Genetics Testing Techniques and Application Flashcards
Genetic Testing Methods
what might be some different scopes of analysis?
- differs according to scope of analysis
- specific location in 1 gene
- more than 1 diff location in same gene
- entire gene sequence
- most of sequence of protein-coding are of the genome (exome)
- most of sequence of whole genome
scope of analysis defines the test to do
Inherited testing
- if we know exact familial variant
- one or more variant associated with disease in question
- one or more variant common among certain population
- more than 1 testing method can be bundled together and needed to get better sensitivity
- insurance billing and reimbursement
Tumor testing
- depnds on goal
- diagnostic testing
- prognosis testing
- treatment
Single gene sequencing
what is it?
1 main type - what is newer?
- determines order of nucleotides
- compares pt sequence to reference sequence
- Sanger sequencing
- multiple next gen sequencing (faster, bigger scope)
detects single nucleotide changes
Single gene sequencing
When to use it? (2)
When not to use it? (3)
- when family mutation is not known
- one specific gene is accompanied by condition we are monitoring or detecting
- when family mutation is known (use targeted mutation)
- family history suggestive of more than 1 hereditary syndrome
- syndrome has multiple candidate genes (use a panel)
Deletion/Duplication analysis
AKA CNV analysis
consist of molecular probes with fluorescent tags that attach to a specific DNA sequence
- detect small deletions or duplications (FAR)
Deletion/Duplication analysis
When to use it? (2)
When not to use it? (2)
- use when deletions/dup are accompanied with condition in question (spinal muscular atrophy)
- gene sequencing is negative but there is a high possibility of genetic involvement in condition tested
- when single gene sequencing didn’t give any results that showed mutations
- don’t use if family mutation is known and is not related to CNV
- more than 1 hereditary syndrome involved (use panel)
Targeted Mutation Analysis
AKA Mutation probe, panel
- molecular probes attach to a specific string of nucleotides that are associated with a certain disease
- fluorescent probe attaches to abnormal nucleotides - looking for diff markers and finding the mutation known
Targeted Mutation Analysis
When to use it? (2)
When not to use it? (3)
- use when family mutation is known
- when we are looking for one or few specific variants (3 site testing for breast or ovarian cancer)
- don’t use when family mutation is unknown (use gene sequencing or multi panel)
- more than 1 hereditary syndrome (panel)
- multiple candidate genes equally possible
Multi-gene panels
AKA Next-generation sequencing (NGS)
compares patient sequence to a reference sequence
Multi-gene panels
When to use it? (3)
When not to use it? (2)
- use when family mutation is unknown
- multiple candidate genes
- more than one hereditary syndrome
- don’t use if family mutation is known (use targeted mutation)
- one gene is likely to be associated with disease of investigation
Whole genome/exome sequencing
Whole exome: analysis of protein coding portion of gene
Whole genome: analysis of coding, regulatory and unknown function regions
Whole genome/exome sequencing
When to use it? (2)
When not to use it? (2)
- use when other testing have no success and hereditary factors strongly suspected
- when more than 1 family member avail for testing (1st or 2nd degree relative)
- don’t use when it is better to use other targeted genetic testing
- when relatives are not available to participate
What are genetic disorders?
what is it caused by? (4)
- disease caused in whole or in part by a change in DNA sequence away from normal sequence
caused by mutation in:
- one gene (monogenic)
- multiple genes (multifactorial inheritance)
- combo of gene mutations and environmental factors
- damage to chromosomes (number or structure of entire chromosomes which carry genes)
group of inherited diseases of blood that affect person’s ability to produce hemoglobin resulting in anemia
Thalassemia
