Evolution Trends of Genomics technology · MiniSeq System MinSeq Series NextSeq Series HiSeq4000 System HiSeq X Series NovaSeq 6000 System Maximum output 1.2 Gb 7.5 Gb 15 Gb 120 Gb

Chalurmpon Srichomthong, M.Sc.Excellence Center for Medical Genetics and GenomicsKing Chulalongkorn Memorial Hospital, The Thai Red Cross SocietyFaculty of Medicine, Chulalongkorn University

Evolution Trends of Genomics Technology

Genomic Medicine“preventive and therapeutic care

is tailored to

an individual genome”

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BloodChemistry

DNASequencing

Digital DataBI + Biology

MeaningPhysicians Scientists

Utility Discovery

Sequencing technology

Sequencing 1.0Sanger sequencing

1.02.0

3.0

4.0

Sequencing 2.0NGS short read

Sequencing 3.0NGS long read

Sequencing 4.0Genome mapping technology

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Real experience- Sanger: 10,000+

- Short read (WES, WGS): illumina 1,000+ BGI 100+

- Long read Pacbio: 100+

Newton prize 2017 Rapid WES

Pacbio’s Training, August 2018

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Sequencing 1.0: Sanger sequencing

• Sequencing by synthesis (SBS)

• DNA polymerase& dye-labelled dideoxynucleotides

• Capillary electrophoresis & fluorescence detection

• 500 – 1,000 bp

6https://www.biotecharticles.com/Genetics-Article/Sanger-Sequencing-Chain-termination-method-of-DNA-Sequencing-3937.html

Sequencing 2.0:Next Generation Sequencing (NGS) short read

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“Massively parallel sequencing technologies”

Template amplification and immobilization Parallel sequencing• Bridge amplification: illumina

• Rolling cycle amplification (DNA Nanoball): BGISEQ• EmPCR: Thermo Fisher

Sequencing 2.0: Illumina

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• Bridge amplification• Sequencing by synthesis (SBS)• Read 75 – 500 bp• Throughput 0.1 – 1,000 Gb

https://bitesizebio.com/13546/sequencing-by-synthesis-explaining-the-illumina-sequencing-technology/

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Model iSeq100System

MiniSeq System MinSeq Series NextSeq Series HiSeq4000 System

HiSeq X Series NovaSeq 6000 System

Maximum output

1.2 Gb 7.5 Gb 15 Gb 120 Gb 1,500 Gb 1,800 Gb 6,000 Gb

Key application

- Small whole-genome sequencing (microbe, virus)

- Targeted gene sequencing

- Long-ranged amplicon sequencing

- Small whole-genome sequencing (microbe, virus)

- Targeted gene sequencing

- Targeted gene expression profiling

- 16S metagenomicsequencing

- Small whole-genome sequencing (microbe, virus)

- Targeted gene sequencing

- 16S metagenomic sequencing

- Small whole-genome sequencing (microbe, virus)

- Exome sequencing

- Whole-transcriptome sequencing

- Exome sequencing

- Whole-transcriptome sequencing

- Large whole-genome sequencing (human, plant, animal)

- Large whole- genome sequencing (human,plant, animal

- Exome sequencing

- Whole-transcriptome sequencing

- Methylation sequencing

On site : https://sapac.illumina.com/systems/sequencing-platforms.html?langsel=/th/

Sequencing 2.0: Illumina

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Sequencing 2.0: BGISEQ

• DNA Nanoball (DNB™) technology

• Sequencing by synthesis (SBS)

11On site : http://en.mgitech.cn/product/Sequencer.html

Sequencing 2.0: BGISEQ

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Sequencing 2.0: Thermo Fisher

• EmPCR

Ion Torrent presentation Mai2012.pdf

• Sequencing by synthesis (SBS)

Application: Small whole genome, Transcriptomes, Gene panel, PGS, ChIP- Seq, metagenomics 13

Sequencing 2.0: Thermo Fisher

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Sequencing 2.0: NGS short read(75 – 300 bp)

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Sequencing 3.0: NGS long read sequencing

• Oxford Nanopore Technology

Read length: 100 Kb

• Pacific Biosciences

>20 Kb (N50)

• 10X genomics; linked-reads

100 Kb

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Application

Platform Read length (Kb) Error rate Application

Oxford Nanopore >100 kb 0.3 - Pathogen detection

Pacific Biosciences >20 Kb (N50)

0.00001(CCS)

0.1 (single read)

- de novo genome assembly- SV and CNV detection- Complex gene sequencing- Expanded repeat detection- RNA isoform sequencing

10X genomics 100 Kb(linked reads)

0.001(NGS short-read)

- de novo genome assembly- SV and CNA detection- Haplotype phasing- Complex gene sequencing

Sequencing 3.0: NGS long read sequencing

Cortical tremor and seizures

Cortical tremor

aCGH, WESWGS: short read

Failed

WGS: long read

(TTTTA)9 -> (TTTTA)800(TTTCA)200

BAFME4

Sequencing 3.0: NGS long read sequencing

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Sequencing 4.0: Genome mapping technologyBionano Genomics

On site : https://bionanogenomics.com/technology/platform-technology/

19https://bionanogenomics.com/wp-content/uploads/2017/02/Bionano_HumanPAG_Hybrid-Scaffolding-White-Paper.pdf

Sequencing 4.0: Genome mapping technologyBionano Genomics

• Hi-c technique + NGS short-read PE20

Sequencing 4.0: Genome mapping technologyDovetail Genomics

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Draft assembly(Contig sequences; N50> 20 kb)

Final assembly

Sequencing 4.0: Genome mapping technologyDovetail Genomics

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BloodChemistry

DNASequencing

Digital DataBI + Biology

MeaningPhysicians Scientists

Utility Discovery

Thank you