john donahue, dna technical leader beaufort county (sc

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?