3 Flashcards
SNPs
○ Synonymous - preserves AA sequence
○ Non-synonymous - does not preserve AA sequence
Both located in coding region of gene
Insertion/Deletion
Variable number tandem repeats (VNTR)
Copy Number Variation (CNV)
Somatic (gene mutations)
-Occurs in somatic cells during MITOSIS
-Passed down to other cells in the individual
-NOT passed down to individual’s offspring (not inherited)
*may or may not affect individual
Polymorphism
A common genetic variation that occurs at a frequency of >1% in a population
*responsible for normal differences between people such as eye color, hair color, blood type, and also drug response
Inherited (gene mutations)
Occurs in gene cells during meiosis
-passed onto offspring
UGT1A1 gene
UGT1A1Gene Product: UDP-glucuronosyltransferase
*this liver enzyme converts unconjugated bilirubin to conjugated bilirubin, making it able to be dissolved/removed
UGT1A1 PK
UDP-glucuronosyltransferase is also the major route of ___
SN-38 elimination
SN-38 is the active metabolite of irinotecan used to treat colorectal cancer
The *28 allele
is associated with reduced UGT1A1 expression and increased drug toxicity
For N polymorphic sites,
there can exist up to 2^N theoretical haplotypes
Inherited variants can be identified in DNA extracted from ____
Somatic mutations are found ____
ANY cell in the body
only in the somatic cell where the mutation occurred or their descendent cells
Genotyping For Inherited Gene Variants
- Identify genetic variants by DNA sequencing
- Develop assay to screen patients for their genotypes (PCR, microarrays, sequencing, SNP arrays)
PCR
Amplifies a single/few copies of DNA fragment
i. To genotype a couple of SNPs or samples
ii. Uses fluorescent dyes for A, C, G, T
iii. Heterozygotes will show a mixed signal for a nucleotide
Custom SNP array
i. To genotype <300 SNPs
ii. Various techniques
DNA microarray
To genotype 1000s of SNPs or samples
- Isolate, label sequence
- Run sequence over probe wells (each well has unique oligonucleotide probes)
- Isolated seq. only stick to complementary probes
- Wash wells
- Scan wells for detection
Sequencing
i. Entire genome is sequenced to identify genotype
ii. Can be costly
iii. Alternatively, exome sequencing, which is just sequencing of exons
Screening For Somatic Gene Variants
● Must collect DNA from the target tissue (note that not all cells in the target tissue will have the mutation)
● Must sequence entire genome of cell to find mutation
● Alternatively, can sequence only functional region of gene
KRAS
● Activated by EGFR
● Common cancer drugs cetuximab and panitumumab block EGFR
● But if there’s a mutation in KRAS (to be ON permanently) that allows it to function without EGFR, these drugs are
ineffective
● Somatic mutation that leads to a change in codon 12 (13)
SO blocking EGFR with a monoclonal antibody will only be effective in tumors with normal KRAS
