SlideShare a Scribd company logo
1 of 1
Download to read offline
Thermo Fisher Scientific • 5791 Van Allen Way • Carlsbad, CA 92008 • www.thermofisher.com
INTRODUCTION
Study of genetic Information from cell-free (cf) DNA provide valuable
opportunities in cancer research and potentially impact future oncology. As an
example, liquid biopsy provide a non-invasive and cost effective solution for
future compared to traditional biopsy tests. Here we report the application of
research based Ion Torrent™ next-generation sequencing (NGS) Oncomine™
cfDNA assays and associated workflow, which is developed to detect somatic
variants at low frequency of 0.1% in cfDNA from plasma.
MATERIALS AND METHODS
Plasma preparation:
Blood samples were collected into EDTA tubes following manufacturer’s
instructions. Plasma was obtained by centrifugation at 1600 x g for 10 min at
4˚C, followed by another spin at 6,000 x g for 30 min at 4˚C to remove any
residual blood cells.
cfDNA/FFPE DNA isolation:
cfDNA was isolated from ~4 mL of plasma using MagMAX™ Cell-Free DNA
Isolation Kit following alternative protocol in User Guide appendix B.
RecoverAll™ Multi-Sample RNA/DNA Isolation Workflow was used to isolate
DNA from FFPE samples following standard protocol.
Library preparation:
Targeted libraries were prepared using the Oncomine™ Lung (or Breast) cfDNA
Assay reagents and user guide instructions for both cfDNA and FFPE DNA.
Sequencing:
The Ion 520™ and Ion 530™ Kit-Chef were used for template preparation on the
Ion Chef™, followed by sequencing on Ion S5™XL system using the Ion 530™
Chip. Lung cfDNA libraries were sequenced as an 8-plex while breast cfDNA
libraries were run as a 12-plex.
Data analysis:
Data analysis was performed in Torrent Suite using the variant Caller plugin.
Yanchun Li, Kris Lea, Priyanka K. Kshatriya, Gu, Jian, Ballesteros-Villagrana, Jeff Schageman, Varun Bagai, Dima Brinza, Richard Chien, Kelli S. Bramlett. 2130 Woodward St. Austin, TX 78744 Thermo Fisher Scientific.
Ion Torrent™ Next Generation Sequencing-Oncomine™ Lung cfDNA assay detected 0.1% low frequency somatic variants in Cell-Free DNA
RESULTS
Figure 1. Workflow for cfDNA analysis using cfDNA Lung Assay. The Oncomine™ cfDNA
assay is a content-optimized solution for NGS cfDNA liquid biopsy research. It includes both
library prep and analysis solutions that enable limit of detection down to 0.1% allelic frequency
(with 20 ng input) for SNV and INDEL hotspots with the flexibility of using as little as 1ng input
DNA. A blood sample to report workflow can be completed in 2 days.
Figure 2. Tagging Technology for rare mutation detection
cfDNA with tumor variant Wild type cfDNA molecule
1. Labeling of DNA molecules
2. PCR amplification and sequencing
Table 1. Detection sensitivity and specificity using Horizon™ cfDNA Reference Standards
with Oncomine™ Lung cfDNA Assay. The Multiplex I cfDNA DNA Reference Standards
(HD780,Horizon™) contains 8 engineered single nucleotide variants (SNVs/SNPs) at a range of
low allelic frequencies (5%, 1%, and 0.1%). Sensitivity and specificity were calculated based on 8
true positive and 149 true negative hotspots covered in Oncomine™ Lung cfDNA Assay. Results
from either duplicates or quadruple experiments.
Horizon Input Sensitivity Specificity
0.0% 20ng
100.0% 100.0%
100.0% 100.0%
0.1% 50ng
91.7% 100.0%
83.3% 100.0%
100.0% 100.0%
91.7% 100.0%
1.0% 10ng
100.0% 100.0%
100.0% 100.0%
5.0% 5ng
100.0% 100.0%
100.0% 100.0%
Gene Variant
Oncomine™
cfDNA Lung
assay
Oncomine™
cfDNA Breast
assay
Digital PCR
KRAS p.G12D
0.20% 0.20% 0.27%
0.17% 0.14% 0.24%
PIK3CA p.E545K
0.15% 0.14% 0.02%
0.11% 0.06% 0.19%
EGFR p.E746_A750delELREA
0.12% *N/A 0.10%
0.11% *N/A 0.12%
EGFR p.L858R
0.07% 0.14% 0.05%
0.06% 0.06% 0.83%
Table 2. Cross Validation of 0.1% Detection sensitivity by Oncomine™ Lung and Breast
cfDNA Assay with digital PCR assay. Data shown is from the Horizon 0.1% control material
when used as input for the Oncomine™ lung and breast cfDNA assays and dPCR assays for the
indicated variants. Allelic frequency of variants was measured using the targeted NGS library
method in the indicated columns. Allelic frequency was validated with digital PCR as an
orthogonal method to measure low frequency variants. Measurements were made in duplicate.
*N/A indicates variants in the Horizon 0.1% control material that are not in the Oncomine™ Breast
cfDNA targeted hotspot file.
Sample Variant
cfDNA input
20ng 10ng 5ng 2ng 1ng 0.5 ng 0.25ng
S1
EGFR
p.L747_E749delLRE
9.4% NA NA 10.4% 14.7% 16.5% 7.9%
S2
KRAS p.G12D 0.2% 0.3% 0.1% 0.2% ** NA NA
MET p.T1010I 47.4% 49.8% 45.5% 47.6% 51.2% NA NA
Table 3. Detection of variants in cfDNA extracted from banked research NSCLC plasma
samples with Oncomine™ Lung cfDNA Assay. Research sample S1 contains a fairly high
frequency variant detected in cfDNA as 9.42% using recommended input of 20ng in the
Oncomine™ Lung cfDNA assay. The variant could still be detected when input was decreased to
0.25 ng of cfDNA. In research sample S2, a variant was identified using 20ng of cfDNA at low
allelic frequency of 0.22%. This variant was successfully detected using input amounts down to 2
ng. A germline variant present in sample S2 was consistently detected at levels ~50% in all input
titration libraries. NA: not tested; **: not detected.
CONCLUSIONS
• Oncomine™ cfDNA Assays provide an easy, quick, and reliable solution for
research in detecting low frequency somatic variant in blood plasma and
tissue
• Oncomine™ cfDNA Assays target specific actionable hotspot regions of genes
for indicated cancer type to create a targeted amplicon library for sequencing
with the Ion Torrent Sequencing System; Oncomine™ Lung cfDNA Assay
(Cat Lot: A31149) is currently available; Oncomine™ Breast and Colon cfDNA
assays coming soon
• The Ion Torrent™ NGS technology and tailored TSS analytical pipeline allows
this assay to detect variants as low as 0.1% limit of detection (LOD);
measured allelic frequencies confirmed by orthogonal measurement
system—dPCR
• The total process time (from plasma/FFPE specimen to result reporting)
could be as short as 32 hours with a total hand on time of ~4 hours;
supporting a lab workflow where you can receive blood samples early on day
1 and have variant calls before you go home on day 2
Sample Variant FFPE Plasma
S1 EGFR p.L858R 71.42% 2.66%
S2 TP53 p.R158L 51.89% 4.32%
S3
METp.T1010I 43.87% 51.75%
KRAS p.G12C 34.62% 0.28%
S4 ND ND ND
S5
EGFR p.L858R 58.44% 7.74%
MET p.T1010I 41.93% 48.74%
TP53 p.Y220C 35.54% 1.93%
S6 TP53 p.R158L 10.19% 1.27%
S7 TP53 p.M237I 0.49% 0.13%
S8 KRAS p.G12A 5.56% 3.02%
S9 MET p.T1010I 68.93% 50.51%
S10
KRAS p.G12V 20.01% 1.70%
KRAS p.G12C 20.03% 1.70%
S11 KRAS p.G12D 25.29% 12%
S12 KRAS p.G12C 19.91% **
S13 KRAS p.G13D 29.90% **
S14 TP53 p.R248L 21.82% 0.34%
S15 TP53 p.R337L 46.84% 0.18%
S16
KRAS p.G12D 3.98% 0.22%
MET p.T1010I 50.42% 47.44%
S17 TP53 p.R273C 4.64% **
S18 KRAS p.G12S 1.25% 6.56%
S19
TP53 p.Y234C 17.16% **
TP53 p.T125T 25.76% **
S20
KRAS p.G13C 2.65% 0.30%
MET p.T1010I 2.21% **
Table 4. Observed frequencies of variants detected from matched FFPE and Plasma
samples. Late stage NSCLC research samples were purchased from BioChain. Sample sets
included solid tumor sample embedded in FFPE and 2–4 mls plasma from blood collected in
EDTA tubes. Bold numbers indicate allelic frequencies as determined using the Oncomine™ Lung
cfDNA assay for the indicated somatic variants. Non-bold frequencies show germline variants
that were also detected in the targeted libraries. For these 6 independent research samples,
there was very high concordance between variants detected in FFPE and cfDNA from matched
plasma from the same research subjects. As expected, higher variant frequencies were observed
in the FFPE solid tumor samples with significantly lower frequencies measured in the matched
cfDNA samples. ND: no detection(negative case); **: not detected.
For Research Use Only. Not for use in diagnostic procedures.
© 2016 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the
property of Thermo Fisher Scientific and its subsidiaries unless otherwise
specified. Horizon is a trademark of Horizon Discovery Group, Inc.
Samples Sensitivity Specificity PPV
0.1%MM 90% 98.4% 94.1%
0.5% >99.9% 98.3% 94.3%
Table 5. Detection Sensitivity and Specificity. The Oncomine™ Lung cfDNA Assay
performance was evaluated using engineered controls (AcroMetrix™ Oncology Hotspot Control)
in background GM24385 genomic DNA diluted to 0.1% or 0.5% allelic frequencies. The control
and background DNA was fragmented to mimic the size of cfDNA. Mean sensitivity and
specificity values were obtained across the expected true positives and true negatives at
oncology hotspot positions.

More Related Content

What's hot

Chapter 2 molecular methods in cancer
Chapter 2 molecular methods in cancerChapter 2 molecular methods in cancer
Chapter 2 molecular methods in cancerNilesh Kucha
 
A short introduction to single-cell RNA-seq analyses
A short introduction to single-cell RNA-seq analysesA short introduction to single-cell RNA-seq analyses
A short introduction to single-cell RNA-seq analysestuxette
 
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...QIAGEN
 
Chapter 1 cancer genome
Chapter 1 cancer genomeChapter 1 cancer genome
Chapter 1 cancer genomeNilesh Kucha
 
Challenges and opportunities in personal omics profiling
Challenges and opportunities in personal omics profilingChallenges and opportunities in personal omics profiling
Challenges and opportunities in personal omics profilingSenthil Natesan
 
Chapter 2.4 tmb and ngs
Chapter 2.4 tmb and ngsChapter 2.4 tmb and ngs
Chapter 2.4 tmb and ngsNilesh Kucha
 
Single-cell RNA-seq tutorial
Single-cell RNA-seq tutorialSingle-cell RNA-seq tutorial
Single-cell RNA-seq tutorialAaron Diaz
 
Next generation sequencing
Next generation sequencingNext generation sequencing
Next generation sequencingUzma Jabeen
 
Liquid biopsy
Liquid biopsyLiquid biopsy
Liquid biopsyDr kusuma
 
The Application of Next Generation Sequencing (NGS) in cancer treatment
The Application of Next Generation Sequencing (NGS) in cancer treatmentThe Application of Next Generation Sequencing (NGS) in cancer treatment
The Application of Next Generation Sequencing (NGS) in cancer treatmentPremadarshini Sai
 
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...QIAGEN
 
Microsatellite instability - What is it? How to test? Applications in Medical...
Microsatellite instability - What is it? How to test? Applications in Medical...Microsatellite instability - What is it? How to test? Applications in Medical...
Microsatellite instability - What is it? How to test? Applications in Medical...Venkata pradeep babu koyyala
 
2 whole genome sequencing and analysis
2 whole genome sequencing and analysis2 whole genome sequencing and analysis
2 whole genome sequencing and analysissaberhussain9
 

What's hot (20)

Chapter 2 molecular methods in cancer
Chapter 2 molecular methods in cancerChapter 2 molecular methods in cancer
Chapter 2 molecular methods in cancer
 
Biomarkers omics 1
Biomarkers omics 1Biomarkers omics 1
Biomarkers omics 1
 
A short introduction to single-cell RNA-seq analyses
A short introduction to single-cell RNA-seq analysesA short introduction to single-cell RNA-seq analyses
A short introduction to single-cell RNA-seq analyses
 
Overview of Single-Cell RNA-seq
Overview of Single-Cell RNA-seqOverview of Single-Cell RNA-seq
Overview of Single-Cell RNA-seq
 
Protein fold recognition and ab_initio modeling
Protein fold recognition and ab_initio modelingProtein fold recognition and ab_initio modeling
Protein fold recognition and ab_initio modeling
 
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...
 
Chapter 1 cancer genome
Chapter 1 cancer genomeChapter 1 cancer genome
Chapter 1 cancer genome
 
ChIP-seq
ChIP-seqChIP-seq
ChIP-seq
 
Challenges and opportunities in personal omics profiling
Challenges and opportunities in personal omics profilingChallenges and opportunities in personal omics profiling
Challenges and opportunities in personal omics profiling
 
Gene expression profiling
Gene expression profilingGene expression profiling
Gene expression profiling
 
Chapter 2.4 tmb and ngs
Chapter 2.4 tmb and ngsChapter 2.4 tmb and ngs
Chapter 2.4 tmb and ngs
 
Single-cell RNA-seq tutorial
Single-cell RNA-seq tutorialSingle-cell RNA-seq tutorial
Single-cell RNA-seq tutorial
 
Liquid biopsy
Liquid biopsyLiquid biopsy
Liquid biopsy
 
Basic Steps of the NGS Method
Basic Steps of the NGS MethodBasic Steps of the NGS Method
Basic Steps of the NGS Method
 
Next generation sequencing
Next generation sequencingNext generation sequencing
Next generation sequencing
 
Liquid biopsy
Liquid biopsyLiquid biopsy
Liquid biopsy
 
The Application of Next Generation Sequencing (NGS) in cancer treatment
The Application of Next Generation Sequencing (NGS) in cancer treatmentThe Application of Next Generation Sequencing (NGS) in cancer treatment
The Application of Next Generation Sequencing (NGS) in cancer treatment
 
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...
 
Microsatellite instability - What is it? How to test? Applications in Medical...
Microsatellite instability - What is it? How to test? Applications in Medical...Microsatellite instability - What is it? How to test? Applications in Medical...
Microsatellite instability - What is it? How to test? Applications in Medical...
 
2 whole genome sequencing and analysis
2 whole genome sequencing and analysis2 whole genome sequencing and analysis
2 whole genome sequencing and analysis
 

Viewers also liked

Computational Methods for detection of somatic mutations at 0.1% frequency fr...
Computational Methods for detection of somatic mutations at 0.1% frequency fr...Computational Methods for detection of somatic mutations at 0.1% frequency fr...
Computational Methods for detection of somatic mutations at 0.1% frequency fr...Thermo Fisher Scientific
 
A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...
A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...
A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...Thermo Fisher Scientific
 
Information Genetic Content (IGC): a comprehensive discovery platform for dis...
Information Genetic Content (IGC): a comprehensive discovery platform for dis...Information Genetic Content (IGC): a comprehensive discovery platform for dis...
Information Genetic Content (IGC): a comprehensive discovery platform for dis...Thermo Fisher Scientific
 
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131Thermo Fisher Scientific
 
High-throughput processing to maximize genomic analysis through simultaneous ...
High-throughput processing to maximize genomic analysis through simultaneous ...High-throughput processing to maximize genomic analysis through simultaneous ...
High-throughput processing to maximize genomic analysis through simultaneous ...Thermo Fisher Scientific
 
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
 
NGS technologies - platforms and applications
NGS technologies - platforms and applicationsNGS technologies - platforms and applications
NGS technologies - platforms and applicationsAGRF_Ltd
 
Ion Torrent Sequencer, Mappers, Variant Callers
Ion Torrent Sequencer, Mappers, Variant CallersIon Torrent Sequencer, Mappers, Variant Callers
Ion Torrent Sequencer, Mappers, Variant CallersVenu Thatikonda
 
Preparing libraries directly from archived FFPE sections blood, saliva, and b...
Preparing libraries directly from archived FFPE sections blood, saliva, and b...Preparing libraries directly from archived FFPE sections blood, saliva, and b...
Preparing libraries directly from archived FFPE sections blood, saliva, and b...Thermo Fisher Scientific
 
Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...
Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...
Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...Thermo Fisher Scientific
 
Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...
Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...
Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...Thermo Fisher Scientific
 
Advances in Breast Tumor Biomarker Discovery Methods
Advances in Breast Tumor Biomarker Discovery MethodsAdvances in Breast Tumor Biomarker Discovery Methods
Advances in Breast Tumor Biomarker Discovery MethodsThermo Fisher Scientific
 
600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...
600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...
600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...Thermo Fisher Scientific
 
Next generation sequencing
Next generation sequencingNext generation sequencing
Next generation sequencingehsan sepahi
 
`Liquid biopsy' using blood test is latest weapon against cancer
`Liquid biopsy' using blood test is latest weapon against cancer`Liquid biopsy' using blood test is latest weapon against cancer
`Liquid biopsy' using blood test is latest weapon against cancerOther Mother
 
High Sensitivity Sanger Sequencing for Minor Variant Detection
High Sensitivity Sanger Sequencing for Minor Variant DetectionHigh Sensitivity Sanger Sequencing for Minor Variant Detection
High Sensitivity Sanger Sequencing for Minor Variant DetectionThermo Fisher Scientific
 
Liquid biopsy in precision medicine
Liquid biopsy in precision medicineLiquid biopsy in precision medicine
Liquid biopsy in precision medicineSeth Taylor
 

Viewers also liked (20)

Computational Methods for detection of somatic mutations at 0.1% frequency fr...
Computational Methods for detection of somatic mutations at 0.1% frequency fr...Computational Methods for detection of somatic mutations at 0.1% frequency fr...
Computational Methods for detection of somatic mutations at 0.1% frequency fr...
 
A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...
A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...
A next Generation Sequencing Approach to Detect Large Rearrangements in BRCA1...
 
Information Genetic Content (IGC): a comprehensive discovery platform for dis...
Information Genetic Content (IGC): a comprehensive discovery platform for dis...Information Genetic Content (IGC): a comprehensive discovery platform for dis...
Information Genetic Content (IGC): a comprehensive discovery platform for dis...
 
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131
 
High-throughput processing to maximize genomic analysis through simultaneous ...
High-throughput processing to maximize genomic analysis through simultaneous ...High-throughput processing to maximize genomic analysis through simultaneous ...
High-throughput processing to maximize genomic analysis through simultaneous ...
 
Ion Torrent Sequencing
Ion Torrent SequencingIon Torrent Sequencing
Ion Torrent Sequencing
 
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...
 
NGS technologies - platforms and applications
NGS technologies - platforms and applicationsNGS technologies - platforms and applications
NGS technologies - platforms and applications
 
Ngs ppt
Ngs pptNgs ppt
Ngs ppt
 
Ion Torrent Sequencer, Mappers, Variant Callers
Ion Torrent Sequencer, Mappers, Variant CallersIon Torrent Sequencer, Mappers, Variant Callers
Ion Torrent Sequencer, Mappers, Variant Callers
 
Preparing libraries directly from archived FFPE sections blood, saliva, and b...
Preparing libraries directly from archived FFPE sections blood, saliva, and b...Preparing libraries directly from archived FFPE sections blood, saliva, and b...
Preparing libraries directly from archived FFPE sections blood, saliva, and b...
 
Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...
Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...
Successful detection of 40 COSMIC hotspot mutations at allelic frequency belo...
 
Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...
Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...
Detection of Low Level Sequence Variants by Sanger Sequencing | ESHG 2015 Pos...
 
Advances in Breast Tumor Biomarker Discovery Methods
Advances in Breast Tumor Biomarker Discovery MethodsAdvances in Breast Tumor Biomarker Discovery Methods
Advances in Breast Tumor Biomarker Discovery Methods
 
600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...
600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...
600 base reads on the Ion S5™ Next-Generation Sequencing System enables accur...
 
Rating Television Food Handling
Rating Television Food HandlingRating Television Food Handling
Rating Television Food Handling
 
Next generation sequencing
Next generation sequencingNext generation sequencing
Next generation sequencing
 
`Liquid biopsy' using blood test is latest weapon against cancer
`Liquid biopsy' using blood test is latest weapon against cancer`Liquid biopsy' using blood test is latest weapon against cancer
`Liquid biopsy' using blood test is latest weapon against cancer
 
High Sensitivity Sanger Sequencing for Minor Variant Detection
High Sensitivity Sanger Sequencing for Minor Variant DetectionHigh Sensitivity Sanger Sequencing for Minor Variant Detection
High Sensitivity Sanger Sequencing for Minor Variant Detection
 
Liquid biopsy in precision medicine
Liquid biopsy in precision medicineLiquid biopsy in precision medicine
Liquid biopsy in precision medicine
 

Similar to Ion Torrent™ Next Generation Sequencing-Oncomine™ Lung cfDNA assay detected 0.1% low frequency somatic variants in Cell-Free DNA

An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...
An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...
An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...Thermo Fisher Scientific
 
Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...
Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...
Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...Thermo Fisher Scientific
 
Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...
Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...
Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...Thermo Fisher Scientific
 
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...Thermo Fisher Scientific
 
Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...
Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...
Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...Thermo Fisher Scientific
 
An NGS workflow to detect down to 0.1% allelic frequency in cfDNA
An NGS workflow to detect down to 0.1% allelic frequency in cfDNAAn NGS workflow to detect down to 0.1% allelic frequency in cfDNA
An NGS workflow to detect down to 0.1% allelic frequency in cfDNAThermo Fisher Scientific
 
trusight-tumor-15-cfdna-white-paper-1170-2016-016
trusight-tumor-15-cfdna-white-paper-1170-2016-016trusight-tumor-15-cfdna-white-paper-1170-2016-016
trusight-tumor-15-cfdna-white-paper-1170-2016-016Andrew Hinton
 
Hotspot mutation and fusion transcript detection from the same non-small cell...
Hotspot mutation and fusion transcript detection from the same non-small cell...Hotspot mutation and fusion transcript detection from the same non-small cell...
Hotspot mutation and fusion transcript detection from the same non-small cell...Thermo Fisher Scientific
 
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...Thermo Fisher Scientific
 
A rapid library preparation method with custom assay designs for detection of...
A rapid library preparation method with custom assay designs for detection of...A rapid library preparation method with custom assay designs for detection of...
A rapid library preparation method with custom assay designs for detection of...Thermo Fisher Scientific
 
Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...
Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...
Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...Thermo Fisher Scientific
 
research paper presentation: HYBRID CAPTURE BASED NGS FOR GENOMIC PROFILING ...
research paper presentation: HYBRID CAPTURE BASED NGS  FOR GENOMIC PROFILING ...research paper presentation: HYBRID CAPTURE BASED NGS  FOR GENOMIC PROFILING ...
research paper presentation: HYBRID CAPTURE BASED NGS FOR GENOMIC PROFILING ...Ikram Ullah
 
Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...
Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...
Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...Thermo Fisher Scientific
 
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...The OncoScan(TM) platform for analysis of copy number and somatic mutations i...
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...Lawrence Greenfield
 
Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...
Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...
Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...Pratik Chandrani
 
Development of a next-generation (NGS) assay for pediatric, childhood, and yo...
Development of a next-generation (NGS) assay for pediatric, childhood, and yo...Development of a next-generation (NGS) assay for pediatric, childhood, and yo...
Development of a next-generation (NGS) assay for pediatric, childhood, and yo...Thermo Fisher Scientific
 
Simultaneous Isolation of RNA & DNA from one FFPE Sample
Simultaneous Isolation of RNA & DNA from one FFPE SampleSimultaneous Isolation of RNA & DNA from one FFPE Sample
Simultaneous Isolation of RNA & DNA from one FFPE SampleQIAGEN
 
Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...
Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...
Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...Thermo Fisher Scientific
 

Similar to Ion Torrent™ Next Generation Sequencing-Oncomine™ Lung cfDNA assay detected 0.1% low frequency somatic variants in Cell-Free DNA (20)

An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...
An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...
An Efficient NGS Workflow for Liquid Biopsy Research Using a Comprehensive As...
 
Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...
Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...
Comparing Mutation Detection Sensitivity from Matched FFPE Tissue and Liquid ...
 
Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...
Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...
Development of a Breast and Lung Cancer Research Panel To Target Therapeutica...
 
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
 
Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...
Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...
Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using...
 
An NGS workflow to detect down to 0.1% allelic frequency in cfDNA
An NGS workflow to detect down to 0.1% allelic frequency in cfDNAAn NGS workflow to detect down to 0.1% allelic frequency in cfDNA
An NGS workflow to detect down to 0.1% allelic frequency in cfDNA
 
trusight-tumor-15-cfdna-white-paper-1170-2016-016
trusight-tumor-15-cfdna-white-paper-1170-2016-016trusight-tumor-15-cfdna-white-paper-1170-2016-016
trusight-tumor-15-cfdna-white-paper-1170-2016-016
 
Hotspot mutation and fusion transcript detection from the same non-small cell...
Hotspot mutation and fusion transcript detection from the same non-small cell...Hotspot mutation and fusion transcript detection from the same non-small cell...
Hotspot mutation and fusion transcript detection from the same non-small cell...
 
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan ...
 
A rapid library preparation method with custom assay designs for detection of...
A rapid library preparation method with custom assay designs for detection of...A rapid library preparation method with custom assay designs for detection of...
A rapid library preparation method with custom assay designs for detection of...
 
Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...
Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...
Circulating Cell Free DNA Targeted Sequencing Workflow | ESHG 2015 Poster PM1...
 
research paper presentation: HYBRID CAPTURE BASED NGS FOR GENOMIC PROFILING ...
research paper presentation: HYBRID CAPTURE BASED NGS  FOR GENOMIC PROFILING ...research paper presentation: HYBRID CAPTURE BASED NGS  FOR GENOMIC PROFILING ...
research paper presentation: HYBRID CAPTURE BASED NGS FOR GENOMIC PROFILING ...
 
Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...
Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...
Rare Mutation Analysis Using Digital PCR on QuantStudio™ 3D to Verify Ion Amp...
 
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...The OncoScan(TM) platform for analysis of copy number and somatic mutations i...
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...
 
Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...
Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...
Molecular-testing-in-Lung-Cancer-_-identification-of-uncommon-mutations-final...
 
PCR
PCRPCR
PCR
 
Development of a next-generation (NGS) assay for pediatric, childhood, and yo...
Development of a next-generation (NGS) assay for pediatric, childhood, and yo...Development of a next-generation (NGS) assay for pediatric, childhood, and yo...
Development of a next-generation (NGS) assay for pediatric, childhood, and yo...
 
Simultaneous Isolation of RNA & DNA from one FFPE Sample
Simultaneous Isolation of RNA & DNA from one FFPE SampleSimultaneous Isolation of RNA & DNA from one FFPE Sample
Simultaneous Isolation of RNA & DNA from one FFPE Sample
 
PCR.pptx
PCR.pptxPCR.pptx
PCR.pptx
 
Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...
Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...
Fusion Gene Detection and Gene Expression Analysis of Circulating RNA in Plas...
 

More from Thermo Fisher Scientific

Why you would want a powerful hot-start DNA polymerase for your PCR
Why you would want a powerful hot-start DNA polymerase for your PCRWhy you would want a powerful hot-start DNA polymerase for your PCR
Why you would want a powerful hot-start DNA polymerase for your PCRThermo Fisher Scientific
 
TCRB chain convergence in chronic cytomegalovirus infection and cancer
TCRB chain convergence in chronic cytomegalovirus infection and cancerTCRB chain convergence in chronic cytomegalovirus infection and cancer
TCRB chain convergence in chronic cytomegalovirus infection and cancerThermo Fisher Scientific
 
Improvement of TMB Measurement by removal of Deaminated Bases in FFPE DNA
Improvement of TMB Measurement by removal of Deaminated Bases in FFPE DNAImprovement of TMB Measurement by removal of Deaminated Bases in FFPE DNA
Improvement of TMB Measurement by removal of Deaminated Bases in FFPE DNAThermo Fisher Scientific
 
What can we learn from oncologists? A survey of molecular testing patterns
What can we learn from oncologists? A survey of molecular testing patternsWhat can we learn from oncologists? A survey of molecular testing patterns
What can we learn from oncologists? A survey of molecular testing patternsThermo Fisher Scientific
 
Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...
Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...
Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...Thermo Fisher Scientific
 
Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...
Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...
Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...Thermo Fisher Scientific
 
Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...
Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...
Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...Thermo Fisher Scientific
 
Liquid biopsy quality control – the importance of plasma quality, sample prep...
Liquid biopsy quality control – the importance of plasma quality, sample prep...Liquid biopsy quality control – the importance of plasma quality, sample prep...
Liquid biopsy quality control – the importance of plasma quality, sample prep...Thermo Fisher Scientific
 
Streamlined next generation sequencing assay development using a highly multi...
Streamlined next generation sequencing assay development using a highly multi...Streamlined next generation sequencing assay development using a highly multi...
Streamlined next generation sequencing assay development using a highly multi...Thermo Fisher Scientific
 
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Thermo Fisher Scientific
 
Development of Quality Control Materials for Characterization of Comprehensiv...
Development of Quality Control Materials for Characterization of Comprehensiv...Development of Quality Control Materials for Characterization of Comprehensiv...
Development of Quality Control Materials for Characterization of Comprehensiv...Thermo Fisher Scientific
 
A High Throughput System for Profiling Respiratory Tract Microbiota
A High Throughput System for Profiling Respiratory Tract MicrobiotaA High Throughput System for Profiling Respiratory Tract Microbiota
A High Throughput System for Profiling Respiratory Tract MicrobiotaThermo Fisher Scientific
 
A high-throughput approach for multi-omic testing for prostate cancer research
A high-throughput approach for multi-omic testing for prostate cancer researchA high-throughput approach for multi-omic testing for prostate cancer research
A high-throughput approach for multi-omic testing for prostate cancer researchThermo Fisher Scientific
 
Why is selecting the right thermal cycler important?
Why is selecting the right thermal cycler important?Why is selecting the right thermal cycler important?
Why is selecting the right thermal cycler important?Thermo Fisher Scientific
 
Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...
Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...
Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...Thermo Fisher Scientific
 
TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...
TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...
TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...Thermo Fisher Scientific
 
Identifying novel and druggable targets in a triple negative breast cancer ce...
Identifying novel and druggable targets in a triple negative breast cancer ce...Identifying novel and druggable targets in a triple negative breast cancer ce...
Identifying novel and druggable targets in a triple negative breast cancer ce...Thermo Fisher Scientific
 
Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...
Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...
Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...Thermo Fisher Scientific
 
Analytical performance of a novel next generation sequencing assay for Myeloi...
Analytical performance of a novel next generation sequencing assay for Myeloi...Analytical performance of a novel next generation sequencing assay for Myeloi...
Analytical performance of a novel next generation sequencing assay for Myeloi...Thermo Fisher Scientific
 
Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...
Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...
Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...Thermo Fisher Scientific
 

More from Thermo Fisher Scientific (20)

Why you would want a powerful hot-start DNA polymerase for your PCR
Why you would want a powerful hot-start DNA polymerase for your PCRWhy you would want a powerful hot-start DNA polymerase for your PCR
Why you would want a powerful hot-start DNA polymerase for your PCR
 
TCRB chain convergence in chronic cytomegalovirus infection and cancer
TCRB chain convergence in chronic cytomegalovirus infection and cancerTCRB chain convergence in chronic cytomegalovirus infection and cancer
TCRB chain convergence in chronic cytomegalovirus infection and cancer
 
Improvement of TMB Measurement by removal of Deaminated Bases in FFPE DNA
Improvement of TMB Measurement by removal of Deaminated Bases in FFPE DNAImprovement of TMB Measurement by removal of Deaminated Bases in FFPE DNA
Improvement of TMB Measurement by removal of Deaminated Bases in FFPE DNA
 
What can we learn from oncologists? A survey of molecular testing patterns
What can we learn from oncologists? A survey of molecular testing patternsWhat can we learn from oncologists? A survey of molecular testing patterns
What can we learn from oncologists? A survey of molecular testing patterns
 
Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...
Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...
Evaluation of ctDNA extraction methods and amplifiable copy number yield usin...
 
Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...
Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...
Analytical Validation of the Oncomine™ Comprehensive Assay v3 with FFPE and C...
 
Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...
Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...
Novel Spatial Multiplex Screening of Uropathogens Associated with Urinary Tra...
 
Liquid biopsy quality control – the importance of plasma quality, sample prep...
Liquid biopsy quality control – the importance of plasma quality, sample prep...Liquid biopsy quality control – the importance of plasma quality, sample prep...
Liquid biopsy quality control – the importance of plasma quality, sample prep...
 
Streamlined next generation sequencing assay development using a highly multi...
Streamlined next generation sequencing assay development using a highly multi...Streamlined next generation sequencing assay development using a highly multi...
Streamlined next generation sequencing assay development using a highly multi...
 
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...
 
Development of Quality Control Materials for Characterization of Comprehensiv...
Development of Quality Control Materials for Characterization of Comprehensiv...Development of Quality Control Materials for Characterization of Comprehensiv...
Development of Quality Control Materials for Characterization of Comprehensiv...
 
A High Throughput System for Profiling Respiratory Tract Microbiota
A High Throughput System for Profiling Respiratory Tract MicrobiotaA High Throughput System for Profiling Respiratory Tract Microbiota
A High Throughput System for Profiling Respiratory Tract Microbiota
 
A high-throughput approach for multi-omic testing for prostate cancer research
A high-throughput approach for multi-omic testing for prostate cancer researchA high-throughput approach for multi-omic testing for prostate cancer research
A high-throughput approach for multi-omic testing for prostate cancer research
 
Why is selecting the right thermal cycler important?
Why is selecting the right thermal cycler important?Why is selecting the right thermal cycler important?
Why is selecting the right thermal cycler important?
 
Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...
Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...
Generation of Clonal CRISPR/Cas9-edited Human iPSC Derived Cellular Models an...
 
TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...
TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...
TaqMan®Advanced miRNA cDNA synthesis kit to simultaneously study expression o...
 
Identifying novel and druggable targets in a triple negative breast cancer ce...
Identifying novel and druggable targets in a triple negative breast cancer ce...Identifying novel and druggable targets in a triple negative breast cancer ce...
Identifying novel and druggable targets in a triple negative breast cancer ce...
 
Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...
Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...
Evidence for antigen-driven TCRβ chain convergence in the melanoma-infiltrati...
 
Analytical performance of a novel next generation sequencing assay for Myeloi...
Analytical performance of a novel next generation sequencing assay for Myeloi...Analytical performance of a novel next generation sequencing assay for Myeloi...
Analytical performance of a novel next generation sequencing assay for Myeloi...
 
Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...
Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...
Estimating Mutation Load from Tumor Research Samples using a Targeted Next-Ge...
 

Recently uploaded

MARKER ASSISTED SELECTION IN CROP IMPROVEMENT
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTMARKER ASSISTED SELECTION IN CROP IMPROVEMENT
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTjipexe1248
 
Substances in Common Use for Shahu College Screening Test
Substances in Common Use for Shahu College Screening TestSubstances in Common Use for Shahu College Screening Test
Substances in Common Use for Shahu College Screening TestAkashDTejwani
 
Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...
Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...
Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...Sérgio Sacani
 
Pests of tenai_Identification,Binomics_Dr.UPR
Pests of tenai_Identification,Binomics_Dr.UPRPests of tenai_Identification,Binomics_Dr.UPR
Pests of tenai_Identification,Binomics_Dr.UPRPirithiRaju
 
Role of herbs in hair care Amla and heena.pptx
Role of herbs in hair care  Amla and  heena.pptxRole of herbs in hair care  Amla and  heena.pptx
Role of herbs in hair care Amla and heena.pptxVaishnaviAware
 
Q3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptx
Q3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptxQ3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptx
Q3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptxArdeniel
 
Contracts with Interdependent Preferences (2)
Contracts with Interdependent Preferences (2)Contracts with Interdependent Preferences (2)
Contracts with Interdependent Preferences (2)GRAPE
 
SCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptx
SCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptxSCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptx
SCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptxROVELYNEDELUNA3
 
Physics Serway Jewett 6th edition for Scientists and Engineers
Physics Serway Jewett 6th edition for Scientists and EngineersPhysics Serway Jewett 6th edition for Scientists and Engineers
Physics Serway Jewett 6th edition for Scientists and EngineersAndreaLucarelli
 
geometric quantization on coadjoint orbits
geometric quantization on coadjoint orbitsgeometric quantization on coadjoint orbits
geometric quantization on coadjoint orbitsHassan Jolany
 
Krishi Vigyan Kendras - कृषि विज्ञान केंद्र
Krishi Vigyan Kendras - कृषि विज्ञान केंद्रKrishi Vigyan Kendras - कृषि विज्ञान केंद्र
Krishi Vigyan Kendras - कृषि विज्ञान केंद्रKrashi Coaching
 
001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...
001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...
001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...marwaahmad357
 
Applied Biochemistry feedback_M Ahwad 2023.docx
Applied Biochemistry feedback_M Ahwad 2023.docxApplied Biochemistry feedback_M Ahwad 2023.docx
Applied Biochemistry feedback_M Ahwad 2023.docxmarwaahmad357
 
Gene transfer in plants agrobacterium.pdf
Gene transfer in plants agrobacterium.pdfGene transfer in plants agrobacterium.pdf
Gene transfer in plants agrobacterium.pdfNetHelix
 
MARSILEA notes in detail for II year Botany.ppt
MARSILEA  notes in detail for II year Botany.pptMARSILEA  notes in detail for II year Botany.ppt
MARSILEA notes in detail for II year Botany.pptaigil2
 
Basic Concepts in Pharmacology in molecular .pptx
Basic Concepts in Pharmacology in molecular  .pptxBasic Concepts in Pharmacology in molecular  .pptx
Basic Concepts in Pharmacology in molecular .pptxVijayaKumarR28
 
Role of Herbs in Cosmetics in Cosmetic Science.
Role of Herbs in Cosmetics in Cosmetic Science.Role of Herbs in Cosmetics in Cosmetic Science.
Role of Herbs in Cosmetics in Cosmetic Science.ShwetaHattimare
 
soft skills question paper set for bba ca
soft skills question paper set for bba casoft skills question paper set for bba ca
soft skills question paper set for bba caohsadfeeling
 

Recently uploaded (20)

MARKER ASSISTED SELECTION IN CROP IMPROVEMENT
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTMARKER ASSISTED SELECTION IN CROP IMPROVEMENT
MARKER ASSISTED SELECTION IN CROP IMPROVEMENT
 
Substances in Common Use for Shahu College Screening Test
Substances in Common Use for Shahu College Screening TestSubstances in Common Use for Shahu College Screening Test
Substances in Common Use for Shahu College Screening Test
 
Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...
Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...
Digitized Continuous Magnetic Recordings for the August/September 1859 Storms...
 
Pests of tenai_Identification,Binomics_Dr.UPR
Pests of tenai_Identification,Binomics_Dr.UPRPests of tenai_Identification,Binomics_Dr.UPR
Pests of tenai_Identification,Binomics_Dr.UPR
 
Role of herbs in hair care Amla and heena.pptx
Role of herbs in hair care  Amla and  heena.pptxRole of herbs in hair care  Amla and  heena.pptx
Role of herbs in hair care Amla and heena.pptx
 
Q3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptx
Q3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptxQ3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptx
Q3W4part1-SSSSSSSSSSSSSSSSSSSSSSSSCI.pptx
 
Contracts with Interdependent Preferences (2)
Contracts with Interdependent Preferences (2)Contracts with Interdependent Preferences (2)
Contracts with Interdependent Preferences (2)
 
SCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptx
SCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptxSCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptx
SCIENCE 6 QUARTER 3 REVIEWER(FRICTION, GRAVITY, ENERGY AND SPEED).pptx
 
Physics Serway Jewett 6th edition for Scientists and Engineers
Physics Serway Jewett 6th edition for Scientists and EngineersPhysics Serway Jewett 6th edition for Scientists and Engineers
Physics Serway Jewett 6th edition for Scientists and Engineers
 
geometric quantization on coadjoint orbits
geometric quantization on coadjoint orbitsgeometric quantization on coadjoint orbits
geometric quantization on coadjoint orbits
 
Krishi Vigyan Kendras - कृषि विज्ञान केंद्र
Krishi Vigyan Kendras - कृषि विज्ञान केंद्रKrishi Vigyan Kendras - कृषि विज्ञान केंद्र
Krishi Vigyan Kendras - कृषि विज्ञान केंद्र
 
Data delivery from the US-EPA Center for Computational Toxicology and Exposur...
Data delivery from the US-EPA Center for Computational Toxicology and Exposur...Data delivery from the US-EPA Center for Computational Toxicology and Exposur...
Data delivery from the US-EPA Center for Computational Toxicology and Exposur...
 
001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...
001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...
001 Case Study - Submission Point_c1051231_attempt_2023-11-23-14-08-42_ABS CW...
 
Cheminformatics tools and chemistry data underpinning mass spectrometry analy...
Cheminformatics tools and chemistry data underpinning mass spectrometry analy...Cheminformatics tools and chemistry data underpinning mass spectrometry analy...
Cheminformatics tools and chemistry data underpinning mass spectrometry analy...
 
Applied Biochemistry feedback_M Ahwad 2023.docx
Applied Biochemistry feedback_M Ahwad 2023.docxApplied Biochemistry feedback_M Ahwad 2023.docx
Applied Biochemistry feedback_M Ahwad 2023.docx
 
Gene transfer in plants agrobacterium.pdf
Gene transfer in plants agrobacterium.pdfGene transfer in plants agrobacterium.pdf
Gene transfer in plants agrobacterium.pdf
 
MARSILEA notes in detail for II year Botany.ppt
MARSILEA  notes in detail for II year Botany.pptMARSILEA  notes in detail for II year Botany.ppt
MARSILEA notes in detail for II year Botany.ppt
 
Basic Concepts in Pharmacology in molecular .pptx
Basic Concepts in Pharmacology in molecular  .pptxBasic Concepts in Pharmacology in molecular  .pptx
Basic Concepts in Pharmacology in molecular .pptx
 
Role of Herbs in Cosmetics in Cosmetic Science.
Role of Herbs in Cosmetics in Cosmetic Science.Role of Herbs in Cosmetics in Cosmetic Science.
Role of Herbs in Cosmetics in Cosmetic Science.
 
soft skills question paper set for bba ca
soft skills question paper set for bba casoft skills question paper set for bba ca
soft skills question paper set for bba ca
 

Ion Torrent™ Next Generation Sequencing-Oncomine™ Lung cfDNA assay detected 0.1% low frequency somatic variants in Cell-Free DNA

  • 1. Thermo Fisher Scientific • 5791 Van Allen Way • Carlsbad, CA 92008 • www.thermofisher.com INTRODUCTION Study of genetic Information from cell-free (cf) DNA provide valuable opportunities in cancer research and potentially impact future oncology. As an example, liquid biopsy provide a non-invasive and cost effective solution for future compared to traditional biopsy tests. Here we report the application of research based Ion Torrent™ next-generation sequencing (NGS) Oncomine™ cfDNA assays and associated workflow, which is developed to detect somatic variants at low frequency of 0.1% in cfDNA from plasma. MATERIALS AND METHODS Plasma preparation: Blood samples were collected into EDTA tubes following manufacturer’s instructions. Plasma was obtained by centrifugation at 1600 x g for 10 min at 4˚C, followed by another spin at 6,000 x g for 30 min at 4˚C to remove any residual blood cells. cfDNA/FFPE DNA isolation: cfDNA was isolated from ~4 mL of plasma using MagMAX™ Cell-Free DNA Isolation Kit following alternative protocol in User Guide appendix B. RecoverAll™ Multi-Sample RNA/DNA Isolation Workflow was used to isolate DNA from FFPE samples following standard protocol. Library preparation: Targeted libraries were prepared using the Oncomine™ Lung (or Breast) cfDNA Assay reagents and user guide instructions for both cfDNA and FFPE DNA. Sequencing: The Ion 520™ and Ion 530™ Kit-Chef were used for template preparation on the Ion Chef™, followed by sequencing on Ion S5™XL system using the Ion 530™ Chip. Lung cfDNA libraries were sequenced as an 8-plex while breast cfDNA libraries were run as a 12-plex. Data analysis: Data analysis was performed in Torrent Suite using the variant Caller plugin. Yanchun Li, Kris Lea, Priyanka K. Kshatriya, Gu, Jian, Ballesteros-Villagrana, Jeff Schageman, Varun Bagai, Dima Brinza, Richard Chien, Kelli S. Bramlett. 2130 Woodward St. Austin, TX 78744 Thermo Fisher Scientific. Ion Torrent™ Next Generation Sequencing-Oncomine™ Lung cfDNA assay detected 0.1% low frequency somatic variants in Cell-Free DNA RESULTS Figure 1. Workflow for cfDNA analysis using cfDNA Lung Assay. The Oncomine™ cfDNA assay is a content-optimized solution for NGS cfDNA liquid biopsy research. It includes both library prep and analysis solutions that enable limit of detection down to 0.1% allelic frequency (with 20 ng input) for SNV and INDEL hotspots with the flexibility of using as little as 1ng input DNA. A blood sample to report workflow can be completed in 2 days. Figure 2. Tagging Technology for rare mutation detection cfDNA with tumor variant Wild type cfDNA molecule 1. Labeling of DNA molecules 2. PCR amplification and sequencing Table 1. Detection sensitivity and specificity using Horizon™ cfDNA Reference Standards with Oncomine™ Lung cfDNA Assay. The Multiplex I cfDNA DNA Reference Standards (HD780,Horizon™) contains 8 engineered single nucleotide variants (SNVs/SNPs) at a range of low allelic frequencies (5%, 1%, and 0.1%). Sensitivity and specificity were calculated based on 8 true positive and 149 true negative hotspots covered in Oncomine™ Lung cfDNA Assay. Results from either duplicates or quadruple experiments. Horizon Input Sensitivity Specificity 0.0% 20ng 100.0% 100.0% 100.0% 100.0% 0.1% 50ng 91.7% 100.0% 83.3% 100.0% 100.0% 100.0% 91.7% 100.0% 1.0% 10ng 100.0% 100.0% 100.0% 100.0% 5.0% 5ng 100.0% 100.0% 100.0% 100.0% Gene Variant Oncomine™ cfDNA Lung assay Oncomine™ cfDNA Breast assay Digital PCR KRAS p.G12D 0.20% 0.20% 0.27% 0.17% 0.14% 0.24% PIK3CA p.E545K 0.15% 0.14% 0.02% 0.11% 0.06% 0.19% EGFR p.E746_A750delELREA 0.12% *N/A 0.10% 0.11% *N/A 0.12% EGFR p.L858R 0.07% 0.14% 0.05% 0.06% 0.06% 0.83% Table 2. Cross Validation of 0.1% Detection sensitivity by Oncomine™ Lung and Breast cfDNA Assay with digital PCR assay. Data shown is from the Horizon 0.1% control material when used as input for the Oncomine™ lung and breast cfDNA assays and dPCR assays for the indicated variants. Allelic frequency of variants was measured using the targeted NGS library method in the indicated columns. Allelic frequency was validated with digital PCR as an orthogonal method to measure low frequency variants. Measurements were made in duplicate. *N/A indicates variants in the Horizon 0.1% control material that are not in the Oncomine™ Breast cfDNA targeted hotspot file. Sample Variant cfDNA input 20ng 10ng 5ng 2ng 1ng 0.5 ng 0.25ng S1 EGFR p.L747_E749delLRE 9.4% NA NA 10.4% 14.7% 16.5% 7.9% S2 KRAS p.G12D 0.2% 0.3% 0.1% 0.2% ** NA NA MET p.T1010I 47.4% 49.8% 45.5% 47.6% 51.2% NA NA Table 3. Detection of variants in cfDNA extracted from banked research NSCLC plasma samples with Oncomine™ Lung cfDNA Assay. Research sample S1 contains a fairly high frequency variant detected in cfDNA as 9.42% using recommended input of 20ng in the Oncomine™ Lung cfDNA assay. The variant could still be detected when input was decreased to 0.25 ng of cfDNA. In research sample S2, a variant was identified using 20ng of cfDNA at low allelic frequency of 0.22%. This variant was successfully detected using input amounts down to 2 ng. A germline variant present in sample S2 was consistently detected at levels ~50% in all input titration libraries. NA: not tested; **: not detected. CONCLUSIONS • Oncomine™ cfDNA Assays provide an easy, quick, and reliable solution for research in detecting low frequency somatic variant in blood plasma and tissue • Oncomine™ cfDNA Assays target specific actionable hotspot regions of genes for indicated cancer type to create a targeted amplicon library for sequencing with the Ion Torrent Sequencing System; Oncomine™ Lung cfDNA Assay (Cat Lot: A31149) is currently available; Oncomine™ Breast and Colon cfDNA assays coming soon • The Ion Torrent™ NGS technology and tailored TSS analytical pipeline allows this assay to detect variants as low as 0.1% limit of detection (LOD); measured allelic frequencies confirmed by orthogonal measurement system—dPCR • The total process time (from plasma/FFPE specimen to result reporting) could be as short as 32 hours with a total hand on time of ~4 hours; supporting a lab workflow where you can receive blood samples early on day 1 and have variant calls before you go home on day 2 Sample Variant FFPE Plasma S1 EGFR p.L858R 71.42% 2.66% S2 TP53 p.R158L 51.89% 4.32% S3 METp.T1010I 43.87% 51.75% KRAS p.G12C 34.62% 0.28% S4 ND ND ND S5 EGFR p.L858R 58.44% 7.74% MET p.T1010I 41.93% 48.74% TP53 p.Y220C 35.54% 1.93% S6 TP53 p.R158L 10.19% 1.27% S7 TP53 p.M237I 0.49% 0.13% S8 KRAS p.G12A 5.56% 3.02% S9 MET p.T1010I 68.93% 50.51% S10 KRAS p.G12V 20.01% 1.70% KRAS p.G12C 20.03% 1.70% S11 KRAS p.G12D 25.29% 12% S12 KRAS p.G12C 19.91% ** S13 KRAS p.G13D 29.90% ** S14 TP53 p.R248L 21.82% 0.34% S15 TP53 p.R337L 46.84% 0.18% S16 KRAS p.G12D 3.98% 0.22% MET p.T1010I 50.42% 47.44% S17 TP53 p.R273C 4.64% ** S18 KRAS p.G12S 1.25% 6.56% S19 TP53 p.Y234C 17.16% ** TP53 p.T125T 25.76% ** S20 KRAS p.G13C 2.65% 0.30% MET p.T1010I 2.21% ** Table 4. Observed frequencies of variants detected from matched FFPE and Plasma samples. Late stage NSCLC research samples were purchased from BioChain. Sample sets included solid tumor sample embedded in FFPE and 2–4 mls plasma from blood collected in EDTA tubes. Bold numbers indicate allelic frequencies as determined using the Oncomine™ Lung cfDNA assay for the indicated somatic variants. Non-bold frequencies show germline variants that were also detected in the targeted libraries. For these 6 independent research samples, there was very high concordance between variants detected in FFPE and cfDNA from matched plasma from the same research subjects. As expected, higher variant frequencies were observed in the FFPE solid tumor samples with significantly lower frequencies measured in the matched cfDNA samples. ND: no detection(negative case); **: not detected. For Research Use Only. Not for use in diagnostic procedures. © 2016 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Horizon is a trademark of Horizon Discovery Group, Inc. Samples Sensitivity Specificity PPV 0.1%MM 90% 98.4% 94.1% 0.5% >99.9% 98.3% 94.3% Table 5. Detection Sensitivity and Specificity. The Oncomine™ Lung cfDNA Assay performance was evaluated using engineered controls (AcroMetrix™ Oncology Hotspot Control) in background GM24385 genomic DNA diluted to 0.1% or 0.5% allelic frequencies. The control and background DNA was fragmented to mimic the size of cfDNA. Mean sensitivity and specificity values were obtained across the expected true positives and true negatives at oncology hotspot positions.