1 USER GUIDE AmpFlSTR Identifiler Direct PCR Amplification Kit for use with: 200 reaction kit (Part no ) 1000 reaction kit (Part no ) Publication Part Number Rev. J For Forensic or Paternity Use Only.
2 Information in this document is subject to change without notice. DISCLAIMER: LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON- INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF. Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept the terms and conditions of all applicable Limited Use Label Licenses. TRADEMARKS 2015 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. AmpliTaq Gold is a registered trademark of Roche Molecular Systems, Inc. Windows and Windows Vista are trademarks of Microsoft Corporation. FTA and Whatman are trademarks of Whatman International Ltd. Buccal DNA Collector is a trademark of Bode Technology Group, Inc. NUCLEIC-CARD and FLOQSwabs are trademarks of Copan Italia S.P.A.
3 Contents About This Guide Revision history Purpose CHAPTER 1 Overview Product overview Purpose Substrate examples Product description About the primers Loci amplified by the kit Allelic ladder Workflow Instrument and software overview Data collection and analysis software Instrument and software compatibility About multicomponent analysis How multicomponent analysis works Materials and equipment Kit contents and storage Standards for samples CHAPTER 2 Perform PCR Optimize PCR cycle number Select samples and prepare plates Determine optimum conditions Treated paper substrates: prepare reactions Sample prep guidelines Prepare the reactions Untreated paper substrates: prepare reactions Sample prep guidelines Prepare the reactions Swab substrates: prepare reactions Sample prep guidelines Prepare the sample lysate Prepare the reactions Store the sample lysate Perform PCR AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 3
4 Contents CHAPTER 3 Perform Electrophoresis Allelic ladder requirements Section /3100-Avant and 3130/3130xl instruments Set up the 3100/3100-Avant and 3130/3130xl instruments for electrophoresis Reagents and parts Electrophoresis software setup and reference documents Prepare samples for electrophoresis on the 3100/3100-Avant or 3130/3130xl instruments Section /3500xL instruments Set up the 3500/3500xL instruments for electrophoresis Reagents and parts Electrophoresis software setup and reference documents Prepare samples for electrophoresis on the 3500/3500xL instruments Section instrument Set Up the 3730 instrument for electrophoresis Reagents and parts Electrophoresis software setup and reference documents Prepare samples for electrophoresis on the 3730 instrument CHAPTER 4 Analyze Data Section 4.1 GeneMapper ID Software Overview of GeneMapper ID Software Instruments Before you start Set up GeneMapper ID Software for data analysis File names Before using the software for the first time Import panels and bins Create an analysis method General tab settings Allele tab settings Peak Detector tab settings Peak Quality tab settings Quality Flags tab settings Create a size standard Analyze and edit sample files with GeneMapper ID Software Examine and edit a project For more information Section 4.2 GeneMapper ID-X Software Overview of GeneMapper ID-X Software Instruments Before you start AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
5 Contents Set up GeneMapper ID-X Software for data analysis File names Before using the software for the first time Import panels, bins, and marker stutter Create an analysis method General tab settings Allele tab settings Peak Detector tab settings Peak Quality tab settings SQ & GQ tab settings Create a size standard Analyze and edit sample files with GeneMapper ID-X Software Examine and edit a project For more information CHAPTER 5 Experiments and Results Overview Importance of validation Experiment conditions Accuracy, precision, and reproducibility SWGDAM guideline SWGDAM guideline Accuracy Precision and size windows Extra peaks in the electropherogram Causes of extra peaks Stutter products Addition of 3 A nucleotide Artifacts Characterization of loci SWGDAM guideline Nature of the polymorphisms Mapping Species specificity SWGDAM Guideline Sensitivity SWGDAM guideline Blood on FTA cards Buccal cells on FTA or Indicating FTA cards and buccal cells on Bode DNA Collectors.. 81 Effect of DNA quantity on results Stability SWGDAM guideline DNA on FTA cards DNA on buccal swabs AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 5
6 Contents Population data SWGDAM guideline Overview Population samples used in these studies Identifiler Direct Kit allele frequencies Evaluation of Hardy-Weinberg equilibrium Concordance studies Mutation rate Additional mutation studies Probability of identity Probability of paternity exclusion APPENDIX A Troubleshooting APPENDIX B Ordering Information Equipment and materials not included APPENDIX C Plate Layouts Example PCR plate layout Example electrophoresis plate layout APPENDIX D PCR Work Areas Work area setup and lab design PCR setup work area Amplified DNA work area APPENDIX E Safety Chemical safety Specific chemical handling Biological hazard safety Bibliography Documentation and Support Related documentation Obtain support Limited Product Warranty Index AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
7 About This Guide IMPORTANT! Before using this product, read and understand the information the Safety appendix in this document. Revision history Revision Date Description A May 2009 New document. B August 2009 Add Experiments and Results chapter. C October 2009 Update screen shots for Panel Manager. D September 2010 Change copyright page information. E July 2011 Add 200-reaction kit, Bode Buccal DNA Collector, Prep-n-Go Buffer, and 3100-Avant, 3130, and 3500/3500xL Genetic Analyzer information. F October 2011 Add information for Prep-n-Go Buffer to Experiments and Results chapter. G March 2012 Change copyright page information. H May 2012 Add heat protocol for buccal swab lysate preparation. Add results for additional swab types. J February 2015 Add information for the ProFlex PCR System. Purpose The AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide provides information about our instruments, chemistries, and software associated with the AmpFlSTR Identifiler Direct PCR Amplification Kit. AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 7
8 About This Guide Purpose 8 AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
9 1 Overview Product overview Workflow Instrument and software overview Materials and equipment Product overview Purpose The AmpFlSTR Identifiler Direct PCR Amplification Kit is a short tandem repeat (STR) multiplex assay optimized to allow direct amplification of single-source: Blood and buccal samples on treated paper substrates without the need for sample purification. Blood and buccal samples collected on untreated paper substrates and treated with Applied Biosystems Prep-n-Go Buffer. Buccal samples collected on swab substrates and treated with Applied Biosystems Prep-n-Go Buffer The Identifiler Direct Kit amplifies 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vwa, TPOX, D18S51, D5S818, and FGA) and the sex-determining marker, Amelogenin, in a single PCR reaction. Substrate examples Product description Treated paper: Copan NUCLEIC-CARD system or Whatman FTA cards Untreated paper: Bode Buccal DNA Collector or 903 paper Swab: Copan 4N6FLOQSwabs The Identifiler Direct Kit contains all the necessary reagents for the amplification of human genomic DNA. The reagents are designed for use with the following Applied Biosystems instruments: Applied Biosystems 3100/3100-Avant Genetic Analyzer Applied Biosystems 3130/3130xl Genetic Analyzer Applied Biosystems 3500/3500xL Genetic Analyzer Applied Biosystems 3730 Genetic Analyzer GeneAmp PCR System 9700 with the Silver 96-Well Block GeneAmp PCR System 9700 with the Gold-plated Silver 96-Well Block Veriti 96-Well Thermal Cycler ProFlex PCR System AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 9
10 1 Chapter 1 Overview Product overview About the primers Loci amplified by the kit The Identifiler Direct Kit employs the same primer sequences as used in the AmpFlSTR Identifiler PCR Amplification Kit. Degenerate primers for the loci D8S1179, vwa, and D16S539 are included in the AmpFlSTR Identifiler Direct Primer Set to address mutations in the primer binding sites. The addition of the degenerate primers allows for the amplification of those alleles in samples containing the mutations without altering the overall performance of the Identifiler Direct Kit. Non-nucleotide linkers are used in primer synthesis for the following loci: CSF1PO, D13S317, D16S539, D2S1338, and TPOX. For these primers, non-nucleotide linkers are placed between the primers and the fluorescent dye during oligonucleotide synthesis (Butler 2005, Grossman et al., 1994, and Baron et al., 1996). Non-nucleotide linkers enable reproducible positioning of the alleles to facilitate inter-locus spacing. The combination of a five-dye fluorescent system and the inclusion of non-nucleotide linkers allows for simultaneous amplification and efficient separation of the 15 STR loci and Amelogenin during automated DNA fragment analysis. Table 1 shows the loci amplified, their chromosomal locations, and the corresponding fluorescent marker dyes. The AmpFlSTR Identifiler Direct Allelic Ladder is used to genotype the analyzed samples. The alleles contained in the allelic ladder, and the genotype of the AmpFlSTR Identifiler Direct Control DNA 9947A, are also listed in the table. Table 1 AmpFlSTR Identifiler Direct PCR Amplification Kit loci and alleles Locus designation Chromosome location Alleles included in Allelic Ladder Dye label Control DNA 9947A D8S , 9 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 6-FAM 13, 13 D21S11 21q11.2-q21 24, 24.2, 25, 26, 27, 28, 28.2, 29, 29.2, 30, 30.2, 31, 30, , 32, 32.2, 33, 33.2, 34, 34.2, 35, 35.2, 36, 37, 38 D7S820 7q , 7, 8, 9, 10, 11, 12, 13, 14, 15 10, 11 CSF1PO 5q , 7, 8, 9, 10, 11, 12, 13, 14, 15 10, 12 D3S1358 3p 12, 13, 14, 15, 16, 17, 18, 19 VIC 14, 15 TH01 11p15.5 4, 5, 6, 7, 8, 9, 9.3, 10, 11, , 9.3 D13S317 13q , 9, 10, 11, 12, 13, 14, 15 11, 11 D16S539 16q24-qter 5, 8, 9, 10, 11, 12,13, 14, 15 11, 12 D2S1338 2q , 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 19, 23 D19S433 19q , 10, 11, 12, 12.2, 13, 13.2, 14, 14.2, 15, 15.2, 16, NED 14, , 17, 17.2 vwa 12p12-pter 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 17, 18 TPOX 2p23-2per 6, 7, 8, 9, 10, 11, 12, 13 8, 8 D18S51 18q21.3 7, 9, 10, 10.2, 11, 12, 13, 13.2, 14, 14.2, 15, 16, 17, 15, 19 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 Amelogenin X: p ; Y: p11.2 X, Y PET X D5S818 5q , 8, 9, 10, 11, 12, 13, 14, 15, 16 11, 11 FGA 4q28 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 26.2, 27, 28, 29, 30, 30.2, 31.2, 32.2, 33.2, 42.2, 43.2, 44.2, 45.2, 46.2, 47.2, 48.2, 50.2, , AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
11 Chapter 1 Overview Product overview 1 Allelic ladder Figure 1 shows the allelic ladder for the Identifiler Direct Kit. See Allelic ladder requirements on page 28 for information on ensuring accurate genotyping. Figure 1 GeneMapper ID-X Software plot of the AmpFlSTR Identifiler Direct Allelic Ladder AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 11
12 1 Chapter 1 Overview Workflow Workflow Perform PCR Obtain samples Treated or untreated paper substrates Obtain samples Swab substrates Prepare samples or Prepare samples Lyse in Prep-n-Go Buffer Harris Manual Punch CPA200 or CPA300 instrument Prepare reactions Untreated paper only: Prep-n-Go Buffer AmpFlSTR Identifiler Direct PCR Amplification Kit Prepare reactions AmpFlSTR Identifiler Direct PCR Amplification Kit Perform PCR GeneAmp PCR System 9700 Cycler ProFlex PCR System Veriti 96-Well Thermal Cycler Perform electrophoresis 3100/3100-Avant Genetic Analyzer 3130/3130xl Genetic Analyzer 3500/3500xL Genetic Analyzer 3730 Genetic Analyzer Analyze data GeneMapper ID-X Software GeneMapper ID Software 12 AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
13 Chapter 1 Overview Instrument and software overview 1 Instrument and software overview This section provides information about the data collection and analysis software versions required to run the Identifiler Direct Kit on specific instruments. Data collection and analysis software Instrument and software compatibility The data collection software provides instructions to firmware running on the instrument and displays instrument status and raw data in real time. As the instrument measures sample fluorescence with its detection system, the data collection software collects the data and stores it. The data collection software stores information about each sample in a sample file (.fsa files for 31xx and 3730 instruments and.hid files for 3500 instruments), which is then analyzed by the analysis software. Instrument Data collection software Analysis software 3100/3100-Avant 1.1 (3100) 1.0 (3100-Avant) /3130xl /3500xL 3500 Series Data Collection Software v1.0 GeneMapper ID Software v3.2.1 GeneMapper ID-X Software v1.0.1 or later GeneMapper ID-X Software v1.2 or later We conducted validation studies for the Identifiler Direct Kit using these configurations. About multicomponent analysis Life Technologies fluorescent multi-color dye technology allows the analysis of multiple loci, including loci that have alleles with overlapping size ranges. Alleles for overlapping loci are distinguished by labeling locus-specific primers with different colored dyes. Multicomponent analysis is the process that separates the five different fluorescent dye colors into distinct spectral components. The four dyes used in the Identifiler Direct Kit to label samples are 6-FAM, VIC, NED, and PET dyes. The fifth dye, LIZ, is used to label the GeneScan 500 LIZ Size Standard or the GeneScan 600 LIZ Size Standard v2.0. How multicomponent analysis works Each of these fluorescent dyes emits its maximum fluorescence at a different wavelength. During data collection on Life Technologies instruments, the fluorescence signals are separated by a diffraction grating according to their wavelengths and projected onto a charge-coupled device (CCD) camera in a predictably spaced pattern. The 6-FAM dye emits at the shortest wavelength and is displayed as blue, followed by the VIC dye (green), NED dye (yellow), PET dye (red), and LIZ dye (orange). Although each of these dyes emits its maximum fluorescence at a different wavelength, there is some overlap in the emission spectra between the dyes (Figure 2). The goal of multicomponent analysis is to correct for spectral overlap. AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 13
14 1 Chapter 1 Overview Materials and equipment Figure 2 Emission spectra of the five dyes used in the Identifiler Direct Kit Normalized Emission Dyes 6-FAM VIC NED PET LIZ Wavelength (nm) Materials and equipment Kit contents and storage The Identifiler Direct Kit contains sufficient quantities of the following reagents for 200 reactions (Part no ) or 1000 reactions (Part no ) at 25 µl/reaction. IMPORTANT! The fluorescent dyes attached to the primers are light-sensitive. Protect the primer set, amplified DNA, allelic ladder, and size standard from light when not in use. Keep freeze-thaw cycles to a minimum. Table 2 Kit Contents and Storage Component Description 200 reaction 1000 reaction Storage AmpFlSTR Identifiler Direct Master Mix AmpFlSTR Identifiler Direct Primer Set AmpFlSTR Identifiler Direct Control DNA 9947A AmpFlSTR Identifiler Direct Allelic Ladder Contains enzyme, salts, dntps, carrier protein, and 0.04% sodium azide Contains forward and reverse primers to amplify human DNA targets. Contains 2 ng/μl human female cell line DNA in 0.04% sodium azide and buffer. See Table 1 on page 10 for profile. Contains amplified alleles. See Table 1 on page 10 for a list of alleles included in the allelic ladder. 2 tubes, 1.25 ml each 2 tubes, 1.25 ml each 1 bottle, 12.5 ml 15 to 25 C upon receipt, 2 to 8 C after initial use 1 bottle, 12.5 ml 1 tube, 50.0 µl 1 tube, 50.0 µl 1 tube, 50.0 µl 1 tube, 100 µl The Control DNA 9947A is included at a concentration appropriate to its intended use as an amplification control (i.e., to provide confirmation of the capability of the kit reagents to generate a profile of expected genotype). The Control DNA 9947A is not designed to be used as a DNA quantitation control and laboratories may expect to see variation from the labelled concentration when quantitating aliquots of the Control DNA 9947A. 14 AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
15 Chapter 1 Overview Materials and equipment 1 Standards for samples For the Identifiler Direct Kit, the panel of standards needed for PCR amplification, PCR product sizing, and genotyping are: AmpFlSTR Identifiler Direct Control DNA 9947A A positive control for evaluating the efficiency of the amplification step and STR genotyping using the AmpFlSTR Identifiler Direct Allelic Ladder. GeneScan 500 LIZ Size Standard or GeneScan 600 LIZ Size Standard v2.0 Used for obtaining sizing results. These standards, which have been evaluated as internal size standards, yield precise sizing results for Identifiler Direct Kit PCR products. Order the GeneScan 500 LIZ Size Standard (Part no ) or the GeneScan 600 LIZ Size Standard v2.0 (Part no ) separately. AmpFlSTR Identifiler Direct Allelic Ladder Developed for accurate characterization of the alleles amplified by the Identifiler Direct Kit. The Allelic Ladder contains most of the alleles reported for the 15 autosomal loci. Refer to page 10 for a list of the alleles included in the Allelic Ladder. AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 15
16 1 Chapter 1 Overview Materials and equipment 16 AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
17 2 Perform PCR Optimize PCR cycle number Treated paper substrates: prepare reactions Untreated paper substrates: prepare reactions Swab substrates: prepare reactions Perform PCR Optimize PCR cycle number Before using the Identifiler Direct Kit for the first time, perform a single initial sensitivity experiment to determine the appropriate cycle number to use during internal validation studies and operational use of the Identifiler Direct Kit. This experiment accounts for instrument-to-instrument and sample-to-sample variations. If you are processing multiple sample type and substrate combinations (for example, buccal samples on treated paper and buccal samples on swabs), perform separate sensitivity experiments for each sample type and substrate to be used for testing. The Identifiler Direct Kit is optimized to amplify unpurified: Single-source blood samples on treated paper or untreated paper Buccal samples on treated paper, untreated paper, or swabs When amplifying single-source, unpurified samples using the Identifiler Direct Kit, you should expect to see greater variation in peak height from sample to sample than is expected with purified samples. Careful optimization of the cycle number will help to minimize this variation. Select samples and prepare plates 1. Select 26 of each sample+substrate type. Ensure the selected samples represent a typical range of samples analyzed in your laboratory. IMPORTANT! The number of samples recommended for this study has been chosen to allow you to complete electrophoresis using a single 96-well plate, thus minimizing the impact of run-to-run variation on the results. Examples of PCR and electrophoresis plate layouts are provided on page Prepare the samples and the reactions as described in the protocols later in this chapter. Prepare sufficient PCR reagents to complete amplification of three replicate plates. 3. Create three identical PCR plates (see page 107 for a suggested plate layout). 4. Amplify each plate using a different cycle number to determine the optimum conditions for use in your laboratory. Suggested cycle numbers for different sample type and substrate combinations are listed below: AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 17
18 2 Chapter 2 Perform PCR Optimize PCR cycle number Sample type Substrate Treated paper Untreated paper Swab Blood 25, 26, 27 cycles 25, 26, 27 cycles N/A Buccal 26, 27, 28 cycles 26, 27, 28 cycles 26, 27, 28 cycles Note: Our testing has not included blood samples on swab substrates. This sample type is not frequently used for the collection of database or casework reference samples. Note: To minimize the effect of instrument-to-instrument variation, use the same thermal cycler to amplify all three plates. To maximize result quality, prepare and amplify Plate 1 then repeat for Plates 2 and 3. Do not prepare all three plates simultaneously. Determine optimum conditions 1. Run the PCR products on the appropriate CE platform using the recommended protocol; see Chapter 3, Perform Electrophoresis on page Based on the results of the sensitivity study, select the appropriate PCR cycle number for future experiments. Our studies indicate the optimum PCR cycle number should generate profiles with the following heterozygote peak heights, with no instances of allelic dropout and minimal occurrence of off-scale allele peaks. Instrument Heterozygous peak height 31xx RFU 3500 Series ,000 RFU 18 AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
19 Chapter 2 Perform PCR Treated paper substrates: prepare reactions 2 Treated paper substrates: prepare reactions Sample prep guidelines Prepare the reactions Do not add water to the wells on the reaction plate before adding the punches. If your laboratory is experiencing static issues with the paper discs, you may prepare and dispense the 25 µl reaction mix into the wells of the reaction plate before adding the punches. Make the punch as close as possible to the center of the sample to ensure optimum peak intensity. Increasing the size of the punch may cause inhibition during PCR amplification. For manual punching: Place the tip of a 1.2 mm Harris Micro-Punch on the card, hold the barrel of the Harris Micro-Punch (do not touch the plunger), gently press and twist 1/4-turn, then eject the punch in to the appropriate well on the reaction plate. For automated punching: Please refer to the User Guide of your automated or semi-automated disc punch instrument for proper guidance. 1. Add samples to the reaction plate: Well(s) Add the following to wells of a MicroAmp Optical 96-Well Reaction Plate... Negative control Test samples Positive control 1.2 mm blank disc 1.2 mm sample disc For 25 cycles 3 µl of Control DNA 9947A IMPORTANT! Do not add a blank disc to the positive control well. For 26 and 27 cycles For 28 cycles 2 µl of Control DNA 9947A 1 µl of Control DNA 9947A Note: The volumes of positive control are suggested amounts and may be adjusted if peak heights are too high or too low for your optimized cycle number. 2. Calculate the volume of each component needed to prepare the reactions, using the table below. Reaction component Volume per reaction Master Mix 12.5 µl Primer Set 12.5 µl Note: Include additional reactions in your calculations to provide excess volume for the loss that occurs during reagent transfers. IMPORTANT! The Identifiler Direct Kit has been optimized for a 25-µL PCR reaction volume to overcome the PCR inhibition expected when amplifying unpurified samples. Using a lower PCR reaction volume may reduce the ability of Identifiler Direct Kit chemistry to generate full STR profiles. AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide 19
20 2 Chapter 2 Perform PCR Treated paper substrates: prepare reactions 3. Prepare reagents. Thaw the Master Mix and the Primer Set, then vortex for 3 seconds and centrifuge briefly before opening the tubes or bottles. IMPORTANT! Thawing is required only during first use of the kit. After first use, reagents are stored at 2 to 8 C and, therefore, do not require subsequent thawing. Do not refreeze the reagents. 4. Pipet the required volumes of components into an appropriately sized polypropylene tube. 5. Vortex the reaction mix for 3 seconds, then centrifuge briefly. 6. Dispense 25 µl of the reaction mix into each reaction well of a MicroAmp Optical 96-Well Reaction Plate. 7. Seal the plate with MicroAmp Clear Adhesive Film or MicroAmp Optical Adhesive Film. IMPORTANT! If using the 9700 thermal cycler with silver or gold-plated silver block and adhesive clear film instead of caps to seal the plate wells, place a MicroAmp compression pad (Part no ) on top of the plate to prevent evaporation during thermal cycling. The Veriti Thermal Cycler does not require a compression pad. 8. Centrifuge the plate at 3000 rpm for about 20 seconds in a tabletop centrifuge with plate holders. 9. Amplify the samples in a GeneAmp PCR System 9700 with the silver or gold-plated silver 96-well block or a Veriti 96-well Thermal Cycler or a ProFlex PCR System as described in Perform PCR on page 26. IMPORTANT! The Identifiler Direct Kit is not validated for use with the GeneAmp PCR System 9700 with the aluminium 96-well block. Use of this thermal cycling platform may adversely affect performance of the Identifiler Direct Kit. 20 AmpFlSTR Identifiler Direct PCR Amplification Kit User Guide
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Single Nucleotide Polymorphisms (SNPs) Additional Markers 13 core STR loci Obtain further information from additional markers: Y STRs Separating male samples Mitochondrial DNA Working with extremely degraded
LRmix tutorial, version 4.1 Hinda Haned Netherlands Forensic Institute, The Hague, The Netherlands May 2013 Contents 1 What is LRmix? 1 2 Installation 1 2.1 Install the R software...........................
BigDye Terminator v3.1 Cycle Sequencing Kit Protocol August 27, 2002 12:32 pm, 4337035A_v3.1Title.fm Copyright 2002, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic
QUICK REFERENCE OpenArray Sample Tracker Software For QuantStudio 12K Flex OpenArray Sample Block and the OpenArray Real-Time PCR System Publication Part Number 4460657 Rev. C Revision Date May 2012 Contents
DNA Sequence Analysis Two general kinds of analysis Screen for one of a set of known sequences Determine the sequence even if it is novel Screening for a known sequence usually involves an oligonucleotide
Luciferase Assay System Proto col GoClone Repor ter Construc ts: Sample Protocol for Adherent Cells LightSwitch Luciferase Assay System GoClone Reporter Assay Workflow Step 1: Seed cells in plate format.
Real-time PCR Kit for detection of mutation G1691A in Factor V gene using the Rotor-Gene Analyzer 3000/6000/Q (Corbett Research) Cat.# G0102 Institute of Applied Biotechnologies a.s. User manual Version
Procedures and Recommendations for DNA Sequencing at the Plant-Microbe Genomics Facility Ohio State University Biological Sciences Building Room 420, 484 W. 12th Ave., Columbus OH 43210 Telephone: 614/247-6204;
Detection of Multiple Reporter Dyes in Real-time, On-line PCR Analysis with the LightCycler System Gregor Sagner, Cornelia Goldstein, and Rob van Miltenburg Roche Molecular Biochemicals, Penzberg, Germany
Single Cell-to-CT Kit Protocol For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in this document is subject to change without notice. APPLIED BIOSYSTEMS
PicoMaxx High Fidelity PCR System Instruction Manual Catalog #600420 (100 U), #600422 (500 U), and #600424 (1000 U) Revision C Research Use Only. Not for Use in Diagnostic Procedures. 600420-12 LIMITED
PRODUCT ULLETIN SYR Select Master Mix SYR Select Master Mix Highly specific and sensitive quantitation SYR Select Master Mix offers advanced performance at an affordable price. SYR Select Master Mix is
292PR 01 G-Biosciences 1-800-628-7730 1-314-991-6034 email@example.com A Geno Technology, Inc. (USA) brand name Classic Immunoprecipitation Utilizes Protein A/G Agarose for Antibody Binding (Cat.
USER GUIDE One Shot TOP10 Competent Cells Catalog Numbers C4040-10, C4040-03, C4040-06, C4040-50, and C4040-52 Document Part Number 280126 Publication Number MAN0000633 Revision A.0 For Research Use Only.
Real-time quantitative RT -PCR (Taqman) Author: SC, Patti Lab, 3/03 This is performed as a 2-step reaction: 1. cdna synthesis from DNase 1-treated total RNA 2. PCR 1. cdna synthesis (Advantage RT-for-PCR
Unzipping Genes MBPCR014 Beta-Thalassemia Detection Kit P r o d u c t I n f o r m a t i o n Description: Thalassemia is a group of genetic disorders characterized by quantitative defects in globin chain
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Stratagene QPCR Mouse Reference Total RNA Instruction Manual Catalog #750600 Revision C.0 For Research Use Only. Not for use in diagnostic procedures. 750600-12 LIMITED PRODUCT WARRANTY This warranty limits
User Bulletin TaqMan SNP Genotyping Assays May 2008 SUBJECT: Replacing TaqMan SNP Genotyping Assays that Fail Applied Biosystems Manufacturing Quality Control In This Bulletin Overview This user bulletin
Matt Kramer Introduction to Post PCR Cleanup Overview Why post PCR amplification cleanup? Enhancing human identity testing Introduction to QIAGEN MinElute post PCR cleanup technologies MinElute as a tool
Applied Biosystems 7500/7500 Fast Real-Time PCR System User Guide for the 21 CFR Part 11 Module in SDS Software v1.4 Introduction Installation Logging in to the SDS Software Configuring the 21CFR11 Module
TissueDirect TM Multiplex PCR System Technical Manual No. 0173 Update Date 10112010 I Description.. 1 II Applications 2 III Key Features.. 2 IV Shipping and Storage. 3 V Simplified Procedures. 3 VI Detailed
USER GUIDE Publication Part Number 4463722 Rev. A Revision Date April 2011 For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in this document is subject
USER GUIDE HID Real-Time PCR Analysis Software Version 1.2 for use with: 7500 Real-Time PCR Instruments Quantifiler DNA Quantification Kits Publication Number MAN0009819 Revision C.0 For Research, Forensic,
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Development of two Novel DNA Analysis methods to Improve Workflow Efficiency for Challenging Forensic Samples Sudhir K. Sinha, Ph.D.*, Anne H. Montgomery, M.S., Gina Pineda, M.S., and Hiromi Brown, Ph.D.
Forensics @ NIST Gaithersburg, MD DNA Stability Studies: FTA vs 93 Margaret C. Kline Overview History of DNA storage studies at NIST Stability at different temperatures and different papers Review Anal
Re-evaluation of the Current NMI01 STR Sizing System of Cannabis DNA Ryan P. Clarke * Department of Forensic Science University of New Haven Prof. Heather Miller Coyle Department of Forensic Science University
Data Analysis on the ABI PRISM 7700 Sequence Detection System: Setting Baselines and Thresholds Overview In order for accuracy and precision to be optimal, the assay must be properly evaluated and a few
Primer Express Software Version 3.0 Getting Started Guide Before You Begin Designing Primers and Probes for Quantification Assays Designing Primers and Probes for Allelic Discrimination Assays Ordering
SPARK DNA Sample Prep Kit Ion Torrent (SPK0002-V08) Frequently Asked Questions Under what circumstances would I use SPARK DNA Sample Prep Kit for Ion Torrent? Enzymatics SPARK DNA Sample Prep Kit for Ion
Overview This chapter provides information for troubleshooting automated DNA sequencing results from capillary electrophoresis runs. Assumptions Using Controls suggestions listed in this chapter assume