Biology 3594A Lecture Notes - Lecture 16: Microsatellite Instability, Synonymous Substitution, Genotoxicity
13 May 2018
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Hyper and Ultra mutation: specific number of mutations per Mbp. Number is stated clearly in the paper, it mathematically determined a cutoff
Mutation burden or load are used interchnageablely
Definition: 2 parts: load/burden and mutation
Mutation: changes in linear DNA sequence, heritable
Burden/load: aggregate number, collecting all mutations. Studying it in the context of cancer and coming at it from a negative perspective, causing a deleterious
phenotype
Powerful technology because of its coverage: covers entire genome, not restricted to a specific chromosome or probes on an array
Can use it on living organisms
Driver and passenger can be plural, there can be more than one
Driver dictates phenotype that you’re seeing e.x. rapid cell growth. That mutation has led to the phenotype. If you can design a drug against a phenotype you could
stop the phenotype
Passengers might be contributing to phenotype somewhat, might be silent, do not appear to have major influence on phenotype of the cell
When you’re treating a cancer and block a driver, a passenger can get into the driver’s seat, increase its influence on the cells
With remission or a bad turn in a cancer, we start thinking about all the passengers and trying to treat those, figure out which passenger is now expressed in the cell
Very dynamic process between driver and passenger
Clastogenic agents: 17 beta estradiol, acetaldehyde, cyclophosphamide
Can be external or internal, exogenous or endogenous
Cleave DNA and create ss or ds breaks, chromosomal fragments
MSI-H- microsatellite instability
Repeats of either 2-4ish nucleotides, very short
Micro = small size
Satellite = repetitive DNA collected by centrifugation
Instability = they expand and contract
H = high amount of expansion and contraction
Can be characteristic of certain cancers
POLD1 and POLE tackling diff DNA strands
Paper defined hypermutation and found genes that have mutations for that
Intrinsic and extrinsic
APOBEC is intrinsic, editing DNA in bad way, hyperediting and causing mutations.
Extrinsic: chemotherapy agent: tobacco smoke, UV light –both leading to hypermutation
Particular change in amino acid was bad, not amino acid itself that was important
Didn’t lose amino acid, it’s the new amino acid there that drives the cancer
One particular codon is really bad even though a synonymous mutation –want to know why. Maybe tRNA abundance
Can’t treat all synonymous codons the same way
NGS –be able to figure out how much of the tumour has this mutation, a little or a lot?
Variant allele fraction –detect a mutational change, can relate this to how much of that tumor has that change, and related it to timing. Determined by the coverage
or read depth (if you have 150 reads how many are variant? Larger number of reads occur earlier, smaller number of reads variant occurred later, learn about timing
and dynamics of tumour development –associated with patient survival).
Good or bad prognostic information –know when and what they should be treating
All clusters have something to do with replication and ultrahypermutation
Divide a piece of paper into 3 parts and know a few features: signature, gene hit, nature of cancer, adult or child, POLE, POLD, microsatellite instability,
ultrahypermutation
Variant allele fraction told about timing, and survivorship
Unsupervised clustering, big graph
8 clusters, found that the clusters had particular signatures, diff characteristics of gene affected, classified the cancers themselves (child and adult), a particular
cluster was associated with a particular tissue
There are more than 5 but should be able to come up with 5
Big figure with clusters 1-8
Talking about variant allele fraction again, just a diff way of asking
Carp paper: beta estradiol
Two genotoxic assays (comet, micronucleus). Genotoxic is all cleavage. Cytotoxic is cell death: tunel and caspase
In the intro of the paper
Anthropogenic (people are putting this into water), know it is bioactive
Present, detectable, causing phenotypic changes, suspected to have cytotoxic and genotoxic effects (4)
There are more
Carp are present where the estradiol is (aquatic), they exist in the zone of the water where it might be concentrated (bottomfeeders), in some countries like Mexico
carp are economically important, may want to use it as sentinel for other species, easy to catch and sample so can get it as an environmental biomonitoring
Lec 16 Tasmanian Tiger Genome
May 13, 2018
2:51 PM
3594 Page 1
Document Summary
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