5. Sample & Assay Technologies
Complete Biological Story
Built on Pathway / Network Analysis
Angiogenesis
Inflammation
Pathway
Cell cycle
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6. Sample & Assay Technologies
Patient sample =
Wild-type =
Determining DNA Differences
ATGCCATCTGGGACGGGTCAGTAG
ATGCCATCTGTGACGGGTCAGTAG
How could that SINGLE base difference make the person sick?
Let’s look at the amino acids that are translated in both samples:
Patient sample DNA =
Amino Acid Sequence =
ATG CCA TCT GGG ACG GGT CAG TAG
Met P S G T G Q Stop
Valine
Glycine
Compare the two amino acid sequences:
Patient sample AA Sequence =
Wild-Type AA Sequence =
Met P S G T G Q Stop
Met P S V T G Q Stop
If the wild-type protein, with the Valine positioned here, looked like:
and in the patient sample, it is a Glycine, and it looks like:
Well….the protein just won’t work.
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7. Sample & Assay Technologies
What is NGS (Next Generation Sequencing)?
Massively Paralleled Sequencing
Instead of sequencing a DNA sequence from
Sequence many small pieces at the same time
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8. Sample & Assay Technologies
When doing NGS analysis, what are you looking for?
Easy-to-use workflow and Data output
Detection of Low Prevalence Somatic Mutation in FFPE Lung Adenocarcinoma Sample
Human Lung Cancer GeneRead DNASeq Gene panel was used to enrich 20 genes in genomic DNA isolated from three
FFPE lung adenocarcinoma and one FFPE normal lung samples. Sequencing data was analyzed using QIAGEN NGS
Data Analysis Web Portal and high quality variants were filtered.
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9. Sample & Assay Technologies
Your NGS research needs
Identify low frequency DNA mutation variants
Work with low quality DNA samples, such as FFPE
samples
Focus efforts on a focused set of genes important to
their research
Simple methodology to make variant calls
Selective sequencing saves sequencing capacity
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10. Sample & Assay Technologies
Traditional NGS Workflow
Isolate DNA
Library Prep & Quantification
NGS
Sequence Analysis &
Variant ID
• Whole genome analysis
• Too much irrelevant data
• Poor quality reads / coverage
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11. Sample & Assay Technologies
New NGS Workflow with Targeted Enrichment
80 ng
Achieve more sensitive mutation detection
with 1 additional step
• Focused on your genes of interest
• Why look at all 20,000
genes in the human
genome when you are
interested in only a few?
• Enables deep sequencing to ID
low frequency mutation / rare
variants
• Integrated controls to assess
target enrichment
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12. Sample & Assay Technologies
Target Enrichment: Principles
Multiplex PCR-enabled enrichment of gene of interest
We provide primer sets that produce overlapping PCR products
• For any gene or set of genes in the human genome
Division of non-adjacent gene primer sets into
4 tubes increases amplification specificity.
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14. Sample & Assay Technologies
Complete Analysis Workflow
With integrated controls to assess sample quality / TE process
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15. Sample & Assay Technologies
NGS Sequence Analysis and Variant ID Software
FREE Complete & Easy to use Data Analysis with Web-based Software
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16. Sample & Assay Technologies
Read Mode: Paired End vs Single End
Goal: Increased # of Reads / Amplicon
Sequence of Interest:
TACGCATCGATGCGGTAACTGCTGATCGTCGTAGTGCTAGCTGA
Single End Sequencing:
TACGCATCGATGCGGTAACTGCTGATCGTCGTAGTGCTAGCTGA
Paired End Sequencing (both ends are sequenced):
TACGCATCGATGCGGTAACTGCTGATCGTCGTAGTGCTAGCTGA
AGTCGATCGTGATGCTGCTAGTCGTCAATGGCGTAGCTACGCAT
17. Sample & Assay Technologies
How Genes on Panels Are Selected
Comprehensive Cancer Panel (124 genes)
Disease Focused Gene Panels (20 genes)
Breast cancer
Liver cancer
Colon Cancer
Lung Cancer
Gastric cancer
Ovarian Cancer
Leukemia
Prostate Cancer
Genes with High Relevance
Biologically relevant gene content
Clinically relevant: Published association with the
disease state
– Multiple Publically accessible databases
– Text mining tools
– Manually curated
Genes Involved in Disease
ALSO AVAILABLE: Custom Panels from ANY GENE
or COLLECTION OF GENES in Human Genome
Technically relevant gene content
Most frequently mutated genes
Specific feedback from the thought leaders
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18. Sample & Assay Technologies
Targeted Enrichment: Panel Information
19. Sample & Assay Technologies
Targeted Enrichment: Panel Information
20. Sample & Assay Technologies
NGS Target Enrichment Design Strategy
Commonly encountered issues solved by GeneRead Algorithm
•
Design Coverage
• How much of the gene is covered by your amplicons
•
Sequence Coverage Uniformity
• How much ease base pair is covered: Ideally, it should be uniform
•
Specificity
• % of reads mapped back to your sequence of interest
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21. Sample & Assay Technologies
GeneRead DNAseq Gene Panel: Performance data
% Covered by Design
Design coverage
GeneRead DNAseq
Custom Panel
GeneRead DNAseq
Lung Cancer Panel
GeneRead DNAseq
Comprehensive Cancer Panel
Discover more potential variants by covering more exons
for genes of interest in assay design
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22. Sample & Assay Technologies
GeneRead DNAseq Gene Panel: Performance data
Sequence coverage uniformity
GeneRead DNAseq
Custom Panel
GeneRead DNAseq
Lung Cancer Panel
GeneRead DNAseq
Comprehensive Cancer Panel
More bases sequenced above minimum read depth,
generating more high-quality consensus calls.
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23. Sample & Assay Technologies
GeneRead DNAseq Gene Panel: Performance data
Specificity
(% on-target reads)
Specificity (On-target reads)*
GeneRead DNAseq
Custom Panel
GeneRead DNAseq
Lung Cancer Panel
GeneRead DNAseq
Comprehensive Cancer Panel
No wasting of sequencing capacity
* On-Target Reads= Number of reads on target out of total number of reads per run
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24. Sample & Assay Technologies
DNAseq Gene Panel Application Data
KRAS:G12V is present in all three FFPE lung adenocarcinomas
Detection of Low Prevalence Somatic Mutation in FFPE Lung Adenocarcinoma Sample
Human Lung Cancer GeneRead DNASeq Gene panel was used to enrich 20 genes in genomic DNA isolated from three
FFPE lung adenocarcinoma and one FFPE normal lung samples. Sequencing data was analyzed using QIAGEN NGS
Data Analysis Web Portal and high quality variants were filtered.
NOTE: KRAS mutations confirmed by either Pyro or ARMS mutation assays (qBiomarker Somatic Mutation PCR Array)
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25. Sample & Assay Technologies
Next-generation sequencing workflow
Where does Library Quantification fit within the NGS workflow?
Purification
and
amplification
Sample
enrichment
Library
preparation
Next generation
sequencing run
Result
verification
(Optional)
GeneRead (DNAseq) Library
Quantification and QC System
Why do you want to:
1. quantify their NGS DNA libraries
2. know the quality of their NGS DNA libraries?
You have to, in order to ensure high quality reads
Sequencing runs are expensive and time consuming, therefore, you want to ensure that
downstream sequencing analyses are performed on samples of adequate quality for
NGS technology.
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26. Sample & Assay Technologies
Your needs
Potential problems in NGS if library not quantified
NGS methodology needs
Too much DNA
Mixed signals and un-resolvable data
Too little DNA
Reduced sequencing coverage
Reduced read depth
Empty runs
Increase cost per run
Wasted time
Your needs
Simple and easy to perform method, with convenient and highthroughput format
Fast
Reliable and accurate quantification of sequencing targets
Unmet need: Assess quality of target enriched DNA
Efficient use of NGS capacity
Potential methods for library QC
qPCR
Bioanalyzer
Qubit
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27. Sample & Assay Technologies
Why choose qPCR for NGS Library Quantification?
1. BioAnalyzer measures total nucleic acids
- Why is this a problem?
2. Low limit of detection
3. Consistency of results
-
For each technology, the greater the
concentration of each sample (X-axis),
the greater the # of clusters
-
This should be a linear relationship
-
Only qPCR provides this
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28. Sample & Assay Technologies
NGS Library Quantification Made Easy
Adapters can be quantified with qRT-PCR
Step 1: You have your DNA (whole genome or target enriched)
Step 2: You prepare the DNA library for NGS by adding (via ligation) NGS platformspecific adapters
NOTE: The adapters are short pieces of DNA
Step 3: We provide you 2 reagents:
1. Pre-aliquoted dilutions of the standard
2. qPCR Primer Assays that detect the adapters
Step 4: You perform qPCR with your sample. It should fall between our standard curve
created with 5 sequential 10-fold dilutions. THAT is your library concentration to use in
preparing your NGS analysis.
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29. Sample & Assay Technologies
NGS Library Quantification Made Easy
Adapters can be quantified with qRT-PCR
Step 1: You have your DNA (whole genome or target enriched)
Step 2: You prepare the DNA library for NGS by adding (via ligation) NGS platformspecific adapters
NOTE: The adapters are short pieces of DNA
Step 3: We provide you 2 reagents:
1. Pre-aliquoted dilutions of the standard
2. qPCR Primer Assays that detect the adapters
Step 4: You perform qPCR with your sample. It should fall between our standard curve
created with 5 sequential 10-fold dilutions. THAT is your library concentration to use in
preparing your NGS analysis.
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30. Sample & Assay Technologies
GeneRead Library Quantification System
NGS library quantification for any sequencing application
, Ion Proton
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31. Sample & Assay Technologies
GeneRead DNAseq & LQ System: Summary
Focused:
Biologically relevant content selection enables deep sequencing on
relevant genes and identification of rare mutations
Flexible:
Mix and match any gene of interest
NGS platform independent:
Functionally validated for IT PGM, MiSeq/HiSeq
Integrated controls:
Enabling quality control of prepared library before sequencing
Free, complete and easy of use data analysis tool
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32. Sample & Assay Technologies
GeneRead DNAseq Panel & Library Quant System for NGS
Questions?
Contact Technical Support: 9 AM – 6 PM M – F ET
Contact: 1-800-742-4368 OR support@SABiosciences.com
Shankar Sellappan, Ph.D. (Global Product Manager)
Shankar.Sellappan@QIAGEN.com
Ph.D. Trained Application Scientists
Available Before, During, and After Your Experiments for Consultation / Help
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