Genomics Quiz #1 Terminology

NDSU 2025 PSCI 417

PGx

Pharmacogenomics

There are _______ base pairs and ________ genes in the human genome.

3 Billion base pairs

20,000 genes

SNPs

Single Nucleotide Polymorphism. DNA sequence differs by a single nucleotide.

Transposition

Removal & transfer of a segment of DNA from one site to another of the same or different chromosome.

GWAS

Genome Wide Association Studies

Scans many different genomes to associate specific genetic variations w/ particular diseases.

SAEC

Serious Adverse Effects Consortium

INDELs

Insertion-Deletions.

DNA sequence differs by and insertion/deletion of a single/multiple nucleotides.

CNVs

Copy Number Variations.

Gene duplication; a single gene may occur multiple times of the same or different chromosomes.

STRs

Short-Tandem Repeats.

Short sequences repeated multiple times over.

BAC

Bacterial Artificial Chromosome

VNTRs

Variable-Number Tandem Repeats.

Other regions of the genome contain repeats with variable number of repetitions.

Genome

All the genetic material of an organism. Including material that encodes proteins, Functional RNA, and non-coding DNA sequences.

Genetic Variation

Differences between corresponding genomic sequences of individuals or populations.

Gene Promoters

May be “Housekeeping”, “Tissue Specific”, or “Inducible”. A single gene may have multiple promoters.

Activates genes to be synthesized/used.

Reasons for Mutations (5)

1. Errors during duplication

2. Radiation

3. Chemical Mutagens

4. Methylation/Deamination

5. Inefficient DNA repair enzymes

Somatic vs. Germinal Mutations

Somatic: mutations that happened to the body cells and are not passed down from genetics

Germinal: genetic mutations that come from sex genes and will be passed on to future generations

HGNC

HUGO Gene Nomenclature Committee

DNA Polymerase

Builds new strands of DNA by attaching to a stretch of dsDNA

Sanger Sequencing

Primer Extension/Chain-Termination, ddNTP addition

Most popular, adaptable, easily scaled.

Sequencing by ligation

1) High throughput, good for re-sequencing

2) Short-Read Lengths (non-ideal for de novo assembly)

Pyrosequencing

Measures chain extension by pyrophosphate monitoring. Releases visible light.

1) larger read length

2) high reagent cost

3) high error rate

Sequencing by Synthesis

highest output instrument exome, transcriptomic whole genome and targeted resequencing

NGS Next Generation Sequencing

Measures hydrogen ions that are released during the polymerization of the DNA.

Phenotype

Change in gene translation

Genotype

Change in encoding DNA

Linked Genes

Genes are close together & on the same chromosome. (Likely associated w/ eachother)

Genetic Map Distance

a measure of the relative location of genes on a chromosome, based on the frequency of meiotic recombination (crossovers) between them

centiMorgans (cM)

Corresponds to the % chance of a chromosomal recombination

Genomic Analysis

Provides insight into overall genetic make up of a person and genetic variation in their genes.

Transcriptomes

Specifically the mRNA molecules present in a tissue or cell type.

Epigenomes

DNA modifications that don’t change the DNA sequence, but regulate transcription.

Can be influenced by life experiences to environmental factors.

Stigmatization (Genetic Discrimination)

Treating a person differently than others based on genetic information

Race

Social Construct; based on physical characteristics and shared ancestry.

Ethnicity

Social Construct; based on heritage, language, traditions, and geographic origin.

Federal Law: GINA

Genetic Information Non-discrimination Act (GINA) (2008)

• Prohibits genetic discrimination in health insurance/employment

Risks of PGx research: (3)

Physical Risk: associated w/ ADRs or Non-Effective Medications

Time-Delay in initiating treatment.

Psychological Risks: Being excluded from a treatment option, not being offered a treatment

Informed Consent

Patient should be informed about risks/benefits of participation in medical treatment, procedure, or experimental intervention.

Patient must also understand what is being explained.

Patent

license granted by government conferring the temporary right to exclude others from making, using, or selling an intervention