Bulk Next-Generation Sequencing (NGS) refers to high-throughput sequencing techniques that analyse genetic material from a population of cells or organisms, providing a comprehensive view of the genetic makeup, gene expression, or epigenetic modifications across the sampled population.

Key Advantages of Bulk NGS:

• High-throughput: Capable of sequencing millions to billions of DNA or RNA fragments simultaneously.
• Cost-effective: More affordable than traditional methods when sequencing large genomes or many samples.
• Comprehensive: Provides a broad overview of genetic information, capturing a wide range of variations and expression profiles.

Limitations:

• Loss of Cellular Resolution: Bulk NGS provides averaged data across all cells in the sample, which can mask the heterogeneity present in cell populations.
• Requires High-Quality DNA/RNA: Degraded samples can lead to incomplete or biased sequencing data.

Credit: BioLizard

Below is a brief overview of the main types of bulk NGS methods:

1. Whole Genome Sequencing (WGS)

• Purpose: Provides a complete DNA sequence of an organism's genome.
• Applications: Identifying genetic variations, studying evolutionary relationships, and detecting rare mutations.
• Process: All genomic DNA is fragmented, sequenced, and then assembled to represent the entire genome.
• GCTU Services: KAPA DNA HyperPrep, Illumina DNA Prep, Custom kit, Sequencing Only

2. Whole Exome Sequencing (WES)

• Purpose: Focuses on sequencing the exonic regions of the genome, which code for proteins.
• Applications: Detecting mutations that affect protein-coding genes, particularly in genetic diseases.
• Process: Captures and sequences only the exome, which is about 1-2% of the genome.
• GCTU Services: Illumina RNA Prep with Exome Enrichment, Custom kit, Sequencing Only

3. Targeted Sequencing

• Purpose: Sequences specific regions of the genome, such as a panel of genes of interest.
• Applications: Diagnosing genetic disorders, validating mutations, or studying specific pathways.
• Process: Uses probes to capture and sequence only the targeted regions.
• GCTU Services: Custom kit, Sequencing Only

4. RNA Sequencing (RNA-Seq)

• Purpose: Quantifies gene expression by sequencing RNA, providing a snapshot of the transcriptome.
• Applications: Studying gene expression profiles, alternative splicing, and identifying novel transcripts.
• Process: RNA is converted to cDNA, which is then sequenced and mapped to the genome to quantify expression levels.
• GCTU Services: KAPA RNA HyperPrep (ribodepletion from Human, Mouse, Rat or Bacteria using Illumina RiboZero), QuantSeq 3' FWD, Custom kit, Sequencing Only

5. Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

• Purpose: Identifies the binding sites of DNA-associated proteins, such as transcription factors.
• Applications: Studying protein-DNA interactions, epigenetic regulation, and identifying regulatory elements.
• Process: Chromatin is immunoprecipitated using antibodies against a specific protein, and the bound DNA is sequenced.
• GCTU Services: Sequencing Only

6. Bisulfite Sequencing (BS-Seq)

• Purpose: Maps DNA methylation patterns across the genome.
• Applications: Studying epigenetic modifications and their impact on gene expression and disease.
• Process: DNA is treated with bisulfite, converting unmethylated cytosine to uracil, while methylated cytosine remains unchanged, and then sequenced.
• GCTU Services: Twist Human Methylome kit, Sequencing Only

7. ATAC-Seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing)

• Purpose: Identifies open chromatin regions, indicating active regulatory elements.
• Applications: Studying chromatin accessibility, gene regulation, and enhancer activity.
• Process: Tn5 transposase inserts sequencing adapters into accessible chromatin regions, which are then sequenced.
• GCTU Services: Sequencing Only

8. Shotgun Metagenomics

• Purpose: Sequences the collective DNA from a mixed community of organisms, typically microbial communities.
• Applications: Characterising microbial diversity, studying microbial functions, and exploring the interactions within ecosystems (e.g., human gut microbiome, soil microbiome).
• Process: All DNA from an environmental sample is fragmented and sequenced randomly (shotgun approach), allowing for the identification and quantification of different organisms and their genetic content.
• GCTU Services: Illumina DNA Prep, KAPA DNA HyperPrep, Custom kit, Sequencing Only

9. Small RNA Sequencing

• Purpose: Specifically sequences small RNA molecules, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs).
• Applications: Studying gene regulation, identifying novel small RNAs, and understanding RNA interference and other post-transcriptional regulatory mechanisms.
• Process: Small RNAs are isolated, converted to cDNA, and then sequenced to identify and quantify these regulatory molecules.
• GCTU Services: Qiagen miRNA kit, Custom kit, Sequencing Only

Bulk NGS methods are foundational in genomics, enabling wide-ranging applications from basic research to clinical diagnostics. Please visit our Services page to see our off the shelf bulk sequencing services. We also offer a 'Sequencing Only' service for user prepared NGS libraries.

We can also perform any library preparation method required under our 'Custom' route - please reach out to genomics@qub.ac.uk to discuss.