Amplification Kits GlobalFiler And GlobalFiler IQC PCR

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GlobalFiler and GlobalFiler IQC PCRAmplification KitsUSER GUIDEfor use with:GlobalFiler PCR Amplification Kit (Cat. No. 4476135 and 4482815)GlobalFiler IQC PCR Amplification Kit (Cat. No. A43565)Publication Number 4477604Revision FFor Research, Forensic, or Paternity Use Only. Not for use in diagnostic procedures.

Life Technologies Ltd 7 Kingsland Grange Woolston, Warrington WA1 4SR United KingdomFor descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.The information in this guide is subject to change without notice.DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. 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. 4477604RevisionDateF03 October 2019DescriptionE07 July 2016DSeptember 2015Remove Master Mix Additive. Add the ProFlex PCR Systems. Add information aboutartifacts identified at the TH01 locus and TPOX locus. Add Section 5.2 “Performanceverification after BSA component replacement”. Update branding.CSeptember 2014Change storage conditions from 2 months to 6 months. Add Veriti Thermal Cyclerverification information.BApril 2014AAugust 2013 Add information for the GlobalFiler IQC PCR Amplification Kit: pages 9–12, 14, 16,18–19, 26, 30, 36–40, 43–45, 50, 52–56, 149–170, 174.Update 3500 software information: pages 19, 28, 175, 184. Update GeneMapper ID‑X Software: pages 176, 186.Add information on 30 cycles with 500-ng sample concentration to Chapter 1,Chapter 2, and Chapter 5. Add references to 3500 Series Data Collection 3 andGeneMapper ID-X v1.5. Add section on amplification artifacts to Chapter 5.Non-technical changes: Reorganize Chapter 1 and Chapter 5. Add data to Chapter 5 concerning the evaluation of Hardy-Weinberg equilibrium. Add information about the Quantifiler HP and Trio DNA Quantification Kits. Update thetroubleshooting table.New documentTrademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Windows is a trademarks ofMicrosoft Corporation. FTA is a trademark of GE Healthcare. NUCLEIC-CARD is a trademark of Copan Italia S.P.A., and used by Thermo FisherScientific under their permission. MiniTab is a trademark of Minitab Inc. JMP is a trademark of SAS Institute Inc. 2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents CHAPTER 1 Product information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Product description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Kit overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Validated DNA input amounts and PCR cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10About the primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Dyes used in the kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Loci amplified by the kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Standards and controls that are required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 GlobalFiler Allelic Ladder profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 GlobalFiler IQC Allelic Ladder profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 GlobalFiler kit DNA Control 007 profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 GlobalFiler IQC kit DNA Control 007 profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Contents and storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 GlobalFiler kit contents and storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 GlobalFiler IQC kit contents and storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Required materials not supplied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Instrument and software compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 CHAPTER 2 Perform PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21DNA quantification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Importance of quantification before STR analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Effect of DNA quantity on results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Methods of quantifying DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21212122Before you begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Prepare low-TE buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Thaw reagents (before first use of the kit) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Prepare the amplification kit reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Perform PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Direct amplification (GlobalFiler kit only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26GlobalFiler and GlobalFiler IQC PCR Amplification Kits User Guide3

Contents CHAPTER 3 Perform electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Allelic ladder requirements for electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Materials required for electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Set up the 3500/3500xL instruments for electrophoresis (before first use of the kit) . . . . 28Electrophoresis software setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Perform spectral calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Set up the 3130/3130xl instruments for electrophoresis (before first use of the kit) . . . . .Electrophoresis software setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Obtain and activate 6-dye license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Perform spectral calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30303032Prepare samples for electrophoresis (3500 Series and 3130 Series instruments) . . . . . . . 32 CHAPTER 4 Analyze data with GeneMapper ID‑X Software . . . . . . . 34 Overview of GeneMapper ID‑X Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Allelic ladder requirements for data analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35File names and versions used in this section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Set up the GeneMapper ID‑X Software for analysis (before first use of the kit) . . . . . . . . Workflow: Set up GeneMapper ID‑X Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Check panel, bin, and stutter file versions on your computer . . . . . . . . . . . . . . . . . . . .(If needed) Download newer versions of panel, bin, and stutter files . . . . . . . . . . . . .Import panels, bins, and marker stutter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .(Optional) Define custom table or plot settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .363636373741Create an analysis method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Create an analysis method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Analysis method settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Create a size standard definition file if needed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48About the GS600 LIZ (60– 460) size standard definition file . . . . . . . . . . . . . . . . . . . . 48Create a size standard definition file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 Analyze and edit sample files with GeneMapper ID‑X Software . . . . . . . . . . . . . . . . . . . . . 50Examine or edit a project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 For more information on using the GeneMapper ID‑X Software . . . . . . . . . . . . . . . . . . . . . 51 CHAPTER 5 Assess the PCR reaction with the InternalQuality Control System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Overview of the Internal Quality Control System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Evaluate the PCR reaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Balanced profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Ski slope profile with decreased or missing IQCL peak height (inhibition) . . . . . . . . .Ski slope profile with balanced IQC peaks (degradation) . . . . . . . . . . . . . . . . . . . . . . . .No sample peaks with balanced IQC peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .No sample peaks with extreme inhibition of IQC peaks . . . . . . . . . . . . . . . . . . . . . . . . .4525354555656GlobalFiler and GlobalFiler IQC PCR Amplification Kits User Guide

Contents CHAPTER 6 Experiments and results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57Importance of validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57Experiment conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57Laboratory requirements for internal validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58Developmental validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 2.2.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.9.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .PCR components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Thermal cycling temperatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .PCR cycle number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .585858585960Accuracy, precision, and reproducibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Accuracy observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Precision and size window description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Precision observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6161616464Extra peaks in the electropherogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Causes of extra peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Extra peaks: Stutter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Extra peaks: Addition of 3' A nucleotide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Extra peaks: Artifacts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Extra peaks: Amplification-related artifacts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .787878889091Characterization of loci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Loci in this kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Nature of polymorphisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Inheritance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Genetic linkage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95959595969696Species specificity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97SWGDAM Guideline 3.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97Nonhuman study observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Effect of DNA quantity on results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Sensitivity observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98989899Stability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Degraded DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Effect of inhibitors—hematin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Effect of inhibitors—humic acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100100100101103Mixture studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Mixture study overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Mixture study observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103103104105GlobalFiler and GlobalFiler IQC PCR Amplification Kits User Guide5

ContentsResolution of genotypes in mixed samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105Limit of detection of the minor component . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106Population data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .SWGDAM guideline 3.7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Population data overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Loci in the kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Population samples used in these studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Concordance studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Probability of Identity definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Probability of identity observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Probability of paternity exclusion observation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107107108108108108108109126CHAPTER 7 Performance verification after BSAcomponent replacement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130BSA component overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130Experiment overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .131131131132Sensitivity study results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132Sensitivity study results: Allele recovery, average peak height, stuttercomparison, and NTCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132Sensitivity study results: Intralocus, intracolor, and intercolor balance . . . . . . . . . . 135Stability study results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137Inhibitor study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137Degraded DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138Population study results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138Mixtu

For Research, Forensic, or Paternity Use Only. Not for use in diagnostic procedures. GlobalFiler and GlobalFiler IQC PCR Amplification Kits USER GUIDE for use with: GlobalFiler PCR Amplification Kit (Cat. No. 4476135 and 4482815) GlobalFiler IQC PCR Ampli

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DB Dream Beams ( Ford I-Beams) DJM Complete DJM lowering Kits DS Drop Spindles EH Leaf Spring Eye Hangers EL End Links (for anti sway-bars) FK Complete Flip Kits HS Hanger / Shackle Kits (leaf spring rear ends) K One box complete kits LB Aluminum Lowering Block Kits RK Complete Rear Kits SB Steel Lowering Block Kits SE Shock Extenders SH Leaf .

SERIES A, AV, HV; 3/4, 1, 1-1/8" BORE SERIES A, AV, HV MEDIUM DUTY CYLINDERS 3/4, 1, 1-1/8" BORE PARTS LIST AND REPAIR KITS REPAIR KITS Full unit description required followed by -H9010 NOTE: Repair kits include all seals and bushings. SEAL KITS Full unit description required followed by -H9000 NOTE: Seal kits include all seals and backup rings.

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49 7432 98375-0 7 info@vizaar.com vIsIo DoC system kits 1 Visio 1.1 vIsIo system kits 1.1 Visio system kits including: n Visio documentation system n High power, longlife Led light source n s-Video cable n composite cable n power supply n Visio p2 probe Benefit from the pre-selected system kits vIsIo BoX system kits

Accurately Measuring Global Risk of Amplification Attacks using AmpMap Soo-Jin Moon†, Yucheng Yin†, Rahul Anand Sharma†, Yifei Yuan§ , Jonathan M. Spring , Vyas Sekar† †Carnegie Mellon University, §Alibaba Group, CERT/CC , SEI, Carnegie Mellon University Abstract Many recent DDoS attacks rely on amplification, where an

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