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Whole genome sequencing

Overview

A genome is the entire DNA sequence of an organism. The DNA contains the instructions for how a living organism is formed. Whole genome sequencing (WGS) is a next generation sequencing application that determines the entire DNA sequence all at once. The alternative to WGS is targeted next generation sequencing, which sequences part of the genome.

How do you sequence an entire genome?

The first genome sequenced was the genome of a bacterium that causes bacterial influenza, Haemophilus influenzae. This bacterial genome was sequenced in 1995, using shotgun sequencing whereby you randomly sequence short fragments of the genome and then reassemble using bioinformatics tools [1]. When the Human Genome Project sequenced the first human genome in 2001, shotgun sequencing was also used, but, since the human genome is so much larger than a bacterial genome, the human genome was not fully sequenced. Part of the problem was the time required to perform shotgun sequencing. Next generation sequencing allows sequencing reactions to be completed in a much shorter amount of time. Whole genome sequencing involves extracting DNA from an organism’s tissue, preparing a library by adding adapters that attach the DNA to the sequencing machine, determining the sequence of the DNA using a machine, and lastly, using bioinformatics to interpret the sequencing results. The sequencing step is usually performed on Illumina sequencing machines. Sequencing starts with single-stranded DNA and fills in the opposite strand, using fluorescence to identify each base, or molecule of DNA, as it is added to the strand.

Benefits of whole genome sequencing

WGS provides the most comprehensive data about a given organism. Using next generation sequencing can deliver large amounts of data in a short amount of time. Since you are profiling the entire genome, it allows for the discovery of previously unknown genes or variants. As scientists work toward precision medicine and personalized treatment, WGS may point to genes that do not cause disease but could aid in choosing the best therapy for an individual. WGS could even reveal genetic predispositions that could be mediated through lifestyle or environmental changes to aid in prevention.

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Discovery
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Speed
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Ease-of-use

What do you need to perform whole genome sequencing?

Since WGS starts with DNA, you first need to extract DNA from your tissue or cell sample. How much DNA is needed for whole genome sequencing? WGS can be performed with as little as 100 ng of DNA. If you don’t need data from the whole genome, targeted sequencing can be performed with as little as 1 ng of DNA. You will need to prepare libraries using a library preparation kit and adapters. Adapters may come with barcodes, or indexes, that help identify the sample or specific molecules in the sample and aid in multiplexing. Since sequencing machines are very expensive, sequencing services can carry out the sequencing step for you. Analysis can be performed with a variety of available free bioinformatics tools.

What is whole genome sequencing used for?

Variants are also called mutations and are points in the genome that differ between organisms. WGS can be used to determine variant frequencies, or how often a difference occurs within populations of organisms, and to associate genetic variants with disease through genome-wide association studies (GWAS). In a GWAS, WGS on two populations is done to compare trait differences with genetic differences—to associate identified traits with identified variants. WGS was first used for clinical diagnostics in 2009, but time and costs have limited its use in this area [2, 3]. As the price of WGS decreases, it is becoming more common as a diagnostic tool. Having achieved the “$1000 genome”, multiple companies are pushing towards the next goal of the “$100 genome” [4–6].

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NGS 101 application guide

This detailed overview walks you through major advances in sequencing technology, types of next generation sequencing, their applications and more.

Downstream uses of WGS

Cancer research

Next generation sequencing technologies are ideal for screening hundreds or thousands of variants, making these methods appealing for assessing the substantial genetic diversity of cancers.

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Genotyping

Genotyping by sequencing is a technique used in agriculture for molecular breeding and trait/marker selection. Whether you are focused on a few markers for marker-assisted selection or on thousands of markers for genomic selection, whole genome sequencing can help accelerate your plant or animal improvement programs.

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xGen Stubby Adapter and Unique Dual Index Primer Pairs

Ensure maximum accuracy in your NGS reads with xGen Stubby Adapter and Unique Dual Indexing (UDI) Primer Pairs. A convenient indexing option for a variety of applications from whole-genome to targeted sequencing, the kit provides adapters and unique i5 and i7 primer pairs that can be used with TruSeq™-compatible library prep for sequencing on Illumina instruments.

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Lotus DNA Library Prep Kit

The Lotus DNA Library Prep Kit enables streamlined preparation of high-quality next generation sequencing (NGS) libraries from double-stranded DNA (dsDNA)—generate libraries suitable for PCR-free, PCR-amplified, and targeted sequencing applications on Illumina platforms.

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References

  1. Fleischmann RD, Adams MD, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science (New York, N.Y.) 269(5223):496–512.
  2. Welch JS, Westervelt P, et al. (2011) Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA 305(15):1577–1584.
  3. Lunshof JE, Bobe J, et al. (2010) Personal genomes in progress: from the Human Genome Project to the Personal Genome Project. Dialogues Clin Neurosci 12(1):47–60.
  4. Hayden EC (2014) Technology: The $1,000 genome. Nature 507(7492):294–295.
  5. Herper M (2017) Illumina promises to sequence human genome for $100—but not quite yet. Forbes. [Accessed Dec 30, 2019]
  6. McMorrow D (2010) The $100 genome: Implications for the DoD. The MITRE Corporation. Report number JSR-10-100.