Next Generation Sequencing

Dylan Young

Biomedical Engineering

What is DNA? • Molecule composed of

• Adenine (A)

• Guanine (G)

• Cytosine (C)

• Thymine (T)

• Paired as either AT or CG

• Provides genetic instructions for every living organism

What is sequencing? • Process of determining the order of nucleotides within DNA

• Includes any technology that is used to determine the order or A, T, C, and G

• This information impacts

• Medical diagnoses

• Biotechnology

• Forensic Biology

• Virology

Long-term Goal of Sequencing

• To achieve cost and time effective whole-genome sequencing for individual patients

Human Genome Project • International project to sequence the entire human genome

• Remains the world’s largest collaborative biological project

• United States, United Kingdom, France, Germany, Canada, China, Japan

• Began in 1990

• Project sequenced a small group of individuals then assembled them together to form a complete sequence for each chromosome

• Employed the Sanger Sequencing Method

Sanger Method • Invented in 1970

• Process

• Short primer is added to a strand of DNA

• DNA polymerase is then used to add complementary nucleotides

• Reaction is stopped by removing an oxygen from the ribonucleotide (termination)

• Chain terminating nucleotide marked by inserting dye

• Extension products then separated by Capillary Electrophoresis

• Electrical field moved negatively charged DNA fragments towards a positive electrode

• Laser excited the fragments as they move through a window, and a unique wavelength is emitted for each base pair

Human Genome Project Results

• Project was completed in 2003

• 3 Billion base pairs were sequenced

• Total Cost for complete genome sequencing

• $2.7 Billion

Where to go next

• Increase sequencing speed

• Decrease sequencing cost

• Achieve practical, patient specific whole-genome sequencing

• By 2005, Sanger sequencing could

• Sequence 18 kilobases per one sequencing run

• Cost ~$10million per whole genome sequence

Next Generation Sequencing (NGS)

• NGS was invented in 2005

• Utilized most successfully by Illumina Inc.

• Repetitively Analyzes short sequences of DNA (100-150 base pairs) in parallel

• Allows for millions of fragments to be analyzed simultaneously

How it works 1. Strand of DNA is cleaved into segments

2. Cleaved segment is ligated to adaptors and annealed to a slide

3. Slide is flooded with fluorescently labeled nucleotides and DNA polymerase

1. Terminator is added to each nucleotide to ensure only one base is added at a time

4. DNA polymerase then adds corresponding base pair to the section of cleaved DNA and an image is taken of the slide

5. Terminator is then removed to allow the next base to be added

6. This process is repeated for every base pair of the cleaved segment

7. Images are then run through a machine that detects the base pair at each site by color

8. Full sequence is then reconstructed

Efficacy and Price

• In 2005,

• NGS could sequence 1 Gigabase of data per run

• As of 2014,

• 1.4 Terabases of data per run

• 45 Human genomes can be sequenced in a single day

• $1000

Discussion

• NGS has provided

• 1000X increase in data/run

• Can sequence a whole-genome 200,000X faster than the Sanger method

• Costs 3,000,000X less than the original Human Genome Project

• Clear superiority over Sanger Method

References • 1] Morozova, O. and Marra, M. (2008). Applications of next-generation sequencing technologies in functional

genomics. Genomics, 92(5), pp.255-264.

• [2] van Dijk, E., Auger, H., Jaszczyszyn, Y. and Thermes, C. (2014). Ten years of next-generation sequencing technology. Trends in Genetics, 30(9), pp.418-426.

• [3] EMBL-EBI Train online. (2017). Illumina sequencing. [online] Available at: https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/what-next-generation-dna-sequencing/illumina- [Accessed 26 Sep. 2017].

• [4] National Human Genome Research Institute (NHGRI). (2017). DNA Sequencing Costs: Data. [online] Available at: https://www.genome.gov/sequencingcostsdata/ [Accessed 26 Sep. 2017].

• [5] National Human Genome Research Institute (NHGRI). (2017). The Cost of Sequencing a Human Genome. [online] Available at: https://www.genome.gov/27565109/the-cost-of-sequencing-a-human-genome/ [Accessed 26 Sep. 2017].

• [6] National Human Genome Research Institute (NHGRI). (2017). DNA Sequencing Fact Sheet. [online] Available at: https://www.genome.gov/10001177/dna-sequencing-fact-sheet/ [Accessed 26 Sep. 2017].

• [7] Illumina.com. (2017). DNA Sequencing | Understanding the genetic code with NGS. [online] Available at: https://www.illumina.com/techniques/sequencing/dna-sequencing.html [Accessed 26 Sep. 2017].

• [8] Illumina. (2017). An introduction to Next-Generation Sequencing Technology. [online] Available at: https://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf [Accessed 25 Sep. 2017]