Next-generation sequencing technologies

• What is the main advantage of the sequencing step in NGS?

  It reads millions of DNA fragments simultaneously
• What does the analysis step in NGS involve?

  Aligning reads to reference sequence and identifying variants
• How many copies are made during library preparation in NGS?

  Millions of identical copies
• What type of data is produced in the Sequencing step?

  The Sequencing step produces raw sequencing reads, which are then aligned and analyzed in the Analysis step.
• What are the drawbacks of the Ion Torrent sequencing platform?

  • Short length reads
  • Accuracy
• How does the Analysis step differ from the Sequencing step?

  • Sequencing generates the raw sequencing data
  • Analysis involves aligning the reads, identifying variants, and interpreting the sequencing results
• What are the applications of next-generation sequencing (NGS)?

  • Identifying genetic mutations
  • Understanding diseases
  • Studying entire genomes
  • Analyzing large DNA regions
• What is a key advantage of NGS over traditional sequencing methods?

  It is faster and cheaper than Sanger sequencing
• What are the advantages of the Illumina sequencing platform?

  Sensitivity, Amount of generated data with same DNA, High throughput
• In what scenario would NGS be particularly useful?

  Studying entire genomes or large DNA regions
• What does NGS stand for?

  Next-generation sequencing
• What are the 4 main steps in the DNA sequencing process shown in the image?

  1. Extraction
  2. Library Prep
  3. Sequencing
  4. Analysis
• What is the first step in the DNA sequencing process shown in the image?

  Extraction
• What factors do NGS platforms trade-off?

  Cost, speed, accuracy, read length, data output
• What are the characteristics of different NGS platforms?

  • Each platform has unique strengths
  • Trade-offs exist between:
  • Cost
  • Speed
  • Accuracy
  • Read length
  • Data output
  • Suitable for various experimental designs
• What are the drawbacks of the Pacific Biosciences sequencing platform?

  Costs, Large amounts of starting material, Error rate with CLR mode
• How is NGS transforming biological research and healthcare?

  By enabling advanced genetic analysis and applications
• What are the advantages of the Pacific Biosciences sequencing platform?

  Long reads, High accuracy with CCS mode, Direct detection of epigenetic modifications
• What is the purpose of the Adapter Ligation PCR step in the Library Prep process?

  The Adapter Ligation PCR step attaches adapters to the fragmented DNA to allow for amplification and sequencing.
• What are the applications of NGS in various fields?

  • Disease diagnosis: Identifying genetic mutations
  • Personalized medicine: Tailoring treatments to genetics
  • Drug development: Discovering drug targets and predicting responses
  • Evolutionary studies: Tracking genetic changes over time
• What are the drawbacks of the BGI Group sequencing platform?

  Short length reads
• What are the key features of NGS technologies?

  • Extraction: DNA is isolated from samples
  • Library Prep: DNA fragments converted into a sequencing library
  • Sequencing: Parallel sequencing reads millions of DNA fragments
  • Analysis: Software aligns reads to reference and identifies variants
• What are the drawbacks of the Sanger sequencing platform?

  • Sensitivity
  • Scalability
  • Sample input requirements
• How does next-generation sequencing (NGS) differ from Sanger sequencing?

  NGS sequences millions of fragments simultaneously
• What are the drawbacks of the Illumina sequencing platform?

  Costs for low target numbers, Short length reads
• What is the strategy for Sanger Sequencing?

  Multiple simultaneous reactions for a single gene. Use for the analysis of regions with specific primers.
• What are the pros of Sanger Sequencing?

  Low cost & high precision, Short turnaround time, Straightforward, standardized data interpretation
• What does the high-throughput approach in NGS create?

  Massive amounts of digital sequencing data
• What are the advantages of the Oxford Nanopore Technologies sequencing platform?

  Very long reads, Direct sequencing of RNA, Detection of RNA modifications
• What is the first step in the NGS workflow?

  Extraction
• What are the pros and cons of NGS compared to Sanger sequencing?

  NGS is high scale but has complex data
• What is the first step in the DNA sequencing workflow?

  Extraction
• What is the final step in the NGS workflow?

  Analysis
• What are the main features comparing Sanger sequencing and NGS?

  • Sanger Sequencing:
  • Strategy: Single reactions
  • Analysis: Regions with primers
  • Pros: Low cost, fast, simple
  • Cons: Small sequence, single species
  • NGS:
  • Strategy: Massively parallel
  • Analysis: Whole genomes
  • Pros: High scale, versatile
  • Cons: Complex data, long setup
• What is the first step in NGS technologies?

  DNA is isolated from samples
• What are the advantages of the Ion Torrent sequencing platform?

  • Costs
  • Speed
• Why is NGS ideal for large-scale genetic studies?

  It analyzes many DNA fragments simultaneously
• What are the main steps in the analysis workflow?

  • FASTQ
  • BAM
  • VCF
• What are the main steps in the library prep process?

  • Fragmentation
  • Template
  • PCR or RT-PCR
  • Adapter Ligation PCR
  • Sequencing Library
• What is created during the library preparation step?

  A sequencing library