DNA Electrophoresis Protocols for Forensic Genetics PDF
Preview DNA Electrophoresis Protocols for Forensic Genetics
M M B ™ ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 DNA Electrophoresis Protocols for Forensic Genetics Edited by Antonio Alonso Instituto Nacional de Toxicología y Ciencias Forenses, Servicio de Biología, Madrid, Spain Editor Antonio Alonso, Ph.D. Instituto Nacional de Toxicología y Ciencias Forenses Servicio de Biología, Madrid, Spain [email protected] ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-460-5 e-ISBN 978-1-61779-461-2 DOI 10.1007/978-1-61779-461-2 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011943292 © Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or d issimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com) Preface At present, most of the validated forensic DNA profi ling procedures are based on high- resolution and high-throughput capillary electrophoresis separation and detection systems of PCR amplicons obtained from DNA genomic markers with different inheritance pat- terns (autosomal, Y-chromosome or X-chromosome linked, and mitochondrial DNA). A high degree of standardization has been achieved in the fi eld of typing procedures for PCR products obtained with fl uorogenic labeled primers, separated by capillary electrophoresis, and detected by the fl uorescence emission induced by laser on a CCD camera. Current systems have acquired a high degree of accuracy and precision in the identifi cation of allelic variants (with a resolution of one base), and also an improvement in the sensitivity of PCR amplicon detection (with reproducible signals even from picograms of DNA template). Another advantage of current capillary electrophoresis systems (with 5–6 multichannel detection technology) is a greater capacity for simultaneous detection of multiple markers. It can be detected up to 15–26 short tandem repeats (STRs) multiallelic markers, perform simultaneously about 50 biallelic single nucleotide polymorphisms (SNPs) or detect 4-dye- terminator sequencing reactions in a single capillary electrophoresis injection. Human forensic identifi cation is currently performed using commercial kits for STR multiplexing. Basically there are two sets of standardized STR markers in the criminal DNA databases around the world: the European standard set of 12 STR markers and the USA CODIS standard of 13 STR markers. They form together a standard of 18 STR markers in total. Development of mini-STR markers and their recent incorporation into commercial kits have improved the application of these markers in severely degraded DNA samples. Other source of human genetic variation used in forensic casework is the analysis of sex chromosome markers. The Y-chromosome STR haplotypes are of special interest in the specifi c analysis of the male component of DNA mixtures that are very frequently faced by forensic labs in sexual assault cases. Another application of Y-STR haplotyping using a commercial multiplex PCR system of 17 loci, is the identifi cation of human remains and missing persons checked against the appropriate reference samples of paternal relatives. As regards X-chromosome STR analysis, it provides complementary analysis in some kinship defi ciency cases. The automated sequence analysis of mitochondrial DNA hypervariable regions is espe- cially important in the analysis of forensic samples negative for nuclear DNA, or when it is necessary to identify human remains by comparing them with maternal relatives. Multiplex PCR-CE assays of autosomal SNP markers have been developed for human individualization of degraded samples and as a complementary tool in paternity testing. The analysis of autosomal, Y-chromosome, and mtDNA SNPs with well-differentiated allele or haplotype frequencies among global population-groups has been also applied to the inference of likely ancestry. DNA Electrophoresis Protocols for Forensic Genetics offers a comprehensive coverage of the most modern current electrophoretic protocols and interpretation guidelines used in forensic genetics for the analysis of amplifi ed human DNA fragments and DNA sequencing. v vi Preface It includes protocols for profi ling of autosomal STRs (s ee Chapters 1 – 3 , and 1 3 – 15 ), Y-STRs ( see Chapter 4 ), X-STRs ( see Chapter 5 ), autosomal SNPs and INDELS ( see Chapters 6 – 8 , 10 ), Y-SNPs ( see Chapter 9 ), mtDNA-SNPs ( see Chapter 11 ), and mtDNA hypervariable regions HV1 and HV2 (s ee Chapters 1 9 – 21 ). Besides the use of DNA electrophoresis on different applications for human identifi ca- tion (criminal investigations, kinship analysis, degraded samples, low template DNA, etc.) the book also covers some interesting electrophoretic protocols for molecular identifi cation of nonhuman species with interest in forensic botany (s ee Chapters 1 7 and 1 8 ), forensic veterinary (s ee Chapters 1 6 , 22 , and 23 ), and microbial forensics (s ee Chapter 2 6 ). Finally the book explores novel forensic applications of capillary electrophoresis to target messenger RNA markers for body fl uid identifi cation (s ee Chapter 1 2 ), and some forensic applications of microchip capillary electrophoresis (s ee Chapters 2 4 and 25 ). DNA Electrophoresis Protocols for Forensic Genetics has been written by highly recog- nized professionals and specialists from different forensic DNA laboratories around the world dealing with casework and using validated technology and high quality standards. This book was made possible, thanks to them. Madrid, Spain Antonio Alonso Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi PART I CURRENT PROTOCOLS ON CAPILLARY ELECTROPHORESIS OF AMPLIFIED DNA FRAGMENTS 1 An Overview of DNA Typing Methods for Human Identification: Past, Present, and Future . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Robyn Thompson, Silvia Zoppis, and Bruce McCord 2 Capillary Electrophoresis and 5-Channel LIF Detection of a 26plex Autosomal STR Assay for Human Identification. . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Carolyn R. Hill 3 Capillary Electrophoresis of MiniSTR Markers to Genotype Highly Degraded DNA Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Michael D. Coble 4 Interpretation Guidelines of a Standard Y-chromosome STR 17-plex PCR-CE Assay for Crime Casework. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Lutz Roewer and Maria Geppert 5 Capillary Electrophoresis of an X-Chromosome STR Decaplex for Kinship Deficiency Cases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Leonor Gusmão, Cíntia Alves, Iva Gomes, and Paula Sánchez-Diz 6 A 48-plex Autosomal SNP GenPlex™ Assay for Human Individualization and Relationship Testing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 Carmen Tomas, Claus Børsting, and Niels Morling 7 Typing of 49 Autosomal SNPs by Single Base Extension and Capillary Electrophoresis for Forensic Genetic Testing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 Claus Børsting, Carmen Tomas, and Niels Morling 8 A 34-plex Autosomal SNP Single Base Extension Assay for Ancestry Investigations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 C. Phillips, M. Fondevila, and Maria Victoria Lareau 9 SNaPshot® Minisequencing Analysis of Multiple Ancestry-Informative Y-SNPs Using Capillary Electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 Maria Geppert and Lutz Roewer 10 Capillary Electrophoresis of 38 Noncoding Biallelic Mini-Indels for Degraded Samples and as Complementary Tool in Paternity Testing. . . . . . . . . . . . . . . . . . . . 141 Rui Pereira and Leonor Gusmão vii viii Contents 11 Capillary Electrophoresis of an 11-Plex mtDNA Coding Region SNP Single Base Extension Assay for Discrimination of the Most Common Caucasian HV1/HV2 Mitotype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159 Peter M. Vallone 12 Capillary Electrophoresis of a Multiplex Reverse Transcription-Polymerase Chain Reaction to Target Messenger RNA Markers for Body Fluid Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 Cordula Haas, Erin Hanson, and Jack Ballantyne 13 DNA Extraction from Aged Skeletal Samples for STR Typing by Capillary Electrophoresis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 René Huel, Sylvain Amory, Ana Bilić, Stojko Vidović, Edin Jasaragić, and Thomas J. Parsons 14 Interpretation Guidelines for Multilocus STR Forensic Profiles from Low Template DNA Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199 Zoran M. Budimlija and Theresa A. Caragine 15 Interpretation Guidelines for Mixed-STR Multilocus Electrophoretic Profiles. . . . . 213 Juan Antonio Luque 16 Capillary Electrophoresis Analysis of a 9-plex STR Assay for Canine Genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231 Barbara van Asch and António Amorim 17 Capillary Electrophoresis of DNA from Cannabis sativa for Correlation of Samples to Geographic Origin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241 Heather Miller Coyle 18 Capillary Electrophoresis of Multigene Barcoding Chloroplast Markers for Species Identification of Botanical Trace Evidence. . . . . . . . . . . . . . . . . . . . . . . 253 Gianmarco Ferri, Beatrice Corradini, and Milena Alù PART II CAPILLARY ELECTROPHORESIS AND DNA SEQUENCING 19 Capillary Electrophoresis of Big-Dye Terminator Sequencing Reactions for Human mtDNA Control Region Haplotyping in the Identification of Human Remains. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267 Marta Montesino and Lourdes Prieto 20 Capillary Electrophoresis of Human mtDNA Control Region Sequences from Highly Degraded Samples Using Short mtDNA Amplicons . . . . . . . . . . . . . . 283 Odile M. Loreille and Jodi A. Irwin 21 Interpretation Guidelines of mtDNA Control Region Sequence Electropherograms in Forensic Genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301 Manuel Crespillo Marquez 22 Capillary Electrophoresis of mtDNA Cytochrome b Gene Sequences for Animal Species Identification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Adrian Linacre 23 Sequence Analysis of the Canine Mitochondrial DNA Control Region from Shed Hair Samples in Criminal Investigations. . . . . . . . . . . . . . . . . . . . . . . . . 331 C. Berger, B. Berger, and W. Parson Contents ix PART III ADVANCES IN MICROCHIP CAPILLARY ELECTROPHORESIS 24 Integrated Sample Cleanup and Microchip Capillary Array Electrophoresis for High-Performance Forensic STR Profiling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351 Peng Liu, Susan A. Greenspoon, Stephanie HI Yeung, James R. Scherer, and Richard A. Mathies 25 Microchip Capillary Electrophoresis Protocol to Evaluate Quality and Quantity of mtDNA Amplified Fragments for DNA Sequencing in Forensic Genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367 Coro Fernández and Antonio Alonso 26 Microchip Capillary Electrophoresis of Multi-locus VNTR Analysis for Genotyping of Bacillus Anthracis and Yersinia Pestis in Microbial Forensic Cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381 Andrea Ciammaruconi Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
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