Forensic DNA Typing Protocols (Methods in Molecular Biology, 1420)

✍ Scribed by William Goodwin (editor)

• Publisher: Humana
• Year: 2016
• Tongue: English
• Leaves: 298
• Category: Library

✦ Synopsis

This volume presents a series of protocols and methods, some of which are not widely used by researchers/practitioners, and will aid in the execution of different laboratory techniques. Forensic DNA Typing Protocols, Second Edition is arranged into a series of related chapters. Chapter 1-3 examines two different aspects of RNA analysis for body fluid identification. Chapters 4-7 focuses on the storage of biological materials and the extraction of DNA from hard tissues. Chapters 8-10 present methods for monitoring the quality of DNA extracts, and steps to aid in the purification of DNA. Chapters 11-16 talk about methods on non-standard markers, such as INDELs, Y chromosome STRs, and mitochondrial DNA. Detailed procedures and data analysis for phenotypes and ancestry are explored in Chapter 17-19. The last chapter (20) looks at the application of DNA typing to the identification of non-human material to species level. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions 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.

Practical and thorough, Forensic DNA Typing Protocols, Second Edition, is a valuable resource for forensic specialists, researchers, and anyone interested in the field of forensic science.

✦ Table of Contents

Preface
Contents
Contributors
Chapter 1: Collection of Samples for DNA Analysis
1 Introduction
2 Exhibit Triaging, Pre-examination Preparation, and Sample Targeting
2.1 Multidisciplinary Evidence Recovery
2.2 Contamination Risk Reduction
2.3 Sample Targeting and Ordering
3 Sampling
3.1 Choice of Sampling Method
3.2 Swabbing
3.3 Tapelifting
4 Record Keeping, Packaging, and Storage
4.1 Record Keeping
4.2 Packaging and Storage
5 Notes
References
Chapter 2: Body Fluid Identification Using mRNA Profiling
1 Introduction
2 Equipment and Materials
2.1 General Supplies and Equipment
2.2 RNA Extraction with the RNeasy® Plus Mini Kit (QIAGEN GmbH) and RNA/DNA Coextraction with the AllPrep® DNA/RNA Mini Kit (QIAGEN GmbH)
2.3 RNA Extraction with Arcturus® PicoPure® RNA Isolation Kit (Life Technologies)
2.4 DNase Treatment with the TURBO DNA-Free Kit™ (Life Technologies)
2.5 Reverse Transcription
2.6 PCR of cDNA
2.7 Post-PCR Purification
2.8 mRNA Profiling: Capillary Electrophoresis
3 Methods
3.1 RNA/DNA Coextraction with the AllPrep® RNA/DNA Mini Kit (QIAGEN GmbH)
3.2 RNA Extraction with the RNeasy® Plus Mini Kit (QIAGEN GmbH)
3.3 RNA Extraction with the Arcturus® PicoPure® RNA Isolation Kit (Life Technologies)
3.4 Post-RNA Purification DNase Treatment with the TURBO DNA-Free Kit™ (Life Technologies)
3.5 cDNA Synthesis
3.6 cDNA PCR
3.7 Post-PCR Purification with the MinElute® PCR Purification Kit (QIAGEN)
3.8 mRNA Profiling: Capillary Electrophoresis
4 Notes
References
Chapter 3: mRNA Profiling for Vaginal Fluid and Menstrual Blood Identification
1 Introduction
2 Materials
2.1 General Supplies and Equipment
2.2 RNA Isolation
2.3 Reverse Transcription
2.4 PCR
2.5 Electrophoresis
3 Methods
3.1 RNA Isolation from Biological Stains
3.2 Reverse Transcription
3.3 Multiplex PCR
3.4 Capillary Electrophoresis
3.5 Interpretation of the Results
4 Notes
References
Chapter 4: Preservation of and DNA Extraction from Muscle Tissue
1 Introduction
2 Materials
2.1 Preservatives
2.2 DNA Extraction
3 Methods
3.1 Reference Samples
3.2 Preservation of Tissue in the Field
3.3 Preparation of Reference Samples and Controls
3.4 Preparation of Tissue Samples
3.5 Preparation of Salt-Saturated DMSO–EDTA Solution
3.6 Extraction of DNA (See Note 20)
3.7 Genotyping
4 Notes
References
Chapter 5: DNA Extraction: Organic and Solid-Phase
1 Introduction
2 Organic Extraction (Phenol–Chloroform)
2.1 Materials and Equipment
3 Method
4 Solid-Phase Nucleic Acid Extraction
4.1 Qiagen Investigator® Kit Using the EZ1® Bio-Robot Workstation
4.2 Materials and Equipment
5 Method
6 PrepFiler® Express™ and Express BTA™ Forensic DNA Extraction Kits Using AutoMate Express™
6.1 Materials and Equipment
7 Method
8 Notes
References
Chapter 6: Extraction of DNA from Skeletal Remains
1 Introduction
2 Materials
2.1 Skeletal Sample Preparation and Cleaning (Dried)
2.2 Intact Tooth Preparation and Cleaning (Dried)
2.3 Organic Extraction of Powdered Skeletal Samples or Teeth (Dried)
2.4 Nonorganic Extraction for Both Skeletal Samples and Teeth (Dried)
2.5 Skeletal Sample Preparation and Cleaning (Fresh)
2.6 Intact Fresh Tooth Preparation and Cleaning (Fresh)
2.7 Nonorganic Extraction for Both Skeletal Samples and Teeth (Fresh)
3 Methods
3.1 Sample Selection
3.2 Skeletal Sample Preparation and Cleaning (Dried)
3.3 Intact Tooth Preparation and Cleaning (Dried)
3.4 Organic Extraction for both Dried Skeletal Samples and Teeth (Dried)
3.5 Nonorganic Extraction for Both Skeletal Samples and Teeth (Dried)
3.6 Skeletal Sample Preparation and Cleaning (Fresh)
3.7 Intact Fresh Tooth Preparation and Cleaning (Fresh)
3.8 Nonorganic Extraction for Both Skeletal Samples and Teeth (Fresh)
4 Notes
References
Chapter 7: Extraction of DNA from Human Skeletal Material
1 Introduction
2 Materials
2.1 Chemicals
2.2 Consumable  Goods
2.3 Equipment
3 Methods
3.1 Measures for Preventing and Detecting DNA Contamination
3.2 Reagent Preparation
3.2.1 Preparation of 5 % Alconox
3.2.2 Preparation of 80 % Ethanol
3.2.3 Preparation of 0.5 M Ethylene Diamine Tetra Acetic Acid (EDTA) (pH 8.0)
3.2.4 Preparation of 1 μg/μl cRNA
3.2.5 Preparation of 1 M DTT
3.3 Bone and Tooth Sample Preparation
3.3.1 Bone and Tooth Sample Selection
3.3.2 Bone and Tooth Sample Cleaning
3.3.3 Bone and Tooth Sample Powdering
3.3.4 Bone and Tooth Sample Decalcification
3.4 DNA Extraction and Purification
3.4.1 Extraction of DNA
3.4.2 Purification of DNA
4 Notes
References
Chapter 8: The Development and Use of Internal Amplification Controls (IACs) with DNA Profiling Kits for Forensic DNA Analysis
1 Introduction
2 Materials
2.1 Reagents
2.2 Preparation of Solutions
2.3 Kits Needed
2.4 Primers
2.5 Plasmid pBR322 DNA
2.6 Instruments Used
3 Methods
3.1 Generation of IACs
3.1.1 Designing of IACs Primers
3.1.2 Generation of the IACs
3.1.3 Purification of IAC Template
3.1.4 Quantification of DNA
3.1.5 Calculation of Copy Number
3.2 Use of IACs with DNA Profiling Kit
3.2.1 Optimization of the IAC Amplification
3.2.2 Running of the Samples with Capillary Electrophoresis
3.2.3 Interpretation of the Results Using IACs as Quality Control Markers
4 Notes
References
Chapter 9: NucleoSpin® XS Columns for DNA Concentration and Clean-Up
1 Introduction
2 Materials
3 Methods
3.1 NucleoSpin® XS Concentration and Cleanup Methods
3.1.1 NucleoSpin® XS Concentration and Cleanup of Extracts
3.1.2 NucleoSpin® XS Cleanup of Existing DNA Extracts
4 Notes
References
Chapter 10: Purification of PCR Products to Improve STR Profiles
1 Introduction
2 Equipment and Materials
2.1 General Supplies and Equipment
3 Methods
3.1 Purification of PCR Products Using Amicon® Filter Units
3.2 Capillary Electrophoresis of Purified PCR Amplicons
4 Notes
References
Chapter 11: Analysis of 30 Biallelic INDEL Markers Using the Investigator DIPplex® Kit
1 Introduction
2 Materials
2.1 Equipment and Materials
2.1.1 General Supplies and Equipment
2.2 Investigator® DIPPlex Kit Contents
3 Methods
3.1 PCR Amplification
3.2 Capillary Electrophoresis
4 Notes
References
Chapter 12: Analysis of Mitochondrial Control Region Using Sanger Sequencing
1 Introduction
2 Materials
2.1 PCR
2.2 Gel Electrophoresis
2.3 Sequencing
3 Methods
3.1 Initial PCR
3.1.1 Full Control Region Strategy
3.1.2 Midi-Mito Strategy
3.2 PCR Quality Check
3.3 PCR Cleanup
3.4 Sequencing
3.5 Sequencing Cleanup and Electrophoresis
3.6 Sequence Analysis
4 Notes
References
Chapter 13: Whole Human Mitochondrial DNA Sequencing
1 Introduction
2 Materials
2.1 DNA Extraction
2.2 PCR
2.3 Agarose Gel
2.4 PCR Purification
2.5 DNA Sequencing
2.6 DNA Sequencing Purification
3 Methods
3.1 Puncher and Cutting Square Cleaning Procedure
3.2 DNA Extraction from FTA Discs
3.3 Polymerase Chain Reactions (PCRs)
3.3.1 First-Round (multiplex) PCR
3.3.2 Second-Round (Simplex) PCR
3.4 Agarose Gel Electrophoresis
3.5 PCR Purification
3.5.1 Zymo-Spin Column PCR Purification
3.5.2 Zymo Silicon-A Plate PCR Purification
3.6 DNA Sequencing
3.7 Sequencing Reaction Cleanup
3.8 Data Analysis
4 Notes
References
Chapter 14: In-Solution Hybridization for the Targeted Enrichment of the Whole Mitochondrial Genome
1 Introduction
2 Materials
2.1 Bait Preparation
2.2 Library Preparation
2.3 Enrichment of Target
2.4 Bait-Library-
3 Methods
3.1 Preparation of Bait
3.1.1 Long-Range PCR
3.1.2 Annealing of Biotinylated Adapters
3.1.3 Blunt-End Repair of Bait
3.1.4 Ligation of Adaptors to Bait
3.2 Library Preparation
3.2.1 Fragmentation
3.2.2 End Repair, Ligation of Adaptors, and Indexing
3.2.3 Optional (See Note 7)
3.3 Enrichment
3.3.1 Bead-Bait Complex Preparation
3.3.2 Prepare Target DNA for Enrichment
3.3.3 Prepare Bait-
3.3.4 After Hybridization
3.3.5 Enrichment PCR
4 Notes
References
Chapter 15: Enhanced DNA Profiling of the Semen Donor in Late Reported Sexual Assaults: Use of Y-Chromosome-Targeted Pre-amplification and Next Generation Y-STR Amplification Systems
1 Introduction
2 Materials
2.1 General Equipment and Supplies
2.2 Manual Organic DNA Extraction (See Note 1)
2.3 DNA Extraction Concentration and Purification
2.4 DNA Quantitation (See Note 3)
2.5 Y-Chromosome-
2.6 Next Generation Commercial Y-STR Kit Amplification
2.7 Capillary Electrophoresis (See Note 7)
3 Methods (See Note 8)
3.1 Post-coital Sample Collection
3.2 Manual Organic DNA Extraction
3.3 DNA Extraction Concentration and Purification (MinElute) (See Notes 10 and 11)
3.4 DNA Quantitation
3.5 Y-Chromosome-
3.6 Next Generation Y-STR Amplification (See Note 16)
3.6.1 AmpFlSTR® Yfiler® Plus PCR Amplification Kit
3.6.2 PowerPlex® Y23 System (Promega)
3.7 Capillary Electrophoresis
4 Notes
References
Chapter 16: Analysis of Rapidly Mutating Y Chromosome Short Tandem Repeats (RM Y-STRs)
1 Introduction
2 Materials
2.1 FTA® Extraction: Reagents and Equipment
2.2 PCR Amplification and Analysis
3 Methods
3.1 Blood/Saliva Stained FTA Punch Purification (See Notes 2 and 3)
3.2 PCR Amplification
3.3 Capillary Electrophoresis and Analysis
3.4 Genotyping of Commercial Controls
4 Notes
References
Chapter 17: A Practical Guide to the HIrisPlex System: Simultaneous Prediction of Eye and Hair Color from DNA
1 Introduction
2 Materials
2.1 HIrisPlex Multiplex PCR Assay
2.2 HIrisPlex Multiplex Primer Extension Assay
2.3 Purification of Amplification Products (PCR and SBE)
2.4 Electrophoresis and Genotyping Software
2.5 HIrisPlex Online Prediction Tool
3 Genotyping Methods
3.1 HIrisPlex Assay
3.2 Primer Preparation
3.3 PCR Multiplex Reaction Mix
3.4 Multiplex PCR Conditions
3.5 Purification of the PCR Product
3.6 Single Base Extension (SBE) Reaction
3.7 Multiplex SBE Conditions
3.8 Purification of the SBE Product
3.9 Capillary Electrophoresis
3.10 Analysis Methods
3.10.1 HIrisPlex Genotype Scoring
3.10.2 HIrisPlex Prediction Model
3.10.3 Understanding the HIrisPlex Prediction Probability Values
4 Notes
References
Chapter 18: Inference of Ancestry in Forensic Analysis I: Autosomal Ancestry-Informative Marker Sets
1 Introduction
2 Materials
3 Methods
3.1 The Revised SNPforID 34-Plex Forensic Ancestry Test
3.1.1 PCR Amplification of 34-Plex
3.2 Eurasiaplex, a Complimentary Test to 34-Plex for Differentiating Europeans and South Asians
3.3 The 46-Plex AIM-Indel Ancestry Test
3.4 Inference of Ancestry from STR Data
3.5 Alternative SNP-Based Forensic Ancestry Tests
3.6 Redesigning Forensic Ancestry Sets for NGS: Selecting AIM-SNPs for Power and Population Divergence Balance
3.7 Concluding Remarks
4 Notes
References
Chapter 19: Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data
1 Introduction
2 Materials
3 Methods
3.1 Collection of Ancestry Reference Data with the SPSmart Browser
3.2 STRUCTURE Software
3.2.1 Background on STRUCTURE Analysis
3.2.2 Preparation of a STRUCTURE Input File
3.2.3 How to Run STRUCTURE Software
3.2.4 STRUCTURE Associated Software
3.2.5 What Information Can Be Obtained from STRUCTURE?
3.3 The Snipper Web Portal
3.3.1 Background on Snipper Analysis
3.3.2 Preparation of a Snipper Input File
3.3.3 How to Run Snipper
3.3.4 Evaluating Snipper Output
3.4 Principal Component Analysis (PCA)
3.4.1 Background  on PCA
3.4.2 Preparation of PCA Input Files
3.4.3 Creating a PCA Plot
3.4.4 What Information Can Be Obtained from PCA?
3.5 Casework Example of a Custom Ancestry Inference: The 11-M Madrid Bomb Attack
4 Notes
References
Chapter 20: Species Determination: The Role and Use of the Cytochrome b Gene
1 Introduction
2 Materials
3 Methods
3.1 PCR Amplification of Part of the Cyt b Locus
3.2 Confirmation  of PCR
3.3 Sequencing of PCR Products
3.3.1 PCR Cleanup
3.3.2 Cycle Sequencing Method
3.3.3 Separation of Sequenced Fragments
3.4 Analysis of Results
3.5 Analyses of DNA Data
4 Notes
References
Index