講義主題：資料科學與基因體研究的應用 講者資訊： 北醫大 臨藥所 周宛萱

1. Data Science in
Genome Studies
資料科學於基因
體研究的應用
PRESENTED BY 周宛萱 Wan-Hsuan (Ocean) Chou

2. About me
台北醫學大學臨床藥物基因體學暨蛋白質
體學碩士學位學程
Master Program for Clinical
Pharmacogenomics and
Pharmacoproteomics, TMU
台北醫學大學藥學系
College of Pharmacy, TMU
Research assistant, WCC
lab, Pharmacy Dept., TMU
Pharmacist
Secretary General, 2017
IPSF World Congress
Contact Person, PSA-Taiwan
Education Experiences
Pharmacy, Genomics, Data Science
German, International Affairs,
Public Affairs
Fields of interest

3. CONTENTS
基因體研究的簡介與發展
大型基因體研究與生物資料庫
基因體研究的未來趨勢
資料科學學習心得與資源分享
1
2
3
4

4. PART ONE
基因體研究的簡
介與發展

5. 基因體研究近代簡史
“Nuclein”
1871
Double helix DNA
1953
Sanger sequencing
1977
Friedrich Miescher, Switzerland
James Watson, USA
Francis Crick, UK
Frederick Sanger, UK
Virus genome“phiX174”

6. Human Genome Project
1990
2003-
Characterize all genes
ENCODE project
2003
Human
2010
Neanderthal
2002
Mouse
2005
Chimpanzee
2002-2005-2010
Human genetic variant pattern
International Hapmap Project
2008-2015-
Variants across ethnicities
1KGP
基因體研究近代簡史
1990-2003-
NIH; Celera co.(1998-)
1983
Location of
HTT gene
1995
H. Influenzae
1996
Yeast
1999
Human ch22
2000
Drosophila
2001
Draft of
Human genome
2013
Zebrafish
Eurobiobank
Victorian cancer biobank
Biobank
Japan
Taiwan Biobank
200K+100K
UK10K
4K+6K
Genomics England
100K
NHS + UKbiobank
500K
2010-
Genotype-tissue expression
GTEx project
2005-
Cancer genome
TCGA

7. PART TWO
大型基因體研究
與生物資料庫

8. Human Genome Project
2001
Drafts of Human Genome
2003
Complete of HGP
2009
GRCh37 ≈ hg19
2010
GRCh38 = hg38
Human Genome
“HGP’s goal is to determine the sequence of
nucleotide base pairs that make up human DNA.”
GRCh37 hg19
Genome Reference
Consortium (GRC)
UCSC Genome Browser
1, 2, 3, 4, ….X, Y, MT chr1, chr2, chr3,
chr4, …..chrX, chrY, chrM
MT: NC_012920 chrM: NC_001807

9. Hapmap Project
Phase 1 Phase 2 Phase 3
sample n 269 270 1115
populations 4
YRI, CEU, CHB, JPT
4
YRI, CEU, CHB, JPT
11
YRI, CEU, CHB, JPT
ASW, CHD, GIH, LWK
MEX, MKK, TSI
center Hapmap International
Consortium
Perlegen Broad & Sanger
SNPs n 1.1 M 3.8 M (phase 1+2) 1.6 M
publication Nature. 2005 Oct
27;437(7063):1299-320.
Nature. 2007 Oct
18;449(7164):851-61.
Nature. 2010 Sep
2;467(7311):52-8.
“Hapmap Project aimed to develop a haplotype map (HapMap) of the human
genome, to describe the common patterns of human genetic variation.”

10. ENCODE Project
“Encyclopedia of DNA Elements”
“ENCODE Project aimed to identify functional
elements in the human genome.”

11. TCGA
• RNA-Seq
• WXS
• miRNA-Seq
• Genotyping array
• Methylation array
• Diagnostic slide
• Tissue slide
• ATAC-Seq
• WGS
• Targeted sequencing
Experiments
• Sequencing reads
• Single nucleotide variation
• Clinical
• Biospecimen
• Transcriptome profiling
• Copy number variation
• DNA methylation
Data

12. 1KGP
“extensive catalog of human genetic variation”
“Extension of the International HapMap Project”
Hapmap Project 1KGP
Release 2010 2015
Technology genotyping Whole genome sequencing
Sample number 1115 2504
populations 11
YRI, CEU, CHB, JPT
ASW, CHD, GIH, LWK
MEX, MKK, TSI
26
ASW, ACB, BEB, GBR, CDX, CLM,
ESN, FIN, GWD, GIH, CHB, CHS, IBS,
ITU, JPT, KHV, LWK, MSL, MXL, PEL,
PUR, PJL, STU, TSI, YRI, CEU

13. GTex Project
“Genotype-Tissue Expression (GTEx) project”

14. 人體生物資料庫
• Governments
• Research institutes
• Hospitals
• Biotech companies/ pharma
Biobank owners
Biobanks Worldwide (2015)
317+
4
14
23
90
186
0
50
100
150
200
middle
east
oceania asia europe north
america
count

15. PART THREE
基因體研究的未
來趨勢

16. Biobank
Publication
Market value
Nature Biotechnology 30, 141-147 (2012)
Dove Press 2, 29-42 (2014)

17. Multi-Omics
Nature Rev Genet 16, 85 (2015)
RNA-seq Methylation miRNA-seq
Machine learning
Clin Cancer Res. 15;24(6):1248-1259 (2018)
Functional analysis

18. Clinical application
Clin Cancer Res. 1;23(11):2630-2639 (2017)

19. Single-cell genomics
Bulky Single-cell

20. PART FOUR
資料科學學習心
得與資源分享

21. DATACAMP
• R
• Python
• SQL
Technology
• Career track
• Skill track
Track
• Git
• Shell
• Spreadsheet
“DataCamp offers interactive R, Python, Sheets,
SQL and shell courses. All on topics in data
science, statistics and machine learning. ”

22. 機器學習百日馬拉松
• Thematic Learning
• Python
• Jupyter notebook
• Github
• Kaggle
• CPU/ GPU
• Community (Q&A)
• Online lessons
• Onsite lessons
Features
1. 資料清理數據前處理
2. 資料科學特徵工程技術
3. 機器學習基礎模型建立
4. 機器學習調整參數
5. 非監督式機器學習
6. 深度學習理論與實作
7. 初探深度學習使用 Keras
8. 深度學習應用卷積神經網路
9. Bonus 進階補充
Themes

23. KAGGLE
• Problem-based learning
• Data resources
• Cooperation
• Competitions
Features
“Kaggle is an online community of data scientists
and machine learners. ”

24. Workshops
GATK workshop (國網中心)
EPIDEMIOLOGY GENOMICS (中研院)
Workshops

25. 資料科學學習心得
Discussion
Learning material Data resource
Practice

26. THANKS
FOR YOUR
LISTENING
PRESENTED BY 周宛萱 Wan-Hsuan (Ocean) Chou
ocean.chou@tmu.edu.tw
感謝聆聽