Strahl: Genomics/proteomics

Front 1

Epigenetics

Back 1

Effect on gene or genome function that is not specified in DNA sequence itself (e.g. histone post-translational modifications)

Front 2

Epigenetic regulators

Back 2

Chromatin remodeling complexes
Histone modifications
Histone variants
DNA methylation

Front 3

Blotting and hybridization

Back 3

1. Separate molecules by electrophoresis according to size
2. Transfer to solid support membrane
3. Probe for sequence (hybridization for nucleic acid; antibodies for proteins)

Front 4

Southern blots

Back 4

Target: genomic DNA
Examines gene structure, organization, size, and copy number
Ex. Her2/new copy number in breast cancer

Front 5

Northern blots

Back 5

Target: RNA
Examines gene expression: transcript size, alternate transcripts, related transcripts, gene regulation, expression levels

Front 6

Western blots

Back 6

Target: protein
Goal: examine protein levels and post-translational modifications
Ex. HIV testing

Front 7

PCR

Back 7

Each cycle yields 2 copies
35 cycles yields 2^35 = 34.4 billion copies

Front 8

Reverse Transcriptase PCR

Back 8

Detects specific mRNAs
Amplification of RT-derived cDNA

cDNA = DNA made from mRNA and reverse transcriptase

Front 9

Real Time PCR

Back 9

High-throughput quantification of DNA and RNA
Quencher
Release of quencher releases fluorescence into solution

Useful: determining number of gene copies (e.g. Her2), quantitating level of RNA viral infection, comparing expression of suspect genes in normal versus diseased tissues or tumors (e.g. p53, RB, ER)

Front 10

Microarrays

Back 10

Gene expression profiling

Global changes in transcriptome
Understanding disease etiology
Distinguishing disease subtypes (molecular signature)
IDing new diagnostic markers
Revealing new therapeutic targets

Front 11

Microarrays and cancer

Back 11

Help distinguish primary tumor type on basis of gene expression

Front 12

AML and ALL

Back 12

Difficult to distinguish using traditional cytological, cytogenetic and biochemical assays

But different drugs work better for each, so need to know

Use a microarray

Front 13

AmpliChip

Back 13

Determines likelihood of certain drugs to be metabolized faster
Looks for common genetic mutations and/or variations in cytochrome enzymes

Front 14

MammaPrint

Back 14

Examines gene signature of cancer-related genes in breast tumors
Determines likelihood that breast cancer will return within 5 to 10 years
Determines low risk or high risk for tumor recurrence

Front 15

ChIP-Seq

Back 15

Obtains transcription and chromatin factor binding sites

Front 16

Proteomics: key technologies

Back 16

Mass spec
Tissue microarrays
Protein microarrays

Used to identify early-stage ovarian cancer

Front 17

Mass spec

Back 17

Mass of proteins, peptide fragments upon digestion, and post-translational modifications

Front 18

Protein microarrays

Back 18

Protein-protein interaction studies