software updates to support 6-dye chemistry implementation

1 Life Technologies™ | 1 Life Technologies™ |

Software Updates to Support 6-dye Chemistry Implementation

2 Life Technologies™ |

GlobalFilerTM Express Workflow Solutions


6-Dye Summary

Chemistry/ Standards

GeneMapper® ID-‐X So5ware

v1.4

Service

3730 DNA Analyzer /

31xx GeneEc Analyzers

3500 GeneEc Analyzer

Data CollecEon So5ware

1 2 3

31xx/3730 only All Instruments


What CE instrument are you currently using for casework?

A.  310 B.  3100 C.  3130 D.  3500


Product Overview 3500 Data CollecEon 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 exis8ng, 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 CollecEon GMID-‐X v1.2 QC 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 normalization

Data 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 OperaEons

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)


3500 Data CollecEon v2 New RFID SeZngs

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


Calibration and Maintenance Calendar

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

R = User-specified repeating tasks


Calibration and Maintenance Reports 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 Reinjec8ons

Sizing Table

Plot view with plot op8ons: by dye, overlay, off scale


Improved Signal Consistency: NormalizaEon Methods

§  Factory StandardizaEon: Hardware-‐based calibra8on for more consistent instrument to instrument performance

§  Internal Standard (IS) NormalizaEon: Chemistry and So[ware based method for more consistent signal across capillaries, injec8ons and instruments

•  User enabled •  U8lizes re-‐designed GeneScan™ 600 LIZ® Size Standard •  Sample level peak heights are scaled rela8ve to the intensity of the co-‐injected size standard compared to an op8mized average size standard peak height (Normaliza8on 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

%C

V

Instrument to Instrument Peak Height Consistency


Are you interested in using the normalizaEon feature of the 3500?

A.  Yes, definitely! B.  We are looking into it, but are unsure C.  No D.  I have never heard of this before!


Data Scaling Considerations

§  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

3130xl

3500xL

3000

9000


Comparison of 3130xl and 3500xL Data

PAT = 50 RFU PAT = 175 RFU 3130xl 3500xL

Identification of appropriate analysis thresholds promotes consistency of analysis outcome


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


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 v1.4 Sample Info Tab

Consumable information tracked via RFID

Normalization Factor Value


Product Overview 3130/3730 Data CollecEon So5ware v4 Updates

§  Windows® 7 Professional SP1 u8lizes a newer, becer, fully supported opera8ng system §  New Dell OpEplex XE -‐ 4 GB RAM, 500 GB RAID Disk replaces exis8ng, 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 seZngs updated pump control values to be in line with system specifica8ons §  Modern Licensing Technology u8lizing on-‐line so[ware registra8on §  Data migraEon from UDC3.0, 3.1 -‐> UDC4.0 §  Oracle 180 day password expira8on fix §  MAC address Holix integrated §  BigDye® Direct mobility files §  GeneMapper® ID-‐X So5ware CompaEbility: .fsa sample files generated by this so[ware can be viewed and analyzed with all versions of GeneMapper® ID-‐X or GeneMapper® ID So[ware.


Data CollecEon AddiEonal InformaEon

§  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

28 Life Technologies™ | 28 Life Technologies™ |

GeneMapper® ID-X v1.4 Updates


Product Overview GeneMapper® ID-‐X v1.4 Value ProposiEon

§  A single data analysis tool that significantly reduces the amount of 8me required to perform data review, mixture analysis and staEsEcal calculaEons on rou8ne and casework forensic samples.

§  Expert system and mixture interpretaEon capabiliEes introduced specifically to handle expanded core loci set of GlobalFilerTM Kit, minimizes data review 8me and provides an addi8onal layer of quality assurance to the review and interpreta8on process.

§  Long-‐standing, trusted approach to fragment analysis (same validated algorithms from GeneMapper ID) minimizes valida8on and implementa8on burdens.

§  CriEcal component of a complete, validated soluEon providing op8mized and validated workflow solu8on – to address expanding data processing and interpreta8on needs.


Product Overview GeneMapper® ID-‐X v1.4 So5ware Updates

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

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

haplotypes in a single sample •  Enabled spike detecEon switch to turn on/off automated spike detec8on for sample type

= ‘’sample’’ (similar to the allelic ladder spike detec8on switch from v1.1.1) •  Latest analysis files (including GlobalFiler™ panels and bins and GlobalFiler™ Example

Data) •  Windows® 7 and XP compa8ble •  Issues Addressed: Updated ‘redefine sample file path’ for .hid (3500) files, minor update

to exis8ng popula8on data

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

v1.3.


31

Y Marker Handling Panel and Bin Func4onality

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


32

Y Marker Handling Amelogenin Cross Check (ACC) PQV

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


33

Y Marker Handling Amelogenin Cross Check (ACC) PQV


34

Y Marker Handling ACC PQV Results for GlobalFiler


35

Y Marker Handling ACC PQV – GQ/CGQ

New ACC GQ SeZng: By adjus8ng 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 weigh8ng contributes to the status of Quality Value flags for GQ and in-‐turn CGQ.


36

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 ACC PQV


37

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


38

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.


Are you interested in using the Mixture Tool?

A.  Yes, we are already using it B.  We plan to start using it soon C.  We are looking into it, but unsure D.  No, we are not interested at this time E.  Mixture tool? You have one of those?????


40

Y Marker Handling Allele Labeling Option

Existing

Project Op8on> Duplicate Homozygous Alleles op8on – Y marker alleles (designated in the Panel Manager) are displayed with a single label


41

Spike Detection Switch Sample & Controls

Enhanced to allow you to disable spike detec8on for samples and controls. Expands disable/enable spike detec7on func7onality introduced for allelic ladders in v1.1.1


Updated Spike DetecEon Rules


§  GeneMapper® ID-‐X So5ware Version 1.4 User BulleEn PN4477684 Rev B Contains informa8on on the new features, so[ware valida8on and installa8on instruc8ons

§  Updates to ID-‐X So5ware Help -‐ informa8on on 6 dye specific features, func8onality and troubleshoo8ng

§  So5ware Release Notes includes overview of new features and system requirements

§  So5ware ValidaEon CerEficate covers valida8on of GlobalFiler™ and Legacy

AmpfℓSTR® Kits on the 3130, 3730 and 3500 CE plalorms For more informaEon go to http://idx.appliedbiosystems.com

GeneMapper® ID-‐X User DocumentaEon


Thank You

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software updates to support 6-dye chemistry implementation

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