Genetic Variation

Question 1

Genetic Variation Leading to an Observed Effect

Answer 1

• Variation must occur in protein coding genes
• May be dangerous or beneficial

Question 2

Primary Goal of Genome Sequence Projects

Answer 2

• Mapping out each chromosome w/ high resolution
• Underlying DNA sequences determined and annotated to identify coding and noncoding DNA regions
• Provides insight on the mechanisms of inherited diseases and genetic variability

Question 2

DNA Polymorphism

Answer 2

• Presence of one of two or more alleles at a chromosomal region, locus (differences in DNA sequence between people)
• Differs in single nucleotide base or no. of tandem repeats
• Resides MOSTLY in noncoding regions
• Allows for assembly of high density genetic maps, hence called DNA Markers
• Includes SNPs, VNTRs, CNVs

Question 3

DNA Markers

Answer 3

• Polymorphisms in DNA sequence that vary among individuals
• Act as genetic landmarks → can be used to track inheritance and locate nearby genes (genetic linkage)
• Also used to identify individuals (DNA profiling)
• Assembly of high-density genetic maps
• SNPs, CNVs, VNTRs
• Seen through microarray analysis, PCR, DNA sequencing, southern blot

Question 4

SNPs

Answer 4

Single nucleotide polymorphisms

• Single base-pair variations in DNA
• One of the most common types of genetic variation!
• Brought about by single nucleotide base substitutions
• SNPs near/linked a certain gene used as DNA markers for that specific gene
• SNPs on genes are passed down from parent to child

Location:

• Found in coding and noncoding regions
• 1/350 base pairs, hence millions of SNPs

Question 5

Detecting SNPs

Answer 5

Through DNA microarray analysis! We want to detect SNPs that are near genes as they act as DNA markers.

• Oligonucleotides that match common allele AND all possible variant SNP alleles are attached to wells
• Oligonucleotides of known sequence w/ complimentary nucleotide to SNP allele
• Fragments of cDNA of individual hybridized to the chip
• Possible to match emergent fluorescent patterns based on which SNP an individual has, including info to determine homo/heterozygous for each SNP
• Two possible SNP alleles which show different fluorescence
• Reveals variation in populations…

Question 6

VNTRs

Answer 6

Variable Number of Tandem Repeats.

• Short DNA sequences (~10–100 base pairs) repeated in tandem (back-to-back along the chromosome)
• Number of repeat units varies between individuals
• Typically found in noncoding regions
• Do not usually affect phenotype (often neutral)
• Source of differences between species
• Identified using PCR and gel electrophoresis

Question 7

How to detect VNTRs

Answer 7

PCR and gel electrophoresis. Used in the identification of individuals based on their DNA profiles. VNTR determines genetic familiy relationships and forensic relationships.

• Tandem repeat sites are targeted and amplified w/ sequence-specific primers targeting flanking regions of variable repeats
• Amplified DNA fragments can then be separated and detected using gel electrophoresis
• Smaller fragments move faster/further, larger fragments move slower, different individuals show different band patterns based on VNTR length
• Genetic profiles can then be compared across individuals

Question 8

Silent Variations

Answer 8

Variation in the DNA that occurs in noncoding DNA

• No effect as there is no change in protein

Question 9

Variations in Coding Genes

Answer 9

• Results in altered gene product / protein
• Can be dangerous

Question 10

Sickle Cell Anemia

Answer 10

• Characteristic variations in alleles are passed down from parent to child
• Cellular phenotype: Variation of the haemoglobin protein results in a sickled shape instead of biconcanve round
• Physiological phenotype: Oxygen is not carried as efficiently, blocking of the capillaries leading to anemia and acute pain

Question 11

Genotype

Answer 11

Representation of the pair of alleles carried by a person

Question 12

Phenotype

Answer 12

Cell or bodies’ interpretation of the genotype

• Observable characteristics

Question 13

Genotype Combinations of Sickle Cell Anemia Alleles!

Answer 13

• Beta-globin protein gene lies on chromosome 11 (autosome)

HOMOZYGOUS HBA:

• Functional beta-globin w/ biconcave shape (cellular phenotype)
• Healthy RBC and individual (physiological phenotype)

HOMOZYGOUS HBS:

• HbS is sickle cell genotype results from single nucleotide polymorphism in beta hemoglobin gene –> AA sub of glutamine to valine –> altered teriatary structure of protein
• Homozygous for HbS alleles –> nonfunctional beta-globin w/ rod shape —-> cells assume a sickled shape (cellular phenotype)
• Decreased efficiency of hemoglobin to bind to oxygen, sickle cell individual (physiological phenotype)

HETEROZYGOUS HBA/HBS

• No symptoms of sickle cell anemia!!! though cells exhibit both protein variants
• Some of the beta-hemoglobin will be rod shaped, others will be normal
• Heterozygotes produce enough of normal hemoglobin to overcome abnormal hemoglobin

Question 14

Selective Advantageous of Heterozygous HbA/HbS individuals

Answer 14

In regions prominent w/ malaria… heterozygotes are resistant

• Homozygous is harmful at cellular phenotype and functioning level, but advantageous in these regions regardless

Question 15

Haplotypes p.t. Sickle Cell Anemia

Answer 15

• A haplotype is a group of linked alleles or SNPs on the same chromosome that are inherited together
• Different sickle cell alleles arose independently in multiple populations
• 5 distinct β-globin haplotypes are found in regions with high prevalence of sickle cell anemia
• Each haplotype is associated with a specific pattern of SNPs in the β-globin gene region

Question 16

CNV

Answer 16

Copy Number Variations

• Variations in gene copy number
• Contributes to genetic differences between individuals
• Can occur in coding/noncoding regions
• Duplications/deletions of region in a genome
• Gene duplications are found adjacent to eachother

Question 17

How to identify CNVs

Answer 17

• Based on relative fluorescence intensities that are detected during DNA microarray analysis
• Greater no. of copies = higher fluorescence

Question 18

AMY1 gene

Answer 18

• Codes for starch digesting enzyme, amylase
• Detectable no. of copy number differences along chromosome 1 w/ varying individuals w/ varying ancestry
• Low starch diets –> fewer copies
• High starch diets –> more copies
• Gene copy variations are a direct reflection of selective pressures, where extra copies aid in digesting starch (BENEFICIAL)