HID Validation: The 3500 Series Genetic Analyzers

Transcription

1

2 Outline Scope Materials and Reagents Validation Elements Selection of Validation Data Additional Sources of Validation Information User Bulletin 2

3 Validation Scope Hardware and Reagents HID Validation: Instruments (3) 8 Capillary Instruments (3500) (3) 24 Capillary Instruments (3500xL) Size Standard GeneScan 600 LIZ Size Standard v2.0 GeneScan 500 ROX Size Standard Profiler Plus / Cofiler do not use normalization Polymer and Array POP-4 and 36 cm Capillary Array 3

4 Validation Scope Sample Summary HID Validation: Test Name Samples Input Replicates Genotype Concordance and Reproducibility 40 male and 42 female gdna samples 4 racial groups Controls 1-2 ng total DNA 1 replicate per sample 2 injections Sizing Precision and Accuracy Allelic ladder 1 µl per well See below Sensitivity and Normalization 007 control DNA 3 gdna samples STR: 0.125ng, 0.5ng, 1ng, 6ng Minifiler: 0.125ng, 0.25ng, 0.5ng,.75ng 5 replicates for DNA samples 3 replicates for NTC 4 injections Mixture Analysis 4 pairs of male and female gdna Mixture ratios 1:0, 1:1, 1:3, 1:5, 1:9, and 0:1 Recommended concentrations per kit 1 replicate per sample Resolution Allelic Ladder Research material 1 µl per well 24 replicates 4

5 Validation Scope AmpFlSTR Kits Identifiler Minifiler SGM Plus Yfiler Sinofiler SEfiler Plus Profiler Plus Cofiler Identifiler Direct Identifiler Plus NGM 5

6 Precision and Accuracy

7 Precision and Accuracy Example Configurations for Standard Deviation Within Injection Across Injections 3500xL 8 data points per mean 12 injections per plate 12 columns 3 Instruments 12 data points per mean 4 injections per plate 8 rows 3 Instruments 7

8 3500 Sizing Precision Study: Within an Injection of Identifiler Allelic Ladder 8

9 3500 Sizing Precision Study: Across Multiple Injections of Identifiler Allelic Ladder Samples Injections 3500xL - 4 Injections 96 Replicates of Identifiler Allelic Ladder 9

10 Introduction to Normalization

11 Sources of CE Variation (3100) Raman Intensity, 3100 file: INSTRUMENT DATA Mod2B.xls Numerous optical components, capillary array y = x R 2 = Electrophoresis, injection Sample and sample preparation A/D Units median= Stdev = Average = Stdev/ average = 0.13 Series1 Linear (Series1) Instrument Almost 2-fold difference in signal from over 100 instruments from the factory floor 11

12 Normalization: What is it? HID Validation: This feature normailzes signal variations associated with instrument, capillary array, sample salt load, and injection variability among capillaries and instruments Normalization can be applied during primary analysis of the data Before normalization After normalization 12

13 Normalization: Definitions HID Validation: Normalization Target (NT) The expected average RFU for eleven peaks in the GeneScan 600 LIZ v2 size standard used for normalization Normalization Factor Normalization Target divided by the Average peak height of the subset of peaks in the GeneScan 600 LIZ v2 size standard used for normalization Normalization Factor Threshold The passing range for Normalization Factor (default range is 0.3 to 3.0) 13

14 Sources of Variation by Normalization Method 39% Instrument to Instrument largest source of variation 14 %CV Internal standard Normalization greatest reduction in variation 40% 35% 30% 25% 20% 15% 10% 5% 0% 33% 31% 25% 24% 24% 20% 19% 12% 11% 5% 4% 3% 3% 0% No Norm Factory only Int Std only Levels of Normalization 0% Factor+IntStd 4% 14% 13% Total 5% Instrument to Instrument Within Cap to Cap Injection to Injection Sources of Variation

15 Sensitivity and GeneScan 600 LIZ Size Standard v2.0

16 Sensitivity Study: Average Peak Height across a Range of DNA Input Amounts AmpFlSTR MiniFiler TM PCR Amplification Kit H1126 Genomic DNA # ng 0.25ng 0.50ng 0.75ng H1152 Genomic DNA # H1161 Genomic DNA #3 OO7 Control DNA Standard Peak Height ng 00.25ng 0.50ng ng Normalization Method Factory Only Factory + Internal Std 16

17 Sensitivity Study: Average Peak Height by Dye for 1ng DNA Input AmpF lstr Identifiler PCR Amplification Kit Peak Height Disabled Enabled Internal Standard Normalization

18 Size Standard Peak Height Consistency Study: Five AmpFlSTR PCR Amplification Kits GeneScan 600 LIZ Size Standard v Peak Height GS600 Peak Height Identifiler Identifiler Direct Identifiler Plus Minifiler TM NGM TM Lot 1 Lot 2 Lot 3 GS600 Lot Number 18

19 Size Standard Peak Height Consistency Study: %CV for 5 Different AmpFlSTR Kits GeneScan 600 LIZ Size Standard v2.0 % CV 19 Size Standard Peak Height Consistency 6 instruments 3 lots of size standard

20 Internal Standard Normalization: Injection to Injection Peak Height Consistency GeneScan 600 LIZ Size Standard v Normalization Method Factory Only Factory + Internal Std % CV Lot 1 Lot 2 Lot 3 Size Standard Peak Height Consistency 6 instruments 3 lots of size standard 20

21 Resolution and Baseline Evaluation

22 Resolution SEfiler Plus (SE33 triplet) and Identifiler (TH01 9.3/10) Allelic Ladders 160 injections per instrument on 6 instruments Research STR markers greater than 300 base pairs were also developed with single base pair differences (data not shown) 22

23 Baseline Noise - Developmental Evaluation G5 Average Noise (10x SD) 10x Average Std. Dev RFU 20 0 FAM VIC NED PET LIZ TOTAL Data generated during the Sensitivity experiment was then used to confirm the level of pull up and the peak amplitude threshold setting. 23

24 Pull-up 360 Samples at 6 ng template HID Validation: % 24

25 Additional Studies and Validation Documentation

26 Identifiler Direct HID Validation: Capillary 3500xL 0 8 Capillary gdna, 25 cycles Three 3500xl and three 3500 instruments. Mother plate split into 6 daughter plates. 26

27 Additional Studies HID Validation: Genotype Concordance 100% Concordant with 3130xL GeneMapper ID-X v1.2 Evaluation Normalization and RFID documentation functionality performed as expected Average Mx values obtained in the Mixture Study were similar to the 3130xl 27

28 Validation Documentation HID Validation: AAFS and ISHI Posters Bode Conference Presentations User Bulletin containing developmental validation in progress 28

29 Legal FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners. For those who require IVD-marked devices, the 3500 Dx and 3500xL Dx Genetic Analyzers and system accessories meet the requirements of the In Vitro Diagnostic Medical Devices Directive (98/79/EC). The 3500 Dx and 3500xL Dx systems are for distribution and use in specific European countries only. For more information about the 3500 Dx Series Systems, contact your Applied Biosystems representative. 29

30 Thank you!