Forensic DNA Analysis: Methods and Protocols (Methods in Molecular Biology, 2685)

Description

This volume focuses on the latest techniques used in forensic DNA analysis. The chapters include a comprehensive collection of extraction, quantification, STR amplification, and detection methods for routine forensic samples, including manual, semi-automated, and automated procedures using both home-brew and commercial products. The chapters also discuss probabilistic modeling software and specialized start-to-finish procedures for mitochondrial DNA analysis, archived latent fingerprints, latent DNA, rapid DNA profiling, and next-generation sequencing. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and practical, Forensic DNA Analysis: Methods and Protocols is a valuable resource for researchers interested in learning more about forensic DNA analysis procedures. Preface Contents Contributors Part I: Introduction Chapter 1: Forensic DNA Analysis: An Overview of the Laboratory Process 1 Introduction 2 Universal Precautions Against Contamination and Compromise 3 Routine Guidance for DNA Processing 3.1 Separation of Question and Reference Samples 3.2 DNA Extraction and Purification 3.3 DNA Quantification 3.4 STR Amplification 3.5 STR Profile Detection 4 Additional Guidance 4.1 Water 4.2 Tris-EDTA (TE) Buffer Versus Water 5 Summary 6 Notes References Part II: DNA Extraction and Purification Chapter 2: Organic Extraction of Nucleic Acids Using Ethanol Precipitation or Microcon Centrifugal Filter Purification Methods 1 Introduction 2 Materials 2.1 Equipment 2.2 Consumables 2.3 Reagents 3 Methods 3.1 Sample Preparation and Lysis: Swabs and Stains 3.2 Sample Preparation and Lysis: Tissue Samples 3.3 Sample Preparation and Lysis: Bones 3.4 Sample Preparation and Lysis: Teeth 3.5 Sample Preparation and Lysis: Differential Procedure for Mixed Body Fluid Stains 3.6 Organic Isolation of DNA 3.7 Microcon Purification 3.8 Ethanol Precipitation Purification 4 Notes References Chapter 3: Manual Silica-Based DNA Extractions 1 Introduction 1.1 Background 1.2 Silica DNA Extraction Chemistry 2 Materials 2.1 DNA Extraction via QIAamp DNA Blood Mini Kit or QIAamp DNA Mini Kit 2.2 DNA Extraction via QIAamp DNA Investigator Kit 2.3 DNA Extraction via DNA IQ System 3 Methods 3.1 Extraction of Reference Blood or Buccal Samples Using QIAamp DNA Blood Mini Kit or QIAamp DNA Mini Kit 3.2 Extraction of Blood, Buccal, Saliva, or Touch DNA Samples Using QIAamp DNA Investigator Kit 3.3 Extraction of Blood, Buccal, Saliva, or Touch DNA Samples Using DNA IQ System 4 Notes References Chapter 4: Applied Biosystems PrepFiler Forensic DNA Extraction Kit (Manual and Semi-automated via AutoMate Express) 1 Introduction 1.1 Background 1.2 Sample Lysis 1.3 DNA Isolation and Purification 1.4 DNA Concentration and Elution 1.5 The AutoMate Express Forensic DNA Extraction System 2 Materials 2.1 Manual PrepFiler Extractions 2.2 Semi-automated PrepFiler Extractions Using the AutoMate Express 2.3 Shared Materials for Manual and Robotic Extractions 3 Methods 3.1 Preparation for Manual Extraction 3.2 Sample Lysis for Manual Extraction 3.3 DNA Isolation and Purification for Manual Extraction 3.4 DNA Concentration and Elution for Manual Extraction 3.5 Preparation for the Semi-automated PrepFiler Express Standard and BTA Extraction Using the AutoMate Express 3.6 Sample Lysis for Semi-automated PrepFiler Express Standard and BTA Extraction Using the AutoMate Express 3.7 DNA Extraction on the AutoMate Express Robot 3.8 Post-Run Instrument Maintenance 3.9 Bi-weekly Instrument Maintenance 3.10 Monthly Instrument Maintenance 3.11 Yearly Instrument Maintenance 4 Notes References Chapter 5: Robotic DNA Extraction Utilizing Qiagen BioSprint 96 Workstation 1 Introduction 2 Materials 2.1 Reagents and Supplies 2.2 Equipment 2.3 Reagent Preparation 3 Methods 3.1 DNA Extraction of Liquid Blood 3.2 DNA Extraction from Bloodstain Cards 3.3 DNA Extraction from Buccal Swabs 3.4 Robotic Processing Steps 4 Notes References Chapter 6: DNA Extraction of Bone Through Demineralization 1 Introduction 2 Materials 2.1 Equipment 2.2 Supplies 2.3 Reagents 3 Methods 4 Notes References Chapter 7: Differential Extraction with Purification via Organic/Microcon and Promega DNA IQ Methods 1 Introduction 2 Materials 2.1 General Reagents and Supplies 2.2 Organic Differential Extraction 2.3 DNA IQ System Differential Extraction 3 Methods 3.1 Differential Lysis Procedure 3.2 Organic Extraction with Microcon DNA Purification 3.3 DNA IQ Extraction and Purification 4 Notes References Chapter 8: DNA Purification from Bloodstains and Buccal Cells/Saliva on FTA Cards 1 Introduction 2 Materials 3 Method 3.1 Purification from Blood on FTA Cards 3.2 Purification from Buccal Cells/Saliva on FTA Indicating Cards 4 Notes References Part III: DNA Quantification Chapter 9: Yield Gel via Quantitative Gel Electrophoresis 1 Introduction 2 Materials 2.1 Agarose Gel Equipment and Supplies 2.2 Agarose Gel Reagents 3 Methods 3.1 Agarose Gel 3.2 DNA Standard Preparation 3.3 Sample and Control Preparation 3.4 Loading on Agarose Gel and Electrophoresis 3.5 Capture Gel Image 3.6 Data Interpretation 4 Notes References Chapter 10: Quantitative PCR of Alu Repeats Using PowerUp SYBR Green Master Mix 1 Introduction 2 Materials 3 Methods 3.1 Plate Layout Form Setup 3.2 SDS Plate Document Setup 3.3 DNA Standards Preparation 3.4 qPCR 96-Well Plate Preparation 3.5 Running the Reaction Plate on the 7500 Real-Time System 3.6 qPCR Data Analysis and Interpretation 4 Notes References Chapter 11: Quantitation of DNA Using the Applied Biosystems Quantifiler Trio DNA Quantification Kit 1 Introduction 2 Materials 3 Methods 3.1 Preparation of DNA Quantification Standards 3.2 Preparation of the Reaction Plate 3.3 Processing the Reaction Plate 3.4 Evaluation of the Standard Curve and Interpretation of Data 4 Notes References Chapter 12: QIAGEN´s Investigator Quantiplex Pro Kit 1 Introduction 2 Materials 3 Methods 3.1 Preparation of DNA Standards 3.2 Quantification Setup 3.3 Creating an Instrument Plate Record and Starting a Run on the 7500 3.4 Analyzing a Run 4 Notes References Part IV: STR Amplification Chapter 13: DNA Amplification Using Promega´s PowerPlex Fusion Systems (5C and 6C) 1 Introduction 2 Materials 2.1 PowerPlex Fusion 5C System 2.2 PowerPlex Fusion 6C System 2.3 All Amplification Protocols 2.4 Direct Amplification of Lytic Storage Cards (see Note 6) 2.5 Direct Amplification of Nonlytic Storage Cards (see Note 7) 2.6 Direct Amplification of Swabs 3 Methods 3.1 Amplification of Extracted DNA Using PowerPlex Fusion 5C in a Full Reaction Volume 3.2 Amplification of Extracted DNA Using PowerPlex Fusion 5C in a Half Reaction Volume 3.3 Amplification of Extracted DNA Using PowerPlex Fusion 6C in a Full Reaction Volume 3.4 Amplification of Extracted DNA Using PowerPlex Fusion 6C in a Half Reaction Volume 3.5 Direct Amplification of Lytic Storage Cards Using PowerPlex Fusion 5C in a Half Reaction Volume 3.6 Direct Amplification of Nonlytic Storage Cards Using PowerPlex Fusion 5C in a Half Reaction Volume 3.7 Direct Amplification of Swabs Using PowerPlex Fusion 5C in a Half Reaction Volume 3.8 Direct Amplification of Lytic Storage Cards Using PowerPlex Fusion 6C in a Half Reaction Volume 3.9 Direct Amplification of Nonlytic Storage Cards Using PowerPlex Fusion 6C in a Half Reaction Volume 3.10 Direct Amplification of Swabs Using PowerPlex Fusion 6C in a Half Reaction Volume 4 Notes References Chapter 14: Amplification of Extracted DNA and Direct Amplification with the PowerPlex Y23 System 1 Introduction 2 Materials 2.1 Materials Necessary for All Amplification Protocols 2.2 Direct Amplification of Lytic Storage Cards (see Note 3) 2.3 Direct Amplification of Nonlytic Storage Cards (see Note 4) 2.4 Direct Amplification of Swabs 3 Methods 3.1 Amplification of Extracted DNA 3.2 Direct Amplification of Lytic Storage Cards Using Half Reaction Volume 3.3 Direct Amplification of Nonlytic Storage Cards 3.4 Direct Amplification of Swabs 4 Notes References Chapter 15: Applied Biosystems´ GlobalFiler PCR Amplification Kit 1 Introduction 2 Materials 3 Methods 3.1 Preparing DNA Samples and PCR Amplification Master Mix 3.2 Preparing Amplification Reactions 3.3 Thermal Cycler Instrument Operation 4 Notes References Chapter 16: QIAGEN´s Investigator 24plex QS and GO! PCR Amplification 1 Introduction 2 Materials 2.1 General Materials 2.2 Amplification with Investigator 24plex QS 2.3 Direct Amplification with Investigator 24plex GO! 3 Methods 3.1 Amplification with Investigator 24plex QS Kit 3.2 Direct Amplification (Investigator 24plex GO! Kit) with FTA or Non-FTA Blood Samples 3.3 Half Reaction, Direct Amplification (Investigator 24plex GO! Kit) with Buccal Swab Samples 4 Notes References Chapter 17: Low Volume STR Amplification Options: Coupling with Standard or Fast PCR, Traditional or Normalized DNA Extraction... 1 Introduction 2 Materials 2.1 STR Amplification 2.2 Normalized DNA Extraction 2.3 Capillary Electrophoresis Detection 3 Method 3.1 3 μL or 6 μL STR Amplification 3.2 Normalized DNA Extraction via ChargeSwitch 3.3 Traditional Capillary Electrophoresis Detection 3.4 Alternative Capillary Electrophoresis Detection (POP-6 and 22 cm Array) 4 Notes References Part V: STR Profile Detection and Interpretation Chapter 18: Capillary Electrophoresis with Applied Biosystems´ 3500 Genetic Analyzer 1 Introduction 2 Materials 3 Methods 3.1 Turning the Instrument On 3.2 Turning the Instrument Off 3.3 Loading the Anode Buffer Container (ABC) 3.4 Loading the Cathode Buffer Container (CBC) 3.5 Maintenance Wizards 3.6 Spatial Calibrations 3.7 Spectral Calibrations 3.8 Preparing the Instrument for Electrophoresis 3.9 Sample Plate Set Up 3.10 Processing the Plate on the Instrument 3.11 Monitoring Electrophoresis in Progress 4 Notes References Chapter 19: Likelihood Ratio Calculation Using LRmix Studio 1 Introduction 1.1 Background 1.2 Likelihood Ratio Calculations Using LRmix Studio 1.3 Additional Analyses Available in LRmix Studio 2 Materials 3 Methods 3.1 Preparation of DNA Profile Files 3.2 Set Up of LRmix Studio for Statistical Analysis 3.3 Probability of Drop-Out Calculation 3.4 Additional Analyses in LRmix Studio 3.5 Printing a LRmix Studio Report 4 Notes References Part VI: Specialized Samples Chapter 20: Mitochondrial DNA Analysis 1 Introduction 2 Materials 2.1 General Materials 2.2 Extraction 2.3 Amplification 2.4 Primer Sequences 2.5 Product Evaluation 2.6 Purification and Sequencing 2.7 Capillary Electrophoresis 2.8 Sequence Assembly 3 Methods 3.1 Chelex Extraction Method for Reference Bloodstains 3.2 Chelex Extraction Method for Reference Buccal Swabs 3.3 Chelex Isolation of DNA 3.4 Organic Extraction Method for Loose Hairs 3.5 Organic Extraction Method for Bone 3.6 Organic Extraction Method for Bloodstains and Buccal Swabs 3.7 Mitochondrial DNA Amplification 3.8 Mitochondrial DNA Product Evaluation 3.9 Enzymatic Purification/Sequencing of Mitochondrial DNA 3.10 Sequence Assembly and Analysis 4 Notes References Chapter 21: An Optimized Forensic DNA Analysis Workflow for Obtaining STR Results from Archived Latent Fingerprints 1 Introduction 2 Materials 2.1 DNA Extraction 2.2 Re-purification with Centri-Sep Spin Columns 3 Methods 3.1 DNA Sampling 3.2 DNA Extraction with QIAamp DNA Investigator Kit 3.3 Re-purification with Centri-Sep Spin Columns 4 Notes References Chapter 22: Detection of Latent DNA Using a DNA Binding Dye 1 Introduction 2 Materials 2.1 Reagents and Supplies 2.2 Equipment 3 Methods 3.1 Reference Samples 3.2 Evidential Items 4 Notes References Chapter 23: Rapid DNA Profile Development with Applied Biosystems RapidHIT ID System 1 Introduction 1.1 Background 1.2 STR Profile Generation on the RapidHIT ID 1.3 STR Profile Generation on with the RapidLINK Software 2 Materials 2.1 Consumables 2.2 RapidHIT ID Kits 2.3 Equipment 3 Methods 3.1 Set-Up of a Sample Run on the RapidHIT ID System 3.2 Viewing and Exporting the Results in the RapidHIT ID Software 3.3 General Instrument Usage and Maintenance 3.4 Replacing the Primary Cartridge 3.5 RapidHIT ID Software Configuration (Only for Supervisor and/or Administrator Login) 3.6 Analyzing Samples in RapidLINK 3.7 Secondary Analysis with GeneMarker HID 4 Notes References Chapter 24: Next-Generation Sequencing: ForenSeq DNA Signature Prep Kit with the Illumina MiSeq FGx 1 Introduction 1.1 Background 1.2 Library Preparation Using the ForenSeq DNA Signature Prep Kit 1.3 Sequencing on the MiSeq FGx 2 Materials 2.1 Library Preparation 2.2 Sequencing Specific Materials 3 Methods 3.1 Library Preparation-Amplification 1: Amplification and Tagging of Loci Targets 3.2 Library Preparation-Amplification 2: Enrichment of Targets-Amplification and Attachment of Indices 3.3 Library Preparation-Sample Purification-Removal of Left-over Amplification Reagents 3.4 Library Preparation-Sample Normalization-To Create Equal Sample Representation During Sequencing 3.5 Library Preparation-Pooling of Sample Libraries 3.6 Denaturation and Dilution of Pooled Libraries and Cartridge Loading for Sequencing 3.7 Instrument Setup and Performing a Run 3.8 Perform a Post-Run Wash 4 Notes References Index