Pharmacogenomics Flashcards
1
Q
how many cells in the human body
A
30-40 trillion
2
Q
how many different types of cells
A
200
3
Q
how many cells die each day and are replaced?
A
100 billion
4
Q
what are the cell cycle phases
A
G1, S, G2, M, G0
5
Q
what is G1
A
cell grows and prepares for DNA synthesis
Cell is getting bigger, enzymes, and molecules required for synthesis are prepared
6
Q
what is the S phase
A
DNA replication
One copy into 2 copies (doubling of DNA material)
7
Q
what is the G2 phase
A
cell continues to grow and prepare for mitosis
Has to accumulate the molecules for mitosis, cell continues to get bigger in order to divide into 2 cells (don’t want small daughter cells)
8
Q
what is the M phase
A
mitosis: cell stops growth and starts division
Further divided into 4 phases: prophase, pro-metaphase, metaphase, telophase, cytokinesis
9
Q
what is G0 phase
A
cell has left the cell cycle and stopped dividing
Daughter cells can keep dividing or leave the cell cycle
Cell is stable and doing biological functions
Some cells leave and become permanent: neurons
10
Q
where are the checkpoints in the cell cycle?
A
G1 and G2
11
Q
what happens at the G1 checkpoint?
A
DNA synthesis
Checks if the cell is ready for DNA synthesis (problem with unwinding, etc)
12
Q
what happens at the G2 checkpoint
A
preparation for mitosis
Checks whether the cell is ready for mitosis (does it have all the molecules)
13
Q
what is the R point
A
cell commits to the cycle for division
Before the R: cell is growing and is preparing for DNA synthesis (requires growth factors)
After R: no longer needs growth factors, it is now an AUTOMATIC process
Happens 2-3 hours before the S phase
G1 checkpoint and R point happen very closely together
14
Q
how many pairs of chromosomes
A
23 pairs
22 autosomes
1 pair of sex chromosomes
15
Q
what is a chromosome
A
Complex of DNA molecules and proteins
16
Q
how many base pairs in a DNA molecule
A
50-250 million base pairs
17
Q
how many base pairs and genes in an average chromosome
A
130 million base pairs
2500-5000 genes
18
Q
what do the non-coding regions do?
A
regulate gene functions
Only 10% of human chromosomes code for genes
19
Q
what is a microband
A
3-5 million base pairs and 60-120 genes
20
Q
what is the chromosome structure?
A
Chromosome–>chromatin fiber–>nucleosome–>histone–>gene–>nucleotide
21
Q
what are the nucleotide base pairs
A
A-T: 2 H bonds
C-G: 3 H bonds
22
Q
what is a histone
A
DNA wraps around a histone polymer
2 linker regions of DNA: H1 anchors the 2 DNA linkers to the histone atomer
H2A and H2B are paired; H3 and H4 are paired
Also called DNA beads
23
Q
what is a gene
A
A portion of chromosomal DNA sequence required for the production of a polypeptide (protein) or a functional RNA molecule
24
Q
what is the size of a small gene vs a large gene?
A
small-1.5 kb
large-2000kb
25
which is the biggest gene?
DMD gene
26
what is the size of mature mRNA compared to the gene?
1/10th
| Small genes encode for proteins but bigger genes have introns that will be spliced out
27
what are the 4 nucleotides in mRNA
A, U, G, C
28
how many nucleotides in a codon
3
29
what does the first/second letter in a codon dictate?
tells you the amino acids made
30
what happens if the 3rd nucleotide is changed?
can end up with the same amino acid or a different one
31
what is transcription
gene-->mRNA
32
what is translation
mRNA-->protein
33
how many genes expressed in a typical human cell
15,000 genes expressed
Pattern of expression is different from one cell to another (brain vs. cardiac)
Genes may be different and expression may be different
34
how do eukaryotic genes differ from prokaryotic
have introns and exons
35
what is a gene malfunction often found in cancer patients
Tp53
36
what are promoters
DNA sequences that promote gene expression
Required for gene transcription (mRNA synthesis)
Typically located upstream of genes
RNA polymerase binding site
Direct the exact place to initiate DNA transcription
Determine when and how a gene is transcribed
Promoter methylation represses gene transcription
37
how many base pairs in the human genome
3 million
38
how many genes
19,000
39
how many base pairs and genes in the mitochondrial DNA genome
17 thousand base pairs
| 38 genes
40
what is ENCODE
Encyclopedia Of DNA Elements (ENCODE)
| Annotation of functional elements encoded in human genome
41
what is an SNP?
Single nucleotide polymorphisms
| Small stretches of DNA that differ in only ONE base
42
what is the most common type of genetic variation
SNP
| even occurs in identical twins
43
what is the frequency of SNPs
1/1000 to 1/200-300 bases
44
how many coding SNPs in each gene?
approx. 5
Happen in the coding areas: effect will be shown in the protein structure
SNP in the first/second codon letter: will get different proteins
SNP in the third codon: may get the same protein may not
45
what happens if an SNP occurs in a non-coding region?
no effect
46
what happens if a SNP occurs in a regulatory region
changes expression level
47
what happens if a SNP occurs in a coding region
can change protein structure which may alter function
| <1% occur in coding regions
48
how many SNPs occur between 2 individuals on average
1 SNP every 1250 bases
49
what is a CNV
copy number variation
| Variation among people in the number of copies for a particular gene or DNA sequence
50
how do CNVs occur
Recombination based and replication based mechanisms
| DNA replication errors are repaired leading to variation
51
how do CNVs differ from SNPs
Higher de novo locus-specific mutation rate than for SNPs
Happens at a certain locus (hotspots)
SNPs occur everywhere
52
how much of the human genome is affected by CNVs
approx 13%
Gene duplication and exon shuffling: predominant mechanism for genome evolution
Multiple axons in a gene: axons from different genes get combined to make new genes
53
what are the 4 mechanisms of CNVs
deletion, duplication, segmental duplication, inversion
54
what is an INDEL
insertions and deletions of small pieces of DNA
55
do INDELs have an impact on humans health and susceptibility to disease
YES
56
what are the 5 categories of INDELs
1. insertion/deletion of single base pair: If this happens in the frame of coding region: results in a frame shift
2. Expansion by 1 base pair: 3 codons inserted into the gene
3. multi-base pair expansion (2-15 repeats)
4. Transposon insertions: insertions of mobile elements
5. Random DNA sequence insertions or deletions
57
what is an ILU fragment
Small pieces of DNA that moves within the same chromosome or different chromosome
300 base pairs, encodes 1 domain
Occurs 10-15 times in the whole genome and can move up to 1 million times in the cell
58
what are 3 examples of INDELs causing disease
Cystic fibrosis: 3 base pair deletion in CFTR gene (In frame deletion: 1 whole amino acid is deleted, so it doesn’t cause a shift in the coding of the other amino acids)
Huntigtons: triplet repeat expansion (>35 CAG repeats in gene HTT)
Breast cancer: 6.2-kb deletion of BRCA2 gene
59
what is a large scale variation
Large portions of DNA repeated or missing for no known reasons in healthy people
This heterogeneity may underlie disease susceptibility
Only occur in certain parts of the genome: not evenly distributed
60
what are structural variations
Involves kilobase-megabase sized deletions, duplications, insertions, inversions, and complex combinations of rearrangements
Genome structural changes are involved
61
what is an example of a hot spot for a structural variation
short arm of chromosome 1
Has many of the tumor suppressors (people who get cancer often have deletions in the short arm of chromosome 1)
1 is the biggest chromosome
62
what is balanced translocation vs. unbalanced translocation
unbalanced: chromosome A gives a piece to chromosome B but B doesnt give anything back
balanced: both receive genetic material
63
what is an example of balanced translocation
Philadelphia chromosome
Balanced translocation of chromosomes 9 and 22
Create BCR-ABL gene
Leads to acute lymphocytic leukemia (ALL) and chronic myeloid leukemia (CML)
64
what is genetics
Study of heredity
Specific gene
Function and composition of a single gene
65
what is genomics
Study of entirety
Entire genome
Addresses all genes and their relationships
66
what is pharmacogenetics
Study the genetic basis for variability in drug response between individuals
67
what is pharmacogenomics
Development of drug therapies (drug and dose) to compensate for genetic differences in patients
68
what are the 6 principles of pharmacogenomics
```
Determining appropriate dosing
Avoiding necessary toxic treatments
Ensuring maximal efficacy
Reducing adverse side effects
Developing novel treatments
Explaining variable response to drugs
```
69
How does Tamoxifen and CYP2D6 relate to pharmacogenomics
Tamoxifen is for breast cancer
Converted by CYP 2D6 to endoxifen to be active
6-10% european population deficient in CYP 2D6: efficacy is likely to be low-->seek alternative treatment
CYP 2D6: 114 SNPs and metabolize 223 drugs
Extensive metabolizers: live longer as they are able to convert more of pro-drug into active drug
Reduced metabolism: need to give a higher dose to those with reduced metabolism in order to achieve the same therapeutic concentration BUT also increase the risk of toxicity and s/e
70
what is DMD
Duchenne Muscular Dystrophy
Happens in 1/3500 male births (X-chromosome linked, muscle weakness, scar tissue formation, inflammation)
Caused by mutations in the dystrophin gene (DMD)
Mutations in gene DMD occur throughout the whole length, prevalently characterized by large deletions and single point mutations
71
what is Eteplirsen
Exon skipping therapy
Treats some types of DMD (NOT A CURE)
Causes excision of exon 51 during pre-mRNA splicing
The shortened dystrophin has approx. 50% of normal function
72
what is Eteplirsen MOA
Loses the gene 49 and 50 causing it to be out of frame and have a premature stop codon
Drug causes a small portion of the gene to be lost but it is still functional
73
what are the 4 Ps of personalized medicine
Predictive: patient has no disease but we know the genomics, we have to tell them their risk based on the genome
Preventative
Personalized: patient already has the disease but based on their genomic background we provide the right drug
Participatory
74
why are SNPs important to consider in clinical trials
Correlation of drug response to genetic background
Prediction of dose response and adverse effects
Pinpoint common SNP sets for patients who do not respond to a drug
75
how are SNPs related to Vit D and breast cancer risk?
Heterozygotes of one SNP have a statistically significant association with a low risk of breast cancer
Diverse associations with breast cancer risk for a few of the tested SNPs, depending on whether Vit D level was high or low
76
how is warfarin affected by SNPs
Warfarin metabolized by CYP2C9
CYP2C9 (39 SNPs)
People with these variants generally need a lower warfarin dose
77
what is gene expression profiling
Measurement of the expression and activity of thousands of genes at once (genomics and transcriptomics)
Get a global picture of cellular function
Identify association of gene expression profiles with disease susceptibility and development, drug metabolism, and adverse effects
78
gene expression profiling technologies
DNA microarrays
Differential gene expression (DEGs)
Single-cell gene expression
Gene expression profiling based on alternative RNA splicing
Gene expression analysis on biopsy samples
Serial analysis of gene expression (SAGE)
Gene expression profiling of WBC
In vivo gene expression by molecular imaging
79
what is the first approved cancer drug targeted to genetic mutation
Vitrakvi (Larotrectinib)
For adults and children with solid tumors that test positive for NTRK gene fusions without a known acquired resistance mutation
Known acquired resistance mutations: G623R, G696A, F617L
80
how many personalized drugs were approved by the FDA from 2013-2017
1/4 drugs approved by FDA was a personalized medicine
| Approved 16 in 2017
81
what is imatinib
Approved for chronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL)
Inhibit BCR-ABL tyrosine kinase
Inhibits proliferation and induce apoptosis of BCR-ABL positive cells
BCR-ABL gene: translocation from chromosome 22 causes leukemia
Tablets: 100mg and 400mg
CML: 400mg OD
ALL: 600mg OD
82
what are the 3 receptors that are overexpressed in breast cancer
Estrogen, progesterone, and human epidermal growth factor 2
83
what is trastuzumab
Approved for HER2-subtype breast cancer
MAB targeting HER2/neu/Erbb2 protein
Binds to the subdomain 4 of HER2 protein
IV infusion: 1st infusion-->90 mins, if well tolerated-->30mins
ADRs: chills, fever, body pain, weakness, nausea
84
what is pertuzumab
Mab binds to subdomain 2 of HER2 protein
Blocks homodimerization of HER2 and heterodimerization of HER2-HER3
Inhibit HER2 signaling pathway and decrease cell growth
Trastuzumab+ pertuzumab+ docetaxel for metastatic and recurrent HER2 breast cancer
85
what is T-DM1
Conjugate of trastuzumab (T) and emtansine (DM1)
Emtansine which is a potent cytotoxic agent, is cleaved from T-DM1 and released inside breast cancer cells
Treat HER2+ metastatic breast cancer and early stage HER2+ breast cancer after surgery
IV q3wks
14 cycles in total for early stage HER2+ breast cancer
86
what is gefitiib
Inhibitor of epidermal growth factor receptor (EGFR)
Signaling via EGF-EGFR promotes DNA synthesis, proliferation, migration, and survival
Prescribed for non-small cell lung cancer with EGFR exon 19 deletion or exon 21 L358R mutation
Works inside the cell: cytoplasmic domain of the receptor
87
what is cetuximab
Mab against EGFR
Head and neck cancer and colorectal cancer
Antibodies work outside of the cell because they are too large to get inside
