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Single Nucleotide Polymorphisms (SNPs) – Detailed Notes


Single Nucleotide Polymorphisms (SNPs) – Detailed Notes


1. Definition

SNPs are single base-pair variations in the DNA sequence that occur at a specific position in the genome among individuals of a species.
Example: At a specific locus, one individual may have A while another has G:
Copy code

Individual 1: …A T C G A T…  
Individual 2: …A T C G G T…
SNPs are the most common type of genetic variation in most organisms.


2. Characteristics of SNPs


Single base change: Involves substitution of one nucleotide for another (A↔G, C↔T).
Biallelic nature: Most SNPs have only two alleles in a population.
Widespread in the genome: Found in coding regions (exons), non-coding regions (introns, promoters, intergenic regions).
Stable inheritance: Passed from generation to generation like other genetic markers.
Frequency: Occur approximately every 100–300 bp in the human genome.


3. Types of SNPs


SNPs are categorized based on location or effect on gene function:


A. Based on genomic location


Coding region SNPs (cSNPs):
Found in exons.
Can be:
Synonymous (silent): No change in amino acid.
Non-synonymous (missense): Changes amino acid → may affect protein function.
Nonsense: Creates a stop codon → truncated protein.
Non-coding region SNPs:
Located in introns, promoters, enhancers, or intergenic regions.
Can affect gene expression or splicing.
Regulatory SNPs (rSNPs):
Affect gene transcription or regulatory element binding.


B. Based on type of nucleotide change
Transition: Purine ↔ Purine (A↔G) or Pyrimidine ↔ Pyrimidine (C↔T)
Transversion: Purine ↔ Pyrimidine (A↔C, A↔T, G↔C, G↔T)
Indels (not strictly SNPs): Insertions or deletions of a single base.


4. Detection Methods of SNPs
SNPs can be detected using molecular techniques:
A. PCR-based methods
Allele-specific PCR (AS-PCR): Primers match specific SNP alleles.
PCR-RFLP: Restriction enzyme cuts DNA at SNP site.
B. Microarray-based methods
SNP arrays detect thousands of SNPs simultaneously using hybridization.
C. DNA sequencing
Sanger sequencing: Low throughput, accurate for individual SNPs.
Next-generation sequencing (NGS): High throughput, genome-wide SNP detection.
D. Other methods
TaqMan assays: Fluorescent probes for allele detection.
MALDI-TOF Mass spectrometry: Detects mass differences between alleles.
5. Applications of SNPs


Genetic mapping:
SNPs are used as molecular markers in constructing genetic linkage maps.
Association studies:
Genome-wide association studies (GWAS) link SNPs with disease susceptibility or traits.
Population genetics:
SNPs are used to study genetic diversity, evolutionary history, and migration patterns.
Marker-assisted selection (MAS):
In plants and animals, SNPs assist in selecting desirable traits.
Forensic analysis:
SNPs are used in identity testing, paternity testing, and ancestry analysis.
Pharmacogenomics:
SNPs help predict drug response and adverse reactions.

6. Advantages of SNPs


Abundant and widely distributed in the genome.
Stable and inherited in a Mendelian fashion.
Co-dominant markers: can distinguish heterozygotes and homozygotes.
Amenable to high-throughput automated detection.
Suitable for population-wide studies.


7. Limitations of SNPs


Usually biallelic, so less informative than multi-allelic markers like SSRs.
Functional consequences not always clear.
Detection may require expensive technology (arrays, NGS).
Rare SNPs may be missed in low-coverage studies.
8. Examples

SNP associated with lactose tolerance: -13910 C/T upstream of the LCT gene.
SNP in CYP2C9 gene: affects drug metabolism (warfarin sensitivity).
Plant breeding: SNPs used in rice, maize, and wheat to select yield-related traits.

Advantages

Abundant, stable, co-dominant, high-throughput


Limitations
Biallelic (less informative), expensive detection, may not affect function



SNP (Single Nucleotide Polymorphism) – 50 MCQs



What does SNP stand for?
a) Single Nucleotide Protein
b) Single Nucleotide Polymorphism ✅
c) Simple Nucleotide Pair
d) Short Nucleotide Polymorphism
SNP is a type of:
a) Chromosomal mutation
b) Single base-pair variation ✅
c) Large deletion
d) RNA modification
SNPs are most commonly:
a) Multi-allelic
b) Biallelic ✅
c) Triallelic
d) Rarely found in humans
SNPs occur approximately every:
a) 1–10 bp
b) 10–50 bp
c) 100–300 bp ✅
d) 1000–2000 bp
Which type of SNP is found in coding regions but does not change the amino acid?
a) Missense
b) Nonsense
c) Synonymous ✅
d) Frameshift
A non-synonymous SNP results in:
a) No change in protein
b) Amino acid change ✅
c) DNA replication
d) RNA splicing
Which SNP introduces a premature stop codon?
a) Synonymous
b) Missense
c) Nonsense ✅
d) Regulatory
Transition SNPs involve:
a) Purine ↔ Purine or Pyrimidine ↔ Pyrimidine ✅
b) Purine ↔ Pyrimidine
c) Indels
d) Large rearrangements
Transversion SNPs involve:
a) Purine ↔ Purine
b) Pyrimidine ↔ Pyrimidine
c) Purine ↔ Pyrimidine ✅
d) None of the above
SNPs in promoters or enhancers are called:
a) Coding SNPs
b) Regulatory SNPs ✅
c) Synonymous SNPs
d) Intergenic SNPs
Which is the most common type of SNP in the human genome?
a) Transition ✅
b) Transversion
c) Indel
d) Nonsense
SNPs are most frequently found in:
a) Exons
b) Introns and intergenic regions ✅
c) Ribosomal RNA genes
d) Mitochondrial DNA only
SNP detection can be done using:
a) PCR ✅
b) ELISA
c) Western blot
d) Northern blot
Which SNP detection method is high-throughput and genome-wide?
a) Sanger sequencing
b) PCR-RFLP
c) Next-generation sequencing (NGS) ✅
d) Allele-specific PCR
SNP arrays work based on:
a) Protein hybridization
b) DNA hybridization ✅
c) RNA transcription
d) Antibody binding
Which assay uses fluorescent probes for SNP detection?
a) PCR-RFLP
b) TaqMan assay ✅
c) Northern blot
d) Microarray
SNPs are co-dominant markers. This means:
a) Only dominant allele is detected
b) Can distinguish homozygotes and heterozygotes ✅
c) Cannot detect heterozygotes
d) Only used in bacteria
SNPs are useful in:
a) GWAS ✅
b) Protein crystallography
c) Enzyme kinetics
d) RNA splicing only
SNPs are less informative than SSRs because they are:
a) Abundant
b) Biallelic ✅
c) Stable
d) Co-dominant
Which plant is widely studied using SNP markers?
a) Arabidopsis ✅
b) E. coli
c) Yeast
d) Drosophila
SNPs in genes that affect drug response are used in:
a) Forensics
b) Pharmacogenomics ✅
c) Plant breeding
d) Population genetics
SNPs can be used to construct:
a) Protein tertiary structures
b) Genetic linkage maps ✅
c) RNA secondary structures
d) Chromosome staining
SNP detection using restriction enzymes is called:
a) PCR-RFLP ✅
b) Allele-specific PCR
c) NGS
d) TaqMan assay
SNPs are inherited in:
a) Random fashion
b) Mendelian fashion ✅
c) Only maternal fashion
d) Only paternal fashion
SNPs in coding regions that do not alter protein function are called:
a) Non-synonymous
b) Synonymous ✅
c) Nonsense
d) Regulatory
SNPs associated with lactose tolerance are located in:
a) LCT gene promoter ✅
b) Coding region of insulin gene
c) Exon of hemoglobin gene
d) Mitochondrial DNA
SNPs used in forensics help in:
a) Disease treatment
b) Identity and paternity testing ✅
c) Drug metabolism
d) Crop yield improvement
Which factor affects SNP frequency in a population?
a) Population size ✅
b) Protein structure
c) RNA concentration
d) Primer design
SNPs are useful for studying:
a) Evolutionary relationships ✅
b) Protein folding
c) Enzyme kinetics
d) Metabolic pathways
Which SNP type results in a different amino acid?
a) Synonymous
b) Missense ✅
c) Nonsense
d) Silent
Which SNP type results in truncated protein?
a) Missense
b) Nonsense ✅
c) Synonymous
d) Regulatory
SNP detection in high-throughput labs often uses:
a) ELISA
b) Capillary electrophoresis ✅
c) Western blot
d) Southern blot
SNPs in CYP2C9 gene affect:
a) DNA replication
b) Drug metabolism ✅
c) Protein folding
d) Crop yield
SNPs are abundant and stable, making them:
a) Poor genetic markers
b) Useful molecular markers ✅
c) Rarely used
d) Only used in animals
Which SNP detection method is suitable for a single locus in a small sample?
a) PCR-RFLP ✅
b) Microarray
c) NGS
d) GWAS
SNPs in plants are used for:
a) Yield trait selection ✅
b) Protein crystallization
c) RNA interference
d) Enzyme assays
Most SNPs in humans are:
a) Synonymous
b) Non-coding ✅
c) Frameshift
d) Nonsense
Allele-specific PCR uses primers that:
a) Bind to any DNA
b) Match specific SNP alleles ✅
c) Cut DNA
d) Bind RNA
SNP mutation occurs mainly due to:
a) Slipped-strand mispairing
b) Base substitution ✅
c) Large deletion
d) RNA editing
SNPs are useful in GWAS because they:
a) Affect protein folding
b) Serve as markers for trait association ✅
c) Detect RNA expression
d) Sequence proteins
SNP markers are considered co-dominant because they:
a) Show all alleles present ✅
b) Only detect dominant alleles
c) Cannot detect heterozygotes
d) Are random
Which is an example of a regulatory SNP?
a) SNP in promoter of LCT gene ✅
b) SNP in coding exon
c) Synonymous SNP
d) SNP in mitochondrial DNA
SNPs are more abundant than:
a) SSRs
b) Indels ✅
c) Chromosomes
d) Proteins
SNPs affecting gene expression are called:
a) Synonymous
b) Non-synonymous
c) Regulatory ✅
d) Missense
SNP arrays can detect:
a) Single locus only
b) Thousands of loci simultaneously ✅
c) Protein concentration
d) RNA sequences
SNPs can be used in:
a) Plants, animals, and microbes ✅
b) Only humans
c) Only bacteria
d) Only crops
TaqMan assay uses:
a) Fluorescent probes ✅
b) Restriction enzymes
c) Gel electrophoresis
d) Northern blot
Which of the following is a limitation of SNPs?
a) Biallelic → less informative ✅
b) Highly abundant
c) Co-dominant
d) Stable
SNP-based population studies help in:
a) Drug metabolism
b) Evolution and diversity studies ✅
c) RNA transcription
d) Protein folding
SNPs are detected by sequencing because:
a) Sequencing identifies single base changes ✅
b) Sequencing detects proteins
c) Sequencing measures enzyme activity
d) Sequencing detects RNA






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