1. No category

iPLEX® Pro Sample ID Panel*
A highly accurate, rapid research method for
sample identification and quantification
February 2013
* The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures
Agenda
Applications & Use
Content
Biochemistry
Data Analysis with Live Demo
Getting Started
Q&A
2
February 27, 2013
.
The Importance of Sample Identification in
Research Studies
Laboratory procedures are not 100% foolproof
Samples can be mislabeled or contaminated
Leads to repeat experiments, time delays, and/or
retraction of publications
Challenge of the research community is to ensure
correct samples are used and reported in research
studies
3
February 27, 2013
.
Applications for Sample Identification
4
Cell line authentication
Chain of Custody events
Sample replicate pairing
Tumor vs. non-tumor pairing
Sample QC
Library barcoding
February 27, 2013
.
Use Case Scenarios
Application
Use Case
Example(s)
Outcome
Cell Line
Authentication
Verify identity
(One cell line)
Cell Line1 = Cell Line1
Expected Match
Cell Line1 ≠ Cell Line1
Unexpected Mismatch
Verify identity
(Multiple cell lines)
Cell Line1 = Cell Line2
Unexpected Match
Cell Line1 ≠ Cell Line2
Expected Mismatch
Our software provides easy summary reports
5
February 27, 2013
.
Use Case Scenarios
Application
Use Case
Example(s)
Outcome
Tumor vs. NonTumor
Single patient
(One tumor)
T1 = N 1
Expected Match
T1 ≠ N 1
Unexpected Mismatch
Single patient
(Multiple tumors)
T1A = N 1 = T1B
Expected Match
T1 = N 1 ≠ T1B
Unexpected Mismatch
Our software provides easy summary reports
6
February 27, 2013
.
SNP Genotyping as a Method for Sample
Identification
Key publications provided the basis for the iPLEX® Pro Sample ID Panel*
* The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures
7
February 27, 2013
.
Benefits of Sample Identification using the
MassARRAY® System
For use with cell lines, FFPE tissue, blood, NGS
libraries
Comprehensive SNP coverage for sample
identification and QC
High-throughput panel with minimal input DNA and
reagent usage
Automated reports for convenient, rapid sample
comparisons within a single plate or against an
entire database
Relevant for tracking and qualifying samples in your
MassARRAY® or NGS workflow
* The MassARRAY System is for Research Use Only. Not for use in diagnostic procedures
8
February 27, 2013
.
iPLEX® Pro Sample ID Panel*
Comprehensive Coverage
44 SNP loci across genome
High overall heterozygosity to
adjust for population stratification
(45-55%)
Not in exon or variable regions
High overlap with SNP for ID and
original ABS Sample ID panels
Low random match for error and
high confidence
Not intended for forensic, parentage, ethnic identification,
or monozygotic twins.
* The iPLEX® Pro Sample ID Panel is for Research Use Only. Not for use in diagnostic procedures
9
February 27, 2013
.
Quality Control Check Provided for Each Sample
Not enough SNPs for an accurate match or mismatch (N = 30)
Not enough amplifiable copies (N < 500, 1 ng)
Key for qualifying formalin-fixed paraffin embedded tissue
Don’t waste sample, time, or reagents that would not be suitable
for a MassARRAY®* or NGS run
Quickly pass or fail samples to reduce time & material costs
* The MassARRAY System is for Research Use Only. Not for use in diagnostic procedures
10
February 27, 2013
.
iPLEX® Pro Sample ID Panel*
Biochemistry
Robust biochemistry
PCR amplification followed by
iPLEX® Pro primer extension
Convenient assay
Single multiplexed well with 52
markers (44 SNPs, 3 Gender, 5
Copy Number)
Minimal DNA required (10 ng)
Low running cost per sample
*The iPLEX Pro Sample ID Panel is for Research Use only. Not for use in diagnostics procedures.
11
February 27, 2013
.
Use Case Scenarios
Tumor to Normal Comparisons
Advantages of Upfront QC
Quantify amplifiable copies postextraction
Ensure normal to tumor samples are
correctly paired
Pass or fail samples prior to library
prep, sequencing, or MassARRAY®*
panels
“Molecular barcode” can be stored
in database for future reference
Non-tumor
Tumor
Extract DNA
Sample ID
(Primary QC)
MassARRAY® Panel (or NGS)
Tumor to Normal Comparison
* The MassARRAY System is for Research Use Only. Not for use in diagnostic procedures
12
February 27, 2013
.
Use Case Scenarios
NGS Library Tracking
Sample ID with Libraries
13
A rapid technical QC method
for tracking samples
Ensure interesting results are
not an artifact of sample mixup
Sequence analysis can be
conducted in parallel
Requires ~10 µl library to
obtain a molecular barcode
February 27, 2013
Normal
Tumor
NGS Library
Prep
Sequence
Sample ID
Sequence
Normal to Tumor
Comparison
.
Sample ID
Barcoding NGS Libraries vs. Sample Identification
Illumina Barcoding
Multiple samples are pooled
together for a sequencing run
Barcode tags are used to
differentiate reads for each
sample
Sequenom iPLEX Pro Sample ID Panel*
Use in parallel to ensure the right
samples are contained within the
library pool
Expected match or mismatch
using Sample ID signature for
each barcoded sample
?
Combine NGS
barcoding with
Sample ID
*The iPLEX Pro Sample ID Panel is for Research Use only. Not for use in diagnostics procedures.
14
February 27, 2013
.
iPLEX® Pro Sample ID Panel
Data Analysis
Perfect match:
+10 for non-tumor vs. non-tumor;
+5 non-tumor vs. tumor
Penalty scores for any mismatches of
individual SNPs
Non-tumor vs. tumor comparison
ignores any normal heterozygote SNP
calls for LOH
Quickly assess samples for
all 44 SNPs at a glance
*iPLEX Pro Sample ID Panel is for Research Use only. Not for use in diagnostics procedures.
15
February 27, 2013
.
iPLEX® Pro Sample ID Panel*
Software and Database
Compare samples
within selected plates
and against a
database
Compare samples only
within a selected set of
plates
LIVE DEMO
*iPLEX Pro Sample ID Panel is for Research Use only. Not for use in diagnostics procedures.
16
February 27, 2013
.
iPLEX® Pro Sample ID Panel*
Getting Started
Catalog Number
Description
Format
25093
iPLEX Pro Sample ID Reagent Set
- Sample ID PCR Primer Mix
- Sample ID Extend Primer Mix
- Q-Mix for copy number
- PCR Reagents
- SpectroCHIP 96 (10)
10 x 96
960
25094
iPLEX Pro Sample ID Reagent Set
- Sample ID PCR Primer Mix
- Sample ID Extend Primer Mix
- Q-Mix for copy number
- PCR Reagents
- SpectroCHIP 384 (2)
2 x 384
768
No. Samples
*iPLEX Pro Sample ID Panel Reagents sets and SpectroCHIP are for Research Use only. Not for use in
diagnostics procedures.
17
February 27, 2013
.
Summary
Key Takeaways
Use Sample ID
with NGS
18
February 27, 2013
Minimal DNA
required, low
cost per sample
Low random match
probability
(1.0 x 10-18)
.
Contact Information
Thank You
For more information, please contact:
Your local Sales Manager or Applications Scientist
www.sequenom.com
19
February 27, 2013
.
Q&A Session