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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
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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
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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
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CRISPR/Cas Genome Editing
• CRISPR/Cas is the bacteria adaptive immune
system, later introduced in other organisms
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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
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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)