Gene mapping and gene sequencing basics MCQs With Answer

Gene mapping and sequencing basics MCQs With Answer is designed for M.Pharm students to build a strong conceptual and practical foundation in genetic mapping and DNA sequencing technologies relevant to pharmacology and drug discovery. This set of questions emphasizes core principles—linkage analysis, recombination frequency, physical vs genetic maps, marker systems (RFLP, SSR, SNP), and sequencing strategies (Sanger, NGS, long-read platforms). It also covers data interpretation topics such as read coverage, Phred quality scores, alignment, variant calling, and applications like GWAS and targeted sequencing. These MCQs focus on analytical thinking and real-world laboratory considerations to help students integrate molecular genetics into pharmacological research and personalized medicine.

Q1. Which unit is commonly used to express genetic distance based on recombination frequency?

• Base pair (bp)
• CentiMorgan (cM)
• Kilobase (kb)
• Megabase (Mb)

Correct Answer: CentiMorgan (cM)

Q2. What does a recombination frequency of 1% between two loci usually indicate?

• They are 1 megabase apart on the chromosome
• They are 1 centiMorgan apart
• There is no linkage between them
• The loci are identical

Correct Answer: They are 1 centiMorgan apart

Q3. Which marker type provides the highest density and is most suitable for high-throughput genotyping in mapping studies?

• RFLP (Restriction Fragment Length Polymorphism)
• SSR (Simple Sequence Repeat)
• SNP (Single Nucleotide Polymorphism)
• AFLP (Amplified Fragment Length Polymorphism)

Correct Answer: SNP (Single Nucleotide Polymorphism)

Q4. Which sequencing method is considered the gold standard for accuracy and is frequently used to validate variants?

• Oxford Nanopore sequencing
• Illumina short-read sequencing
• Sanger dideoxy sequencing
• PACBIO SMRT sequencing

Correct Answer: Sanger dideoxy sequencing

Q5. What does a Phred quality score (Q) of 20 indicate about a base call?

• Probability of incorrect base call is 1 in 100
• Probability of incorrect base call is 1 in 10
• Probability of incorrect base call is 1 in 1000
• Probability of incorrect base call is zero

Correct Answer: Probability of incorrect base call is 1 in 100

Q6. In paired-end sequencing, what key advantage do paired reads provide for genome assembly?

• They double the base quality of single reads
• They allow direct detection of SNPs without mapping
• They provide linking information across repeats to scaffold contigs
• They eliminate the need for library preparation

Correct Answer: They provide linking information across repeats to scaffold contigs

Q7. Which algorithm or tool is commonly used for fast short-read alignment to a reference genome?

• BLASTn
• MAFFT
• BWA (Burrows-Wheeler Aligner)
• ClustalW

Correct Answer: BWA (Burrows-Wheeler Aligner)

Q8. What is the main difference between genetic (linkage) maps and physical maps?

• Genetic maps measure physical distances in base pairs; physical maps use recombination rates
• Genetic maps are based on recombination frequency; physical maps are based on actual DNA sequence distance
• Genetic maps only apply to prokaryotes; physical maps only apply to eukaryotes
• Genetic maps require sequencing; physical maps do not

Correct Answer: Genetic maps are based on recombination frequency; physical maps are based on actual DNA sequence distance

Q9. What is linkage disequilibrium (LD) most directly describing?

• Physical breakage of DNA strands
• Non-random association of alleles at different loci
• Equal recombination frequency across a chromosome
• Mutation rate at a single nucleotide

Correct Answer: Non-random association of alleles at different loci

Q10. Which sequencing platform is best known for very long read lengths useful in resolving structural variants and repetitive regions?

• Illumina HiSeq
• Ion Torrent
• PacBio SMRT or Oxford Nanopore
• Sanger sequencing

Correct Answer: PacBio SMRT or Oxford Nanopore

Q11. What does ‘coverage’ or ‘depth’ mean in the context of next-generation sequencing?

• Number of different libraries prepared for one sample
• Average number of times a nucleotide is read during sequencing
• Physical distance between paired reads
• Percentage of GC content in the genome

Correct Answer: Average number of times a nucleotide is read during sequencing

Q12. In linkage mapping for drug response traits, what does a high LOD score indicate?

• Low likelihood that a marker and trait are linked
• High likelihood of linkage between marker and trait locus
• The marker is a sequencing artifact
• The recombination frequency is greater than 50%

Correct Answer: High likelihood of linkage between marker and trait locus

Q13. Which library preparation strategy enriches for coding regions and is cost-effective for detecting exonic variants?

• Whole-genome shotgun sequencing
• RNA-seq
• Whole-exome sequencing (targeted capture)
• Bisulfite sequencing

Correct Answer: Whole-exome sequencing (targeted capture)

Q14. Which of the following is a common cause of false positive variant calls in NGS data?

• High sequencing depth across the region
• Presence of PCR duplicates and systematic sequencing errors
• Perfect mappability of reads
• High base quality scores (Q30+)

Correct Answer: Presence of PCR duplicates and systematic sequencing errors

Q15. What is the primary goal of de novo genome assembly?

• Map reads to an existing reference genome
• Determine gene expression levels
• Reconstruct the genome sequence from reads without using a reference
• Identify protein structures from sequence

Correct Answer: Reconstruct the genome sequence from reads without using a reference

Q16. Which marker system detects length polymorphisms due to variation in short tandem repeats and is useful for population genetics?

• SNP arrays
• SSR (microsatellites)
• RNA-seq derived markers
• PCR-RFLP

Correct Answer: SSR (microsatellites)

Q17. In variant calling pipelines, which step directly follows read alignment to the reference genome?

• Library preparation
• Variant annotation with clinical databases
• Marking/removing PCR duplicates and base quality recalibration
• De novo assembly

Correct Answer: Marking/removing PCR duplicates and base quality recalibration

Q18. Which experimental design is most appropriate for mapping recessive mutations in model organisms using next-generation sequencing?

• Single individual sequencing with no crosses
• Bulked segregant analysis (BSA) or mapping-by-sequencing using pooled progeny
• Transcriptome profiling of wild-type only
• ChIP-seq of regulatory elements

Correct Answer: Bulked segregant analysis (BSA) or mapping-by-sequencing using pooled progeny

Q19. What is a scaffold in genome assembly terminology?

• A single continuous read from the sequencer
• A set of contigs ordered and oriented using paired-end or long-range information
• A raw sequencing library before fragmentation
• A database of known gene annotations

Correct Answer: A set of contigs ordered and oriented using paired-end or long-range information

Q20. Which analysis is most appropriate for identifying genomic loci associated with complex drug-response traits in a human population?

• Linkage mapping in an F2 cross
• Genome-wide association study (GWAS)
• De novo assembly of a single individual’s genome
• Sanger sequencing of a housekeeping gene

Correct Answer: Genome-wide association study (GWAS)

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