Shane Flashcards
What is the primary economic advantage of Next Generation Sequencing (NGS) over Sanger Sequencing for large-scale genomic projects?
A) NGS has a lower cost per megabase (€0.05/Mb) compared to Sanger Sequencing (€500/Mb).
B) NGS has a higher throughput per run.
C) NGS requires less sample preparation.
D) NGS has a faster run time.
A
Which sequencing technology is known for using reversible dye terminators and a polymerase for sequencing?
A) SOLiD
B) Ion Torrent
C) Illumina
D) Oxford Nanopore
C
What is a key challenge of using single DNA molecules as sequencing templates in technologies like Pacific Biosciences and Oxford Nanopore?
A) High cost of sequencing
B) Difficulty in keeping single molecules stable during sequencing
C) Requirement for clonal amplification
D) Low throughput per run
B
How does Illumina’s reversible terminator chemistry contribute to its sequencing process?
A) It allows for single molecule sequencing without amplification.
B) It enables massively parallel detection on immobilized molecular colonies.
C) It eliminates the need for imaging during sequencing.
D) It reduces the error rate to below 1%.
B
What distinguishes Ion Torrent sequencing from other NGS technologies in terms of data acquisition?
A) It uses bridge amplification for clonal amplification.
B) It sequences DNA on a chip without requiring imaging.
C) It relies on reversible dye terminators.
D) It has the longest read lengths among NGS technologies.
B
Which of the following is a significant advantage of PacBio sequencing despite its high error rate?
A) High throughput per run
B) Very long read lengths, averaging 10-15kb and up to 40kb
C) Low cost per run
D) Short run time
B
What is the principle behind the detection method used in Oxford Nanopore sequencing?
A) Imaging every cycle to detect base incorporation
B) Measuring the current flow through a nanopore as DNA bases pass through
C) Using reversible dye terminators for base detection
D) Observing DNA modifications during sequencing
B
Which sequencing technology is characterized by a very high error rate ranging from 5-40%?
A) Illumina
B) SOLiD
C) Ion Torrent
D) Oxford Nanopore
D
What determines the spacing of molecular clusters on an Illumina flow cell?
A) The type of polymerase used
B) The initial seeding of single molecules onto the flow cell
C) The length of the DNA fragments
D) The temperature of the sequencing reaction
B
What is the main advantage of paired-end sequencing in Illumina technology?
A) It reduces the error rate.
B) It allows for sequencing of longer fragments by reading both ends.
C) It eliminates the need for clonal amplification.
D) It increases the throughput per run.
B
How does Ion Torrent sequencing detect nucleotide incorporation?
A) By measuring changes in pH
B) By imaging fluorescent signals
C) By observing DNA modifications
D) By measuring current flow through a nanopore
A
What is a common strategy to mitigate the high error rate in PacBio sequencing?
A) Using shorter read lengths
B) Performing multiple passes of the same molecule
C) Increasing the concentration of polymerase
D) Reducing the sequencing speed
B
What is the typical range of read lengths achievable with Oxford Nanopore sequencing?
A) 100-500bp
B) 1-5kb
C) 5-50kb
D) 50-100kb
C
What is the purpose of imaging every cycle in Illumina sequencing?
A) To detect DNA modifications
B) To measure the incorporation of reversible dye terminators
C) To stabilize single DNA molecules
D) To amplify the DNA fragments
B
What is a key advantage of sequencing on the chip in Ion Torrent technology?
A) It allows for real-time data acquisition.
B) It eliminates the need for clonal amplification.
C) It reduces the overall cost of sequencing.
D) It increases the read length.
A
How does PacBio sequencing enable the observation of DNA modifications?
A) By using reversible dye terminators
B) By measuring changes in pH
C) By detecting changes in the polymerase kinetics
D) By imaging fluorescent signals
C
Which of the following are commercial products offered by Oxford Nanopore?
A) MinION and GridION
B) SOLiD and Ion Torrent
C) Illumina and PacBio
D) Sanger and Nanopore
A
What makes Illumina’s sequencing chemistry robust and reliable?
A) The use of single molecule sequencing
B) The use of reversible dye terminators and a polymerase
C) The elimination of imaging steps
D) The high throughput per run
B
What is a common cause of errors in Ion Torrent sequencing?
A) Misincorporation of nucleotides
B) Inaccurate pH measurement
C) Incomplete dye terminator removal
D) Polymerase slippage
B
What is a limitation of PacBio sequencing in terms of throughput?
A) Low throughput per run (~1 million reads on PacBio SEQUEL machine)
B) Short read lengths
C) High cost per run
D) Long run time
A
What percentage of the human genome is covered by whole exome sequencing?
A) 0.1%
B) 1%
C) 10%
D) 50%
B
What percentage of disease-causing mutations are found in the exome?
A) 50%
B) 65%
C) 85%
D) 95%
C
What is the purpose of the Agilent Sure Select Capture Array in whole exome sequencing?
A) To amplify DNA fragments
B) To hybridize target sequences
C) To sequence DNA directly
D) To visualize DNA fragments
B
How many patients’ cancer tissues were collected for the Cancer Genome Atlas (TCGA) project?
A) 1,000
B) 5,000
C) 11,000
D) 20,000
C
What is the primary goal of sequencing both cancer tissue and normal tissue in cancer genome sequencing?
A) To identify inherited mutations
B) To find genetic changes and suggest possible therapies
C) To measure gene expression levels
D) To detect epigenetic modifications
B
Which of the following genes is commonly known to be mutated in various cancer types?
A) TP53
B) MYH7
C) CFTR
D) HBB
A
Which pathway is commonly associated with cancer mutations?
A) Wnt
B) MAPK
C) PI3K/AKT
D) All of the above
D
Which gene mutation is targeted by the drug Gefitinib?
A) BRAF
B) EGFR
C) HER2
D) MET
B
Approximately how many Mendelian diseases have been solved since 2008?
A) 500
B) 1,000
C) 2,000
D) 4,000
C
What gene mutation was identified in Nicholas Volker, the first child saved by Next Generation DNA Sequencing?
A) BRCA1
B) XIAP
C) CFTR
D) TP53
B
What percentage of circulating DNA in maternal blood is foetal DNA during pregnancy?
A) 1-2%
B) 4-10%
C) 15-20%
D) 25-30%
B
What is a key advantage of using target gene panel sequencing over whole genome sequencing?
A) Higher accuracy
B) Smaller, more manageable data sets
C) Longer read lengths
D) Lower error rates
B
In target enrichment, what is used to capture regions of interest?
A) Biotinylated probes
B) PCR primers
C) Fluorescent dyes
D) Restriction enzymes
A
How many targets can be sequenced at a time using amplicon sequencing?
A) 1-10
B) 26-1536
C) 2000-5000
D) 10,000-20,000
B
Which Illumina panel targets 94 genes associated with a predisposition towards cancer?
A) TruSight One Panel
B) TruSight Cardio Panel
C) TruSight Inherited Disease Panel
D) TruSight Cancer Panel
D
What is the first step in the enrichment-based library preparation workflow?
A) Hybridization of biotinylated probes to targeted regions
B) DNA isolation
C) Sequencing
D) Data analysis
B
According to the diagram on cancer genome sequencing, what is the final step before treatment planning?
A) DNA/RNA extraction
B) Sequencing
C) Alignment to reference genome
D) Integration and interpretation
D
In the SureSelect Target Enrichment System, what is used to select targeted regions after hybridization?
A) Magnetic streptavidin beads
B) Fluorescent markers
C) PCR amplification
D) Gel electrophoresis
A
Which pathway is NOT commonly associated with cancer mutations according to the lecture?
A) Wnt
B) PI3K/AKT
C) Ras/Raf
D) Insulin signaling
D
According to the diagram on targeted sequencing panels, what is the compatibility of the TruSight HLA v2 Sequencing Panel?
A) MiniSeq, MiSeq, and NextSeq Series
B) HiSeq Series only
C) PacBio Series
D) Ion Torrent Series
A
What is a DNA microarray (DNA Chip)?
A) A collection of microscopic DNA spots attached to a solid surface
B) A method for sequencing DNA
C) A technique for amplifying DNA
D) A tool for visualizing DNA fragments
A
What is the function of DNA probes on a microarray?
A) To amplify DNA sequences
B) To bind fluorescently labelled target sequences
C) To sequence DNA directly
D) To visualize DNA fragments
B
Who developed the concept of DNA microarrays in the mid-1980s?
A) Edwin Southern
B) Patrick Brown
C) Mark Schena
D) Lehrach’s group
D
What is the core principle behind DNA microarrays?
A) Amplification
B) Hybridisation
C) Sequencing
D) Visualization
B
Which type of DNA microarray uses photolithography to place probes on a glass or silicon surface?
A) Spotted DNA arrays
B) Oligonucleotide arrays
C) Ink-jet microarrays
D) BAC clone arrays
B
What is a disadvantage of spotted DNA arrays?
A) High cost
B) Limited probe length
C) Speed and spotting distance
D) Low specificity
C
What technology does Affymetrix use to place probes on a surface?
A) Ink-jet printing
B) Photolithography
C) PCR amplification
D) Gel electrophoresis
B
How is the fluorescence signal quantified in gene expression microarrays?
A) By a spectrometer
B) By a laser scanner
C) By a microscope
D) By a flow cytometer
B
Which fluorescent dyes are commonly used to label DNA in microarray experiments?
A) Cy3 and Cy5
B) FITC and TRITC
C) DAPI and Hoechst
D) Alexa Fluor 488 and 594
A
What is the purpose of analyzing RNA quality using capillary electrophoresis in the microarray workflow?
A) To determine the concentration of RNA
B) To check the integrity of RNA
C) To label the RNA
D) To hybridize the RNA
B
What components are typically included in the hybridization solution for DNA microarrays?
A) SDS, SSC, dextran sulfate, blocking agent, and formamide
B) Ethanol, EDTA, Tris buffer, and NaCl
C) Acetone, glycerol, HEPES buffer, and MgCl2
D) Methanol, acetic acid, PBS, and BSA
A
How long is the microarray typically hybridized for?
A) 1-2 hours
B) 4-6 hours
C) 12-24 hours
D) 24-48 hours
D
What is the purpose of the MammaPrint dx 70-gene expression array?
A) To diagnose breast cancer
B) To predict the risk of breast cancer recurrence
C) To sequence the entire genome
D) To identify mutations in the BRCA1/2 genes
B
How does the MammaPrint dx array help physicians?
A) By determining the stage of cancer
B) By identifying the type of cancer
C) By predicting whether a patient will benefit from chemotherapy
D) By sequencing the patient’s genome
C
According to the diagram on DNA microarray analysis, what is the first step in the workflow?
A) Labeling DNA with fluorescent dyes
B) Hybridizing samples to the microarray
C) Analyzing RNA quality
D) Growing or acquiring samples for comparison
D
n the gene expression microarray diagram, what does a green fluorescent probe indicate?
A) Gene expression in normal cells only
B) Gene expression in disease cells only
C) Gene expression in both normal and disease cells
D) No gene expression
A
What is a key advantage of spotted DNA arrays according to the diagram?
A) High specificity
B) Low cost and in-house production
C) High throughput
D) Long read lengths
B
What is the role of photolabile groups in Affymetrix oligonucleotide microarrays?
A) To bind fluorescent dyes
B) To break in response to light and allow probe sequence determination
C) To amplify DNA sequences
D) To visualize DNA fragments
B
At what step in the workflow is the label added to the DNA samples?
A) During RNA extraction
B) During reverse transcription or after amplification
C) During hybridization
D) During data analysis
B
According to the MammaPrint dx diagram, what does each row represent?
A) A gene expression profile for a tumour sample
B) A type of cancer
C) A fluorescent dye
D) A hybridization solution
A
