shane Flashcards
- What is a key advantage of Next-Generation Sequencing (NGS) over Sanger sequencing?
A) NGS is more accurate than Sanger sequencing
B) NGS is significantly cheaper per megabase of sequence data
C) Sanger sequencing can process more DNA in parallel than NGS
D) NGS requires cloning DNA fragments before sequencing
Answer: B) NGS is significantly cheaper per megabase of sequence data
- Which of the following sequencing technologies is the most widely used today?
A) SOLiD (Life Technologies)
B) Illumina
C) Ion Torrent
D) Pacific Biosciences (PacBio)
Answer: B) Illumina
- What is the major drawback of Oxford Nanopore sequencing?
A) Short read lengths
B) Low throughput
C) High error rate (5-40%)
D) Requirement for PCR amplification
Answer: C) High error rate (5-40%)
- Why is PCR amplification not required in PacBio sequencing?
A) It uses reversible terminator chemistry
B) It sequences DNA directly as it passes through a nanopore
C) It captures long reads using single-molecule real-time (SMRT) technology
D) It relies on chemical fluorescence for detection
Answer: C) It captures long reads using single-molecule real-time (SMRT) technology
- What is the function of reversible terminators in Illumina sequencing?
A) To allow stepwise addition of nucleotides during sequencing cycles
B) To permanently terminate DNA synthesis
C) To selectively bind to adenine bases only
D) To directly sequence RNA instead of DNA
Answer: A) To allow stepwise addition of nucleotides during sequencing cycles
- What is a major advantage of Illumina paired-end sequencing?
A) It increases read accuracy and alignment quality
B) It only sequences one DNA strand at a time
C) It uses chemical fluorescence instead of imaging
D) It eliminates sequencing errors completely
Answer: A) It increases read accuracy and alignment quality
- In an Illumina sequencing run, what does a high fluorescence intensity at a cycle indicate?
A) That many clusters contain the same nucleotide incorporation at that position
B) That sequencing has failed\
C) That no DNA has been synthesized
D) That the sample contains only A-T rich regions
Answer: A) That many clusters contain the same nucleotide incorporation at that position
- How does Ion Torrent sequencing detect nucleotides?
A) By measuring changes in pH caused by proton release during DNA polymerization
B) By detecting fluorescent signals\
C) By sequencing DNA through a nanopore
D) By using mass spectrometry to differentiate bases
Answer: A) By measuring changes in pH caused by proton release during DNA polymerization
. What is a major limitation of Ion Torrent sequencing?
A) High cost per base compared to Illumina
B) Difficulty in distinguishing homopolymer regions (e.g., AAAA or TTTT stretches)
C) Short read lengths compared to Sanger sequencing
D) Low sequencing speed
Answer: B) Difficulty in distinguishing homopolymer regions (e.g., AAAA or TTTT stretches)
- What is the main advantage of PacBio sequencing over Illumina?
A) Higher accuracy in single-pass reads
B) Ability to sequence long reads (>10 kb) without amplification
C) Lower cost per base
D) Requires lower DNA input for sequencing
Answer: B) Ability to sequence long reads (>10 kb) without amplification
- How does Oxford Nanopore sequencing detect DNA bases?
A) By measuring changes in electrical current as DNA bases pass through a nanopore
B) By detecting fluorescence emitted by labeled nucleotides
C) By analyzing differences in mass-to-charge ratios
D) By using chemical probes to bind specific bases
Answer: A) By measuring changes in electrical current as DNA bases pass through a nanopore
- What is a major challenge in Oxford Nanopore sequencing?
A) Short read lengths
B) Very high sequencing cost
C) High error rates compared to other sequencing technologies
D) Requirement for specialized imaging equipment
Answer: C) High error rates compared to other sequencing technologies
- In an NGS read quality graph, what does a sharp decline in Phred score towards the end of the reads indicate?
A) Increased sequencing errors in later cycles
B) Higher confidence in base calls
C) Shorter fragment lengths in the library
D) Better sequencing accuracy
Answer: A) Increased sequencing errors in later cycles
- In an Illumina cluster density image, what does a high-density cluster pattern suggest?
A) Overloading of DNA onto the flow cell, leading to poor sequencing quality
B) An optimal number of DNA fragments for sequencing
C) Poor nucleotide incorporation
D) Uneven base distribution in the genome
Answer: A) Overloading of DNA onto the flow cell, leading to poor sequencing quality
- Which sequencing technology would be most suitable for detecting structural variants and large genomic rearrangements?
A) Illumina short-read sequencing
B) Oxford Nanopore long-read sequencing
C) Sanger sequencing
D) Ion Torrent sequencing
Answer: B) Oxford Nanopore long-read sequencing
- Why is NGS preferred for clinical diagnostics over Sanger sequencing?
A) It allows parallel sequencing of millions of DNA fragments
B) It has lower error rates than all other sequencing methods
C) It does not require bioinformatics for data analysis
D) It is the only method that can detect single-nucleotide polymorphisms (SNPs)
Answer: A) It allows parallel sequencing of millions of DNA fragments
- What is a key challenge in analyzing large NGS datasets?
A) High computational demand for alignment and variant calling
B) Lack of software tools for analysis
C) Limited accuracy of NGS technologies
D) NGS data cannot be used for human genetics studies
Answer: A) High computational demand for alignment and variant calling
- What is the major reason for using single-cell sequencing?
A) To study cellular heterogeneity within tissues
B) To replace bulk RNA sequencing
C) To identify large chromosomal deletions
D) To increase sequencing read lengths
Answer: A) To study cellular heterogeneity within tissues
- What is the purpose of bioinformatics in NGS analysis?
A) To assemble, align, and analyze sequencing data
B) To manually inspect all sequencing reads
C) To replace the need for sequencing experiments
D) To directly visualize nucleotide sequences
Answer: A) To assemble, align, and analyze sequencing data
- Which of the following is an emerging trend in sequencing technology?
A) Ultra-long read sequencing (>100 kb)
B) Reducing the use of sequencing in clinical settings
C) Increased reliance on Sanger sequencing
D) Complete elimination of sequencing errors
Answer: A) Ultra-long read sequencing (>100 kb)
- What percentage of the human genome is covered by Whole Exome Sequencing (WES)?
A) 0.1%
B) 1%
C) 10%
D) 50%
Answer: B) 1%
- Why is Whole Exome Sequencing (WES) an effective method for identifying disease-causing mutations?
A) It sequences only the promoter regions of genes
B) It focuses on protein-coding genes, where 85% of disease-causing mutations occur
C) It does not require bioinformatics analysis
D) It sequences all non-coding regions of the genome
Answer: B) It focuses on protein-coding genes, where 85% of disease-causing mutations occur
- What is the significance of The Cancer Genome Atlas (TCGA) project?
A) It sequenced all known cancer patients worldwide
B) It established a database of genomic mutations linked to different cancer types
C) It focused exclusively on lung cancer genomics
D) It aimed to eliminate all cancer mutations
Answer: B) It established a database of genomic mutations linked to different cancer types
- What is the difference between inherited and somatic mutations in cancer?
A) Inherited mutations are acquired over a lifetime, whereas somatic mutations are present from birth
B) Somatic mutations occur only in germline cells
C) Inherited mutations are passed from parents, whereas somatic mutations arise spontaneously in somatic cells
D) Somatic mutations affect all cells in an individual
Answer: C) Inherited mutations are passed from parents, whereas somatic mutations arise spontaneously in somatic cells
- What is a “driver mutation” in cancer?
A) A mutation that provides a selective growth advantage to cancer cells
B) A mutation that causes only benign tumors
C) A mutation that affects only non-coding regions of DNA
D) A mutation that does not contribute to tumorigenesis
Answer: A) A mutation that provides a selective growth advantage to cancer cells
- How does genomic sequencing contribute to precision oncology?
A) It identifies mutations that can be targeted with specific drugs
B) It replaces the need for chemotherapy
C) It eliminates all mutations in cancer cells
D) It provides a universal treatment for all cancer patients
Answer: A) It identifies mutations that can be targeted with specific drugs
- In lung cancer treatment, why is it important to identify EGFR mutations before prescribing EGFR inhibitors?
A) Only patients with EGFR mutations will respond to these targeted therapies
B) EGFR inhibitors work on all cancer types
C) Mutations in EGFR indicate resistance to treatment
D) EGFR mutations do not affect drug response
Answer: A) Only patients with EGFR mutations will respond to these targeted therapies
- Why is exome sequencing useful for diagnosing Mendelian diseases?
A) Mendelian disorders are caused by mutations in protein-coding regions
B) It detects structural variations in non-coding regions
C) It can sequence the entire human genome
D) It eliminates all genetic disorders
Answer: A) Mendelian disorders are caused by mutations in protein-coding regions
- What was the first case where exome sequencing successfully diagnosed and treated a rare disorder?
A) Cystic fibrosis
B) Miller syndrome (DHODH mutations)
C) Huntington’s disease
D) Breast cancer (BRCA mutations)
Answer: B) Miller syndrome (DHODH mutations)
- How was exome sequencing used to save Nicholas Volker?
A) It identified a mutation in the XIAP gene, leading to a bone marrow transplant
B) It confirmed he had no genetic mutations
C) It was used to develop an experimental chemotherapy drug
D) It found a cure for all genetic disorders
Answer: A) It identified a mutation in the XIAP gene, leading to a bone marrow transplant
- How early in pregnancy can fetal DNA be detected in maternal blood?
A) Immediately after conception
B) 4-5 weeks
C) 20 weeks
D) At birth
Answer: B) 4-5 weeks
- What is the main advantage of fetal DNA sequencing over amniocentesis?
A) It is non-invasive and poses no risk to the fetus
B) It provides 100% accuracy in detecting genetic conditions
C) It is cheaper than traditional prenatal screening
D) It does not require maternal blood samples
Answer: A) It is non-invasive and poses no risk to the fetus
- Which chromosomal abnormalities can fetal DNA sequencing routinely detect?
A) Down syndrome (Chr. 21), Trisomy 18, and Trisomy 13
B) Only X-linked disorders
C) Only recessive single-gene disorders
D) All genetic conditions
Answer: A) Down syndrome (Chr. 21), Trisomy 18, and Trisomy 13
- What is the purpose of targeted gene panel sequencing?
A) To analyze specific genes associated with a disease while reducing sequencing costs
B) To sequence the entire genome of an individual
C) To replace whole-genome sequencing in all applications
D) To identify environmental risk factors for disease
Answer: A) To analyze specific genes associated with a disease while reducing sequencing costs
- What is a key advantage of using targeted gene panels over whole-genome sequencing (WGS)?
A) Smaller, more manageable datasets for analysis
B) More accurate for detecting large chromosomal deletions
C) Identifies all possible mutations in the genome
D) Does not require bioinformatics tools
Answer: A) Smaller, more manageable datasets for analysis
- What are the two main methods for targeted sequencing?
A) Hybridization-based target enrichment and amplicon sequencing
B) Sanger sequencing and RNA-seq
C) Whole-genome sequencing and whole-exome sequencing
D) PCR and fluorescence microscopy
Answer: A) Hybridization-based target enrichment and amplicon sequencing
- How does hybridization-based target enrichment work?
A) By using biotinylated probes to capture regions of interest, followed by magnetic isolation
B) By sequencing the entire genome and filtering unwanted regions
C) By amplifying all coding and non-coding sequences indiscriminately\
D) By directly visualizing DNA fragments under a microscope
Answer: A) By using biotinylated probes to capture regions of interest, followed by magnetic isolation
- What is a major advantage of amplicon sequencing in targeted panels?
A) It allows for high-multiplex sequencing of small regions
B) It can sequence the entire genome
C) It does not require PCR amplification
D) It is more accurate than whole-genome sequencing
Answer: A) It allows for high-multiplex sequencing of small regions
- What clinical applications commonly use targeted sequencing panels?
A) Hereditary cancer risk screening
B) Population genetics
C) Ancient DNA analysis
D) Forensic fingerprinting
Answer: A) Hereditary cancer risk screening
- What is the main reason for using predesigned targeted sequencing panels?
A) They provide well-validated gene sets for specific diseases
B) They eliminate sequencing errors completely
C) They can analyze all genes in the human genome
D) They do not require sequencing instruments
Answer: A) They provide well-validated gene sets for specific diseases
