Biology 3594A Study Guide - Final Guide: Multiplex Polymerase Chain Reaction, Somatic Hypermutation, Cancer Cluster
13 May 2018
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Lecture 14 Flashcards
Front (Term)
Back (Definition)
Parameters to consider for the use of
assays (9)
1. Scope/capability: how much is detected
2. Resolution/scale: chromosome, nt, etc.
3. Cost/expertise
4. What is detected
5. Method Principle
6. Application: discovery or validation
7. Targets: number and nature
8. Perspective: nt, locus, genome
9. Where does the assay take place
Difference between target of
Discovery and Validation/Confirmation
assays
Discovery assays are not targeting a specific locus or base pair,
very broad
Validation/confirmation assays are more specific (cast assay,
multiplex PCR)
"Comprehensive Analysis of
Hypermutation in Human Cancer"
- what the paper is about
Classify different hypermutations in humans
- look for different driver mutations and passenger mutations
- identify signatures of diff types of hypermutations so that
people can make therapeutic targets
- hypermutations divided into 3 clusters based on phenotype,
helps better diagnose in the clinic
- paper focuses on 3 clusters
Experimental Design and Rationale
- motivation
- question
- materials
- methods (4)
- what are they trying to discover
- clinical implications
Motivation
- understand mutational processes of carcinogenesis, so they
can classify tumors into clinically-relevant subgroups
- helps inform diagnosis, treatment and prognosis of cancer
Question: what drives hypermutation?
Materials: 81 000 tumours (child and adult)
Methods: NGS, WGS, WES, gene panel sequencing
Discover
- mutational mechanisms
- evolutionary dynamics underlying hypermutation
- the role of exogenous mutagens
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Back (definition: scope/capability: how much is detected, resolution/scale: chromosome, nt, etc, cost/expertise, what is detected, method principle, application: discovery or validation, targets: number and nature, perspective: nt, locus, genome, where does the assay take place. Discovery assays are not targeting a specific locus or base pair, very broad. Validation/confirmation assays are more specific (cast assay, multiplex pcr) Look for different driver mutations and passenger mutations. Identify signatures of diff types of hypermutations so that people can make therapeutic targets. Hypermutations divided into 3 clusters based on phenotype, helps better diagnose in the clinic. Understand mutational processes of carcinogenesis, so they can classify tumors into clinically-relevant subgroups. Helps inform diagnosis, treatment and prognosis of cancer. Parameters to consider for the use of assays (9) Clinical implications: improve management of patients and families. Polymerases that are error prone when they are mutated.
