Post on 19-Mar-2020
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Illumina’s VeriSeq™ NIPT Solution
Fast, Accurate, Accessible Non-Invasive Prenatal Testing (NIPT)
Caroline Thureau
Ass. Dir. Clinical Business Illumina
Izmir, 5th of May 2018
For In Vitro Diagnostic Use. Not available in all countries or regions.
2
Presentation Outline
Introducing the VeriSeq NIPT Solution and workflow
VeriSeq NIPT technical innovations
VeriSeq NIPT clinical accuracy study results
Q&A – visit the Incekaralar booth
3
The VeriSeq NIPT Solution
A Revolution for “In-lab” NIPT Testing
Streamlined
Easy to run
PCR-Free Assay
Fast
26 Hour turn around*
96 or 48 Spls/Batch
Confidence
Highly accurate results
Report on more samples
Automated NIPT for detection of aneuploidy of chromosomes 21, 18, 13, X & Y
For In Vitro Diagnostic Use. Not available in all countries or regions
*From accessioned sample to clinical report
CE-IVD marked CE-IVD marked
4
Sample Preparation
VeriSeq NIPT Sample Prep CE-IVD marked Kits
Two CE-IVD marked kit options: 96 & 48 Sample
Versions
Include reagents and consumables for preparing
cfDNA sequencing libraries from plasma
PCR-Free
For In Vitro Diagnostic Use. Not available in all countries or regions.
VeriSeq NIPT SolutionAutomated Laboratory Workflow
VeriSeq NIPT Microlab STAR
Blood to prepared library ~8 hours/batch
– ~2 hours of user hands on time
5
VeriSeq NIPT SolutionAutomated Laboratory Workflow
Sequencing Analysis Clinical Report
Assay software installed on
on-site server
Analysis performed on-site
Evaluation of fetal fraction
and chromosomal ratios for
chromosomes 21, 18, 13, X,
and Y
CE-IVD marked software
Aneuploidy classifications
for chromosomes 21, 18 ,13,
X, and Y
Individualized Fetal
Aneuploidy Confidence
Test (iFACT)
Fetal Fraction Estimate
Other QC metrics
2 x 36 base pair sequencing
48 sample multiplex
~13 hour run (overnight)
For In Vitro Diagnostic Use. Not available in all countries or regions
Batch Analysis and Report
6
VeriSeq NIPT SolutionAutomated Laboratory Workflow
Key Technical Innovations
For In Vitro Diagnostic Use. Not available in all countries or regions
Paired-
end
sequencing
Fetal
fraction
estimatorLLR
iFACT
QC
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Fetal Fraction Estimation Methods in Illumina NIPT
The Coverage Profile Method
Fragment Size Distribution1
Some genomic regions are enriched,
and some depleted with higher fetal
fraction
Training data from 20K CLIA samples
used to create a model to estimate FF
based on coverage profile
1 The VeriSeq NIPT Solution software uses both coverage profiling and fragment
size information in the estimation of fetal fraction
Fragment size distribution,
determined from the analysis of PE
sequencing data, can be used in the
estimation of fetal fraction
FF from Chr Y
FF
fro
m f
rag
siz
e
Fetal Maternal
All charts: Illumina internal data on file
Comparison of maternal and fetal size distribution
of cfDNA fragments
Numerous studies have shown that
cfDNA of fetal origin is shorter than
cfDNA of maternal origin. Therefore,
fetal signal is higher in shorter
fragments.
For In Vitro Diagnostic Use. Not available in all countries or regions
8
Analysis of Sequence Output: Alignment
CGATTTAACT
…ACCACGATTTAACTGGAGTAAAGACTTCCAGGTACCGATCTAGCCT…
Millions of “counts” per sample
GACTTCCAGG
Count:
AGGTACCGAT
Human Genome
Alignment
CGATTTAACT
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CountingFetal
cfDNA
Maternal
cfDNA
Chromosomes: 1 2 3
……
Trisomy 2121
10% more Chr21
cfDNA in T21
VS
Analysis of Sequence Output: Counting by Sample and chromosome scoring
Not to Scale
10
Log Likelihood Ratio (LLR)Incorporates aneuploidy score and fetal fraction information
Fetal fraction
An
eu
plo
idy s
co
re
Expected distribution of
affected samples
Expected distribution of
unaffected samples
LLR incorporates the
estimated fetal fraction of a
sample when assessing
the probability of being
affected.
Likely unaffected sample
(closest to unaffected
distribution)
For In Vitro Diagnostic Use. Not available in all countries or regions
11
Log Likelihood Ratio (LLR)Incorporates aneuploidy score and fetal fraction information
Fetal fraction
An
eu
plo
idy s
co
re
Expected distribution of
affected samples
Expected distribution of
unaffected samples
LLR incorporates the
estimated fetal fraction of a
sample when assessing
the probability of being
affected.
Equivalent aneuploidy
signals are more likely to
be affected for lower fetal
fractions
Likely affected sample
(closest to affected
distribution)
For In Vitro Diagnostic Use. Not available in all countries or regions
12
iFACTIllumina’s innovative approach to ensuring excellent results
even at low fetal fraction
individualized Fetal Aneuploidy Confidence Test
iFACT1 is a dynamic threshold that is assessed for each sample.
For samples with low fetal fraction, iFACT determines whether there is
enough sequencing coverage to make a call.
– Results can be determined even for samples with low fetal fraction.
– iFACT allows results to be determined on the maximum number of
samples.
– Samples that do not pass this quality metric threshold do not provide
a call.
1 The VeriSeq™ NIPT Solution Assay Software has iFACT, which uses sequencing coverage and fetal fraction. The VeriSeq™
NIPT Analysis Software (16 Samples) uses a QC metric based on sequencing coverage alone.
For In Vitro Diagnostic Use. Not available in all countries or regions
13
Total Plasma Aliquots Available, n 3,107
Total Quality Control Failure, n(%) 21 (0.68)
Failed iFACT 11
Data Outside Expected Range 8
Fragment Distribution Outside of Normal Range 2
Total Reported 3,086
With Clinical Reference for Autosomes 3,057
With Clinical Reference for Sex Chromosomes 3,082
The Clinical Accuracy StudySample Exclusion
Data on file. Illumina, Inc. February 2017.
For In Vitro Diagnostic Use. Not available in all countries or regions
14
VeriSeq NIPT Solution ResultsOverall Performance Metrics for Autosomes
a CI based on Wilson’s score method.
Trisomy 21 Trisomy 18 Trisomy 13
Sensitivity, % (n/N) 98.9% (90/91) 90.0% (18/20) 100.0% (8/8)
2-Side 95% CIa (94.0%,99.8%) (69.9%,97.2%) (67.6%,100.0%)
Specificity, % (n/N)>99.9%
(2965/2966)
99.9%
(3034/3037)
99.9%
(3045/3049)
2-Side 95% CIa (99.8%,100.0%) (99.7%,100.0%) (99.7%,99.9%)
Data on file. Illumina, Inc. February 2017.
For In Vitro Diagnostic Use. Not available in all countries or regions
15
Percent Concordance of VeriSeq NIPT Solution Results
For Fetal Sex Classification with
Clinical Reference Standard Outcome
a Percent concordance is calculated as the number of samples in which the VeriSeq™ NIPT Solution fetal sex classification is consistent with the clinical
reference standard classification, divided by the total number of samples with the same clinical reference standard classification and valid VeriSeq™ NIPT
Solution results. Outcomes are based on 3,082 samples, as 4 did not have a clinical reference.b Represents monosomy X. c 1 sample was 49, XXXXY, classified as “Sex chromosome not reportable”.
Newborn Physical Exam
Outcome
[No Cytogenetic Results]
Cytogenetic Results
Female Male XX XY MXb XXX XXY XYY Otherc
Percent Concordanta99.9%
(1371/1373)
99.9%
(1420/1422)
97.4%
(147/151)
100.0%
(118/118)
100.0%
(6/6)
80.0%
(4/5)
100.0%
(5/5)
100.0%
(1/1)
Not
Applicable
Data on file. Illumina, Inc. February 2017.
For In Vitro Diagnostic Use. Not available in all countries or regions.
16
VeriSeq NIPT Solution Clinical Accuracy Study Implications
Data on file. Illumina, Inc. February 2017.
The observed sensitivities and specificities for VeriSeq NIPT in determining fetal
aneuploidy for chromosomes 21, 18, 13, X and Y are vastly superior to
traditional serum screening.
The VeriSeq™ NIPT Solution utilizes iFACT, a quality metric which enables
detection of fetal aneuploidy at fetal fraction estimations of 4% or less.
The VeriSeq™ NIPT Solution demonstrated fewer false positive results which
may result in fewer invasive diagnostic tests compared to serum screening. This
may lead to fewer procedure-related pregnancy losses.
For In Vitro Diagnostic Use. Not available in all countries or regions
17
Thank You!Questions?
• Easy to implement, Automated, PCR-free workflow
• Integrated, CE-IVD marked sample preparation and analysis
• Hands-on training and support from Illumina
• Fastest sample accession to report time (~26 hours total)
• 2 hours “hands on time” per batch of 48 or 96 samples
• High-throughput
• Industry leading low failure rate
• Large (>3k sample) clinical accuracy study
• Reduce invasive procedures and patient anxiety
Streamlined
Fast
Confidence
Automated NIPT for detection of aneuploidy of chromosomes 21, 18, 13, X & Y
For In Vitro Diagnostic Use. Not available in all countries or regions