Advances in targeted

sequencing
Accelerate your NGS workflows with the
new QIAseq chemistry

Boo Sook Yee, Ph.D.

Genomics Application Specialist, OSEA

Legal disclaimer

QIAGEN products shown here are intended for molecular biology applications. These products are not intended for the diagnosis, prevention or
treatment of a disease.
For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit instructions for use or user operator manual.
QIAGEN instructions for use and user manuals are available at www.qiagen.com or can be requested from QIAGEN Technical Services (or your
local distributor).

Advances in targeted sequencing 2

Detection of several types of biomarkers is a cornerstone of
oncology
Biomarkers

NGS is the ideal technology

to efficiently and cost-
effectively detect DNA- and
Single nucleotide variant (SNV) Fusions RNA-based biomarkers
Insertion deletions (InDel) Exon skipping
Gene expression
Copy number variation (CNV) and miRNA
Tumor mutational burden (TMB)

Microsatellite instability (MSI)

Methylation

Advances in targeted sequencing 5

Current challenges in NGS workflow for oncology biomarker
analysis

Inability to confidently call low

variant allele frequency (VAF) Limited panel
sensitivity

Optimizing an NGS panel requires High sample Incompatibility with low-yield

Deep
expertise in chemistry and Challenges input
expertise and low-quality samples
bioinformatics requirements

Time
consuming Library preparation is often
a multi-day workflow

Advances in targeted sequencing 6

UNGS Workflow

Instruments QIAcube Connect

QIAxpert Illumina or Thermo
QIAsymphony QIAxcel
Sequencer
EZ2 Connect QIAxcel Rotorgene

Sample QC Library QC FASTQ

Sample DNA or RNA Library Report
NGS run Data analysis Interpretation
extraction Preparation

Kits/Solutions

QIAamp, DNeasy, RNeasy, QIAseq Targeted Panel Qiagen Clinical Insight

CLC Genomics Workbench
Interpret (QCII)
miRNeasy

May 24, 2023 7

May 24, 2023 9
QIAGEN provides superior solutions for every step of the workflow

QIAseq Targeted DNA Sequencing

• Better coverage of GC-rich regions and enhanced sequencing uniformity due to optimized
PCR chemistry

• Reduced bias and false positives due to unique molecular indices (UMIs)

Data analysis
• Easy-to-run analyses with pre-built, optimized QIAseq workflows

• Sensitive variant detection with tuned algorithms that process UMIs

• Seamless VCF file upload for interpretation in QCI-I for QIAseq

Variant interpretation
Integrated
• Generates variant reports using the vast QIAGEN Knowledge Base NGS
Solutions
• Reveals biological context for variants, including actionable information

• Provides full transparency for supporting literature

10
QIAGEN has developed technology and workflow improvements
Address the challenges and increasing complexity of biomarkers

QIAseq Consolidated workflow Unique molecular Unique dual

foundational
QIAseq Multimodal (DNA+RNA)
+ indices (UMIs) + indices (UDIs) + Single primer extension (SPE)
element

Low sample Comprehensive

Efficient use of Cost-effective
input; compatible Robust panel No risk of sample and deep
Benefit material and lab
with challenging sensitivity mixup biomarker
per sample
resources sequencing
samples coverage

No need to split
precious samples Detect both
Confidently call
known and novel
Total nucleic Higher low VAF/MAF High uniformity
fusions
Impact to acid input 10–40 percentage of and specificity
Correct data set
patients ng clinical samples enable
assigned to
and the received can be multiplexing of
Single samples Depth of
processed (FFPE, more samples
lab consolidated cfDNA)
Detect lowly coverage for
(↓$)
NGS workflow = expressed biomarkers such
50% reduction in fusions as CEBPA and
FTE time TERT promoter

MAF: mutant allele frequency; VAF: variant allele frequency

May 24, 2023 Styleguide 2022 1111
QIAseq technology enable sensitive and reliable variant detection

Unique molecular indices (UMIs) – high confidence variant detection even at low allele frequencies
• UMIs tag each molecule within the sample prior to amplification

• Distinguish PCR-induced artifacts present at low copies from true variants

Unique dual indices (UDIs) – accurate read assignment and maximum flow cell utilization
• UDIs track each sample with high resolution

• High confidence in demultiplexing your samples

Robust panel
sensitivity

Advances in targeted sequencing 12

QIAseq technology provides high compatibility with challenging
samples

Low DNA input requirement

• Minimum DNA input requirement – as low as 10 ng

• Allows for higher percentage of incoming samples to be processed (e.g., FFPE , cfDNA)

Compatible
with low-input
samples

Advances in targeted sequencing 13

Introducing QIAseq Targeted DNA Pro to accelerate your time to
results

Introduction of enzymatic clean-ups

• Significant reduction of hands-on time

• Higher recovery of DNA molecules

Elimination of custom sequencing primer

• Easy sequencing set up

• Maximizing flowcells to multiplex QIAseq with non-QIAseq libraries

Automation-friendly workflow Easy-to-use

and Fast
• Easy to automate reagents and workflow

Advances in targeted sequencing 14

QIAseq Targeted DNA Pro

Building on the recognized performance of the QIAseq Targeted DNA Panels

HASTP = QIAseq Human Actionable Solid Tumor Panel

HCCP = QIAseq Human Comprehensive Cancer Panel

“Among the five commercial kits using UMIs, the QIAGEN HASTP showed the highest mean depth of unique coverage
followed by the QIAGEN HCCP”

Data source: Chung, J. et al. (2019) Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier. BMC Genomics 20, 216.

Advances in targeted sequencing 16

Continuous workflow improvements with QIAseq Targeted DNA Pro

QIAseq Targeted DNA QIAseq Targeted DNA Pro

Time (hours)

12

10

8
Sample to sequencing-ready library within 6 hours

0
Incubation time Hands-on time Total turn-around time

Advances in targeted sequencing 17

QIAseq Targeted DNA Pro workflows

For Illumina sequencers For Thermo Fisher sequencers

FFPE DNA Repair

Fragmentation

Adapter Ligation with UMIs

Enzymatic Clean up
Target Enrichment

Enzymatic Clean up
Universal PCR

Bead Cleanup

Advances in targeted sequencing 18

QIAseq Targeted DNA Pro enables detection of somatic and germline
variants with a broad range of panel offerings
Comprehensive cancer and disease-specific panels

Hereditary cancer research

Research panels Focus panels
panels

1 Comprehensive Cancer 1 Comprehensive Cancer 1 Comprehensive Cancer

2 Brain Cancer 2 Brain Cancer 2 Breast and Ovarian cancer

3 Breast Cancer 3 Breast Cancer 3 Colorectal Cancer

4 Colorectal Cancer 4 Colorectal Cancer 4 Pancreatic Cancer

5 Lung Cancer 5 Lung Cancer 5 Prostate Cancer

6 Myeloid Neoplasms 6 Myeloid Neoplasms 6 Hematologic Malignancies

Genes implicated in solid tumors Genes and variants implicated in solid Genes implicated in hereditary solid
and hematologic malignancies tumors and hematologic malignancies tumors and hematologic malignancies

Coming in April 2022 – Hereditary Comprehensive and Cancer Research Panels

Advances in targeted sequencing 19

QIAseq Targeted DNA Pro delivers high specificity and uniformity

Total number of Panel size Specificity Uniformity (0.2x

Cat. No. Product name
primers* (bases) (on target with primer%) mean base UMI%)

PHS-3000Z Comprehensive Cancer Research Panel 12,264 997,783 95.03 99.46

PHS-001Z Breast Cancer Research Panel 2534 203,082 95.02 99.73
PHS-002Z Colorectal Cancer Research Panel 3430 282,246 96.22 98.82
PHS-003Z Myeloid Neoplasms Research Panel 6848 574,579 96.05 99.63
PHS-004Z Brain Cancer Research Panel 2742 199,053 93.55 98.32
PHS-005Z Lung Cancer Research Panel 2571 207,663 96.31 99.66
PHS-3100Z Comprehensive Cancer Focus Panel 2990 102,488 91.72 98.59
PHS-101Z Breast Cancer Focus Panel 633 30,391 92.99 99.92
PHS-102Z Colorectal Cancer Focus Panel 1000 38,219 87.34 96.74
PHS-103Z Myeloid Neoplasms Focus Panel 1680 65,577 92.18 99.93
PHS-104Z Brain Cancer Focus Panel 649 8,398 85.70 82.08
PHS-105Z Lung Cancer Focus Panel 759 34,958 91.59 99.98

Specificity and uniformity are defined based on NA12878 testing

Advances in targeted sequencing 20

QIAseq Targeted DNA Legacy Panels
Panel
Breast cancer panel
Colorectal cancer panel
Myeloid Neoplasms panel
Lung cancer panel
Actionable solid tumor panel
BRCA1 and BRCA2 panel
BRCA1 and BRCA2 Plus panel
Pharmacogenomics panel
Mitochondria panel
Inherited disease panel
Cancer Predisposition panel
HRR Panel
Comprehensive cancer panel
Tumor Mutation Burden (TMB) panel
MSI
TMB + MSI
Advances in targeted sequencing
Ordering information
333502, 333505; DHS-001Z
333502, 333505; DHS-002Z
333502, 333505; DHS-003Z
333502, 333505; DHS-005Z
333502, 333505; DHS-101Z
333502, 333505; DHS-102Z
333502, 333505; DHS-103Z
333502, 333505; DHS-104Z
333502, 333505; DHS-105Z
333512, 333515; DHS-3011Z
333502, 333505; DHS-3013Z
333512, 333515; DHS-110Z
333512, 333515; DHS-3501Z
333802, 333805; DHS-6600Z
333802, 333805; DHS-7700Z
333802, 333805; DHS-8800Z
21
Flexibility to accommodate new content without compromising on
quality

or

_
Catalog panel Primers for new content Custom panel

Method Description
GeneGlobe QIAseq Targeted DNA Pro Custom Online tool to quickly design your own QIAseq Targeted DNA Pro Custom Panel
Builder

Enterprise Genomics Solutions (EGS) Team of genomics experts to develop and optimize an integrated QIAseq Targeted DNA
Pro Custom solution that meets your requirements

Advances in targeted sequencing 22

Sample to Insight solution for QIAseq Targeted DNA Pro

Sample Library Data Data

preparation preparation NGS run interpretation
analysis

• QIAamp DNA Mini Kit
• QIAamp DNA FFPE Adv Kit
• QIAamp DNA Circulating
Nucleic Acid Kit
• QIAseq Targeted DNA Pro
Panels (Catalog and Custom)
• QIAseq Targeted DNA Pro
Indexes
• Illumina sequencers • QIAGEN CLC Genomics • QIAGEN Clinical Insight
Workbench Interpret
• Thermo Fisher sequencers

Advances in targeted sequencing 23

QIAseq Targeted DNA Pro accelerates your journey to high-quality
results

01 Sample to sequencing-ready
libraries in less than 6 hours

02 Improved workflow and UMI

capture efficiency for
challenging samples

03 High sensitivity for detecting

low-variant allele frequencies

Advances in targeted sequencing 30

Thank you for your attention. Questions?
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Fisher Scientific or its subsidiaries). Registered names, trademarks, etc. used in this document, even when not specifically marked as
such, may still be protected by law. PROM-20511-001 © 2022 QIAGEN, all rights reserved.