A Bioinformatic Pipeline For Detecting Genetic Risk Factors With Clinical Significance: A Personalized Medicine Approach / Elsayed Abdelaal Elsayed

Supervisor: Mohamed A. El-Helw

Thesis (M.A.)—Nile University, Egypt, 2018 .

"Includes bibliographical references"

Contents:
Chapter 1 Introduction and Background ................................................................................. 12
1.1 Bioinformatics definition ...................................................................................... 12
1.2 Sequencing History and techniques ..................................................................... 12
1.2.1 First Generation Technologies ................................................................... 15
1.2.2 Next Generation Sequencing (NGS) Techniques ....................................... 17
1.2.3 Next generation Sequencing Applications ................................................. 21
1.3 Personalized Medicine ......................................................................................... 23
1.3.1 Personal Genome ....................................................................................... 25
1.3.2 Personalized Medicine in Oncology ........................................................... 34
1.4 NGS data analysis pipeline ................................................................................... 37
1.5 Pharmacogenomics .............................................................................................. 40
1.6 Bioinformatics and Personalized Medicine .......................................................... 42
1.6.1 Bioinformatics Solutions supports Precision Medicine ............................. 43
1.6.2 Bioinformatics Challenges in Personalized Medicine ................................ 44
1.7 Our work in the Egyptian Genomes ..................................................................... 45
1.8 Useful tools and their links ................................................................................... 45
1.9 Next Generation Sequencing algorithms ............................................................. 48
Chapter 2 Literature Survey .................................................................................................... 49
Chapter 3 Methodology .......................................................................................................... 53
3.1 Study group and ethical approval ........................................................................ 53
3.2 Clinical characteristics of study group .................................................................. 53
3.3 Raw reads statistics .............................................................................................. 54
3.4 Biochemical Analysis ............................................................................................ 55
3.4.1 Sample collection, DNA isolation and whole genome sequencing ............ 55
3.5 Bioinformatics analysis ......................................................................................... 55
3.5.1 Raw Reads concatenation .......................................................................... 58
3.5.2 Quality Control ........................................................................................... 58
3.5.3 Alignment of reads to reference ................................................................ 58
3.5.4 Variant Calling & SNPs identification ......................................................... 59
3.5.5 Annotation and functional analysis of variants ......................................... 59
7
3.5.6 SNPs filtration ............................................................................................ 60
3.5.7 Novel SNPs counting .................................................................................. 60
Chapter 4 Results and Findings ............................................................................................... 61
4.1 Statistics ............................................................................................................... 61
4.2 Candidate genes ................................................................................................... 61
4.3 Variants analysis ................................................................................................... 67
Chapter 5 Discussion ............................................................................................................... 73
5.1 Sample 1 (EGY1) ................................................................................................... 73
5.2 Sample 2 (EGY2) ................................................................................................... 74
5.3 Sample 3 (EGY3) ................................................................................................... 74
5.4 Sample 4 (EGY4) ................................................................................................... 75
5.5 Sample 5 (EGY5) ................................................................................................... 75
5.6 Sample 6 (EGY6) ................................................................................................... 76
5.7 Sample 7 (EGY7) ................................................................................................... 76
5.8 Sample 8 (EGY8) ................................................................................................... 77
5.9 Sample 9 (EGY9) ................................................................................................... 77
Chapter 6 Conclusion and Future work ..........

Abstract:
Personalized medicine is the new revolution which may replace the traditional medicine in the upcoming years. In the present study we use Bioinformatics technologies and tools which gives a dozen of facilities to improve our understanding to everyone problem with more specific and customized tools points to the exact specific mutation present in individuals and clinical correlation.
A totally nine sample collected from Egyptian females was aged 41±14.35 years old. A clinical examination was conducted for each of them; weight, height (Ht) and waist circumference (WC) were measured. Body mass index (BMI) was calculated according to WHO. Blood pressure was measured for each individual. According to manufacturer's protocol. DNA Library preparation was performed agreeing with the manufacturer’s instructions for sequencing on HiSeq2000 (Illumina, San Diego, CA, USA). For demultiplexing and conversion to FASTQ format, CASAVA 1.8.2 (Illumina) was used. Also, raw data have been submitted to the Sequence Read Archive under the overarching accession number SRP136979.
We got and identify candidate genes and variants associated with obesity, T2D, metabolic syndrome and tumors for example EGY1 we found the mutations rs1801265, rs72478580, rs351855, rs846664 and rs17261572 associated with conditions Dihydropyrimidine dehydrogenase deficiency, Multiple fibroadenomas of the breast, Cancer progression and tumor cell motility, Beta-Glucopyranoside Tasting or Alcoholism addiction risk and Polyagglutinable erythrocyte syndrome in respective order.
In this study we reported clinically significant variants for each subject with associated condition. These findings give a helpful recommendation to improve the quality of life and early detection of suspected diseases and follow up prophylactic plan. The availability of this complete nine Egyptian genomes and variants allow further aid studies aimed to understanding genetic diversity, identifying clinically relevant changes and assessing disease burden in the Egyptian population.

Text in English, abstracts in English.