Next-generation sequencing Technology Overview

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1 Next-generation sequencing Technology Overview UQ Winter School 2018 Christopher Noune, PhD AGRF Melbourne

genome(s) (shotgun) or a single region(s) (amplicon) Massively Parallel Millions of

Dominated by 3 Companies Illumina Thermo-Fisher Roche-454 (Discontinued) Modifications

2 What is NGS? Ion Torrent PGM (Thermo-Fisher) MiSeq (Illumina) High-Throughput Can sequence whole genome(s) (shotgun) or a single region(s) (amplicon) Massively Parallel Millions of short DNA fragments (reads) sequenced at once Currently Second-Generation Sequencing Dominated by 3 Companies Illumina Thermo-Fisher Roche-454 (Discontinued) Modifications of Sequencing-by-Synthesis (SBS) H+ detection (semi-conductor) Phosphate detection (chemiluminescence) Reversible dye-terminators (fluorometry) GS FLX Titanium XL+ (Roche-454)

3 Time for an Adventure! What s Next in NGS?

4 The #1 Sequencing Platform Currently Available SBS Technology Identifies A/C/T/G By Detecting Fluorescents

6 Illumina Platforms ~1.2 Gb 4 mill reads 2x 150 bp ~7.5 Gb 25 mill reads 2x 150 bp ~15 Gb 25 mill reads 2x 300 bp ~120 Gb 400 mill reads 2x 150 bp ~1.5 Tb 5 bill reads 2x 150 bp ~1.8 Tb 6 bill reads 2x 150 bp ~6 Tb 20 bill reads 2x 150 bp

7 Illumina Applications Whole-Genome Shotgun Metagenomics Ultra-Deep Amplicon Sequencing 16s, ITS, custom targets Shotgun RNA Sequencing ChIPseq Gene Panels Contig -1 Reads Contig -2 Contig -3 Contig -4 Contig -5 Contig -6

diversity libraries can cause quality issues Slower run

8 Illumina Summary Pros Lots of data Lowest error rates Multiple platform selection Paired-end reads Cons Low diversity libraries can cause quality issues Slower run times (4 hrs 3 days) Short read lengths Gets a new transformation every year

9 The #2 Sequencing Platform Currently Available SBS Technology NGS Semiconductors Detecting Hydrogen Ions (ph) Capillary Electrophoresis 1 st Gen Sequencing Sanger Fluorescent Detection Gold Standard

11 SeqStudio Genetic Analyzer (Sanger Sequencing) Ion Torrent Personal Genome Machine Ion Proton Ion GeneStudio S5 The prince of all sequencers 400 bp 900 bp read lengths Low- Throughput Single read 30 min to 1.5 hrs per 96 samples Ion 31x series chips 200 bp 400 bp SE reads 400K 5.5 mill reads 30 Mb 2 Gb 2.3 hrs 7.3 hrs Ion PI series chips 200 bp SE reads 60 mill 80 mill reads ~10 Gb 2 hrs 4 hrs Ion 5xx series chips 200 bp bp SE reads 2 mill 130 mill reads ~ Gb 2 hrs 4 hrs

12 Thermo-Fisher Applications AmpliSeq Panels Metagenomic 16S Cancer Custom Small Genome Shotgun Targeted Sequencing

Gold-standard Sanger sequencing Cons Low data output Lower read quality

13 Thermo-Fisher Summary Pros Fast sequencing run times Scalable data outputs one machine, multiple chips Long SE reads (up to 600 bp) Gold-standard Sanger sequencing Cons Low data output Lower read quality than Illumina Struggles with homopolymers Only SE reads Time consuming library prep

14 The Former King SBS - Pyrosequencing Light based detection of pyrophosphate (chemiluminescence)

15 By This image has been created during "DensityDesign Integrated Course Final Synthesis Studio" at Polytechnic University of Milan, organized by DensityDesign Research Lab in Image is released under CC-BY-SA licence. Attribution goes to "Jacopo Pompilii, DensityDesign Research Lab". - Own work, CC BY-SA 4.0,

16 GS Junior GS FLX Titanium ~35 Mb 10 hrs run time ~ 700 bp SE 100K reads ~700 Mb 23 hrs run time Up to 1 Kb SE 1 M reads

17 Roche to Make a Comeback?

comeback Cons Low data output Discontinued Struggles

18 Roche 454 Summary Pros Relatively quick sequencing run times Long SE reads (up to 1 Kbp) Plotting its comeback Cons Low data output Discontinued Struggles with homopolymers Only SE reads Time consuming library prep

19 The Up-and-Coming Unchained Sequencing by ligation DNA nanoballs (Rolling circle replication) Four-colour fluorophore base detection

20 Porreca, G. J. (2010). Genome sequencing on nanoballs. Nature biotechnology, 28(1), 43.

22 BGISEQ-500 ~200Gb runs ~1 billion reads 2x 100bp PE Limited data and information available

23 Third-Generation Technology Single molecule real time sequencing (SMRT) using Zero-Mode Waveguide Four-colour fluorophore base detection

25 Sequel ~10Gb per SMRT Cell ~400,000 reads ~ 30 min to 20 hrs per SMRT Cell >90 Kbp read lengths - ~30 Kbp average

PacBio Applications Simultaneous Epigenetics Detects modifications through polymerase kinetics Long-Read Whole-Genome Sequencing Long reads

26 PacBio Applications Simultaneous Epigenetics Detects modifications through polymerase kinetics Long-Read Whole-Genome Sequencing Long reads make de novo assembly easier Improved Metagenomic Resolution Whole 16S, 18S & 23S sequencing

27 PacBio Summary Pros Cons Relatively quick sequencing run times (per Cell) Low data output Simultaneous Epigenetics High error rate (~1% - 15%) Super long leads Expensive Improved genome assemblies

28 Third-Generation Technology Nanopore Sequencing Measures changes in electrical field surround the pore

30 MinION ~512 Nanopore channels Gb per 48 Hrs No limit read lengths Low read output Fast library prep GridION Five MinIons fused together Up to 5x MinION flow-cells ~2560 Nanopore channels Gb per 48 Hrs PromethION Up to 48 flow-cells Each flow-cell ~3,000 Nanopore channels (total 144,000) Up to 12 Tb per 48 Hrs

31 Oxford Nanopore Applications Simultaneous Epigenetics Detects modifications through voltage changes Whole-Genome Sequencing Sequence microorganisms with a single read! Improved de novo assemblies of large organisms Improved Metagenomic Resolution Whole 16S, 18S & 23S sequencing

Simultaneous Epigenetics High error rate (~1% - 15%) Ultra

32 Oxford Nanopore Summary Pros Cons Relatively quick sequencing run times Devices still in development Simultaneous Epigenetics High error rate (~1% - 15%) Ultra long leads Not many devices available Fast Library Prep Cheaper than PacBio

33 What s Next in NGS?

Nanopore sequencing using sequencing-by-expansion Label-free Gene

35 Nanopore sequencing using proprietary tags and semi-conductors Solid-state nanopore sequencing using sequencing-by-hybridization Nanopore sequencing using sequencing-by-expansion Label-free Gene Electronic Nano- Integrated Ultra-Sensitive technology. Not much information available.

36 Your Adventure Continues! Whole genome sequencing, variant detection and AI Today RNA-seq, machine learning/ai and data science Tomorrow and Wednesday Visualisations Thursday Modelling - Friday

37 Thank-You! AGRF Brisbane Node AGRF Melbourne Node Matthew Tinning Dr David Hawkes Dr Ken McGrath UQ Winter School AGRF is supported by NCRIS and Bioplatforms Australia

Overview of Next Generation Sequencing technologies. Céline Keime

Overview of Next Generation Sequencing technologies Céline Keime keime@igbmc.fr Next Generation Sequencing < Second generation sequencing < General principle < Sequencing by synthesis - Illumina < Sequencing