Sequencing Technology

Model: PromethION 2

Make: Oxford Nanopore Technologies

Specification:

PromethION is a high-throughput, scalable sequencing platform from Oxford Nanopore Technologies. It’s designed for large-scale genomic projects, offering real-time, long-read sequencing of both DNA and RNA. A compact benchtop device with two flow cell ports, ideal for small-to-medium-sized labs. The PromethION platform can deliver terabases of data. A single flow cell can generate up to 290 Gb of data.

Application:

The PromethION’s long-read capabilities and high throughput make it suitable for a wide range of applications, especially those that benefit from long-range genomic information.

  • Whole-Genome Sequencing: It’s ideal for de novo assembly of large or complex genomes, as long reads help resolve repetitive regions and structural variants that are challenging for short-read technologies.
  • Population-Scale Sequencing: The high throughput makes it suitable for large-scale studies involving many samples, such as human population genomics or cancer research cohorts.
  • Direct DNA/RNA Sequencing: PromethION can sequence native DNA and RNA directly without the need for a separate PCR amplification step. This is crucial for:
    • Epigenetics: Detecting base modifications like DNA methylation, which are read directly from the native molecule.
    • Transcriptomics: Analyzing full-length RNA transcripts and isoforms, providing a complete picture of gene expression.
  • Microbial and Metagenomic Studies: Long reads are highly effective for assembling microbial genomes and for characterizing complex microbial communities in metagenomics, as they can span entire operons and repetitive regions.

Model: MinION

Make: Oxford Nanopore Technologies

Application:

The MinION’s long reads, direct sequencing of native DNA/RNA (allowing base modification detection like methylation), and portability make it highly versatile across various fields:

  • Infectious Disease & Pathogen Surveillance: Rapid identification and characterization of bacteria, viruses, and antimicrobial resistance in clinical or outbreak settings, including in remote locations.
  • Microbial Genomics & Metagenomics: Whole genome sequencing of bacterial and viral isolates, as well as complex microbial community analysis (metagenomics), like in environmental or gut microbiome studies.
  • Human Genomics & Research: Sequencing human genomes/exomes, resolving structural variants, characterizing repetitive regions, and phasing alleles due to the ultra-long read capability.
  • Transcriptomics (RNA Sequencing): Direct RNA sequencing, which eliminates the need for cDNA synthesis and allows for isoform resolution and direct detection of RNA modifications.
  • Epigenetics: Detection of DNA methylation (e.g., 5-methylcytosine) directly from the raw electrical signal without the need for bisulfite conversion.
  • Targeted Sequencing: Focus on specific genomic regions, such as full-length 16S rRNA for species identification, or specific cancer gene panels.

Model: SeqStudio Flex Series

Make: Thermo Fisher Scientific

Application:

1. Sanger Sequencing (Gold Standard)

  • Next-Generation Sequencing (NGS) Confirmation: Re-sequencing key regions to confirm variants found by high-throughput NGS platforms.
  • De novo Sequencing: Sequencing unknown DNA fragments, such as those from plasmids or PCR products.
  • Targeted Resequencing: Analyzing specific genes or regions linked to a defined phenotype.
  • CRISPR-Cas9 Analysis: Verifying and quantifying gene editing events (e.g., indels) using software like TIDE.
  • Microbial Identification: Sequencing ribosomal genes (e.g., 16S rRNA) for bacterial and species identification.

2. Fragment Analysis

  • Human Cell Line Authentication: Using Short Tandem Repeats (STRs) to confirm the identity and purity of cell lines.
  • Microsatellite Analysis (MSA) / STR Analysis: Used extensively in Human Identification (Forensics) and paternity testing.
  • Single-Nucleotide Polymorphism (SNP) Genotyping: Analyzing single base variations, often using methods like SNaPshot.
  • MLPA (Multiplex Ligation-Dependent Probe Amplification): Analyzing human copy number variation (CNV).