1 Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520Final Review Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520
2 Genomic techniques Gene expression profiling TF regulation: ChIP-seqExpression 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)
3 Biological Problems Transcriptional regulation and transcription factors Epigenetics and chromatin factors Human genetics and disease susceptibility Cancer genomics and precision medicine
4 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
5 Statistics and AlgorithmsR, 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
6 CRISPR-Cas: Bacterial Adaptive Immune SystemClustered regularly interspaced short palindromic repeats
7 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
8 CRISPR/Cas Genome EditingCRISPR/Cas is the bacteria adaptive immune system, later introduced in other organisms
9 Genome-Wide CRISPR/Cas9 Knockout ScreensgRNA fold change = log2(Count(t)/Count(0)) Negative selection yields essential genes Positive selection yields growth repressive genes Identify cell-specific and condition-specific essential genes and biomarkers of drug response & resistance Shalem & Zhang, Nat Genet, 2015
10 MAGeCK Findings on Published ScreensWang et al Science 2014 Shalem et al Koike-Yusa et al NBT 2013 MAGeCK: over 1,900 download
11 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)