6-Re-sequencing(华大基因高通量测序内部培训资料).pdfVIP

Genetic variation detection for Solexa Re-sequencing Outline Why Re-sequencing? When Re-sequencing? What type of Re-sequencing? Flowchart of Re-sequencing data analysis Methodology of Re-sequencing based genetic variation detection 1 Why Re-sequencing? Re-sequencing including DNA and RNA sequencing, it aims to get the sequences of a region which is already available. DNA re-sequencing is fundamental for genetic variation identification while RNA sequencing can discover new alternative splicing and digital expression profile analysis. Both are essential tools for biological issue study. • Clinical research, bring science to medicine • Population genetic studies • Association study • Evolutionary ……. 2 When Re-sequencing? • Figure out genetic variation among different individuals • Figure out genetic variation between different strands/species which share recent common ancestor -- Closely evolution relationship between different species (99% identity) • Figure out genetic variation between populations • Survey the diversity of a novo genome with a closely species which already had a genome sequence. • Survey the heterozygosity for a de novo assembly 3 Type of Re-sequencing? – Whole genome Re-sequencing – Target region Re-sequencing • PCR based Re-sequencing • Exon capture Re-sequencing – Expression profile analysis – Epigenetics …. 3.1 Whole genome re-sequencing Genome-wide variation detection (SNP/Short InDels/Structure variation) Chromosome ploidy study (DownSyndrome) 3.2 Target region re-sequencing PCR based re-sequencing and Exome re-sequencing Only sequence target region of interest, usually design based on previous study. cost effective but wet lab inte