Association study of HABP2 polymorphisms and discovery of pathogenic variants by whole exome sequencing in idiopathic recurrent pregnancy loss Jeong Yong Lee Major in Biomedical Science

다국어 초록 (Multilingual Abstract)

Association study of HABP2 polymorphisms and discover of pathogenic variants by whole exome sequencing in idiopathic recurrent pregnancy loss Jeong Yong Lee Department of Life science The Graduate school CHA University (Directed by Professor Nam Keun Kim) Idiopathic recurrent pregnancy loss is defined as at least two pregnancy losses before 20 weeks gestation. About 5 percent pregnant couple experiences. Idiopathic recurrent pregnancy loss are heterogenous disease that various cause such as hormone, abnormal chromosome and intrauterine abnormalities. Although how occur pregnancy loss still unknown and number of biological factors are associated with incidence of pregnancy loss including genetic variants. Whole exome sequencing has conducted by 56 Korean patients of recurrent pregnancy loss and 40 healthy controls DNA from blood samples. Whole exome sequencing data were aligned by bioinformatic analysis and detected variants are annotated by additional machine learning tools which is predict pathogenicity can cause protein alteration. Each variant that filtered are confirmed by Sanger sequencing. We use VEST, CADD and SIFT for annotating tool and various database to detect potential variants. We screened 10 potential variants associated with spontaneous abortion genes in Korean 56 patients by WES bioinformatics analysis. Several positions are detected more than one patient. Detecting genes are associated functionally clustered with secreted function (MUC4; rs200737893, HABP2; rs542838125) and GAS2L2(rs140842796), DNM2(rs763894364) genes are functionally associated with cell projection and cytoskeleton. ABCC6, rs758166222 is the only position that screened two individuals in whole exome sequencing. We genotype six HABP2 polymorphisms and rs2240879 is significantly differences between RPL patients and controls and more than 2 times pregnancy loss experienced patients are differences compared with controls. Also in synergistic effect, hormone level, E2, FSH, TSH are associated with HABP2 polymorphisms and coagulation parameter, PT and aPTT levels are related with HABP2 genotypes. In ANOVA analysis aPTT level change depend on rs3832698 A>del genotype. According to statistical analysis revealed that HABP2 polymorphisms are affect coagulation pathway. Combining whole exome sequencing and machine learning tools are useful tool for potential variants in recurrent pregnancy loss. Using bioinformatic tools, we found 10 potential variants in 9 genes. And genotype HABP2 polymorphisms that understand HABP2 affect coagulation pathway. These whole exome sequencing data in patients are need to understand better for cause RPL.
Keywords : Hyaluronan-binding protein 2, Single nucleotide polymorphisms, bioinfomatics, Factor seven activating protease, Pregnancy, Coagulation, Deep learning

목차 (Table of Contents)

• ACKNOWLEDGEMENTS ⅰ
• TABLE OF CONTENTS ⅱ
• LIST OF TABLES · iv
• LIST OF FIGURES vi
• ABSTRACT viii
• Ⅰ. INTRODUCTION 1
• Ⅱ. MATERIALS AND METHODS 5
• 1. study population 5
• 2 .Annotation and variants filtering · 6
• 3. Additional annotation for potential variants 8
• 4. Validation 9
• 5. Genotyping 11
• 6. Replication of patients and control sample validation 11
• 7. Statistical Analysis 14
• Ⅲ. RESULTS 15
• 1. Bioinformatic analysis by Whole exome sequencing with RPL related gene · 15
• 2. Bioinformatic analysis by Whole exome sequencing with not RPL related gene · 17
• 3. Replication of patients and control sample validation 19
• 4 Characteristics of the Study Population 21
• 5. Genotype analysis of RPL and controls 23
• 6. Genotype combination analysis of polymorphisms with synergistic effects 26
• 7. Haplotype Analysis of Polymorphisms with Synergistic Effects · 28
• 8. Stratified analysis of HABP2 gene and clinical parameter · 32
• 9. Interaction Analysis between Genes and Clinical Factors 37
• 10. One way analysis of variance between clinical parameter and each HABP2
• polymorphisms 49
• Ⅳ. DISCUSSION 68
• Ⅴ. CONCLUSION 80
• REFERENCES · 81
• ⅤI. APPENDIX 93
• ABSTRACT IN KOREAN 157

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