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Dna Diagnosis of Thalassemia from Ancient Italian Skeletons

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Dna Diagnosis of Thalassemia from Ancient Italian Skeletons DNA DIAGNOSIS OF ANCIENT THALASSEMIA DNA DIAGNOSIS OF THALASSEMIA FROM ANCIENT ITALIAN SKELETONS By Dongya Yang, B.Sc., M.Sc. A Thesis Submitted to the School of Graduate Studies in Partial Fulfilment of Requirements for the Degree Doctor of Philosophy McMaster University © Copyright by Dongya Yang, December, 1997 Doctor of Philosophy, 1997 McMaster University (Physical Anthropology) Hamilton, Ontario TITLE: DNA Diagnosis of Thalassemia from Ancient Italian Skeletons AUTHOR: Dongya Yang, M.Sc. (Chinese Academy of Sciences, Beijing, China) B.Sc. (Lanzhou University, Lanzhou, China) SUPERVISOR: Professor Shelley R. Saunders NUMBER OF PAGES: xiv, 211 11 ABSTRACT This thesis reports an attempt to extract DNA from the skeletal remains of five young children who died approximately 1,900 years ago and who were recovered from an Italian archaeological site, Isola Sacra. These skeletons have been tentatively diagnosed as thalassemics based on morphological observations, but alternative diagnoses are also possible. DNA diagnosis was used to attempt to identify thalassemia mutations from the human globin genes extracted from these skeletons. Successful extraction of the human globin genes is largely dependent on two factors: retrieving sufficient amounts of ancient DNA without PCR (Polymerase Chain Reaction) inhibitors, and no contamination from modern DNA. To improve the chances of success, a more efficient and rapid method of extracting DNA from ancient skeletons was developed using a silica-based spin column technique to maximize the yield of amplifiable DNA from ancient skeletons and minimize the risk of the contamination with modern DNA. In a single step, the DNA is concentrated and separated from non-DNA substances that could inhibit PCR. This sufficiently removed PCR inhibitors but without an increased risk of contamination. A comparison test proved that this new approach is superior to current commonly used methods. Upon application of the new method, the evidence suggests that ancient human p-globin genes were extracted from three of the five individuals from Isola Sacra. DNA diagnosis for two of the most common Italian thalassemia mutations, IVS 1-11 a and codon 39 (more than 50% of current Italian thalassemia mutations), 111 revealed that these three individuals did not have these two mutations. However, the present results cannot totally exclude the possibility of thalassemia from these specimens since five other untested mutations might occur in these specimens. Precautions were taken to minimize the risk of contamination. Contamination was also monitored by mtDNA analysis of each individual. No systemic contamination took place in this study but a sporadic contamination was identified with one specimen. The further analysis clearly indicated that the contamination came from the author. This thesis has shown that DNA diagnosis of diseases from ancient remains can be a new, powerful approach to the study of health and disease in past human populations. Technical improvements and revised research strategies are expected to advance DNA diagnoses of ancient diseases. IV ACKNOWLEDGEMENTS First and foremost, I would like to thank my supervisor and mentor, Dr. Shelley Saunders for her unending encouragement, support and tolerance throughout my five years at McMaster. It is her vision about ancient DNA research and her faith in my abilities that have really made this thesis possible. I would also like to thank Dr. Ann Herring for her encouragement and help, which have been far beyond that warranted as a member of my supervisory committee. Her positive thinking and optimistic attitude have helped me through many difficult times. Shelley and Ann have played key roles in my graduate career, and I am honoured and privileged to have been treated by them as a colleague. Thank you, Shelley and Ann. I would also like to thank Dr. John Waye of my supervisory committee for his expert critique of ancient DNA studies and of my own project. His expertise in forensic DNA analysis has been a great help always in keeping my project on right track. I am also indebted to Dr. Edward Glanville for his time and effort taken serving as a member of my supervisory committee. Many thanks go to Barry Eng for his help in almost all technical aspects of this project. His unmatched skill and expertise with DNA have helped me to overcome many technical problems. Thank you, Barry for being a great colleague and a good friend. I am grateful to Chris Dudar for sharing his knowledge and experience with ancient DNA with me. I also extend my thanks to Margie Patterson for her help in the DNA analysis. I would like to thank Dr. Anne Keeleyside for her encouragement, VI help and kindness during my first years at McMaster. Thanks also go to Drs. Charles FitzGerald and Rob Hoppa for their help in my preparation of the oral defence. For their friendship and camaraderie, I extend my thanks to Tina Moffat, Todd Garlie, Tracy Prowse, Clare McVeich, Sylvia Abonyi, Tosha Dupras, Debi Truscott, and Cathy Crinnion. I cannot forget to say thank you to Janis, Cookie and Rosita of the Department for their help during my years at McMaster. I am grateful to Drs. Roberto Macchiarelli and Luca Bondioli of the National Prehistoric Ethnographic "L. Pigorini" Museum of Rome for their permission to access the Isola Sacra specimens and the use of their unpublished data on morphological observations of specimens. Thanks are also due to Alexandra Sperduti and Tracy Prowse for their efforts at gathering morphological skeletal data. I would also like to thank Drs. Wu Liu and Zhenbiao Zhang of the IVPP, Beijing for providing some ancient skeletal samples. Special thanks go to Drs. Christopher Justice and Patricia Seymour for their invaluable friendship. Their help and encouragement in my graduate studies are greatly appreciated. Finally, I am most grateful to my parents, brother and sisters for their faith in my ability and their support of my education. Thanks to my mother-in-law for her time taken baby-sitting my son. A very special thanks goes to my wife, Xiaobang for always encouraging me and believing in me, and to my son, Joshua, a little smart boy, who has inspired me with his unique questions. This research was supported in part by the School of Graduate Studies, McMaster University, the Arts Research Board of McMaster University and the Social Sciences and Humanities Research Council of Canada. Vll TABLE OF CONTENTS ABSTRACT .......................................................... iii ACKNOWLEDGMENTS ............................................... vi LIST OF FIGURES . .. xii LIST OF TABLES .................................................... xiv CHAPTER 1. INTRODUCTION .......................................... 1 1.1. The Study of Health and Diseases of Past Human Populations ........... 1 1.2. Problems with the Diagnosis of Ancient Diseases from Skeletal Remains .. 4. 1.3. Diagnosis of Thalassemia from Ancient Italian Skeletons .............. 10 CHAPTER 2. BACKGROUND .......................................... 14 2.1. Ancient DNA ................................................ 14 2.1.1. History of aDNA Studies ................................ 15 2.1.2. DNA Structure and the PCR Technique .................... 17 2.1.3. Mechanisms of aDNA Degradation ........................ 20 2.1.4. aDNA and the PCR Technique ........................... 24 2.1.5. Retrieval of DNA from Ancient Human Remains ............ 26 2.1.6. Summary ............................................ 31 2.2. Thalassemia ................................................. 32 2.2.1. What Is Thalassemia? .................................. 32 2.2.2. Origins and Distribution of Thalassemia .................... 33 2.2.3. Bone Lesions Caused by Thalassemia ...................... 38 2.2.4. Pathogen Load and Porotic Hyperostosis ................... 40 2.2.5. Diagnosis of Thalassemia from Skeletons ................... 43 Vlll 2.2.6. Molecular Pathogenesis of Thalassemia and DNA Diagnosis .... 44 2.2.7. Summary ............................................ 45 CHAPTER 3. MATERIALS AND METHODS ............................. 47 3.1. Materials .................................................... 47 3.1.1. General Information on the Isola Sacra Site ................. 47 3.1.2. Description of the Isola Sacra Specimens .................. 51 3.1.3. Morphological Diagnosis of Thalassemia from the Isola Sacra Skeletons ........................................... 60 3.1.3.1. Age at Death .................................. 61 3.1.3.2. General Pattern of Bone Manifestation .............. 62 3.1.3.3. Cranial Vault Involvement ....................... 63 3.1.3.4. Cortical Bone/Diploe Ratio ....................... 64 3.1.3.5. Orbital Thickness .............................. 65 3.1.3.6. Facial Bone Involvement ....................... 65 3.1.3.7. Postcranial Skeletal Changes ..................... 65 3.1.4. Bone samples for Evaluating the New Extraction Method ...... 68 3.2. Methods ..................................................... 69 3.2.1. Protocols for DNA Extraction from Ancient Bones ........... 69 3.2.1.1. New Procedures for DNA Extraction ............... 71 3.2.1.2. Evaluating the New Extraction Method by PCR Amplification .................................. 72 3.2.2. DNA Extraction from the Isola Sacra Specimens ............. 73 3.2.2.1. Bone Sample Preparation ....................... 73 3.2.2.2. DNA Extraction ............................... 76 3.2.3. PCR Amplification ofa Highly Repetitive Human-Specific Sequence .........................................
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