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Final Review Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520 Genomic techniques • Gene expression profiling – Expression Microarray and RNA-seq • TF regulation: ChIP-seq • Epigenetic profiling – Methylation array, BS-seq, ChIP-seq, DNase-seq, HiC • GWAS: SNP arrays • Genome sequencing: germline & somatic • High throughput screening – Genetic (si/shRNA, CRISPR screens) and chemical (drug screens) Biological Problems • Transcriptional regulation and transcription factors • Epigenetics and chromatin factors • Human genetics and disease susceptibility • Cancer genomics and precision medicine Binformatics • • • • • • • • • Microarrays (RMA, LIMMA) Ontology and pathway (DAVID, GSEA) Batch removal (COMBAT, SVA) NGS for DNA-seq (FastQC, BWA, STAR) RNA-seq (DESeq, Kalisto, Sluth) ChIP/DNase-seq (MACS, BETA) GWAS (Plink, GCTA) Genome-resequencing (GATK, Mutect) Web resources: GEO, UCSC, CBioPortal Statistics and Algorithms • R, BioConductor and python • Tukey bi-weight, median polish, qnorm, qq plot • Statistical test: t*-test, Chi-sq test, KS test, FDR adjustment • Hierarchical models, generalized linear models • K-means and hierarchical clustering • PCA, SVM • Burrows-Wheeler alignment • EM, Gibbs sampling • HMM, dynamics programming • LASSO and logistic regression • Survival analysis CRISPR-Cas: Bacterial Adaptive Immune System • Clustered regularly interspaced short palindromic repeats 6 CRISPR/Cas9 Knockout • CRISPR guide RNA allows Cas9 to make ds breaks at specific genomic locations in the genome • Repairs on exonic breaks create loss-of function gene knockouts 7 CRISPR/Cas Genome Editing • CRISPR/Cas is the bacteria adaptive immune system, later introduced in other organisms 8 Genome-Wide CRISPR/Cas9 Knockout Screens • gRNA fold change = log2(Count(t)/Count(0)) • Negative selection yields essential genes • Positive selection yields growth repressive genes Shalem & Zhang, Nat Genet, 2015 • Identify cell-specific and condition-specific essential genes and biomarkers of drug response & resistance 9 MAGeCK Findings on Published Screens Wang et al Science 2014 Shalem et al Science 2014 Koike-Yusa et al NBT 2013 MAGeCK: http://mageck.sourceforge.net over 1,900 download 10 Final Exam • Tue 4/26, 11:30am-1pm, Science Center 309A. • Open notes / open computer, but please don’t print and don’t cheat! • Last HW out now and due next Tue • Class participation • ScreenCast video (optional)