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DataMapto

Reference

GenomeMapto

Reference

GenomeIdentification

of

VariantsAnnotationAnnotationNCBI

Database

centralized

pageBioProject

(formerly

Genome

Project)

A

collection

of

genomics,

functionalgenomics,

and

genetics

studies

and

links

to

their

resulting

datasets.

This

resourcedescribes

project

scope,

material,

and

objectives

and

provides

a

mechanism

toretrieve

datasets

that

are

often

difficult

to

find

due

to

inconsistent

annotation,

multipleindependent

submissions,

and

the

varied

nature

of

diverse

data

types

which

are

oftenstored

in

different

databases.GenBank

The

NIH

genetic

sequence

database,

an

annotated

collection

of

all

publiclyavailable

DNA

sequences.

GenBank

is

part

of

the

International

Nucleotide

SequenceDatabase

Collaboration,

which

comprises

the

DNA

DataBank

of

Japan

(DDBJ),

theEuropean

Molecular

Biology

Laboratory

(EMBL),

and

GenBank

at

NCBI.

These

threeanizations

exchange

data

on

a

daily

basis.

GenBank

consists

of

several

divisions,most

of

which

can

be

accessed

through

the

Nucleotide

database.

The

exceptions

arethe

EST

and

GSS

divisions,

which

are

accessed

through

the

Nucleotide

EST

andNucleotide

GSS

databases,

respectively.Computational

Resources

from

NCBI‘s

Structure

Group

A

centralized

page

providingaccess

and

links

to

resources

developed

by

the

Structure

Group

of

the

NCBIComputational

Biology

Branch

(CBB).

These

resources

cover

databases

and

tools

tohelp

inthe

study

of

macromolecular

structures,

conserved s

andproteinclassification,

small

molecules

and

their

biological

activity,

and

biological

pathwaysand

systems.NCBI

Database:

GenomeGenome

Contains

sequence

and

map

data

from

the

wholegenomes

of

over

1000 anisms.

T omes

represent

bothcomple y

sequencedin

progress.

All

three

mainanisms

and

those

for

which

sequencing

iss

of

life(bacteria,archaea

［考古es,］,

and

eukaryota)

are

represented,

as

well

as

manyphages,

viroids,

plasmids,

and

anelles.Genome

Reference

Consortium

(GRC)T ome

Reference

Consortium

(GRC)

maintains

responsibilityfor

the

human

and

mouse

reference

genomes.

Members

consist

of

T ome

Center

at

Washington

University,

the e

TrustSanger

Institute,

the

European

Bioinformatics

Institute

(EBI)

and

theNational

Center

for

Biotechnology

Information

(NCBI).

The

GRCworks

to

correct

misrepresented

loci

and

to

close

remainingassembly

gaps.

In

addition,

the

GRC

seeks

to

providealternateassemblies

for

complex

or

structurally

variant

genomic

loci.

At

theGRC

website

( ),

the

publiccan

viewgenomic

regions

currently

under

review,

report

genome-relatedproblems

and

contact

the

GRC.NCBI

Database:

GeneGene

A

searchable

database

ofgenes,

focusing

on

genomes

that

havebeen

comple y

sequenced

and

that

have

an

active

research

community

tocontribute

gene-specific

data.

Information

includes

nomenclature,chromosomal

localization,

gene

products

and

their

attributes

(e.g.,proteininteractions),

associated

markers,

phenotypes,

interactions,

and

linkstocitations,

sequences,

variation

details,

maps,

expression

reports,

homologs,protein

content,

and

externaldatabases.UniGene

A

database

that

provides

sets

of

transcript

sequences

thatappearto

come

from

the

same

transcription

locus

(gene

or

expressedpseudogene),

together

with

information

on

protein

similarities,

geneexpression,

cDNA

clone

reagents,

and

genomic

location.UniGene

Library

Browser

Thisdatabase

contains

libraries

of

ExpressedSequence

Tags

(ESTs) anized

by anism,

tissue

type

anddevelopmental

stage.UniSTS

A

comprehensive

database

ofsequence

tagged

sites(STSs)derived

from

STS-based

maps

and

other

experiments.

STSs

aredefinedbyPCR

primerpairs

and

are

associated

with

additional

information,

such

asgenomic

position,

genes,

and

sequences.•NCBI

Database:

nucleotide

sequencesNucleotide

Database

A

collection

ofnucleotide

sequences

from

severalsources,

including

GenBank,

RefSeq,

the

Third

Party

Annotation

(TPA)database,

andPDB.

Searching

theNucleotide

Database

will

yieldavailableresults

from

each

of

its

component

databases.RefSeqGene

A

collection

ofhuman

gene-specific

reference

genomicsequences.

RefSeq

gene

is

a

subsetof NCBI’s

RefSeq

database,

and

aredefined

based

on

review

from

curators

of

locus-specific

databases

and

thegenetic

testing

community.

They

form

a

stable

foundation

forreportingmutations,

for

establishing

consistent

intron

and

exon

numberingconventions,

and

for

defining

the

coordinates

of

otherbiologically

significantvariation.

RefSeqGene

isa

part

of

theLocus

Reference

Genomic

(LRG)Collaboration.Reference

Sequence

(RefSeq)A

collection

of

curated,

non-redundant

genomic

DNA,

transcript

(RNA),

andprotein

sequences

produced

byNCBI.

RefSeqs

provideastable

reference

f enome

annotation,

gene

identification

and

characterization,

mutationand

polymorphism ysis,

expression

studies,

and

comparative

yses.The

RefSeq

collection

is

accessed

through

the

Nucleotide

and

Proteindatabases.NCBI

Database:

Protein

sequencesProtein

ClustersA

collection

of

related

protein

sequences

(clusters),consistingof

Reference

Sequenceproteinsencodedbycomplete

prokaryotic

and anelle

plasmids

andgenomes.

The

database

provides

easy

access

toannotation

information,

publications,

s,structures,

external

links,

and ysis

tools.Protein

DatabaseA

database

that

includes

protein

sequence

recordsfroma

variety

of

sources,

including

GenPept,

RefSeq,

Swiss-Prot,

PIR,

PRF,and

PDB.StructuralysisGln406

of

KRT5

(Gln418ofKRT1)

located

at

the

‘g’

positionin

the

heptad

unitGln406

of

KRT5

(Gln418of

KRT1)

engaged

in

ahydrogen

bond

with

Lys352of

KRT14

(Lys386

ofKRT10).KRT5

carrying

the

Q406H(Q418H

for

KRT1)

mutationloses

the

hydrogen

bondinginteraction

with

Lys352

ofKRT14

(Lys386

of

KRT10)PalmoplantarkeratodermaNCBI

Database:

Gene

StructureConserved

Database

(CDD)

A

collection

of

sequencealignments

and

profiles

representing

protein s

conserved

inmolecular

evolution.

It

also

includes

alignments

of

the s

toknown

3-dimensional

protein

structures

in

the

MMDB

database.Database

of

Genomic

Structural

Variation

(dbVar)

The

dbVardatabase

has

been

developed

to

archive

information

associatedwith

large

scale

genomic

variation,

including

large

insertions,deletions,

translocations

and

inversions.

In

addition

to

archivingvariation

discovery,

dbVar

also

stores

associations

of

definedvariants

with

phenotype

information.Database

of

Genotypes

and

Phenotypes

(dbGaP)

An

archive

anddistribution

center

for

the

description

and

results

of

studies

whichinvestigate

the

interaction

of

genotype

and

phenotype.

These

studies

include

genome-wide

association

(GWAS),

medicalresequencing,

molecular

diagnostic

assays,

as

well

as

associationbetween

genotype

and

non-clinical

traits.NCBI

Database:

Structure

sequencesDatabase

of

Major

patibility

Complex

(dbMHC)

An

open,

publicly

accessibleplatform

where

the

HLA

community

can

submit,

edit,

view,

and

exchange

data

relatedto

thehuman

major

patibility

complex.

It

consists

of

an

interactive

AlignmentViewer

for

HLA

and

related

genes,

an

MHCmicrosa lite

database,

a

sequenceinterpretation

site

for

Sequencing

Based

Ty (SBT),

and

a

Primer/Probe

database.Database

of

Short

Genetic

Variations

(dbSNP)

Includes

single

nucleotidevariations,

microsa lites,

and

small-scale

insertions

and

deletions.

dbSontainspopulation-specific

frequency

and

genotype

data,

experimental

conditions,

molecularcontext,

and

map information

for

both

neutral

variations

and

clinical

mutations.Structure

(Molecular

Modeling

Database)

Contains

macromolecular

3D

structuresderived

from

the

Protein

Data

Bank,

as

well

as

tools

for

their

visualization

andcomparative

ysis.Epigenomics

This

resource

enables

users

to

explore

and

visualize

richly-annotatedepigenomics

datasets.

It

provides

a

unique

interface

to

search

and

navigateepigenomic

data

in

the

context

of

biological

sample

information,

as

well

as

tools

toselect,

download

and

view

multiple

sets

of

epigenomic

data

as

tracks

on

genomebrowsers.Database

of

Expressed

Sequence

Tags

(dbEST)

A

divison

of

GenBank

thatcontainsshort

single-pass

readsof

cDNA

(transcript)

sequences.

dbEST

can

be

searcheddirectly

through

the

Nucleotide

EST

Database.NCBI

Gene

Expression

DatabaseGene

Expression

Nervous

System

Atlas

(GENSAT)

Maps

the

expression

ofgenes

in

the

central

nervous

system

of

the

mouse,

using

both

in

situhybridization

and

transgenic

mouse

techniques.

T SATdatabasecontains

a

series

of

images

related

to

gene

expression

experiments.Gene

Expression

Omnibus

(GEO)

Database

A

public

functional

genomicsdata

repository

supporting pliantdata

submissions.

Array-

andsequence-based

data

are

accepted

and

tools

are

provided

to

help

usersquery

anddownload

experiments

and

curated

gene

expressionprofiles.Gene

Expression

Omnibus

(GEO)

Datasets

Stores

curated

geneexpression

and

molecular

abundance

DataSetsassembled

from

teExpression

Omnibus

(GEO)

repository.

DataSet

records

contain

additionalresources,

including

cluster

tools

and

differential

expression

queries.Gene

Expression

Omnibus

(GEO)

Profiles

Stores

individual

geneexpression

and

molecular

abundance

Profiles

assembled

from

t

eExpressionOmnibus

(GEO)

repository.

Search

for

specific

profiles

ofinterest

based

on

gene

annotation

or puted

profilecharacteristics.Database

of

Expressed

Sequence

Tags

(dbEST)

A

divison

of

GenBankthatcontains

short

single-pass

reads

of

cDNA

(transcript)

sequences.

dbESTcan

be

searched

directly

through

the

Nucleotide

EST

Database.NCBI

Clinical

DatabaseOnline

Mendelian

Inheritance

in

Man

(OMIM)

A

database

of

humangenes

and

genetic

disorders.

NCBI

maintains

current

content

and

continuesto

support

its

searching

and

integration

with

other

NCBIdatabases.

However,

OMIM

now

has

a

new

home

at

omim.

,

and

usersare

directed

to

this

site

for

full

record

displays.GeneReviews

A

collection

of

expert-authored,

peer-revieweddiseasedescriptions

on

the

NCBI

Bookshelf

thatapply

genetic

testing

to

thediagnosis,

management,

and

genetic

counseling

of

patients

andfamilieswith

specific

inherited

conditions.GeneTests

A

publicly

funded

medical

genetics

information

resourcedeveloped

for

physicians,

other

healthcare

providers,

and

researchers,available

at

no

cost

to

allinterested

s.Cancer

Chromosomes

A

compilation

ofdata

from

three

sources:

theNCI/NCBISKY/M-FISH

and

CGH

Database,

the

NCI

Mi man

Database

ofChromosome

Aberrations

in

Cancer,

and

the

NCI

Recurrent

Aberrations

inCancer.

The

interface

supports

searching

via

cytogenetic,

clinical,

and/orreferenceinformationClinVar

A

resource

under

development

toprovide

apublic,

tracked

record

ofreported

relationships

among

human

variation

and

observed

health

status.ClinVar

has

a

projected

launch

date

for

late

2011.Comparative

Genomic

DatabaseTaxonomy

Contains

the

names

and

phylogenetic

lineages

of

morethan

160,000 anisms

that

have

molecular

data

in

the

NCBIdatabases.

New

taxa

are

added

to

the

Taxonomy

database

as

dataare

deposited

for

them.PopSet

Database

of

related

DNA

sequences

that

originate

fromcomparative

studies:

phylogenetic,

population,

environmental

and,to

a

lesser

degree,

mutational.

Each

record

in

the

database

is

a

setof

DNA

sequences.

For

example,

a

population

set

providesinformation

on

genetic

variation

within

an anism,

while

aphylogenetic

set

may

contain

sequences,

and

their

alignment,

of

asingle

gene

obtained

from

several

related

anism.Trace

ArchiveA

repository

of

DNA

sequence

chromatograms

(traces),

base

calls,and

quality

estimates

for

single-pass

reads

from

various

large-scalesequencing

projects.NCBI

Education

/

Tool

DatabaseMeSHDatabaseMeSH

(Medical

Subject

Headings)is

the

U.S.

NationalLibrary

of

Medicine'scontrolled

vocabularyfor

indexingarticles

for

MEDLINE/PubMed.

MeSH

terminologyprovides

a

consistent

wayto

retrieve

information

thatmay

use

different

terminology

for

the

same

concepts.NCBI

C++

Toolkit

ManualA

comprehensive

manual

on

the

NCBI

C++

toolkit,including

its

design

and

development

framework,

a

C++library

reference,

software

examples

and

demos,

FAQsand

release

notes.

The

manual

issearchable

online

andcan

be

downloaded

asa

seriesof

PDF

s.NCBI

NGS

DatabaseSequence

Read

Archive

(SRA)

The

SequenceRead

Archive

(SRA)

stores

sequencing

datafrom

the

nextgeneration

of

sequencingplatforms

including

Roche

454

GS

System®,Illumina

Genome yzer®,

Life

TechnologiesAB

SOLiD

System®,

Helicos

BiosciencesHeliscope®,

Complete

Genomics®,

and

PacificBiosciences

SMRT®.GigaScience

/

BGI-ShenzhenAs

of

April

2011:-135.4-

431,399-126.6The

International

Nucleotide

Sequence

Databases

(INSD)

have

beendeveloped

and

maintained

collaboratively

between

DDBJ,

ENA,

and

GenBankAs

of

Aug

2014:-

174.1-

>

431,399-

165.7Microarray

Resources

-mercialtype

in

“microarray”––

/science/biology/chips.html

mittees/MARG/marg.html/ng/chips_interstitial.htmlhttp://w

/–––––––––http

/group/microarray/––htt––

mittees/MARG/MARG_Survey_2000_Pos––

htt

mcresearch.

/resources.htm–––DECIPHER

(DatabasE

of

Genomic

variants

andPhenotype

in

Humans

Using

Ensembl

Resources)an

interactive

web-based

database

which

incorporates

a

suite

oftools

designed

to

aid

the

interpretation

of

genomic

variants(sequence

variants

or

copy

number

variants)

that

by

disruptingnormal

gene

expression

lead

to

disease.enhances

clinical

diagnosis

by

retrieving

information

from

a

varietyof

bioinformatics

resources

relevant

to

the

variant

found

in

thepatient.

The

patient's

variant

is

displayed

in

the

context

of

bothnormal

variation

and

pathogenic

variation

reported

at

that

locusthereby

facilitating

interpretation.an

international

community

of

academic

departments

of

clinicalgenetics

and

rare

disease

genomics

now

numbering

more

than

200centers

and

having

uploaded

more

than

10,000

cases.DECIPHER17q21.3

recurrent

microdeletion

syndrome(Koolen

De

Vries

Syndrome)A

segment

of

thehuman

reference

genome,

viewed

using

Ensembl

with

theDECIPHERtrack

enabled.

Redbars

represent

individual

mutations

for

anonymouspatients

with

deletions

across

this

region,

whilegreen

bars

represent

patients

withduplications

across

this

region.

The

region

shown passes

the

segmentofchromosome

missing

in

patients

with

17q21.3

recurrent

microdeletion

syndrome.Web-accessible

dataGreat

amounts

of

publicly

available

microarray

data

areavailableonthe

InternetCardioGenomics

Program

in

Genomic

Applications–data.html142

microarrays

involving

mouse

models

of

cardiacdevelopment

and

signal

transduction,

includingmeasurements

made

in

time-series.Whitehead

Institute

Center

f enome

Research–bin/cancer/datasets.cgiMicroarrays

from

12

publications

involving

many

typesof

cancer,

including

some

clinical

measurementsassociated

with

each

sampleWeb-accessible

dataChildren’s

National

Medical

Center(HopGenesProgram

in

Genomic

Applications)htt

mcresearch.

/pgadatatable.aspOver500

microarrays

from

many

human

diseases,including

muscular

dystrophy,

dermatomyositis,

andheart

failure,

as

well

as

mouse,

rat

and

dog

models

ofspinal

cord

injury,

pulmonary

disease,

and

heart

failure.Human

Gene

Expression

Index–121

microarrays

from

19

normal

human

tissues.Web-accessible

dataStanford

Microarray

Database–3290

microarrays

measured

across

11

species,

from80publications.National

Center

for

Biotechnology

Information

GeneExpression

Omnibus–2354

microarrays

from

105

types

of

microarrays,

measuredacross

78

experiments.TREX

Program

in

GenomicApplications–565

microarrays

from

mouse

and

rat

models

of

sleep,

infection,hypertension,

and

pulmonary

disease.in

vivo,

in

vitro,

in

httpUnderstandingthe

Structure

ofGenomesUnderstandingthe

Biology

ofGenomesUnderstandingthe

Biology

ofDiseaseAdvancing

the

Science

ofMedicine1990-2003Human

Genome

Project2004-20102011-2020Beyond

2020Genomicplishments

AcrosssImproving

theEffectivenessofHealthcareHGP

to

HapMap

to

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总协调人/牵头单位Genomic

Disorders

Research

CentreKey

ContactsRichard

Cotton–MelbourneHead,

Genomic

Disorders

Research

Centre

Convenor,

Human

Variome

ProjectMing

Qi

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University

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MedicineDirector,

Center

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enetic

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Genomic

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浙江大学-

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浙江大学

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挺,HVP-中国学生自愿者

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