Lecture 7: NGS, Mapping, and Epigenetics

Question 1

SNP

Answer 1

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.

Question 2

NGS

Answer 2

Next Generation Sequencing

Question 3

CGH

Answer 3

Comparative Genomic Hybridization

Two DNA samples are compared (normal vs. patient, normal vs. tumor) to look for regions of duplication or deletion.

Question 4

CNV

Answer 4

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.

Question 5

Mb

Answer 5

Megabase (1 million base pairs)

Question 6

Kb

Answer 6

Kilobase (1 thousand base pairs)

Question 7

GWAS

Answer 7

Genome-Wide Association Study

Question 8

VUS

Answer 8

Variant of Unknown Significance

Question 9

in silico

Answer 9

Performed on the computer.

Question 10

SNP DNA Analysis

Answer 10

Takes advantage of a neutral single nucleotide difference found across the human genome.

Question 11

How would one identify the loss of heterozygosity?

Answer 11

SNP Array. Can be used to map copy number changes (CNC) and loss of sequence from one of the two chromosomes.

Question 12

CNC

Answer 12

Copy number change.

Question 13

What are three ways SNP genomic mapping used?

Answer 13

1. Analysis of suspected genomic lesions in individual patients.
2. Genome wide association studies (GWAS).
3. Ancestry genotyping using ancestry informative markers (AIMS).

Question 14

How are SNPs inherited?

Answer 14

Mendelian-style.

Question 15

A group of multiple SNPs that occur together.

Answer 15

Haplotype.

Question 16

How might the significance of VUSs be resolved in the present time?

Answer 16

Checking parents and databases of information about population variants.

Question 17

What should one expect about VUSs in the future?

Answer 17

With increasing informationin databases, their significance can be ruled either benign or disease-causing.

Question 18

What kind of changes can NGS identify?

Answer 18

1. Recessive conditions (Two mutations in the same gene are needed)
2. Dominant conditions (One mutation is sufficient)

Question 19

Deleterious Mutation

Answer 19

Previously shown to be linked to a phenotype.

Question 20

Medically Actionable Mutations

Answer 20

Previously linked to preventable diseases with later onset.

Question 21

Epigenetics

Answer 21

Used to describe heritable changes in gene expression that arise from changes in the chromosomes without alteration of the DNA sequence.

Question 22

What may be the causes of methylation of DNA?

Answer 22

1. Normal process (different genes needed at different times).
2. Environmental stress or exposure.

Question 23

Can epigenetic modifications be passed on to offspring?

Answer 23

Yes, when imprinting is not reset.

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