Microarray techniques and applications MCQs With Answer

Introduction: Microarray techniques and applications MCQs With Answer provides M.Pharm students a concise, exam-focused review of microarray technology used in cellular and molecular pharmacology. This compilation covers core concepts—from array fabrication, probe design, labeling and hybridization, to data preprocessing, normalization, and downstream analyses like differential expression, clustering and pathway interpretation. Questions emphasize experimental design, quality controls, platform differences (cDNA, oligonucleotide, bead arrays), and practical limitations such as cross-hybridization and dynamic range. Each MCQ includes targeted distractors and clear answers to reinforce learning, prepare for exams, and support research planning or critical evaluation of microarray-based pharmacogenomics and toxicogenomics studies.

Q1. What is the primary difference between cDNA microarrays and in-situ synthesized oligonucleotide arrays?

• cDNA arrays use long DNA fragments printed onto slides; in-situ arrays synthesize short oligonucleotides directly on the surface
• cDNA arrays measure protein levels; in-situ arrays measure DNA methylation only
• cDNA arrays require rolling circle amplification; in-situ arrays use bead-based hybridization
• cDNA arrays use photolithography; in-situ arrays are always glass-supported

Correct Answer: cDNA arrays use long DNA fragments printed onto slides; in-situ arrays synthesize short oligonucleotides directly on the surface

Q2. Which labeling strategy is most commonly used in two-color microarray experiments to control for dye bias?

• Single-color labeling with Cy3 only
• Dye-swap labeling between replicates
• Labeling with radioactive isotopes
• Using biotin-streptavidin detection without dyes

Correct Answer: Dye-swap labeling between replicates

Q3. In microarray data preprocessing, what is the main purpose of normalization?

• To convert fluorescence signals into concentration units
• To remove systematic technical variation so biological differences are comparable
• To identify probe sequences with low GC content
• To multiply all intensities by a constant to increase signal

Correct Answer: To remove systematic technical variation so biological differences are comparable

Q4. Which normalization method is especially used for two-color microarrays to correct intensity-dependent dye biases?

• Quantile normalization
• Loess (local regression) normalization
• RMA (Robust Multi-array Average)
• Median polish

Correct Answer: Loess (local regression) normalization

Q5. What is a key advantage of bead-based (Illumina) microarrays over traditional spotted arrays?

• Bead arrays are restricted to prokaryotic samples only
• Bead arrays offer higher feature redundancy and manufacturing uniformity
• Bead arrays cannot detect SNPs
• Bead arrays require microfluidic channels for hybridization

Correct Answer: Bead arrays offer higher feature redundancy and manufacturing uniformity

Q6. Which quality metric indicates spot morphology and helps flag poor hybridization or printing defects?

• Signal-to-noise ratio (SNR)
• Spot circularity and uniformity metrics (e.g., spot shape)
• False discovery rate (FDR)
• Benjamini–Hochberg adjusted p-value

Correct Answer: Spot circularity and uniformity metrics (e.g., spot shape)

Q7. Comparative Genomic Hybridization (aCGH) microarrays are primarily used to detect:

• Differential gene expression between tissues
• Copy number variations (deletions/amplifications) across the genome
• Protein–DNA interactions
• Alternative splicing events only

Correct Answer: Copy number variations (deletions/amplifications) across the genome

Q8. In an expression microarray experiment, which control is commonly spiked into samples to monitor labeling and hybridization efficiency?

• Housekeeping genes only
• Exogenous RNA spike-in controls of known concentration
• Genomic DNA fragments from the same organism
• Unlabeled competitor oligonucleotides

Correct Answer: Exogenous RNA spike-in controls of known concentration

Q9. What is a major limitation of microarrays compared with RNA-Seq for transcriptome analysis?

• Microarrays have unlimited dynamic range compared to RNA-Seq
• Microarrays cannot detect novel transcripts not represented on the array
• Microarrays directly measure absolute transcript copy numbers
• Microarrays are always more sensitive to low-abundance transcripts

Correct Answer: Microarrays cannot detect novel transcripts not represented on the array

Q10. Which probe characteristic is most important to minimize non-specific hybridization on oligonucleotide arrays?

• High secondary structure propensity
• Similar melting temperature (Tm) across probes and balanced GC content
• Variable probe lengths within the same array feature
• Inclusion of repeat sequences in probe design

Correct Answer: Similar melting temperature (Tm) across probes and balanced GC content

Q11. ChIP-chip combines chromatin immunoprecipitation with microarrays primarily to map:

• RNA-protein interaction sites genome-wide
• Protein–DNA binding sites and transcription factor occupancy
• Global DNA methylation at single-base resolution
• Copy number variation in cancer cells

Correct Answer: Protein–DNA binding sites and transcription factor occupancy

Q12. Which statistical correction is commonly applied when testing thousands of genes to control the expected proportion of false positives?

• Student’s t-test without adjustment
• Benjamini–Hochberg false discovery rate (FDR) correction
• Bonferroni correction applied to each probe individually without consideration
• No correction is necessary for microarray data

Correct Answer: Benjamini–Hochberg false discovery rate (FDR) correction

Q13. For exon arrays used to study alternative splicing, which analysis step is crucial beyond standard gene-level expression?

• Aggregating all probes into a single average only
• Exon-level normalization and splice-index or differential exon usage analysis
• Removing all probes that map to known exons
• Using only genomic DNA as a reference

Correct Answer: Exon-level normalization and splice-index or differential exon usage analysis

Q14. Which hybridization parameter is adjusted to increase stringency and reduce mismatched probe binding?

• Lowering hybridization temperature
• Increasing salt concentration in hybridization buffer
• Raising hybridization/wash temperature and reducing salt concentration
• Adding more fluorescent dye to the sample

Correct Answer: Raising hybridization/wash temperature and reducing salt concentration

Q15. What does a high signal-to-noise ratio (SNR) indicate for a microarray feature?

• The spot intensity is low relative to background
• The measured signal is strong relative to background variability, indicating confident detection
• There is significant cross-hybridization contaminating the signal
• The probe sequence is likely unmappable

Correct Answer: The measured signal is strong relative to background variability, indicating confident detection

Q16. Which application of microarrays is most directly relevant to pharmacogenomics?

• Profiling differential gene expression related to drug response and metabolism
• Mapping protein tertiary structures
• Measuring tissue mechanical properties
• Quantifying small-molecule concentrations in plasma

Correct Answer: Profiling differential gene expression related to drug response and metabolism

Q17. During microarray scanner calibration, which parameter is optimized to avoid signal saturation while maintaining sensitivity?

• Hybridization buffer composition
• Laser power and photomultiplier tube (PMT) gain settings
• Probe synthesis chemistry
• Genome annotation database version

Correct Answer: Laser power and photomultiplier tube (PMT) gain settings

Q18. Which downstream analysis method groups genes with similar expression patterns to infer co-regulation or shared pathways?

• Hierarchical clustering or k-means clustering
• PCR amplification
• Western blotting
• Mass spectrometry-based proteomics

Correct Answer: Hierarchical clustering or k-means clustering

Q19. What is the role of background subtraction in microarray image processing?

• To increase the measured intensity of all spots equally
• To remove local non-specific fluorescence and scanner background from spot signals
• To correct probe sequence mismatches
• To convert intensity values to fold-change directly

Correct Answer: To remove local non-specific fluorescence and scanner background from spot signals

Q20. Why is validation of microarray results by quantitative RT-PCR recommended?

• qRT-PCR uses the same probes and therefore is redundant
• Microarrays provide qualitative but less precise quantitative results; qRT-PCR offers higher sensitivity and specificity for selected transcripts
• qRT-PCR is cheaper for genome-wide discovery
• Validation is not needed if microarray p-values are significant

Correct Answer: Microarrays provide qualitative but less precise quantitative results; qRT-PCR offers higher sensitivity and specificity for selected transcripts

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