genomics dual factors for physical lifecontents.kocw.or.kr/document/wcu/2012/bio_data... · 2007:...
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Genomics Dual Factors for Physical Life◦ Genetic factors for systems healthcare◦ Acquired factors for systems healthcare
Opportunities and Challenges
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Anatomy Microscope/Cell Biology Molecular Biology
Bioinformatics and Systems Biology
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Personal Physical Life = f (Nature, Nurture)Nature: Genes – Personal Genome Project
Nurture: Environment, Food, Exercise, Medication, …
Data Collection Data Mining Understanding/Prediction
G1 G2 … … Gp E1 E2 … … Eq L1 L2 … … Lr
P1
……Pm
Feature SelectionModel-Based Data MiningNew Approaches ?
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1 SNP in every 2kb of genomic sequences Synonymous vs. non-synonymous SNP
1….ATCCTGTACCTACGTGTACAATAGTA…..CTGATCATCTCTATGGG….2….ATCCTGTTCCTACGTGTACAATAGTA….. CTGATCATCTCTATGGG….3….ATCCTGTACCTACGTGTACAATAGTA…..CTGATCAGCTCTATGGG….
1 2 3
SNP1 SNP2
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1G: Sanger
2G: Parallel
3G: Single Molecule
4G: Non-optical
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Human Genome Project Consortium◦ 1990 ~ 2005 (16 years), US$ 3 billion (3조원)◦ Haploid from many anonymous donors (cf. RP11, a male from Buffalo, NY)
Celera Genomics◦ 1998 ~ 2005 (8 yrs), US$ 300 million (3천억원)◦ Consensus from five anonymous donors (including Craig Ventor)
2007: Market, US$ 20 million (2백억원) 2007: Knome, US$ 350,000 (3억5천만원) for diploid sequencing 2009: US$ 100,000 (1억원) – NIH RFP Objective 2011: US$ 20,000 (2천만원) – George Church’s prediction 2014: US$ 1,000 (1백만원) – NIH RFP Objective
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6,099 GWAS studies as of Sep. 6, 201114
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Pharmacogenomics
DNA(SNP) chip
Cf. HER2 Overexpress, Herceptin, Genentech, 199815
Disease risk assessment for 119 diseases◦ Clinical Reports (33) BRCA Cancer Mutations, Celiac Disease (소아지방변증) Diabetes, Parkinson’s Disease, Prostate Cancer, Rheumatoid Arthritis,
Resistance to HIV/AIDS, and so on◦ Research Reports (86) Asthma, Baldness, Bipolar Disorder, Breast Cancer, Food Preference,
Height, Longevity, Memory, Obesity … Ancestry tracking => New International Social networks?◦ Maternal line with mitochondrial DNA◦ Paternal line with Y chromosome
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Interleukin Genetics, Inc. & Amway Global Cost: US$ 100~200 / per kit1. Kit-based sampling from oral cavity2. SBE(Single Base Extension)-based detection of
SNP markers3. Bioinformatics analysis for SNP-to-trait mapping4. Recommendation for nutrition, exercise, and
medication
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Genomic sequences from whole genome parallel sequencing
Image from the sequencing machines (usually discarded after processing)
Raw sequence reads: ~300GB Genome-mapped sequences: ~300GB Binary compressed sequences: ~150GB Intermediate results: ~300GB Over 1TB/sample 1000 Genome => 1PB
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(3 x 109) bp x 30 rd x 3 = ~ 3 x 1011 bytes = ~ 300GB
@HWI-ST621:206:B0202ACXX:1:1101:1216:2021 1:Y:0:ATCACG TitleNTTTANNNNTGAATNNTGTCAAAATTACAGAAGAACTGCAAGAATATCACATGGTACACTCATACAATCTCCACCCANANNNNNNNNNNNNNNNNNTTTGC Base+ Comment##################################################################################################### Base quality@HWI-ST621:206:B0202ACXX:1:1101:1116:2024 1:Y:0:ATCACGNCTTNNNNNCACAGNNTTTAACCTTTCTTTTCTTAGAGCACTTTAGAAACACTCTGCTTGTTATGTCTGCAAGTGGANANNNNNNNNNNNNNNNNNCCTTC+#####################################################################################################
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HWI-ST621:206:B0202ACXX:1:1101:1128:2173 147 chr1 81092578 60 101M = 81092212 -467 AGGGCAGAATACCGTATCCTTGGAAAATTAAATAGTAAGAGGAGAGAGGCTTCAGTGGCAGACCATTCGGAAAGTGTGGGGAAATCCAGGAAGGAAAGTAN ##################################################################################################### XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:100G0HWI-ST621:206:B0202ACXX:1:1101:1022:2177 73 chr3 110819717 37 101M = 110819717 0 NTCCNTTTTCATGCTGCTGATAAAGACATAGCTGAGACTGGGTAATTAAAAAAAAAAGCGGTTTAATGAACTCACAGTTTCACATGGCTGGGGGGGGCTCA ##################################################################################################### XT:A:U NM:i:4 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:0G3A88A2C4
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Clockwork Business Solutions ©
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EDI (Electronic Data Interchange) OCS (Order Communication System) LIS (Laboratory Information System) PACS (Picture Archiving and Communication System) PIS (Pharmacy Information System) CIS (Clinical Information System) EMR (Electronic Medical Records) PHR (Personal Health Records) Etc…
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Molecular snapshots◦ Transcriptomics◦ Proteomics◦ Metabolomics
Electronics Medical Records PACS images Life log Etc…
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Gene1 Gene2 Gene3 Gene4Genome
Transcriptome mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1
mRNA1mRNA1mRNA2mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1mRNA4
Proteome mRNA1Protein1 mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1Protein4
mRNA1mRNA1mRNA1mRNA1mRNA1Protein2’
Transcriptional Regulation
Translational Regulation, Post-translational modification
mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1mRNA1Protein2
Metabolome
Metabolic Regulation
Metabolite-A Metabolite-B Metabolite-C
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A large number of structured tables with text-based fields Different schema for different organizations, cf. HL7 Security and privacy is extremely critical
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High resolution images with structured meta data
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Body composition analyzerTask: Body balance inspection Application: Wellness & fitness programCost: $ 2K
SNP genotypingTask: Individual genetic variation detection in single nucleotide polymorphismApplication: Disease prognosisCost: $ 5K
Expression profiling chipTask: Individual genomic response inspection Application:Disease prognosis (e.g. caner)Cost: $ 10K
Diabetes phoneTask:Measurement of glucose levelApplication: Diabetes, dietary managementCost: $ 400
Genomic profile
Physiologicalsignal
CNV genotypingTask: Individual genetic variation detection at copy number variationApplication: Disease prognosisCost: $ 1M
Healthcare bidetTask: Examination of user’s secretionApplication: Patient monitoring systemCost: $ 400
Diabetes watchTask: Measurement of glucose levelApplication: Diabetes, dietary managementCost: $ 100
PCR-based genetic diagnosisTask: Detection of genetic disease and predisposition to a diseaseApplication: Disease prognosisCost: $ 10K
Life shirtTask: Monitor vital signals (respiration flow, heart rate, sweat) Application:Patient monitoring systemCost: $ 2K
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Yahoo
Overture => Yahoo
Amazon
Auction
Nexon
Blizzard
YouTube
Much more …
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Medical History Health Information
Comprehensive at-home DNA test
NavigenicsNavigenicsRevealing genetic predisposition
Managing health information
Healthcare software solutions
Making personal genetics
23 and me23 and me
Helix HealthHelix Health
deCODEmedeCODEme
Scanning Traits & Disease Tracing Ancestry Features
Microsoft Health VaultMicrosoft Health Vault
Patient ManagementPersonalized Prevention Family History
Complete Scan Cardio Scan Cancer Scan
Nursing Home Application
YOU40
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Data Acquisition Data Mining Information DeliveryPersonal Genomes
- Cheap Sequencing- Accurate Annotation
Personal Life Logging- EMR- Food, Exercise, ..
ULDB- Cloud computing
ULDM- Extreme bias on SV ratio- Dynamic and noisy- Incremental
Biomedical Information Models- Ultra-scale- Multi-level- Multi-precision- Multi-modality
Mobile interactionRecommendationPoint-on-treatments…
Scientific Aspects
Industrial AspectsCreative Business Models
(1) Utilizing existing resources(2) Timely join to new emerging markets(3) Accumulating intellectual properties
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