WHOLE GENOME RE-SEQUENCING

WHOLE GENOME RE-SEQUENCING

Overview – What is genome re-sequencing?

Whole genome sequencing (WGS) or whole genome re-sequencing is a sequencing-based approach for determining the entire genome of an organism. The comprehensive method provides sequencing information on chromosomal and mitochondrial DNA, as well as chloroplast DNA in plants. A decline in sequencing costs makes the approach appealing to researchers looking to sequence the genome of humans, animals, plants or microorganisms. 

Genome re-sequencing is often the preferred method for tracking disease outbreaks, studying disease-associated genetic mutations, advancing evolution genetics or discovering and typing novel organisms. The deep coverage of whole genome sequencing enables the analysis of the full range of genetic variations. Comparative analysis of species at the genome level can be used to infer information on synteny, horizontal gene transfers and orthologs. WGS is an indispensable part of any genome-wide association study (GWAS), where common genetic variants in different individuals are assessed to decide if a variant is related to a particular disease-associated phenotype. GWASs are usually focused on the relationship between single-nucleotide polymorphisms (SNPs) and traits related to major diseases. 

Applications – What are the advantages of genome re-sequencing?

The following are examples of how whole genome re-sequencing can serve research purposes:

  • Comprehensive view of the genome at base resolution
  • Variant calling of SNPs, insertions, deletions, inversions, rearrangements and copy number variations of any size
  • Discovery of potential causative variants 
  • Assembly of novel genomes spanning repetitive and complex genomic regions
  • Annotation of genes in whole genome assemblies
  • Haplotype characterisation
  • Comparative analysis at the genome level
  • Characterisation of pathogen DNA from infected hosts

Workflow – Genome re-sequencing methods & technologies

The first step in WGS is to fragment the genomic DNA into random fragments. During library preparation, specific adapters are ligated to the DNA fragments and the DNA library is sequenced. Depending on the technology, sequencing reads of different lengths are generated. The reads are then aligned to a reference genome. In the absence of a reference genome, the genome can be assembled by overlapping regions of the sequence (see de novo genome sequencing).   

Whole genome re-sequencing versus exome sequencing

The main difference between WGS and whole exome sequencing (WES) is that WGS aims to sequence the entire genome, whereas WES delivers the protein-coding sequences only. A typical WGS project requires approximately 90 Gb of sequencing data versus a WES project, which requires only about 5 to 6 Gb of data as it targets only about 2% of the genome. 

WGS does not require any target enrichment for exons. Whole genome sequencing can also take advantage of long read lengths, for example with the PacBio technology, making it better suited for determinating disease-related attributes such as copy number variations, rearrangements and structural variations. WGS can also provide information on regulatory regions in the non-coding part of the genome, including promoters and enhancers. Additionally, WES is limited to several organisms only, whereas WGS can be used to explore nearly any organism of interest. 

Scientific expertise: genome re-sequencing

GATC Biotech has provided services for NGS since 2006. As the first company to install the most widely used platform for WGS, Illumina HiSeq, GATC Biotech has fully mastered all of the processing steps required for complete genome assembly. 

For de novo genome sequencing, GATC Biotech applies the popular PacBio sequencing platform. With sequencing reads of unmatched length, this sequencing system is ideal for achieving finished novel genomes with a minimum number of misassemblies. GATC Biotech was the first commercial sequencing provider to acquire the PacBio system, offering its customers unrivalled experience in using the platform and in analysing the resulting sequencing reads. 

Publications

Find here, a list of selected research articles supported by GATC Biotech’s sequencing products, as well as the latest publications on genome re-sequencing.

Products related to whole genome re-sequencing

Interested in performing WGS for your project? Then apply our expert genome re-sequencing solution with sequencing reads generated on a leading sequencing platform. Our team of experts will guide you through the planning of the project and our well-trained specialists will handle your samples during library preparation and sequencing. Experts in bioinformatics will then provide you with an  in-depth analysis of your sequencing data.

See how our whole genome re-sequencing service can help advance your research or contact us for more information.

For cases where only the coding regions of the genome are of interest, see how our INVIEW HUMAN EXOME predesigned package can be used to your advantage.  

Further reading on WGS

Ng, P.C., Kirkness, E.F. Whole genome sequencing. Methods Mol Biol. 628, 215 - 26 (2010).
Ekblom, R., Wolf, J.B. A field guide to whole-genome sequencing, assembly and annotation. Evol Appl. 7(9):1026-42 (2014).