My Project
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![Page 1: My Project](https://reader031.fdocument.pub/reader031/viewer/2022012922/554bcd28b4c905706a8b48cd/html5/thumbnails/1.jpg)
유전자 데이터 다루기광우병에서구글까지
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전문가가 되어버리다
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M/MMethionine=Met , Valine = Val
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영국인 은 40%한국 사람은 95%
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gtg/atg
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dbSNP
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단지 하나 차이일뿐인데...
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단일염기 다형성(SNP, Single Nucleotide
Polymorphism)
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모두 23쌍의 염색체를 지님인간은 누구나 서로 99.9%의 유전정보가 동일
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한 인구집단의 유전체에서 1% 이상의 빈도를 보이는 염기서열의 변이
대머리의 56%가 가족력 존재
22%가 유당분해효소 결핍증44%가 귓볼 존재 알츠하이머의 19%가 가족력 존재
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30억 염기쌍이라는 거대한 책의 색인을 작성
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인간 유전체 연구
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여자 3명, 남자 2명의 DNA 샘플을 시작으로 휴먼지놈프로
젝트 시작
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영국, 미국, 캐나다, 일본, 나이지리아 및 중국에서 약 200여 과학자들
아시아, 아프리카 및 미국에서 약 269명의 DNA표본을 이용
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1000명 유전체 프로젝트(1000 Genomes Project)
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한국인 만명에 대한...
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2003년 휴먼지놈프로젝트 $27억2004년 크레이그 벤터 박사 $1억2008년 왓슨 박사 $100만
5년후 $100
-MIT Technology Review 2008년 4월 17일 뉴스-
30억 염기서열 쌍이라는 대용량 데이터 생산과 분석이 현실
다른 오믹스(단백체, 발현체, 대사체 등) 정보와의 통합 분석을 구현할 시점
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점점 커져가는데...
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대량의 연구를 빠른 시간에...
SequencingMicroarrays
High throughput GenotypingPowerful ComputationLab Automation
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생물학 데이터에 대해서
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•1차원 배열 형태의 서열 데이터•다차원 배열 형태의 구조 데이터•매트릭스 형태의 발현 데이터•네트워크 형태의 상호작용 데이터•문서 형태의 텍스트 데이터
자료구조 관점
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서열 데이터DNA, RNA 등의 유전체 데이터
EST서열SNP 데이터
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구조 데이터단백질 3차 구조 데이터질량분석기 데이터
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발현 데이터마이크로어레이 데이터
array CGHChIP-chip
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네트워크 형태pathway
protein interaction
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텍스트 데이터논문, 문헌정보
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유전체 연구
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DatabaseHardware
Agent
Machine LearningAlgorithm
InformationRetrieval
IT와 유전체 연구
Genomic Variation Research
Personalized Medicine
GeneBankSWISS-PROT
Super ComputerCluster
ClusteringPattern recognition
Classfication
Sequence alignment
Biomedical text analysis
Information filteringMonitoring agent
Personal Genome
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Sequence Alignment-Simulated Annealing-Genetic Algorithms
Structure and Function Prediction-Hidden Markov Models-Multilayer Perceptrons-Decision Trees
Molecular Clustering and Classification
-Support Vector Machines-Nearest Neighbor Algorithms
Expression Analysis-Self-Organizing Maps-Bayesian Networks
Machine Learning
Toby SegaranBiotech software company
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Sequence Search with MPI
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GPU를 이용한 병렬 서열 정렬
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웹서비스를 이용한 생물학 매쉬업(Taverna, Myexperiment)
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컴퓨팅 파워 제공(Folding@Home, Korea@Home)
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집단지성을 이용한 퍼즐 맞추기 - foldit
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시맨틱웹(FreeBase)
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유전체 연구 플랫폼
50만개의 SNP Porbe를 포함하고 있는 Affymetrix Genome-Wide Human SNP Assay 5.0
고밀도 SNP array
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Multidimensional Scaling(MDS)북부및서유럽(CEU), 나이지라아계열(YRI), 일본계(JPT), 중국한족(CHB)
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한국인 SNP2,978개의 유전자에 대한12,995개의 SNP
KARE로 생산된 9,603명(Genotype 데이터 18GB)후속 13,000명 생산중
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임상, 역학 데이터
12개 질환군별 센터(심혈관, 뇌신경질환, 당뇨, 피부, 불임, 선천성 기형 등등)안산(대도시), 안성(농촌) 코호
트 등등
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질병 관련 연관성 연구
정상, 환자의 시료를 이용한 표현형(phenotype)에 연관된 SNP 발굴
질환가계 및 질환형제자매를 이용한 연구
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역학 정보 변수
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KSNP(Korean SNP) Browser
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질병 예측
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Genome Browser with Google Maps API
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BioBlogRSS: 전세계의 생물학 블로거
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모든것은 바로 컴퓨터의 힘!SimulationData AnalysisData AcquisitionData ManagementData Archiving
->Scientific Results, PublicationData Integration
Knowledge ManagementCollaboration
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유전체센터의 컴퓨팅파워
18 Node IA2 Cluster 32 Node X86 Cluster
100 Node PPC Cluster
NAS, DAS Storage
Workstation
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해결 해야 할 문제점
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단일 플랫폼
Capacity & Size 증가데이터 생산의 가속화
데이터 부족
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다중 플랫폼
비용 문제지리적 문제
협업을 통한 시너지 창출컴퓨팅 리소스
누구도 접근해보지 못한
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...ATTAGGACCAATAAGTCT...
...ATTAGGAGCAATAAGTCT...
...ATTAGGAGCAATAACTCT...
...ATTAGGAGCAATAAGTCT...
Person 1 +
Person 2 -
Single locus Pair of locii
(+,-)Cost = 0.5M x 5k x 10k
(+,-)Cost = 1/2 x 0.5M x 0.5M x 5k x 10k
0.5M SNP, cohort of 5K individuals, 10k random data set
1 day 120 yr
Computational problem
Text
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기상청
지역별 관측소 자료 + 작년도 오늘 날씨 =
내일 비올 확률 40%
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Realistic Solution
머리카락 + 몸무게 + 키 + 음주습관=
다음주 당뇨
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구글과 생명 공학의 만남
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Google Health BETA
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SNP 정보
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유전자 정보
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나는 누구인가?
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얼마나 유사한가?
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원하는것은?
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Google 검색엔진 -> Google 플랫폼Nutch 검색엔진 -> Hadoop 플랫폼
분석도구의 손쉬운 접근새로운 알고리즘의 개발과 적용대용량의 데이터의 접근
->생물학 데이터 처리를 위한 플랫폼
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플랫폼 그 이상의 플랫폼
모든 연구자들이 아무런 댓가 없이자신의 연구를 수행하고
서로의 의견을 교류 할 수 있는 그런...
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!"#$%&'()*!'+,-.#&!"#"$%&"'()*&$+,-.#/,'(
/++0122"3#4-!'5*"#$%&'(-(*+
!"0*$1,.23"'
4.*(#/,'(5Questions?
Hong ChangBumCenter for Genome ScienceNIH, [email protected]://socmaster.homelinux.org/~hongiiv