified method for routine test purposes, a comparison study of the old and new method must be performed by the laboratory supervisor to ensure that the processing and data evaluation of both methods produces equivalent results. 6 CytoScan™ Assay Automated Workflow Site Preparation Guide—Applied Biosystems™ NIMBUS™ Instrument Chapter 2 Safety precautions and hazards Computer precautions 2 Biohazard If the NIMBUS Instrument becomes contaminated with biohazardous or chemical precautions material, it should be cleaned in accordance with the procedures in the Maintenance section of the MICROLAB® NIMBUS® User Guide (Pub. No. 62965-01). Failure to observe and carry out these maintenance procedures may impair the reliability and correct functioning of the NIMBUS Instrument. If working with biohazardous samples, pay particular attention to cleaning and decontamination procedures when performing the maintenance procedures. Wear gloves when handling the 96 pipetting arm, pedestals, containers, and tips. The NIMBUS Instrument drops used tips into a waste container. When the waste container becomes full, immediately empty it into a laboratory-supplied waste bin. Avoid contact with the discarded tips. Any surfaces on which liquid has been spilled must be decontaminated. Do not use disinfecting materials which contain hypochlorite (Javel water, Chlorox) or bleaching fluids. Computer precautions Take necessary precautions against software viruses and other malicious software. Only use the manufacturer’s original installation CD-ROM sets for the operating system and the original NIMBUS Instrument Software. Only CytoScan™ Post-PCR Software Methods for NIMBUS™ may be used to control the NIMBUS Instrument. Running other software concurrently with CytoScan™ Post-PCR Software Methods.
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