software updates to support 6-dye chemistry...

Software Updates to Support 6-dye Chemistry Implementation

2/8/2013 | Life Technologies™ Proprietary and confidential 2

GlobalFilerTM Express Workflow Solutions


6-Dye Summary

Chemistry/

Standards

GeneMapper®

ID-X Software

v1.4

Service

3730 DNA

Analyzer /

31xx Genetic

Analyzers

3500 Genetic

Analyzer

Data

Collection

Software

1 2 3

31xx/3730 only All Instruments


Product Overview

3500 Data Collection v2 Updates Windows® 7 Professional SP1 utilizes a newer, better, fully supported operating system designed for newer

systems

New Dell Optiplex XE - 4 GB RAM, 500 GB RAID Disk replaces existing, no longer supported computer systems

Modern Licensing Technology with a new license scheme that utilizes on-line registration

RFID warnings have been added for (HID/RUO version only)

Data migration from Data Collection v1 -> v2

Software issues addressed include:− Improved spatial calibration QC checks

− Updated instrument run modules to improve polymer leak detection during array fill operations

− Consumable Usage Statistics Report added

− Consumables Dashboard improvements

− Target EP voltage displayed correctly during run on Sensor Details page

− Hovering tool in the Fragment Results view displays the quality value for OffScale data

− Improved Instrument Error Dialog when reporting fatal instrument errors

GeneMapper® ID-X Software Compatibility: .hid sample files generated by the 3500 Data Collection software v2 can be viewed and analyzed with GeneMapper® ID-X v1.4 – v1.2 Software.

Reagent and consumable lifetime minimum performance values are based on developmental

validation studies and promote the production of high quality data and help minimize instrument

downtime.


3500 System Workflow and Feature Highlights

Instrument Run Set-Up Data Collection GMID-X v1.2QC Analysis

Redesigned laser and

polymer pump block

Pre-packaged consumables

with RFID Tracking

Intuitive Run Set-Up

and system monitoring

Predefined protocols

and HID templates

New oven design

Shorter run times

Optional signal

normalizationData analysis QC

tools and flags

Simplified reinjection

scheme

Upgrade to

GeneMapper® ID-X 1.4 for

Window ® 7 comp

Analyzes .fsa & new

.hid file format

Instrument

Run Set-Up

Data Collection

QC Analysis

GeneMapper®

ID-X v1.4


Dashboard

Key Operations

Maintenance Prompts

Instrument Status

Consumable Gauges


Spatial Calibration Improvements

•Evaluates each peak to confirm that is above the threshold.•Capillary spacing enhanced to look at the spacing difference between cap n and n+1 (which is why the spacing of the last capillary is always 0).

Added the peak threshold to help detect this issue.


Redesigned Consumable Packaging

Pre-filled, quality-controlled reagents

Radio Frequency Identification Tags

− Fixed, passive tags

− Limited read range

− Memory only, cannot be read by the computer and cannot execute code

Comparable per sample running cost to 31xx instruments


Radio Frequency Identification (RFID)

Three independent RFID readers track and record information on four primary consumables (with RFID labels)

Consumables tracked− Polymer

− Cathode Buffer

− Anode Buffer

− Array

Information tracked− Lot numbers

− Part numbers

− Serial numbers

− Dates (expiration and installation)

− Capacity/Usage


Consumables: Polymer Pouch Volume

Excess volume for installation,

wizards and proper pouch

functionality

Purchased volume

- 960 or 384 samples

Provides:

- Predictable cost per sample

- Ease of use

- Data tracking (via RFID)


The use of consumable beyond the manufacturer’s expiry date or on-instrument life can impact data quality and cause damage to the instrument. The cost of repairing such damage is NOT covered by Life

Technologies’ warranty or service plans.

2On-instrument life/sample usage limit is based on whichever limit is reached first. The primary indicator of pouch depletion is the Sample Count.

Injection count is present as a fail safe mechanism for low sample count reinjection scenarios.1Polymer validated for 7 days on instrument and the array for 160 injections

3500 Data Collection v2New RFID Settings


Calibration and MaintenanceCalendar

FR or F = Applied Biosystems recommended tasks, user editable - specify dates

R = User-specified repeating tasks


Calibration and MaintenanceReports and Export Files


QC Analysis: QC Protocol

• QC protocol is the required primary analysis protocol for HID applications

• It defines peak detection, sizing, and quality values

• Factory-provided QC protocols are available in the software or can be created by the user

G5_LS(80-400)+Normalization


QC Analysis: Result Review

Review QC Flag Details – Set Up Reinjections

Sizing Table

Plot view with plot options: by dye, overlay, off scale


Improved Signal Consistency:Normalization Methods

Factory Standardization: Hardware-based calibration for more consistent instrument to instrument performance

Internal Standard (IS) Normalization: Chemistry and Software based method for more consistent signal across capillaries, injections and instruments

• User enabled

• Utilizes re-designed GeneScan™ 600 LIZ® Size Standard

• Sample level peak heights are scaled relative to the intensity of the co-injected size standard compared to an optimized average size standard peak height (Normalization Target)


Signal Normalization Tools

Forensic laboratories with multiple instruments have reported that signal variation between instruments can impact data interpretation

Factory standardization and user-selectable internal standard normalization minimize signal variation between instruments and from injection to injection

%CV

%C

V

Injection to

Injection Peak

Height

Consistency%

CV

Instrument to

Instrument Peak

Height

Consistency


Data Scaling Considerations

3130xl

3500xL

3000

9000

Peak heights on the 3500 ~4x greater than 31XX platforms due to differences in data scaling

Higher peak amplitude threshold required for 3500 analysis if using a static threshold− Use of the Global Cut-off function in the analysis method may allow for fine-tuning of analysis

thresholds


Comparison of 3130xl and 3500xL Data

PAT = 50 RFU PAT = 175 RFU3130xl 3500xL

Identification of appropriate analysis thresholds promotes consistency of analysis outcome


PAT Definition for 3500 DataPAT: 50rfu PAT: 175rfu


Setting Analytical Thresholds

Peak Amplitude Threshold− Minimum suggestion of [Mean Baseline Noise] + [3-10 x SD]

> Default Data Collection value based on G5 Dye Set noise evaluation is ~175 RFU (independent tests recommended on individual instruments and workflows)

− Dependent upon multiple factors including choice of chemistry, injection conditions, injection recipe, instrument platform

− Other considerations

> Artifacts

> Spectral pull-up

> Stutter

Stochastic Threshold− Determine level of confidence for homozygote calls

Consider differential thresholds for casework and database applications


Security, Audit and E-Sig

User Configurable according to laboratory’s needs

Security controls user access to system functions and data

Auditing tracks changes and provides history reports

E-signature requires user-authentication before changes are saved


System Preferences

Default application, polymer and array

Decrease # of spectral borrowing events


GeneMapper® ID-X Software v1.4Sample Info Tab

Consumable

information

tracked via RFID

Normalization

Factor Value


Product Overview3130/3730 Data Collection Software v4 Updates

Windows® 7 Professional SP1 utilizes a newer, better, fully supported operating system New Dell Optiplex XE - 4 GB RAM, 500 GB RAID Disk replaces existing, no longer supported computer systems 6-dye capability view 6 dye data in the Capillaries Viewer, Cap/Array Viewer, and Spectral Viewer windows (+ 6-dye Module to run and analyze 6-dye data) Updated Sapphire pump wizard settings updated pump control values to be in line with system specifications Modern Licensing Technology utilizing on-line software registration Data migration from UDC3.0, 3.1 -> UDC4.0 Oracle 180 day password expiration fix MAC address Hotfix integrated BigDye® Direct mobility files

GeneMapper® ID-X Software Compatibility: .fsa sample files generated by this software can be viewed and analyzed with all versions of GeneMapper® ID-X or GeneMapper® ID Software.


Data Collection

Additional Information

3500 Series Software 2 GETTING STARTED GUIDE PN 4476988 Rev. A. Contains instrument calibration, run setup data review, software licensing information.

3130 Series Data Collection Software 4 GETTING STARTED GUIDE PN 4477796 Rev. A. Contains instrument calibration, run setup data review, software licensing information.

3730/3730xl DNA Analyzer Data Collection Software 4 GETTING STARTED GUIDE PN 4478016 Rev A. Contains instrument calibration, run setup data review, software licensing information.

Online 3500 FAQs www.appliedbiosystems.com/3500hid

• 3500 Webinar Series Considerations for Efficient Implementation of the 3500 Series Genetic Analyzer for Human Identification www.3500Webinar1.com

http://www.appliedbiosystems.com/3500hid

http://www.3500webinar1.com/

GeneMapper® ID-X v1.4 Updates


Product OverviewGeneMapper® ID-X v1.4 Value Proposition

A single data analysis tool that significantly reduces the amount of time required to perform data review, mixture analysis and statistical calculations on routine and casework forensic samples.

Expert system and mixture interpretation capabilities introduced specifically to handle expanded core loci set of GlobalFilerTM Kit, minimizes data review time and provides an additional layer of quality assurance to the review and interpretation process.

Long-standing, trusted approach to fragment analysis (same validated algorithms from GeneMapper ID) minimizes validation and implementation burdens.

Critical component of a complete, validated solution providing optimized and validated workflow solution – to address expanding data processing and interpretation needs.


Product OverviewGeneMapper® ID-X v1.4 Software Updates

• Fragment and mixture analysis to support 4, 5 and 6 dye analysis• Expert system functionality (PQVs) to evaluate Amelogenin and Y marker data quality –

ACC (Amelogenin Cross Check) PQV and Y marker AN PQV• Updated allele labeling functionality to handle both homozygote genotypes and

haplotypes in a single sample• Enabled spike detection switch to turn on/off automated spike detection for sample type

= ‘’sample’’ (similar to the allelic ladder spike detection switch from v1.1.1)• Latest analysis files (including GlobalFiler™ panels and bins and GlobalFiler™ Example

Data)• Windows® 7 and XP compatible• Issues Addressed: Updated ‘redefine sample file path’ for .hid (3500) files, minor update

to existing population data

Validated with data generated from the GlobalFiler™ and Legacy AmpfℓSTR® Kits on the 3130, 3730 and 3500 CE platforms. Concordant with data analyzed using GeneMapper® ID-X v1.3.

2/8/2013 | Life Technologies™ Proprietary and confidential 32 32

Y Marker Handling Panel and Bin Functionality

Y Marker Checkbox is used by the software to apply Y-marker handling rules for ACC PQV, AN PQV, Mixture Analysis and the Duplicate Homozygous Allele Label


Y Marker Handling Amelogenin Cross Check (ACC) PQV - Updated

New Marker Level AMEL/Y Markers PQV:

- Cross checks Amelogenin results with Y marker (selected in the Panel Manager) results

- The ACC PQV flag will fire when Amelogenin and Y marker results are discordant

Y


Y Marker Handling Amelogenin Cross Check (ACC) PQV


Y Marker Handling ACC PQV Results for GlobalFiler


Y Marker Handling ACC PQV – GQ/CGQ

New ACC GQ Setting:

By adjusting the weight of the ACC, the user can be alerted to discordant results between Amelogenin/Y Marker(s) with a Genotype Quality flag (GQ)

ACC weighting contributes to the status of Quality Value flags for GQ and in-turn CGQ.


When the ACC Fails:• Marker header bars (Genotype Quality flag) may fire as yellow or red depending on the weight ACC has for the GQ flag• Quality Value Details Window = Amelogenin/Y marker discordance

Y Marker Handling - UpdatedACC PQV


Y Marker Handling Y Marker AN PQV

Allele Number PQV Threshold:

- A new AN Threshold field has been added for Y Markers

- The AN flag will fire if the number of alleles exceeds the user defined threshold


Y Marker Handling Mixture Analysis

A warning message will be displayed when a sample that contains Y markers is imported into the MA Tool reminding the user that Mixture Analysis does not analyze the Y markers.


Y Marker Handling – update options screenshot?Allele Labeling Option

Existing

Project Option> Duplicate Homozygous Alleles option

– Y marker alleles (designated in the Panel Manager) are displayed with a single label


Spike Detection Switch – UpdatedSample & Controls

Enhanced to allow you to disable spike detection for samples and controls.

Expands disable/enable spike detection functionality introduced for allelic ladders in v1.1.1


Updated Spike Detection Rules


GeneMapper® ID-X Software Version 1.4 User Bulletin PN4477684 Rev BContains information on the new features, software validation and installation instructions

Updates to ID-X Software Help - information on 6 dye specific features, functionality and troubleshooting

Software Release Notes includes overview of new features and system requirements

Software Validation Certificate covers validation of GlobalFiler™ and Legacy AmpfℓSTR® Kits on the 3130, 3730 and 3500 CE platforms

For more information go to http://idx.appliedbiosystems.com

GeneMapper® ID-X

User Documentation - Updated

http://idx.appliedbiosystems.com/


Thank You

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