1 / 8

Next-generation sequencing and PBRC

Next-generation sequencing and PBRC. Next Generation Sequencer Applications. DeNovo Sequencing Resequencing, Comparative Genomics Global SNP Analysis Gene Expression Analysis Methylation Studies ChIP Sequencing-transcription factors, histones, polymerases

ivie
Download Presentation

Next-generation sequencing and PBRC

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Next-generation sequencing and PBRC

  2. Next Generation Sequencer Applications • DeNovo Sequencing • Resequencing, Comparative Genomics • Global SNP Analysis • Gene Expression Analysis • Methylation Studies • ChIP Sequencing-transcription factors, histones, polymerases • Transcriptome Analysis-splicing, UTRs, cSNPs, nested transcripts • MicroRNA Discovery and quantitation • Metagenomics, Microbial diversity • Copy number variation • Chromosomal aberrations • Gene regulation studies

  3. AB SOLiD Ligation sequencing

  4. How many sequence tags* do I need for my gene expression application? • SAGE/CAGE – 2-5 million mappable • miRNA – 10 million mappable • ChIP Seq—10-20 million mappable • Whole Transcriptome from polyA RNA – 40-50 million mappable • Whole Transcriptome from rRNA depleted - >50 million mappable • Whole Transcriptome for Allele Specific Expression - >>50 million mappable SOLiD™ 4 generates >1.4 billion mappable sequences/run (2 slides) Libraries can be multiplexed to decrease the cost/sample according to the application and number of sequences needed. *For human/mouse sized genomes; smaller organisms require fewer sequence tags.

  5. SAGE Sequencing vs. Microarray

  6. Bioinformatics: Geospiza Primary Data Analysis - Images to bases Instrument-specific Sequences + Quality values RunQuality Ref Seq + Alignment Assembly, De Novo Secondary Data Analysis – Bases to alignments/contigs • Applications • Tag Profiling • Small RNA Analysis • Transcriptome seq. • ChIP-Seq • Methylation Analysis • Resequencing • De novo assembly • Algorithms • Eland • Maq • SOAP • Velvet • Newbler • Mapreads • Others … Sample/Library Quality One or more Data sets Tertiary Data Analysis – Experiment Specific • Differential expression • Methylation sites • Binding sites • Gene association • Genomic structure Discovery

  7. Next-gen sequencing: applications • Genome analysis: basic and translational research • Genetics of disease – new frontiers • Exomeresequencing: confirmation of GWAS • Genome sequence as diagnostic tool • Genetic counseling • Epigenome analysis: basic research; biomarkers • Analyses of DNA methylation, transcription factors, histone modifications, non-coding RNA • Epigenomic biomarkers of disease • Gene expression analysis: basic research; diagnostics & biomarkers • Whole transcriptome: all transcribed sequences in a cell • SAGE analysis: expression of known genes • Small RNA: microRNA as regulators of biology • Genotype to phenotype: a new frontier • Pathology: systems biology • Diagnosis: data filtering • Personalized Genomic Medicine: Treatment recommendations

  8. Next-gen sequencing: challenges • Rapid growth in methodology • Technology and equipment changes & upgrades • High demands on informatics: • Staff • Software • Computational resources • New ways of handling data needed: • Interpretation • Publication • Storage

More Related