NGS Sample to Insight Workflows from QIAGEN · Plug-in tools for most applications One solution for all kind of sequencing data Scalable –from desktop to server solutions Most versatile

Sample to Insight

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Erik Söderbäck, Ph.D. ([email protected])

Director Market Development,

Clinical and Applied Genomics, EMEA

Sample to Insight NGS solutions for the forensic laboratory:

the GeneReader System and Universal Workflow Solutions from QIAGEN

Delivering on the promise of NGS

Sample to Insight

NGS Sample to Insight Workflows from QIAGEN

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Ingenuity Variant Analysis

Ingenuity Pathway Analysis

HGMD®

Inova Genomes

QIAGEN® Clinical Insight

Interpret

Biomedical

Genomics

Workbench

Biomedical

Genomics Server

Solution

QIAGEN® Clinical

Insight Analyze

QIAseq Library kits:

- FX Library

- Ultralow Input

- 1-step Amplicon

- Stranded RNA

- miRNA

- methylome

QIAseq Targeted

panels:

- RNA,

- miRNA

- RNAscan (fusions)

- DNA

- MethylSeq

- Custom

QIAamp

- DNA & RNA kits

- Cirkulating NA kits

- Power kits

PAXgene DNA & RNA kits

GeneRead DNA FFPE Kit

RNeasy Kits

exoRNeasy Kits

Ion Torrent

Illumina

GeneReader

GeneReader fully integrated and optimized sample to insight NGS system

Sample to Insight

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Source: www.ngsperspectives.com; n=924; =1%

NGS

workflow

Sample preparation

Tertiary

analysis

Secondary

analysis

Library

construction

Target

enrichment

Sample

technologiesSequencing

Complexity of

data analysis (26%)

Accuracy of

sequencing (3%)

Complexity of

workflow (13%)

Access to

clinical samples (23%)

Regulatory

constraints (12%)

Experimental

design (8%)

Reproducibility

of data (10%)

“What are the biggest bottlenecks for NGS in clinics?”

Sample to Insight

Nucleic

Acid

Extraction

Target

enrichment

Library

Preparation

Clonal

Amplification

Next-

Generation

Sequencing

Data

Analysis &

Inter-

pretation

Sample InsightSample

QCLibrary

QCVariant

Confirmation

QIAGEN GeneReader NGS system

4

The GeneReader™ NGS System is the first complete Sample to Insight®

NGS solution designed for any lab to deliver actionable results.

Sample to Insight

GeneRead Assistant

Support

5

Interpretation

QIAcube/

QIAsymphonyQIAcube GeneRead

QIAcube

Gene

ReaderQCI

Automation

Quality

control QIAxcel

(QC)

Data

management

GeneRead Link / LIMS & IT support / GeneRead DataBank

GeneReader: The First Truly Complete NGS Solution

Offering everything needed from one vendor for NGS solutions

Nucleic Acid

collection &

extraction

Library

preparation

Next-

generation

sequencing

Data

analysis

Integrated

Actionable

Flexible

Affordable

Reliable

A

B

LH

C

Sample to Insight

GeneReader – Three Sequencers In One

6

Integrated

Actionable

Flexible

Affordable

Reliable

Unique Turntable Design

Separate Fluidic Stations

- parallelized fluidics on separate flowcells

Flexible Throughput

- 1-3 flowcells, in parallel or continuous loading

- Same or different applications at the same time

Sample to Insight


7



HGMD®

Inova Genomes


Interpret

Biomedical

Genomics

Workbench

Biomedical

Genomics Server

Solution

QIAGEN® Clinical

Insight Analyze


- FX Library

- Ultralow Input

- Singe Cell RNA/DNA

- 1-step Amplicon

- Stranded RNA

- miRNA

- methylome

QIAseq Targeted

panels:

- RNA,

- miRNA

- RNAscan (fusions)

- DNA

- MethylSeq

- Custom

QIAact Panels

(GeneReader)

QIAamp

- DNA & RNA kits


- Power kits



RNeasy Kits

exoRNeasy Kits

Ion Torrent

Illumina

GeneReader


Sample to Insight

Sample-derived PCR/RT-PCR/NGS inhibitors

In the process of breaking open cells to release

nucleic acids from environmental samples,

amplification inhibitors are also released.

Inhibitors include complex polysaccharides, bile,

bilirubin and heme in stool.*

*Other examples for additional matrices given in Rådström, P. et al. (2004) Pre-PCR processing: Strategies to

generate PCR-compatible samples. Mol. Biotechnol. 26, 133–46.

Sample to Insight

QIAGEN Patented Inhibitor Removal Technology

2009: Removal of PCR inhibitors Technology (U.S. Pat. Number 7,459,548)

IRT Removes the most challenging

inhibitors from DNA samples prior to

purification.

Comparison of soil

samples with and

without IRT:

Inhibitors cause false negatives in qPCR and sequencing analysis.

Sample to Insight

Effect of inhibitor removal

Low levels of contaminating inhibitors can lead to false negatives/aberrant amplification

and/or inhibition of NGS library preparations

IRT + +

+ IRT

IRT

QIAGEN PowerAmp kits (former MoBio kits) are developed with IRT technology

(PowerSoil, PowerWater, PowerBiofilm, PowerFecal etc.)

Samples A260/A280 A260/A230

IRT 1.91 2.03

IRT 1.92 1.99

No IRT 1.87 1.84

No IRT 1.85 1.53

10

Sample to Insight


11



HGMD®

Inova Genomes


Interpret

Biomedical

Genomics

Workbench

Biomedical

Genomics Server

Solution

QIAGEN® Clinical

Insight Analyze


- FX Library

- Ultralow Input


- 1-step Amplicon

- Stranded RNA

- miRNA

- methylome

QIAseq Targeted

panels:

- RNA,

- miRNA

- RNAscan (fusions)

- DNA

- MethylSeq

- Custom

QIAact Panels

(GeneReader)

QIAamp

- DNA & RNA kits


- Power kits



RNeasy Kits

exoRNeasy Kits

Ion Torrent

Illumina

GeneReader


Sample to Insight

QIAseq and QIAact Targeted DNA and RNA Panels

12

Sample to Insight

A new dimension of accuracy – from Sample to Insight

13

Base-calling accuracy of “Super Reads” from Unique Molecular Indexing (UMI)

Sample to Insight

Effect from using Single Primer Extension (SPE) technology: Coverage of GC-rich regions

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CEBPA

GC content

(regionally >90%)

Coverage

GC content

(full exons >90%)

Coverage

CCND1

Dual primer

PCR: <25%

SPE: 100%

Sample to Insight

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QIAseq targeted technology for DNA and RNA panels with molecular barcoding

Genomic & transcriptomics

DNA

SNVs

CNVs

Indels

Structural changes

RNA

Gene expression

Fusions

miRNA

NGSMethylation:

QIAseq panel

for targeted

meSeq

STR:

QIAseq panel

for STR

sequencing

QIAseq and QIAact Panels for Forensics

Sample to Insight

QIAGEN’s HID NGS targeted enrichment panels

MiSeq and IonTorrent sites validated and live with:

• GeneRead DNA Seq Investigator SNP ID Panel

QIAGEN‘s QIAseq NGS panels planned for:

• QIAseq SNP ID Panel (in tests)

• QIAseq SNP Ancestry Panel Global (in tests)

• QIAseq SNP Ancestry Panel ME (in tests)

• QIAseq Mito Panels (in tests)

• QIAseq phenotypic SNP Panel (in design)

• QIAseq methylation panel (in design)

• QIAseq miRNA panel (in design)

• QIAact/QIAseq Missing Persons SNP Panel (ICMP)

• QIAseq STR enrichment panel (in design)

InterpretationTarget

Enrichment

Library

Construction

Sample

PreparationSequencing

Data

Analysis

QIAGEN Universal NGS Solutions

QIAGEN GeneReader Sample to Insight Solutions

16

Sample to Insight


17



HGMD®

Inova Genomes


Interpret

Biomedical

Genomics

Workbench

Biomedical

Genomics Server

Solution

QIAGEN® Clinical

Insight Analyze


- FX Library

- Ultralow Input


- 1-step Amplicon

- Stranded RNA

- miRNA

- methylome

QIAseq Targeted

panels:

- RNA,

- miRNA

- RNAscan (fusions)

- DNA

- MethylSeq

- Custom

QIAact Panels

(GeneReader)

QIAamp

- DNA & RNA kits


- Power kits



RNeasy Kits

exoRNeasy Kits

Ion Torrent

Illumina

GeneReader


Sample to Insight

QIASeqFX

NexteraXT

Comparison FX/NexteraXT example; PROC gene, exons 4-6covera

ge

covera

ge

GC-rich region

Prof. Egbert Schultze Heidelberg (analysis with JSI SeqPilot Software)

coverage

700

Sample to Insight

Biomedical Genomics Workbench

19

De novo sequencing

Whole exome sequencing

Re-sequencing/Targeted Sequencing

MethylSeq

ChIP-seq

RNA-seq

smRNA-seq

Microbiology module

Plug-in tools for most applications

One solution for all kind of sequencing data Scalable – from desktop to server solutions

Most versatile and powerful NGS bioinformatics solution

Sample to Insight

Current Bioinformatics Capabilities to support NGS in Forensic Applications

QIAseqDNA Panels(HID SNP)

Microbiome Genomics

Module

Software Module for

NGS-mtDNAAnalysis

Software Prototype for Genotyping SNP or STR

Based on Clustering

Biomedical Genomics Workbench

Universal software platform “all” bioinformatic applications

• Easy to use

• Agnostic to sequencing and computer platform

• Powerful workflow framework – create and “lock” for production

• Scalable

• Audit trail

• Integration options with other algos, DBs, LIMS, etc.

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Sample to Insight

Biomedical Genomics Workbench: World Class Algorithms

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Import

QC Assays on the

reads

Trimming

Mapping to the

Reference Sequence

QC Assays on the

Mapping

Variant Calling

Variant Annotation

Reporting Results

GeneReader QIAact panel workflow in Workbench:

Sample to Insight

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QIAGEN Clinical Insight (QCI) Analyze for GeneReader – Sample Tracking

Sample to Insight

The ultimate objective of NGS in Molecular Pathology

23For Research Use Only not for use in diagnostic procedures

- Fresh Frozen

- Cytology

- FFPE

- Plasma

- Blood

NGS

integrated

workflow

QCI-I example report

Sample to Insight

The ultimate objective of NGS in Forensics

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- Blood

- Bone

- Swob

- Soil

etc.

NGS

integrated

workflow

”QFI” mock-up report

Sample to Insight

Building Enterprice Solutions Using QIAGEN Tools for Genomics

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Interpret


HGMD®

Inova Genomes

Biomedical

Genomics

Workbench

&

Biomedical

Genomics Server

Solution

QIAGEN® Clinical

Insight Analyze

(Early Access)

QIAseq FX Library

Kits

QIAseq 1-step

Amplicon KIt

QIAseq Ultralow

Input Kit

QIAseq Stranded

RNA Library kit

QIAseqTargeted

RNA Panels

QIAseq miRNA

QIAseq RNAscan

Panels (fusions)

QIAseq DNAseq

Panels v3

QIAamp DNA kits

PAXgene RNA/DNA kits


QIAamp Circulating NA Kit

exoRNeasy Kits

RNeasy Kits

Ion Torrent

Illumina

GeneReader


Sample to Insight

26

Solid

Tumour

Hereditary

diseases

Infectious

disease

QIAcube

EZ1

QIAsymphonyAneuploidi

testing

Extraction Panel/Library

QIAact

Panels

Tertiary

analysis

QCI - Interpret

Secondary

analysis

QCI - Analyse

Sequencing

GeneReader

QIAact &

QIAseq

Panels

IVA and QCI-ICLC

GeneReader /

MiSeq /

NextSeq

16S / WG

+ QIAseq

Library kits

CLCMiSeq

IlluminaIlluminaNextSeq

QIAcube

EZ1

QIAsymphony

Clinical

ExomeCapture +

QIAseq FXIVA and QCI-ICLCNextSeq

QCI-InterpretBMWB /

QCI-Analyse

IVA /

QCI-Interpret

BMWB /

QCI-Analyse

BMWB

BMWB

IVA /

QCI-Interpret

BMWB /

QCI- Analyse

= Present GeneReader Standard Workflows

BMWB

BMWB

QIAcube

EZ1

QIAsymphony

QIAcube

EZ1

QIAsymphony

QIAcube

QIAsymphony

QIAGEN Enterprise Solutions for NGS; Example Hospital Core Lab

QIAseq Library

kits

= Present GeneReader Customized Workflows

Sample to Insight

Standardized Analysis Pipeline Framework for All Clinical Departments

27

Workbench

Clients

IVA

BxWB

Variants

Clinical Exome

Illumina sequecing

QCI-I

QCI-A

GR

Variants

QIAact Panels

GeneReader

Interpret

BxWB

Variants

QIAseq Panels

Illumina sequencing

Custom

Report

QCI-AU GWB

Microbiology

16S and whole genome

Illumina sequencing

Integrated vcf upload manual or API-based vcf upload

Integrated sharing


Example: QIAGEN is using 54 servers in a Swedish hospital IT infrastructure

Sample to Insight

28

Solid

Tumour

Hereditary

diseases

Infectious

disease

QIAcube

EZ1

QIAsymphonyAneuploidi

testing

Extraction Panel/Library

QIAact

Panels

Tertiary

analysis

QCI - Interpret

Secondary

analysis

QCI - Analyse

Sequencing

GeneReader

QIAact &

QIAseq

Panels

IVA and QCI-ICLC

GeneReader /

MiSeq /

NextSeq

16S / WG

+ QIAseq

Library kits

CLCMiSeq

IlluminaIlluminaNextSeq

QIAcube

EZ1

QIAsymphony

Clinical

ExomeCapture +

QIAseq FXIVA and QCI-ICLCNextSeq

Harmonised

reporting

Harmonised

extraction

Harmonised

analysis

QCI-InterpretBMWB /

QCI-Analyse

IVA /

QCI-Interpret

BMWB /

QCI-Analyse

BMWB

BMWB

IVA /

QCI-Interpret

BMWB /

QCI- Analyse

= Present GeneReader Standard Workflows

BMWB

BMWB

Harmonised

enrichment

QIAcube

EZ1

QIAsymphony

QIAcube

EZ1

QIAsymphony

QIAcube

QIAsymphony


QIAseq Library

kits

= Present GeneReader Customized Workflows

Flexibility in

sequencing

equipment

Sample to Insight

QIAGEN NGS Solutions for Forensics

29

QIAGEN Hilden headquarter (in between Duesseldorf and Cologne)

Documents

NGS Sample to Insight Workflows from QIAGEN · Plug-in tools for most applications One solution for all kind of sequencing data Scalable –from desktop to server solutions Most versatile