John Donahue, DNA Technical Leader Beaufort County (SC) Sheriff’s Office QIAGEN Users Meeting, “Models of Efficiency” July 30 th , 2014
John Donahue, DNA Technical Leader Beaufort County (SC) Sheriff’s Office
QIAGEN Users Meeting, “Models of Efficiency” July 30th, 2014
QIAGEN would like to thank our speaker,John Donahue, for his presentation.
Disclaimer:QIAGEN is not affiliated with the Beaufort County (SC) Sheriff’s Office. The views expressed herein are those of the speaker, and do not necessarily express the views of QIAGEN.
For up-to-date licensing information and product-specific disclaimers for QIAGEN products, see the respective QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN Technical Services or your local distributor.
� Beaufort County, SC
� � 2013 population (est.) = 172,000 � By municipality:
� Beaufort (13,000) � Port Royal (11,500) � Bluffton (13,600) � Hilton Head Island (39,000 full time residents)
� 150,000 in summer
Demographics
� � FBI UCR stats, 2012, Beaufort County
� Murder: 12 � Rape: 47 � Robbery: 146 � Property crime: 5,017
� Scaled up to population of 1,000,000 � Murder : 70 � Rape: 273 � Robbery: 850 � Property crime: 29,000
Crime Statistics
� � Lab staff hired January, 2008 � Initial equipment purchased May/June, 2008 � Offsite validation began August, 2008 � Lab construction completed March, 2010 � Onsite validation completed August, 2010 � Lab opened September, 2010 � ISO inspected February, 2011; accredited June, 2011
Laboratory History
� � DNA staff
� 2 (one TL, one examiner) � No additional DNA personnel (technicians, CODIS
administrators, etc.) � 2 DNA staff handle all technical duties (evidence
screening, DNA analysis, quality control, etc.) plus some administrative functions (LIMS, CODIS, safety)
Laboratory Staffing
� � Knew that some automation would be necessary � Automated extraction
� Determined that number of samples to be examined would not require large benchtop robot
� Initially purchased small extraction robot from another vendor but were not satisfied
� Traded up for EZ1 Advanced XL (14 samples per run)
Initial Setup of Laboratory
� � Started casework and then found that manual setup
of quant and amp plates was limiting � Required large amounts of time that could be used for
other tasks � Concerns about sample switches limited the number
of samples that could be processed
Operational Limits
� � Realized that a liquid handling instrument was
required � Large multi-purpose liquid handler was not needed
(EZ1 already used for extraction) � Did not have enough room for large liquid handler � Evaluated QIAgility for automated quant and amp
setup on 96-well plates
Operational Limits
QIAgility
� Dimensions: 21” x 25” x 18”
QIAgility
3 1 2
4
� � Purchased installation and validation services
� At the time we used one quant kit and four STR kits � Casework was increasing and we did not have time to
validate � Validation services by QIAGEN took three days in-
house (including training, building of customized instrument protocols, creation of worksheets)
QIAgility
� � 75% of samples completed in-house, 25% completed
after install team left � Validation document prepared and delivered by
QIAGEN � Following approval of validation, instrument was
placed online � Total time from arrival of team to casework approval
was roughly five months � Lab was about three months late in sending final data
QIAgility
� � QIAgility used for:
� Quant setup of up to 80 samples plus preparation of standard curve dilutions (7 standards + 1 NTC, 2 replicates each)
� PCR setup of up to 64 samples + positive and negative controls with dilution and normalization of samples
� Up to 40 to 45 minutes for each (full plate)
QIAgility
QIAgility
� � Also used for:
� Aliquotting cRNA, DTT into individual tubes � Creation of dilution series/sensitivity studies for
validations
� Can be used for setup of electrophoresis plate � We use a repeating pipette for formamide/ILS mix
and a multichannel pipette for samples
QIAgility
� � 2013 – found that two areas were slowing us down
1. Worksheets � QIAgility uses .csv files for import but we had
multiple electronic forms for extraction, quantification, amplification
2. Increasing number of samples that were not conducive to EZ1 Tip Dance protocol, thus requiring use of spin baskets
Capacity Enhancement
� � Development of Excel workbook
� Sample IDs exported from LIMS � Copy/paste to extraction sheets, quant sheets, quant
results, amp sheets, 3130 setup � All data retained in one workbook � No transcription errors � Import/export functions used for all instrumentation
Solutions
�
Solutions
� Investigator Lyse & Spin Baskets
� � Investigator Lyse & Spin Baskets
� Reduces handling time by about 15-20 minutes per run with no transfers of cutting or supernatant
Solutions
� � Added QIAcube in 2014 for differential washing
� Capable of processing up to 12 differential extractions at same time
� Wash time comparable to manual washing but requires no labor other than run setup
� Touch screen prompts walk examiner through the setup process
Addition of QIAcube
� � Purchased validation services with QIAcube
� All samples processed in two days � STR amplifications performed after departure of
validation team � Final report delivered; competency testing in progress
� Preliminary data indicates that QIAcube recovered more DNA from sperm fractions than manual washing � Likely due to sperm loss in manual wash steps
Addition of QIAcube
124
476 444 534
1362
2017
0
500
1000
1500
2000
2500
2011 2012 2013
Capacity Increase After Automation
Cases
Items
5
20 19 22
57
84
0
10
20
30
40
50
60
70
80
90
2011 2012 2013
Analyst Productivity Per Month
Cases
Items
� � With current equipment and methods (EZ1 AXL (x2),
Lyse&Spin baskets, QIAgility, QIAcube) one person can easily: � Extract � Quantify � Amplify
80+ samples in one day
Capacity Increase
� � Direct amplification of reference standards
� Eliminates extraction and quantification steps � FTA punches and buccal swab lysates added directly
to plate � 40 to 50 minute amplification
� Addition of Rotor-Gene Q for quicker quantification � (RGQ + HYres = roughly 50 minutes)
Future Objectives
�
Questions?