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RarePedia: A tool that integrates scattered information about rare-damaging variants : 레어피디아 : 희귀 손상 변이에 대한 산재된 정보를 통합하는 도구

DC Field Value Language
dc.contributor.advisor김주한-
dc.contributor.author송유림-
dc.date.accessioned2018-12-03T01:50:37Z-
dc.date.available2018-12-03T01:50:37Z-
dc.date.issued2018-08-
dc.identifier.other000000153286-
dc.identifier.urihttps://hdl.handle.net/10371/144073-
dc.description학위논문 (석사)-- 서울대학교 대학원 : 자연과학대학 협동과정 생물정보학전공, 2018. 8. 김주한.-
dc.description.abstractFinding causal factors of various diseases, whether they be environmental factors, stress, aging, and etc. has been the focus of many researchers around the globe. As advancements in science and technology were made, many disease-related genes and mechanisms have been discovered. With the development of DNA sequencing techniques, the sequences of disease-associated genes and specific disease-related genetic variants are being revealed. However, variants that occur at very low frequencies are often ignored, seemingly because there is little known information about these rare variants, which in turn makes rare variant analyses difficult without increasing the sample size.

RarePedia was designed to make a unified collection of information about rare variants. Furthermore, it focuses on deleterious variants that are expected to be related to diseases. RarePedia is another way to use Next Generation Sequencing(NGS) data, and a helpful tool to see organized information previously scattered across many sources.

The ultimate goal of RarePedia is the accumulation of information through additional updates, whenever there is new information about rare and deleterious variants. It can be a way to organize information about rare and deleterious variants that have not been organized systematically.
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dc.description.tableofcontents1. INTRODUCTION 1

2. DATA 3

2.1. Next Generation Sequencing(NGS) data 3

2.1.1. 1000 Genomes Project data 3

2.1.2. Alzheimer's Disease Sequencing Project (ADSP) data 3

2.2. Databases and Resources 4

2.2.1. Databases prepared by ANNOVAR developers 4

2.2.2. Resources used by Oncotator 5

2.2.3. Additional publicly available resources 5

3. METHODS 8

3.1. Filtering scheme for extraction of rare-damaging variants 8

3.1.1. Analysis focused on variants 8

3.1.2. Analysis focused on genes 9

3.2. Annotation of information 10

3.2.1. Annotation with ANNOVAR 10

3.2.2. Annotation with Oncotator 10

3.3. Generation of HTML pages about rare-damaging variants 10

3.4. Validation with publicly available Next Generation Sequencing(NGS) data 11

3.4.1. Statistics from 1000 Genomes Project data 11

3.4.2. Statistics from Alzheimer's Disease Sequencing Project(ADSP) data 11

4. RESULT 13

4.1. Statistics about rare-damaging variants from Next Generation Sequencing(NGS) data 13

4.1.1. Statistics from 1000 Genomes Project data 13

4.1.2. Statistics from Alzheimer's Disease Sequencing Project(ADSP) data 13

4.1.3. Additional Whole Exome Sequencing(WXS) data 14

4.1.4. ClinVar information about variants 14

4.2. Information contained in the HTML page generated by RarePedia 15

5. DISCUSSION 17

6. REFERENCE 20

ABSTRACT(KOREAN) 59
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dc.formatapplication/pdf-
dc.format.mediumapplication/pdf-
dc.language.isoen-
dc.publisher서울대학교 대학원-
dc.subject.ddc574.8732-
dc.titleRarePedia: A tool that integrates scattered information about rare-damaging variants-
dc.title.alternative레어피디아 : 희귀 손상 변이에 대한 산재된 정보를 통합하는 도구-
dc.typeThesis-
dc.contributor.AlternativeAuthorSong Yurim-
dc.description.degreeMaster-
dc.contributor.affiliation자연과학대학 협동과정 생물정보학전공-
dc.date.awarded2018-08-
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