3500 series software...the world leader in serving science 3500 series instrument data collection...

The world leader in serving science

3500 Series Instrument Data Collection Software Version 4.0 and GeneMapperTM ID-X Software v1.6Dr. Anke KrugerManager HID Field Application Specialists Europe

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Data Collection Software v4 enhancements:• Signal optimization • Pull-up reduction• Offscale recovery• Updated Library Organization• Flexible plate loading• Additional features

GeneMapper ID-X v1.6:• Off-scale Data Recovery• Export Options for Probabilistc Genotyping• Peak Detection Algorithm changed• Enhanced Plot and Printing Options• Sorting Improvements

Agenda


3500 Series Instrument Data Collection Software Version 4.0

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Computer Requirements

Operating System

• Win 10 2016 LTSB, 64bit• Java 7 32bit• Tomcat 7.0.82 32bit• Verification testing included: Symantec Endpoint Protection 12 and McAfee

Endpoint Security 10.5 and Windows Defender. • McAfee Endpoint Security may block services startup. See release notes for

details.

Dell OptiPlex XE2 Computer

Updates

• Server Monitor updated • Patch for camera corrupt error• No licensing• FSE installed


Signal optimization

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• Goal: reduce capillary-to-capillary variation within an injection• Spatial approach developed

Signal optimization

• Utilize spatial calibration data• 24-capillary instruments only• Automatically applied

Optical approach: Reduce variation introduced by optics

Optimize Signal

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• Displayed in Spatial Calibration screen• Included in the Spatial calibration report, can be exported or

printed• 8 capillary instruments: factor = 1 for all capillaries

Signal Optimization Factor

Reduce Variation Due to Optics

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Signal Optimization Results


Pull-up Reduction

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Recognizing Pull-up

• Analyzed data: centered under parent peak

• Raw data: same shape as parent peak

Spectral

• Analyzed data: not centered under parent peak

• Raw data: sinusoidal curve

Instrument-Specific

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Pull-Up Reduction in DC v4.0

Pull-up reduction

Addresses spectral (including off-scale)

and instrument-specific pull-up

Utilizes sample-specific spectral data

To enable pull-up reduction

Utilize an Applied Biosystems (AB) STR

kit

Perform spectral calibration using an

AB dye matrix and AB dye set

Choose applicable AB assay

Spectral correction

Takes place prior to creation of .hid files

Raw Data viewed in GeneMapper IDX (all versions) will have the

reduction applied

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Pull-Up Reduction in DC v4.0

• Identified by labeling as allelic ladder sample type

• Identified by density of peaks in profile

Allelic ladders – pull-up reduction DISABLED

• Signal-to-noise ratio

• Number of peaks and dyes detected

• Calibrated matrix will still be applied (i.e. sample-specific spectral data not utilized due to poor quality)

Poor quality samples – pull-up reduction DISABLED

• Adds approximately 2-3 minutes per injection for processing (3500xL)

• Pull-up frequency is reduced

• Peak height percentage of remaining pull-up generally falls within 1-3%

Important Notes

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Improved Data Interpretation – Pull-up

Single-source 1ng sample amplified with the GlobalFiler kit analyzed at 50 RFU31 pull-up edits

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Improved Data Interpretation – Pull-up Reduction

The same GlobalFiler profile analyzed at 50 RFU after pull-up reduction is applied.6 pull-up edits


Off-scale data recovery

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• Capture “off-scale”• Truer peak height• Decrease manual interpretation

• Off-scale data now approaching ~65,000 RFU

• Global filters more effective• Stutter filters more applicable

• Decrease pull-up associated with off-scale peak

• On-scale data not impacted

• Higher 1st pass success rate

Off-Scale Data Recovery (OSR) for Database Samples

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Off-Scale Data Recovery

• Bin data signals saturation• Bin data converted to dye data• Dye data capped at ~32K RFU

values

Saturation

• CCD camera saturation limit is extended (OSR assays)

• More bin data can be utilized• Dye data capped at ~65K RFU

values


GMIDX 1.6 is required to analyze/view OSR data above ~32K RFU.

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Off-Scale Data Recovery Field Testing Results

OSR Disabled(Any6Dye dye set)

OSR Enabled(J6 dye set)

Test Site 1 5 markers in 2 samples 0 markers in 0 samplesTest Site 3 99 markers in 12 samples 4 markers in 1 sample

Test Site 2 5 markers in 2 samples 0 markers in 0 samples

(10) Reference GFE samples(3) GFE Positive Controls

Data from Test Site 1

OSR ON

OSR OFF

Using OSR dye set enables OSR feature – works with AB dyes


Additional Features

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Flexible Plate Loading - 3500 Series

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Added Flexibility and Control – System Preferences

• Instrument settings

• Uncheck “allow runs” options

• Access: admins only

• Results in pre-run validation check error

Choose: hard stop

Admin view

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DC 4.0 Enhancements - Summary

Improved data analysis options• Pull-Up Reduction• Off-Scale Data Recovery (OSR)• Signal Optimization (SO)

Improved user experience• No yearly licensing• Flexible Plate Loading• 6-dye HID Install Standard• Library Assets Updated• Flexible admin preferences for hard stops and warnings• Bi-weekly scheduling• Exportable consumables list• Exportable injection list• Normalization Factor and average peak height in Sample View• EPT for completed/aborted runs

User Bulletin available


GeneMapperTM ID-X Software v1.6

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GMIDX updates including:

• Operating Systems (Win 10, 64bit and Win7, 64 bit compatibilty)

• Off-scale Data Recovery

• Export Options for Probabilistc Genotyping

• Peak Detection Algorithm changed

• Command Line Interface

• Profile Comparsion Tool

• Enhanced Plot and Printing Options

• Sorting Improvements

• Panel and Report Manager Updates

• Support of SeqStudio file format

• ...

Agenda

HID validation expected H2 of 2019

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• Upper limit: ~65,000 RFU

• MUST use GeneMapper™ IDX v 1.6

RFU upper limit extended for DC 4.0

• Global filters more effective

• Stutter filters more applicable

• Decreased pull up

• Higher 1st pass success rate

• On-scale data not impacted

Better peak height estimate

• Peaks will be capped

• Secondary dye colors may be pulled-up to 65K

• Analyze with caution!

Severely off-scale data (>65K RFU)

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Off-Scale Data Recovery (OSR)

41251

29620

v1.6 = Pass

v1.5 = Flagged

OS w/ pink bar


Export for Probabilistic Genotyping

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Probabilistic Genotyping – Data Export

• Two export file type options:• .txt or .csv • Select from the right-hand drop-

down menu

• When you export without stutter:• Labeled allele peaks are identified

as Allele 1 and Allele 2

• When you export with stutter:• Stutter peaks and labeled allele

peaks are labeled sequentially


Enhanced Plot and Printing Options

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Printing

Custom Header

Marker header outlined in color

Bin Color adjusted to improve visibility


Sorting within the Software

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Sorting Within the Software

• Projects sorted by default with most recently created on top

• Analysis Methods and Size Standard drop downs in project window are alphabetical

• Genotype Table can be sorted by Marker only without dye consideration

General Sorting

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Comparison NGM Detect - NGMSelect

Different Samples - One Marker – Different dyes

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Comparison NGM Detect - NGMSelect

Different Samples - One Marker - sample order by selection

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GMIDX v1.6 Details- Summary

Improved data analysis options• Off-Scale Data Recovery (OSR)• Data export for stutter• Peak height detection

Improved user experience• Profile Comparison Tool• CLI• Sorting (projects, drop-down menus, Genotypes Table)• Plots (scrolling, editing/deleting, size standard display, PLI, tables)• Panel manger (v6x, IQS and Ymarker functionality)• Report manger• SS Normalization• Printing (comment, marker header)• SAE: Audit record deletion, log-in list• Seq Studio file support

IT compliance• Win 7 or Win 10• CODIS updates• Chinese Language• Oracle Security

User Bulletin available

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Thank you for your time & attention

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Products described herein are intended for forensic or paternity use only. Not for use in diagnostics procedures.

The content provided herein may relate to products that have not been officially released and is subject to change without notice.

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