evolution trends of genomics technology · miniseq system minseq series nextseq series hiseq4000...
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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
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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
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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
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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
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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)
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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)
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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
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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/
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19https://bionanogenomics.com/wp-content/uploads/2017/02/Bionano_HumanPAG_Hybrid-Scaffolding-White-Paper.pdf
Sequencing 4.0: Genome mapping technologyBionano Genomics
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• 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