Lecture 7: NGS, Mapping, and Epigenetics Flashcards
SNP
Single nucleotide polymorphism.
Changes that may or may not result in a change of the AA sequence. Occur in sets, called haplotypes and are inherited as mendelian characteristics.
NGS
Next Generation Sequencing
CGH
Comparative Genomic Hybridization
Two DNA samples are compared (normal vs. patient, normal vs. tumor) to look for regions of duplication or deletion.
CNV
Copy Number Variation
Alterations of the DNA of a genome that results in the cell having an abnormal or, for certain genes, a normal variation in the number of copies of one or more sections of the DNA.
Mb
Megabase (1 million base pairs)
Kb
Kilobase (1 thousand base pairs)
GWAS
Genome-Wide Association Study
VUS
Variant of Unknown Significance
in silico
Performed on the computer.
SNP DNA Analysis
Takes advantage of a neutral single nucleotide difference found across the human genome.
How would one identify the loss of heterozygosity?
SNP Array. Can be used to map copy number changes (CNC) and loss of sequence from one of the two chromosomes.
CNC
Copy number change.
What are three ways SNP genomic mapping used?
- Analysis of suspected genomic lesions in individual patients.
- Genome wide association studies (GWAS).
- Ancestry genotyping using ancestry informative markers (AIMS).
How are SNPs inherited?
Mendelian-style.
A group of multiple SNPs that occur together.
Haplotype.
How might the significance of VUSs be resolved in the present time?
Checking parents and databases of information about population variants.
What should one expect about VUSs in the future?
With increasing informationin databases, their significance can be ruled either benign or disease-causing.
What kind of changes can NGS identify?
- Recessive conditions (Two mutations in the same gene are needed)
- Dominant conditions (One mutation is sufficient)
Deleterious Mutation
Previously shown to be linked to a phenotype.
Medically Actionable Mutations
Previously linked to preventable diseases with later onset.
Epigenetics
Used to describe heritable changes in gene expression that arise from changes in the chromosomes without alteration of the DNA sequence.
What may be the causes of methylation of DNA?
- Normal process (different genes needed at different times).
- Environmental stress or exposure.
Can epigenetic modifications be passed on to offspring?
Yes, when imprinting is not reset.
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