Eliminating manual steps in a high throughput ... - PerkinElmer
Eliminating manual steps in a high throughput ... - PerkinElmer
Eliminating manual steps in a high throughput ... - PerkinElmer
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<strong>Elim<strong>in</strong>at<strong>in</strong>g</strong> <strong>manual</strong> <strong>steps</strong> <strong>in</strong><br />
a<strong>high</strong> <strong>high</strong>-<strong>throughput</strong> genotyp<strong>in</strong>g workflow<br />
Heiko Cziudaj, COG Meet<strong>in</strong>g, 2010-10-12
The company…<br />
• Founded <strong>in</strong> 1998 as Artemispharmaceuticals GmbH<br />
• Generation of genetically modified mouse models for customers<br />
• KO, cKO, KI, HUM, TTG, KD<br />
• based <strong>in</strong> Cologne<br />
• 120 FTE<br />
• Parent company Taconic, Inc (Hudson, NY)
The lab...<br />
1 FTE for sequenc<strong>in</strong>g<br />
2 FTE for genotyp<strong>in</strong>g
The mission...<br />
Genotyp<strong>in</strong>g:<br />
Dist<strong>in</strong>guish mutants and wildtype mice by size differences of PCR-products<br />
mutated allele<br />
wildtype allele
The trend...<br />
Genotyp<strong>in</strong>g 2010<br />
~ 64.000 Typ<strong>in</strong>gs<br />
2FTE<br />
Genotyp<strong>in</strong>g 2009<br />
63.000 Typ<strong>in</strong>gs<br />
2 FTE<br />
Genotyp<strong>in</strong>g 2008<br />
60.000 Typ<strong>in</strong>gs<br />
3 FTE<br />
Genotyp<strong>in</strong>g 2007<br />
44.000 Typ<strong>in</strong>gs<br />
3FTE
Database portfolio
Process Flow Genotyp<strong>in</strong>g 2009:<br />
Setup<br />
Def<strong>in</strong>e Geno-<br />
Assay<br />
Tail DNA<br />
Assay Dev.<br />
Breed<strong>in</strong>g typ<strong>in</strong>g Task Design Prep<br />
SOP / DB<br />
Manual<br />
Pipett<strong>in</strong>g<br />
Fragment<br />
Analysis<br />
Database<br />
Entry<br />
Quality<br />
Control<br />
Automated Fragment<br />
Database<br />
Quality<br />
Pipett<strong>in</strong>g Analysis Entry Control<br />
Manual tasks<br />
Automated procedures,<br />
no <strong>manual</strong> <strong>in</strong>terferer<strong>in</strong>g
In the beg<strong>in</strong>n<strong>in</strong>g...<br />
Genotyp<strong>in</strong>g results
...now!!
Replacement of EtBr-gels done!<br />
Setup<br />
Def<strong>in</strong>e Geno-<br />
Assay<br />
Tail DNA<br />
Assay Dev.<br />
Breed<strong>in</strong>g typ<strong>in</strong>g Task Design Prep<br />
SOP / DB<br />
Manual<br />
Pipett<strong>in</strong>g<br />
Fragment<br />
Analysis<br />
Database<br />
Entry<br />
Quality<br />
Control<br />
Automated Fragment<br />
Database<br />
Quality<br />
Pipett<strong>in</strong>g Analysis Entry Control<br />
Manual tasks<br />
Automated procedures,<br />
no <strong>manual</strong> <strong>in</strong>terferer<strong>in</strong>g
Aim2 = automated Data import
Automated Data import, 1st concept
...just two clicks for the user!!<br />
al<br />
al<br />
al<br />
al<br />
al<br />
al<br />
al<br />
al
Process Flow Genotyp<strong>in</strong>g 2009:<br />
Setup<br />
Def<strong>in</strong>e Geno-<br />
Assay<br />
Tail DNA<br />
Assay Dev.<br />
Breed<strong>in</strong>g typ<strong>in</strong>g Task Design Prep<br />
SOP / DB<br />
Manual<br />
Pipett<strong>in</strong>g<br />
Fragment<br />
Analysis<br />
Database<br />
Entry<br />
Quality<br />
Control<br />
Automated Fragment<br />
Database<br />
Quality<br />
Pipett<strong>in</strong>g Analysis Entry Control<br />
Manual tasks<br />
Automated procedures,<br />
no <strong>manual</strong> <strong>in</strong>terferer<strong>in</strong>g
Process Flow Genotyp<strong>in</strong>g 2010:<br />
Setup<br />
Def<strong>in</strong>e Geno-<br />
Assay<br />
Tail DNA<br />
Assay Dev.<br />
Breed<strong>in</strong>g typ<strong>in</strong>g Task Design Prep<br />
SOP / DB<br />
Manual<br />
Pipett<strong>in</strong>g<br />
Fragment<br />
Analysis<br />
Export to<br />
Database<br />
Quality<br />
Control<br />
Automated<br />
Pipett<strong>in</strong>g<br />
Fragment Export to Quality<br />
Analysis Database Control<br />
Manual tasks<br />
Automated procedures,<br />
no <strong>manual</strong> <strong>in</strong>terferer<strong>in</strong>g
…everyth<strong>in</strong>g done!!<br />
‣Overview about PCRs per animal facility plate<br />
‣ Creates: - Mastermix recipies (Setup Validator)<br />
- Pipett<strong>in</strong>g <strong>in</strong>structions (Hamilton robotics)<br />
- Layout-file for LabChip (Sample name, position, expected peak )<br />
‣ Automated data entry <strong>in</strong> MouseHouse database<br />
Tails <strong>in</strong> 96well plate<br />
Layout<br />
file<br />
Typ<strong>in</strong>g<br />
results<br />
Typ<strong>in</strong>g<br />
requests<br />
Pipett<strong>in</strong>g<br />
<strong>in</strong>structions<br />
Result<br />
file<br />
Mouse<br />
House<br />
Pipetteted, cycled plates
...Robotics and DB improves lab work<br />
• Autom. Data exchange between MH, LabChip, Hamilton<br />
– Decreases error rate (pipett<strong>in</strong>g, data entry)<br />
• No need for <strong>manual</strong> calculations of mastermixes<br />
– Recipies are just one click away<br />
• Consistency check regard<strong>in</strong>g PCR setup<br />
– Never use wrong controls<br />
• No gel cast<strong>in</strong>g, no ethidium bromide<br />
– Improves work safety<br />
• No bor<strong>in</strong>g paper work for lab staff<br />
– Bor<strong>in</strong>g work <strong>steps</strong> generates <strong>high</strong> error rates<br />
• Results are easy to f<strong>in</strong>d <strong>in</strong> DB<br />
– DB-generated report possible
Acknowledgment<br />
My team:<br />
Kerst<strong>in</strong> Schoebel<br />
Sarah Neu<br />
IT:<br />
Chris Schleiermacher<br />
Christian Schmidt<br />
Cathleen Salomo<br />
Holger Schulz<br />
Thank you for listen<strong>in</strong>g!!!!<br />
i
Our animal plates...<br />
... physically<br />
... <strong>in</strong> silico
PCR-setup
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