The human genome is comprised of more than 3 billion nucleotides, which are the building blocks of our DNA. Hidden in the genome is valuable information about our genetic makeup, which can help inform our healthcare decisions, and allow researchers to discover new things about the human body. Psomagen, a genomic sequencing company, provides whole genome sequencing services to patients, hospitals, and research universities around the world.
What Is Whole Genome Sequencing?
Whole genome sequencing can identify and isolate genetic variations. WGS reconstructs and reads through a patient’s genes to assist the confirmation, prediction, or explanation of a patient’s risk for disease, susceptibility to toxins, and responsiveness to treatment. In a research setting, WGS can help answer complex questions quickly and accurately.
By mapping a patient, animal, or plant’s unique chemical code, whole genome sequencing provides an overall view of their complete set of genes. Instead of narrowing in on a specific section of a DNA sequence, whole genome sequencing analyzes larger data sets to detect single nucleotide variants, insertions, deletions, copy number changes, and large structural variants.
With a wider scope of reference material, whole genome sequencing helps genome experts to develop an understanding of how certain stretches of DNA function and how they’re related. This greater comprehension of how genomes work as a whole is being applied in clinical settings, and to advance research on hundreds of species.
Clinical Whole Genome Sequencing
Through early detection, whole genome sequencing can increase a patient’s chance for reducing or eliminating a disease, or at least its negative effects. By using whole genome sequencing to characterize the traits of a disease, physicians can advise patients (and the wider public) about how to limit the risks their genetic material may pose to a healthful lifestyle.
Whole genome sequencing ensures physicians and patients can have confidence in both proper diagnosis and treatment of genetic disorders.
Revealing the unique differences in base pair mutations helps physicians interpret how certain combinations of DNA impact an organism’s growth and survival. These patterns can identify inherited disorders and define the prognosis of an individual’s disorder. Whole genome sequencing can also predict a patient’s genetic response to a drug, which informs a physician’s recommendation for the amount and type of treatment.
Whole genome sequencing processes the expression and regulation of a patient’s complete set of genes. Because large volumes of data are processed in a short amount of time, there are many medical benefits:
- Provide patients faster, more cost-effective medical experiences
- Chart the course of a disease to mitigate any further damage
- Assess how a patient will be affected by treatment to personalize plans
- Identify all potential genes contributing to a disease instead of only those commonly known to the medical field, advancing healthcare expertise of genetic variations
- Teach a patient to avoid environmental or lifestyle factors in order to moderate their chance of acquiring or worsening a disease
Whole Genome Sequencing for Research
The utilization of genomics in agriculture is known as agrigenomics. WGS can be applied to the study of defective genes and diseases in cattle, sheep, pigs, and more. It can also help researchers learn about crops and plant biology, allowing farmers to make better-informed decisions, and consumers to have a better understanding of the food they’re eating.
The data found in plant DNA is also being used to produce medicines, biofuels, and materials such as cotton and timber. The insight provided by WGS can identify beneficial traits, facilitate breeding, and improve a diverse range of production and conservation efforts around the world.
Psomagen provides a complete solution for variant discovery through two types of sequencing: De novo sequencing and resequencing.
De Novo Sequencing
De novo sequencing assembles long parallel phases of “novel” genetic material, meaning it codes new DNA without referencing an existing amino acid sequence. This type of whole genome sequencing is highly accurate and can replicate or complete a blueprint for complex or polyploid genomes.
This primary generation of genetic material is used to spot chromosome deletions, inversions, or translocations, which may indicate the likelihood or occurrence of a genetic disorder.
Standard data analysis:
- Consensus Sequence (assembled into contigs)
Advanced data analysis:
- Gene Prediction
- Gene Annotation
Resequencing a genome implies the comparison of a common genetic sequence to the newly sequenced data. This type of whole genome sequencing can scan or test for specific genetic variations. Any mutations of the DNA from the standard reference sample will enable new discoveries in research setting and detection of a patient’s potential for disorders in the clinical setting.
Standard data analysis:
- Mapping to the current plant reference genome
- Analysis of mapping statistics
- SNPs and InDels calling
Advanced data analysis:
- SNPs and InDels are mapped to the current versions of SNV and related genome releases.
- Genes, gene structures, change of amino acids and cross-mapping to public databases.
- A variety of options for mapping algorithms, variant detection algorithms, annotations, mapping to public databases, group analysis, and case-control analysis.
- NovaSeq6000 S4 System (151bp Paired end)
- HiSeq X system (151bp Paired end)
- HiSeq2500 / MiSeq System (Paired-end, Mate pair)