BGI 动物案例研讨班课件：6-Genetic Variation identification based on NGS.pdf

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1、Identificationofgeneticvariationsbasedongenomere-sequencingOutline•Background•Genomere-sequencing•Methodology–Geneticvariations–SNPdetection–Othervariations•Practice–Sequencing–Alignment–Basicitems–PracticeoncommandlineBackgroundBackground•SangersequencingBackground•Chipsequencingis

2、outofdate.•NextgenerationSequencing(NGS)timeiscoming…Background•AftergenomeDe-novoassembly…200020022006200720082009Animals:hadbeensequencedwww.ensembl.orgBackground•Re-sequencingiscoming…•Humangenome•Plant/animalgenome•Medical/diseaseresearch•Agriculture/Molecularbreeding•Genomics/c

3、omparativegenomics•Genetics/populationgenetics•Epigenetics•…Re-sequencing•Re-sequencingVs.De-novoassemblyTableDifferencesbetweenre-sequencingandDenovoRe-sequencingDenovoMotiveGeneticvariationsNewgenomeMethodAlignmentAssemblyReferenceYesNoDepth10~20X>50XLibrarySimpleVariousDataqualit

4、yLowHigh………Re-sequencingHELLOFRIENDSWELCOMETOBGISHENZHENHELLRIENDWELCOMOBGIZHENFigureThedifferencesLLOFRIDSWELMOTOBGHENZHbetweenHELLOFSWELMOTOGISHENRe-sequencingandDenovoassemblyHELLOFRIENDSWELCOMOTOBGISHENZHENDenovoRe-sequencing...?HELLRIENDWELCOMEBGIZHENLLOFRIDSWELMETOBGHENZHHELLO

5、FSWELMETOGISHENELLOFRDSWCOMOBGIENZHENOFIIENWELCOMGISHNZHENHELLOFRIENDSWELCOMETOBGISHENZHENRe-sequencing•Re-sequencing:DNAandRNAsequencing–DNAre-sequencingisfundamentalforgeneticvariationidentification.–RNAsequencingcandiscovernewalternativesplicinganddigitalexpressionprofileanalysis

6、.•Whencandore-sequencing?–Figureoutgeneticvariationamongdifferentindividuals–Figureoutgeneticvariationbetweendifferentstrands/specieswhichsharerecentcommonancestor–FigureoutgeneticvariationinpopulationWhattypeofDNAre-sequencing?–WholegenomeRe-sequencing–TargetregionRe-sequencing•PCR

7、basedRe-sequencing•ExoncaptureRe-sequencing•Others–EpigeneticEverythingcandore-sequencing!MethodologyGeneticvariations•Variationsingenome:–Singlenucleotidepolymorphism(SNP)–Shortinsertionanddeletion(InDel)–Structurevariation(SV)–Copynumbervariation(CNV)ATGACGGTATGCTACGAGAT---ATGGCGT

8、AGCTGAAGTCGTACGGAT-