Chapter 8 – Gene Mutations (Molecular Diagnostics, Lela Buckingham)

Which type of point mutation introduces a premature stop codon?
A. Silent mutation
B. Missense mutation
C. Nonsense mutation
D. Conservative substitution

C. Nonsense mutation

A mutation that changes leucine to valine in a protein is best described as
A. Nonsense mutation
B. Frameshift mutation
C. Silent mutation
D. Conservative missense mutation

D. Conservative missense mutation

Insertion of two nucleotides into a coding sequence will most likely
A. Cause a silent mutation
B. Change a single amino acid
C. Cause a frameshift mutation
D. Lead to no functional consequence

C. Cause a frameshift mutation

A trinucleotide repeat expansion in a gene is an example of
A. Point mutation
B. Deletion
C. Nonsense mutation
D. Dynamic mutation

D. Dynamic mutation

Which of the following best describes a dominant negative mutation?
A. Produces no protein
B. Introduces premature stop codon
C. Expands trinucleotide repeats
D. Mutant protein interferes with normal protein function

D. Mutant protein interferes with normal protein function

A silent mutation is least likely to
A. Alter protein function
B. Change the codon sequence
C. Be detected by DNA sequencing
D. Affect mRNA transcription

A. Alter protein function

Which method is best for detecting a known point mutation?
A. Sanger sequencing of entire gene
B. Denaturing HPLC
C. Allele-specific oligonucleotide (ASO) hybridization
D. SSCP

C. Allele-specific oligonucleotide (ASO) hybridization

Which method is most suitable for scanning for unknown mutations?
A. ASO hybridization
B. Allele-specific PCR
C. Sanger sequencing or NGS
D. ELISA

C. Sanger sequencing or NGS

Enzyme immunoassays detect mutations by
A. Sequencing DNA directly
B. Detecting nucleotide mismatches
C. Cleaving DNA at mutation sites
D. Measuring altered or absent protein products

D. Measuring altered or absent protein products

Immunohistochemistry (IHC) is primarily used to
A. Detect DNA point mutations
B. Separate proteins by size
C. Measure enzymatic activity in vitro
D. Localize and visualize protein expression in tissues

D. Localize and visualize protein expression in tissues

High-Performance Liquid Chromatography (HPLC) can detect
A. Nucleotide deletions
B. Trinucleotide repeats
C. mRNA transcripts
D. Hemoglobin variants or protein isoforms

D. Hemoglobin variants or protein isoforms

Gas chromatography is typically used to analyze
A. DNA mutations
B. Protein size
C. RNA splicing errors
D. Volatile compounds or metabolites

D. Volatile compounds or metabolites

Mass spectrometry is used in mutation detection to
A. Amplify DNA sequences
B. Visualize tissues
C. Detect single-nucleotide changes via hybridization
D. Determine protein mass/charge and post-translational modifications

D. Determine protein mass/charge and post-translational modifications

Which hybridization method uses a labeled probe complementary to a known mutation?
A. Southern blot
B. Dot blot
C. Northern blot
D. Allele-specific oligonucleotide (ASO) probe

D. Allele-specific oligonucleotide (ASO) probe

Which of the following is a polymerization-based sequencing method?
A. Dot blot
B. ELISA
C. Mass spectrometry
D. Sanger sequencing

D. Sanger sequencing

Enzymatic cleavage methods for mutation detection rely on
A. Antibody binding
B. Chromatography separation
C. Electrophoretic mobility shift
D. Cleavage at mismatched or specific sites

D. Cleavage at mismatched or specific sites

Which method is most appropriate for screening a population for a new, unknown mutation?
A. ASO hybridization
B. Allele-specific PCR
C. DNA sequencing (Sanger or NGS)
D. Enzyme immunoassay

C. DNA sequencing (Sanger or NGS)

For detecting a previously identified mutation, the fastest and most cost-effective method is
A. NGS
B. DHPLC
C. Mass spectrometry
D. Allele-specific PCR or ASO hybridization

D. Allele-specific PCR or ASO hybridization

In HGVS nomenclature, “c.76A>T” indicates
A. Protein-level change
B. Genomic DNA-level change
C. RNA-level change
D. Coding DNA-level change

D. Coding DNA-level change

A protein-level notation “p.Lys76*” represents
A. Missense mutation
B. Frameshift mutation
C. Silent mutation
D. Nonsense mutation resulting in stop codon

D. Nonsense mutation resulting in stop codon

Which HGVS prefix indicates a genomic DNA sequence?
A. c.
B. r.
C. p.
D. g.

D. g.

Which of the following is the correct gene vs protein notation?
A. BRCA1 protein, BRCA1 (gene)
B. BRCA1 (protein), BRCA1 (gene)
C. BRCA1 gene only
D. BRCA1 (gene), BRCA1 protein

D. BRCA1 (gene), BRCA1 protein

In which scenario would SSCP (single-strand conformation polymorphism) be most useful?
A. Detecting known point mutation with ASO probe
B. Measuring protein expression
C. Identifying post-translational modifications
D. Screening for unknown single-nucleotide changes

D. Screening for unknown single-nucleotide changes

Denaturing HPLC (DHPLC) separates DNA fragments based on
A. Molecular weight
B. Protein charge
C. GC content only
D. Sequence mismatches and melting properties

D. Sequence mismatches and melting properties

A frameshift mutation occurs due to
A. Substitution of one nucleotide
B. Trinucleotide repeat expansion in multiples of three
C. Silent point mutation
D. Insertion or deletion not divisible by three

D. Insertion or deletion not divisible by three

Which detection method is least suitable for a protein-level change?
A. ASO probe hybridization
B. Enzyme immunoassay
C. Immunohistochemistry
D. Mass spectrometry

A. ASO probe hybridization

Which of the following is an advantage of sequencing-based mutation detection?
A. Fastest for high-throughput protein analysis
B. Detects only known mutations
C. Requires antibodies for detection
D. Can identify unknown nucleotide changes anywhere in the target sequence

D. Can identify unknown nucleotide changes anywhere in the target sequence

Which method would be best for analyzing hemoglobinopathies?
A. SSCP
B. ASO probe
C. Enzymatic cleavage assay
D. HPLC

D. HPLC

What is the main purpose of nomenclature standardization (HGVS/HGNC)?
A. Facilitate protein purification
B. Predict patient phenotype automatically
C. Replace sequencing-based methods
D. Ensure consistent reporting of sequence changes and gene names

D. Ensure consistent reporting of sequence changes and gene names

Which method is most suitable for detecting post-translational protein modifications caused by a gene mutation?
A. ASO probe
B. Sequencing
C. DHPLC
D. Mass spectrometry

D. Mass spectrometry

Which detection method is most suitable for identifying a low-frequency mutation in a heterogeneous tumor sample?
A. Sanger sequencing
B. Allele-specific oligonucleotide (ASO) hybridization
C. Single-strand conformation polymorphism (SSCP)
D. Next-generation sequencing (NGS)

D. Next-generation sequencing (NGS)

A patient has a heterozygous deletion in the CFTR gene. Which method would most reliably detect this mutation?
A. DHPLC
B. Multiplex ligation-dependent probe amplification (MLPA)
C. Enzyme immunoassay
D. Mass spectrometry

B. Multiplex ligation-dependent probe amplification (MLPA)

A hemoglobin variant migrates differently on HPLC but is not detected by a DNA probe. Which is the most likely reason?
A. Silent mutation
B. Point mutation in coding DNA
C. Amino acid substitution altering protein charge
D. Frameshift mutation

C. Amino acid substitution altering protein charge

When using HGVS nomenclature, what does “c.35_36insG” indicate?
A. Substitution of G at position 35
B. Deletion of G at position 36
C. Insertion of G between nucleotides 35 and 36
D. Silent mutation at codon 35

C. Insertion of G between nucleotides 35 and 36

Which technique can detect both known and unknown point mutations but requires prior knowledge of the gene sequence?
A. Southern blot
B. DHPLC
C. Mass spectrometry
D. ELISA

B. DHPLC

A patient’s mutation is described as “p.Glu6Val”. Which disease is most likely associated with this mutation?
A. Cystic fibrosis
B. Sickle cell anemia
C. Beta-thalassemia
D. Tay-Sachs disease

B. Sickle cell anemia

Which detection method is most appropriate for screening a large population for a rare, previously identified point mutation?
A. Next-generation sequencing
B. Allele-specific PCR
C. Denaturing HPLC
D. Immunohistochemistry

B. Allele-specific PCR

Which of the following best explains why SSCP can miss some point mutations?
A. Only detects large deletions
B. Depends on protein folding changes
C. Detects only mutations that alter single-strand conformation
D. Only works for RNA sequences

C. Detects only mutations that alter single-strand conformation

A patient has a protein truncating mutation at p.Arg213*. Which molecular mechanism most likely caused this?
A. Frameshift insertion
B. Nonsense point mutation
C. Missense mutation
D. Silent mutation

B. Nonsense point mutation

In a DNA fragment with high GC content, which modification would help improve PCR amplification for mutation detection?
A. Increase Mg2+ concentration
B. Add DMSO or betaine to the reaction
C. Decrease primer annealing temperature below 45°C
D. Use Taq polymerase without proofreading

B. Add DMSO or betaine to the reactio