Next Generation Sequencing at the. Marja Jakobs Core Facility Genomics

Transcription

1 Next Generation Sequencing at the Marja Jakobs Core Facility Genomics

2 Timeline DNA sequencing 1953 Discovery of DNA structure 1961 Sequentional oligosynthesis possible 1977 Sanger sequencing method published (Frederick Sanger) 1983 Development of PCR 1985 Human Genome Project proposed $10 / base 1987 First automated sequencing machine: ABI Human Genome Project officially started 1996 Capillary sequencer: ABI Parallelized adapter / ligation mediated, bead-based sequencing technology launching "Next Generation" sequencing 2003 Human Genome Project completed for $0.01 / base 2005 First Next Generation sequencing system: GS 20, 454 Life Sciences (100 bp) 2006 Solexa (later Illumina): Genome Analyser 2007 Applied Biosystems: SOLiD 2010 Semi Conductor Sequencing by Ion Torrent: PGM & Illumina: H1Seq 2011 Roche / 454: 700 bp readlength, 500 Mb output, Illumina MiSeq 2012 Ion Torrent: Ion Proton 2014 Illumina: NextSeq 2015 Oxford Nanopore: MinION, PromethION, Ion Torrent S5 / S5XL Illumina: HiSeq Illumina: MiniSeq, Human Genome $0,002 / 1000 basen Dideoxynucleotides and radioactive labeled fragments

3 Timeline DNA sequencing 1953 Discovery of DNA structure 1961 Sequentional oligosynthesis possible 1977 Sanger sequencing method published 1983 Development of PCR fl A C G T A A C AC C ACC G ACCG T ACCGT A ACCGTA T 1985 Human Genome Project proposed $10 / base Fluorescent dyes 1987 First automated sequencing machine: ABI Human Genome Project officially started 1996 Capillary sequencer: ABI Parallelized adapter / ligation mediated, bead-based sequencing technology launching "Next Generation" sequencing 2003 Human Genome Project completed for $0.01 / base 2005 First Next Generation sequencing system: GS 20, 454 Life Sciences (100 bp) 2006 Solexa (later Illumina): Genome Analyser 2007 Applied Biosystems: SOLiD 2010 Semi Conductor Sequencing by Ion Torrent: PGM & Illumina: H1Seq 2011 Roche / 454: 700 bp readlength, 500 Mb output, Illumina MiSeq 2012 Ion Torrent: Ion Proton 2014 Illumina: NextSeq 2015 Oxford Nanopore: MinION, PromethION, Ion Torrent S5 / S5XL Illumina: HiSeq Illumina: MiniSeq, Human Genome $0,002 / 1000 basen

4 Timeline DNA sequencing 1953 Discovery of DNA structure 1961 Sequentional oligosynthesis possible 1977 Sanger sequencing method published 1983 Development of PCR 1985 Human Genome Project proposed $10 / base 1987 First automated sequencing machine: ABI Human Genome Project officially started 1996 Capillary sequencer: ABI Parallelized adapter / ligation mediated, bead-based sequencing technology launching "Next Generation" sequencing 2003 Human Genome Project completed for $0.01 / base 2005 First Next Generation sequencing system: GS 20, 454 Life Sciences (100 bp) 2006 Solexa (later Illumina): Genome Analyser 2007 Applied Biosystems: SOLiD 2010 Semi Conductor Sequencing by Ion Torrent: PGM & Illumina: H1Seq 2011 Roche / 454: 700 bp readlength, 500 Mb output, Illumina MiSeq 2012 Ion Torrent: Ion Proton 2014 Illumina: NextSeq 2015 Oxford Nanopore: MinION, PromethION, Ion Torrent S5 / S5XL Illumina: HiSeq Illumina: MiniSeq, Human Genome $0,002 / 1000 basen

5 Timeline DNA sequencing 1953 Discovery of DNA structure 1961 Sequentional oligosynthesis possible 1977 Sanger sequencing method published 1983 Development of PCR 1985 Human Genome Project proposed $10 / base 1987 First automated sequencing machine: ABI Human Genome Project officially started 1996 Capillary sequencer: ABI Parallelized adapter / ligation mediated, bead-based sequencing technology launching "Next Generation" sequencing 2003 Human Genome Project completed for $0.01 / base 2005 First Next Generation sequencing system: GS 20, 454 Life Sciences (100 bp) 2006 Solexa (later Illumina): Genome Analyser 2007 Applied Biosystems: SOLiD 2010 Semi Conductor Sequencing by Ion Torrent: PGM & Illumina: H1Seq 2011 Roche / 454: 700 bp readlength, 500 Mb output, Illumina MiSeq 2012 Ion Torrent: Ion Proton 2014 Illumina: NextSeq 2015 Oxford Nanopore: MinION, PromethION, Ion Torrent S5 / S5XL Illumina: HiSeq Illumina: MiniSeq, Human Genome $0,002 / 1000 basen

6 Timeline DNA sequencing 1953 Discovery of DNA structure 1961 Sequentional oligosynthesis possible 1977 Sanger sequencing method published 1983 Development of PCR 1985 Human Genome Project proposed $10 / base 1987 First automated sequencing machine: ABI Human Genome Project officially started 1996 Capillary sequencer: ABI Parallelized adapter / ligation mediated, bead-based sequencing technology launching "Next Generation" sequencing 2003 Human Genome Project completed for $0.01 / base 2005 First Next Generation sequencing system: GS 20, 454 Life Sciences (100 bp) 2006 Solexa (later Illumina): Genome Analyser 2007 Applied Biosystems: SOLiD 2010 Semi Conductor Sequencing by Ion Torrent: PGM & Illumina: H1Seq 2011 Roche / 454: 700 bp readlength, 500 Mb output, Illumina MiSeq 2012 Ion Torrent: Ion Proton 2014 Illumina: NextSeq Oxford Nanopore: MinION, PromethION, Ion Torrent S5 / S5XL 2015 Illumina: HiSeq 4000 NovaSeq 2016 Illumina: MiniSeq, Human Genome $0,002 / 1000 basen

7 Next Generation Sequencing Mass Parallel Sequencing of unique DNA molecules Main NGS platforms: Roche 454 SOLiD 5500 / Wildfire Illumina Ion Torrent Nanopore PacBio

8 Differences in Sequencing Strategies CONVENTIONAL one sample one tube one reaction one result MPS Pool of molecules one reaction vessel many reactions many results

9 Several strategies Single molecule vs amplified DNA Sequencing by synthesis Sequencing with terminators

10 Two approaches Single molecule SMRT sequencing Detection of incorporation of a single molecule (PAC BIO) Nanopore sequencing Pull a lineair DNA strand through a nanopore (NanoPore) Amplified DNA Amplify a single molecule to obtain a pool of identical molecules Emulsion PCR (IonTorrent) Polony formation (Illumina)

11 Single Molecule Real Time sequencing (PacBio)

12 SMRTbell library

13 Single Molecule sequencing (Oxford Nanopore)

14 Amplified DNA Emulsion PCR (IonTorrent) Polony formation (Illumina)

15 Single vs Amplified Single strand No amplification No bias No copying erros Long reads - Very low signal - High error rate (14%) Amplified DNA Strong signals PCR errors are averaged - PCR bias/errors - Short reads - Loose modifications

16 NovaSeq

17 Next Generation Sequencing platforms CFG Ion Torrent PGM (Personal Genome Machine) Proton Illumina MiSeq HiSeq 4000 (VU)

18 High-throughput sequencing Sanger ABI Ion Torrent PGM / PI Illumina HiSeq MiSeq 4000 Run time sequencer 96 samples / hour 5 / 2.5 hours hours 1-3 days Through put 5 *10 5 x 500 bp 250 * 10 6 bp / year! 30Mb 2Gb per run 6 Gb per run Gb ( Gb) Per lane (per flowcell) sequence length 500 bp bp 2x 150 bp 2x 150 bp Analysis time 15 min sample 1 day - months

19 Workflow Amplified Single Molecule Sequencing Library preparation Emulsion PCR Polony PCR on a slide Semiconductor sequencing (Ion Torrent) Sequencing by synthesis (Illumina) Data Analysis

20 Library preparation platform specific adapter ligation / primers to DNA fragments DNA fragment A B barcode 20

21 Barcoding > multiplex advantages No barcode Libraries epcr Enrichment Deposition barcode

22 Workflow Amplified Single Molecule Sequencing Library preparation Emulsion PCR Polony PCR on a slide Semiconductor sequencing (Ion Torrent) Sequencing by synthesis (Illumina) Data Analysis

23 Illumina Library Rd 1 Seq primer Index Seq Primer P5 P7 INDEX Rd 2 Seq Primer Sequence of intererest

24 Illumina: Sequencing by terminators G C T G A T C A G G G G G G G G C G

25 MiSeq HiSeq Syringe pumps Touch screen monitor optics optics Flow Cell Compartment Flow Cell Compartment Reagent compartment Keyboard & Mouse tray Reagent compartment 1 flowcell, 1 lane, ~25M reads 2 flowcells, 8 lanes each, M reads / lane

26 Workflow Amplified Single Molecule Sequencing Library preparation Emulsion PCR Polony PCR on a slide Semiconductor sequencing (Ion Torrent) Sequencing by synthesis (Illumina) Data Analysis

27 Emulsie PCR Ion OneTouch 2 System Ion Chef

28 Emulsion PCR clonal amplification of DNA fragments A + PCR Reagents B library DNA Mix DNA Library & capture beads (1 cpb) + Emulsion Oil Create Water-in-oil emulsion Micro-reactors Annealing of sequencing primer Break microreactors enrich for DNApositive beads Perform emulsion PCR

29 Emulsion PCR Preferably 1cpb (clonal amplification) Also possible: 2 cpb 1 copy, 2 beads 29

30 Possible outcome emulsion PCR clonal amplification duplicate reads multicopy beads

31 Workflow Amplified Single Molecule Sequencing Library preparation Emulsion PCR Polony PCR on a slide Semiconductor sequencing (Ion Torrent) Sequencing by synthesis (Illumina) Data Analysis

32 Semiconductor Sequencing chip

33 Next Gen Sequencing PPi Ion Torrent: Semiconductor sequencing

34 Fast (real time) Direct Detection dntp Sensing Layer Sensor Plate H + ph Q V DNA Ions Sequence Nucleotides flow sequentially over Ion semiconductor chip One sensor per well per sequencing reaction Direct detection of natural DNA extension, no camera s Millions of sequencing reactions per chip Fast detection, fast cycle time, real time detection Bulk Drain Source Silicon Substrate To column receiver

35 Sequencing Workflow The signal strength is proportional to the number of nucleotides incorporated 4-mer 3-mer T A C G Flow Order TTCTGCGAA 2-mer 1-mer Key sequence Key: TCAG for signal calibration and normalization 35

36 PersonalGenomeMachine Ion Proton Sequencer

37 PGM Chip chamber Chip

38 Data analysis Simplified Next Generation Sequencing Same dataset, different parameters Impossible to assemble manually 38

39 Applications Next Generation Sequencing Genome sequencing: De novo sequencing Metagenome Whole Genome Targeted resequencing Amplicon panels Capture panels RNA sequencing Epigenome sequencing Single Cell Sequencing selected gene panels, mutation analysis(snps, low frequent mutations etc), structural variation (deletions, insertions, inversions, CNVs), whole exome sequencing, mitochondrial sequencing

40 De Novo Sequencing

41 VIDISCA-454 De novo virus discovery Next Generation Sequencing Ion Torrent PGM sequencing Cloning in TA vector Colony-PCR Sequencing of colony-pcr products Michel de Vries

42 Metagenome Sequencing sample Mixed bacterial genomes in the sample DNA cut into fragments Relative abundance of bacterial species Alignment of reads to reference bacterial genome Sequencing

43 Targeted resequencing Multiplex Amplification

44 Coverage distribution (after optimization) 2017 Artec, Olaf Mook

45 Compare reads with reference 2017 Artec, Olaf Mook

46 Applications Next Generation Sequencing Genome sequencing: RNA sequencing: Transcriptome Expression Alternative splicing mirna ncrna.. Epigenome sequencing Single Cell Sequencing

47 More to RNA than messenger RNA Repetitive DNA / RNA Genome Protein -coding <3% mrna Protein Interspread repeats (SINEs,LINEs) Processed pseudogenes Simple sequence repeats Segmental duplication Blocks of tandem repeats Transcriptome Non-coding >80% Circular RNA (circrnas) (100- >4000 nt) Transcriptional RNA trna (70-100nt) rrna ( nt) Translation Translation Small non-coding RNA <300 nt mirna (18-24 nt) Post-transcriptional gene regulation pirna (26-31 nt) Germ line transposon silencing snrna ( 150nt) pre-mrna splicing snorna ( nt) RNA modification, rrna processing scarna RNA modification Y RNA DNA replication, small RNA maturation vrna (88-98nt) sirna (21-23nt) Long non-coding RNA >200 nt 2017 Artec, Brendon Scicluna

48 Relative abundance (%) Relative abundance of RNA species Artec, Brendon Scicluna

49 Relative abundance (%) Relative abundance of RNA species 80 RIN (RNA integrity number) Artec, Brendon Scicluna

50 Relative abundance (%) Relative abundance of RNA species 80 RIN (RNA integrity number) Artec, Brendon Scicluna

51 Relative abundance (%) Relative abundance of RNA species 80 RIN (RNA integrity number) Artec, Brendon Scicluna

52 Approaches for RNA sequencing Gene expression Target poly(a) mrnas (enrich or selectively amplify). Alternative splicing Target exon/intron boundaries by either doing long read sequencing (>300 bp) or paired end read sequencing ( 2 100). mirna (small RNAs) Target short reads using size selection purification because mirnas are in the bp range. Non-coding RNA specific) Directional RNA sequencing is critical (strand- Anti-sense RNA Single cell RNA Consider combining mrna expression with directional RNA sequencing Requires whole transcriptome amplification. Critical challenge is the technical noise created by amplification Artec, Brendon Scicluna

53 Preparing RNA for next generation sequencing The core steps in preparing RNA for NGS analysis are: converting target to double-stranded DNA cdna fragmenting and/or sizing the target sequences to a desired length attaching oligonucleotide adapters to the ends of target fragments quantitating the final library product for sequencing PCR and/or Amplification bias 2017 Artec, Brendon Scicluna

54 2017 Jakobs & Jongejans HTSeq counts Comparison of RNA library prep kits: Kapa mrna Hyper prep kit Kapa total RNA Hyper prep kit with RiboErase Ovation RNA Seq System v2 i.c.w. Ovation Ultralow Library System v2 human mouse

55 Concluding remarks RNA samples contain many types of RNA molecules, not only mrna. Ribosomal RNA is the predominant biotype RNA samples represent molecules at various stages in different ratio s of the RNA life cycle RINs > 6.0 are OK Know your library preparation kits!

56 Applications Next Generation Sequencing Genome sequencing: RNA sequencing: Epigenome sequencing Histon modification and composition Chromatin accessibility Chromatin interaction Single Cell Sequencing

57 Epigenetics Stable heritable traits that cannot be explained by changes in DNA sequence Describes gene regulation processes that drive gene expression in relation to (cell) differentiation and development Genetics (complex) disease Epigenetics Environment Epigenetics: bridge between nature and nurture Artec, Peter Henneman

58 Epigenetic modifications DNA and histon modification go hand in hand. Regulation of gene expression often involves complex chromatin interactions. Altogether this is called the Epigenome Artec, Peter Henneman

59 Epigenetics and NGS DNA-methylation Detecting Histon modifications eg CHIPseq Detecting chromatin accessibility eg ATAC, Mnase, Dnase, FAIRE Detecting chromatin interaction eg HiC

60 Applications Next Generation Sequencing Genome sequencing: RNA sequencing: Epigenome sequencing Single Cell Sequencing Yong Wang, Nicholas E. Navin Advances and Applications of Single-Cell Sequencing Technologies Mol Cell, Volume 58, Issue 4, 2015,

61 Single Cell biology impacts most areas of research Figure 3. Broad Applications of SCS in Biological and Biomedical ResearchPanels illustrating the diverse fields of biology that have been impacted by SCS technologies over the past 5 years. Image credits: neurobiology, Zeynep Saygin (Cell Picture Show); germli... Yong Wang, Nicholas E. Navin Advances and Applications of Single-Cell Sequencing Technologies Mol Cell, Volume 58, Issue 4, 2015,

62 By Kierano - Own work, CC BY-SA 4.0,

63 Individual cells behave differently from the average of many cells

64 Pooled mrna analysis is misleading

65 Pooled cell data can be misleading

66 Level of detail

67 Scaling Single Cell Transcriptomics V Svensson, R Vento-Tormo, SA Teichmann

68 Conditions Single Cell partitioning systems Single cell suspension at high enough concentration No aggregates / clumping No doublets o FACS o Dnase / trypsin treatment o Cell strainer As little manipulation time as possible Avoiding pertubation of transcriptomal profiles in RNA expression Nanoliter protocols technical and cost efficient

69 Flowsorting 384 plate filled with lysis buffer Reversed Transcription cdna Library preparation Sequencing

70 C1 Single cell capture, Fluidigm integrated fluidic circuits C1_fluidigm.mp4

71 Components of RNA seq method Reverse transcription Conversion of RNA to cdna Amplification Amplification of cdna to usable amounts Barcoding & Indexing Labeling library sources Library prep & Analysis Prepare sample for sequencing Data output type nl rxn μl rxn

72 Result cdna synthese C1 1 cell 1 cell 1 cell 2 cells 1 cell 1 cell

73 Chromium Single Cell Solution 10x Genomics microfluidics

74 Droplet encapsulation GEM 10x_Genomics_MMshort.mp4

75 Yields / efficiency Dependent on cell type and viability FACS: 50% - 60% informative wells C1: 50% - 70% capture efficiency Chromium: 50% - 60% informative cells

76 Brief overview of scrna-seq approaches FACS microfluidics Protocol example SMART-seq2 MATQ-seq MARS-seq CEL-seq C1 (SMARTer) DROP-seq InDrop Chromium Seq-well SPLIT-seq Transcript data Full lenght Full lenght 3 end counting 3 end counting Full lenght 3 end counting 3 end counting 3 end counting 3 end counting 3 end counting Platform Plate-based Plate-based Plate-based Plate-based Microfluidics Droplet Droplet Droplet Nanowell array Plate-based Throughput ( cells) Typical read depth (per cell) Reaction volume microliter microliter microliter nanoliter nanoliter nanoliter nanoliter nanoliter nanoliter microliter Haque et al. Genome Medicine (2017) 9:75

77 Conclusions next gen sequencing Works for both research and diagnostics Detection of alternative splicing Expression Receptor rearrangement Virus discovery De novo sequencing Target capture Exomes Whole genomes HT sequencing of large genes chimerism detection Single Cell genomics / transcriptomics

78 Next challenge in NGS Bioinformatics Data analysis Tracking and tracing Interpretation Data storage New developments in analysis software Logistics pre- post PCR laboratories Data and sample tracking

79 The future of medical genetics 1000 dollar genome once in a life time test? Interpretation of data multidiciplinary Whole genome analysis might replace exome sequencing (routine now) Identification of genes for many recessive diseases

80 Future applications Whole Genome Whole Exome Targeted resequencing Epigenome, Conformation LDC, FFPE / Frozen tissue : : Split-Seq

81 Acknowledgements Core Facility Genomics Linda Koster Suzan Kenter Ferry de Klein Bioinformatics Laboratory Aldo Jongejan Perry Moerland Clinical Genetics Martin Haagmans Olaf Mook Clinical Genetics Frank Baas

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85 library prep MiSeq PE *10^6 reads per run HiSeq PE *10^6 reads per laan SR *10^6 reads per laan PGM 200 bp 5*10^6 reads per 318 chip bp 5*10^6 reads per 318 chip 950 Proton 200 bp 70*10^6 reads per chip C1 capture & RNA isolatie & cdna synthese 1.109,41 per IFC (96 captures) library prep 1.211,07 per IFC (96 captures) Chromium 3 lib prep (SC) ~ Per library DNA ~ 400 Per library

86 Structural Variation

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88 mirna sequencing

89 Called vs reference homopolymers

90 Unique Molecular Identifiers Uses large numbers (>10 5 ) of tags in the intial RT primer Each transcript from a given gene is primed with a unique barcode sequence Unique combination of tag and transcript can be used to identify individual RNA molecules Chances of two transcripts receiving the same tag are effectively zero

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95 Reverse transcription Template switch Poly A or random priming Generates full length cdna C1 SMARTer

96 Library Preparation cdna