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Clinical and Molecular Genetic Study of Kindreds with Limbs and Neurological Anomalies

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Clinical and Molecular Genetic Study of Kindreds with Limbs and Neurological Anomalies Clinical and Molecular Genetic Study of Kindreds with Limbs and Neurological Anomalies PhD Dissertation By Muhammad Afzal Human Genetics 2020 Human Genetics Lab, Department of Zoology Faculty of Biological Sciences Quaid-i-Azam University, Islamabad, Pakistan Acknowledgments I offer my humblest and sincere thanks to Almighty ALLAH, Who bestowed me with potential and ability to make a solid contribution to already existing ocean of knowledge and I also feel pleasure to offer thanks for Holy Prophet Hazrat Muhammad (PBUH), Who showed us the right path and enabled us to recognize our creator. This work would not have been possible without the support and encouragement of my teacher Dr. Sajid Malik, under whose supervision I chose this topic and began the thesis. Actually, when I registered at QAU, I was nothing but today I would able to submit this thesis. He always has been a continuous source of encouragement for me. I am grateful to Dean Faculty of Biological Sciences; Prof. Dr. Muhammad Shahab and chairman department of Animal Sciences; Assoc. Prof. Dr. Sajid Malik for providing pre-requisites for this work and thus facilitating this task. Clerical and technical assistant in scientific research is an undeniable important element. So I am righteous in thanking Syed Mujahid Hussain (Lab. assistant), Naeem Masih and Samiullah for their thorough and in time assistance. I am highly thankful to Rana Mazhar (Principal Punjab group of colleges) because he provided me the financial assistance whenever I need at any time at any occasion during the field work and compilation of thesis and he never disappointed me. I am highly grateful to all those families and subjects whose gave their consent and participated in the study. I am also thankful to all those people who helped and facilitated me during field work. I also want to pay special thanks to my PhD juniors Mr. Rana Muhammad Kamran Shabir, Ms. Rehana, Ms. Farwa, Ms. Qandeel, and Saliha Jabeen. All these respected ones assist and helped me in blood samples processing. I am thankful to M. Phil colleagues at Lab of Human Genetics, for their cooperation and nice company, especially, Mr. Salman, Mr. Qazi Waheed, Mr. Naeem, and Muqadssa Naureen. In the end I owe my gratitude to my parents whose countless love, prays and encouragement and I achieved this academic task only because of their efforts and sacrifices that they done for me. _______________ Muhammad Afzal IX List of Contents PLAGIARISM UNDERTAKING ....................................................................................................... AUTHOR’S DECLERATION ………………………………………………………………………………………. CERTIFICATE OF APPROVAL ....................................................................................................... ACKNOWLEDGMENT .................................................................................................................... LIST OF CONTENTS ........................................................................................................................ LIST OF FIGURES ........................................................................................................................... LIST OF TABLES ............................................................................................................................ LIST OF ABBREVIATION ................................................................................................................ GENERAL SUMMARY ....................................................................................................................... 2 CHAPTER 1 1: INTRODUCTION ........................................................................................................................... 4 CHAPTER 2 2: CLINICAL AND EPIDEMIOLOGICAL STUDY OF 103 PROBANDS WITH POLYDACTYLY .................................................................................................................................. 9 2.1: Abstract .................................................................................................................................................... 9 2.2: Introduction ............................................................................................................................................ 10 2.2.1: Clinical spectrum of polydactyly............................................................................................................. 10 2.2.2: Classification, inheritance, and genetics of polydactylies ...................................................................... 11 2.2.3: Polydactyly as a ciliopathy ..................................................................................................................... 15 2.3: Subjects and methods ............................................................................................................................. 16 2.3.1: Exclusion criteria .................................................................................................................................... 17 2.3.2: Statistical analysis .................................................................................................................................. 17 2.4: Results .................................................................................................................................................... 18 2.5: Discussion ............................................................................................................................................... 25 v IX CHAPTER 3 3: A NOVEL MUTATION IN ZRS LOCUS C.287C>A SEGREGATES WITH TRIPHALANGEAL THUMB POLYDACTYLY PHENOTYPE WITH A HIGH DEGREE OF INTRAFAMILIAL VARIABILITY ................................................................................................. 28 3.1: Abstract .................................................................................................................................................. 28 3.2: Introduction ............................................................................................................................................ 29 3.3: Subjects and methods ............................................................................................................................. 37 3.3.1: Polymerase chain reaction (PCR) and Sanger sequencing ..................................................................... 38 3.4: Results .................................................................................................................................................... 40 3.4.1: Clinical report ......................................................................................................................................... 40 3.4.2: Molecular study ..................................................................................................................................... 44 3.5: Discussion ............................................................................................................................................... 45 CHAPTER 4 4: CLINICAL STUDY OF LONGITUDINAL AND TRANSVERSE DEFICIENCIES OF UPPER LIMBS IN FOUR UNRELATED SPORADIC CASES .................................................................. 50 4.1: Abstract .................................................................................................................................................. 50 4.2: Introduction ............................................................................................................................................ 51 4.2.1: Limb reduction defects: ......................................................................................................................... 52 4.3: Subjects and methods ............................................................................................................................. 57 4.4: Results .................................................................................................................................................... 58 4.4.1: Subject A: Longitudinal deficiency of ulna with absence of postaxial fingers ........................................ 58 4.4.2: Subject B: Sever longitudinal deficiency of ulna with absent of certain fingers .................................... 60 4.4.3: Subject C: Complete longitudinal deficiency of ulna in left arm ............................................................ 61 4.4.4: Subject D: Terminal transverse deficiency of upper limb ...................................................................... 64 4.5: Discussion ............................................................................................................................................... 66 vi IV CHAPTER 5 5. CLINICAL AND MOLECULAR STUDY OF TWO INDEPENDENT FAMILIES WITH CENANI-LENZ SYNDACTYLY SYNDROME: ELUCIDATION OF PHENOTYPIC VARIABILITY AND IDENTIFICATION OF NOVEL MUTATIONS ........................................ 69 5.1: Abstract .................................................................................................................................................. 69 5.2: Introduction ............................................................................................................................................ 70 5.3: Subjects and methods ............................................................................................................................. 79 5.3.1: Families recruitment and their assessment ..........................................................................................
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