Introduction to Laboratory Assistant Suite

1. Laboratory
Assistant
Suite

2. Players
Starting May 2011, LAS stems from the joined efforts of IRCC and the Politecnico of Torino
IRCC contribution
• Strategy
• Working- and Data-flow analysis
• User interface definition
• On-site implementation
POLITO contribution
• Database & Data warehouse
• Analytical tools & software features
• IT

3. Goals
Structured data management
• Samples data (biobank)
• Biological data (xenos and cell lines)
• Molecular data (instruments)
• Public data (open access databases)
Integrative analysis management
• Complex queries across multiple databases (including clinical annotations)
• Analysis tools
• Annotations

4. Features
Data Entry
• Real-time
• Time saving
• User friendly
• Error proof
Data Analysis
• Integrative
• Reproducible
• Intuitive
• No programming skills required

5. Technical Specs
• Web-based
• Ad-hoc GUIs
• Relational and NOSQL Databases
• Distributed
• Audit trail
• A mnemonic code (GenID) intrisically represents the most critical attributes of the
main biological entities

6. Genealogy ID
Features
• Unique
• Intrinsic to key biological entities
• Encodes relevant information regarding the history of the entity
• Automatically generated through formal rules
XENOPATIENT ALIQUOT
CRC 0001 LM X 0A 01 001 TUM RL0100
Collection type
Tissue type Lineage Mouse ID Aliquot type
(tumor type, eg colorectal)
(eg liver metastasis) (eg tracks the line (individual mouse (eg RNAlater)
generation event) number)
Collection Event Vector type Passage Explanted Aliquot ID
(sequencial) (eg xeno, original (n° of generations Tissue (individual aliquot
human or cell line) ex-vivo) (eg number)
tumor, lung, liver, et
c.)

7. Data Flow
Tissue Aliquots BIOBANKING
Operation
Treatments
Explants Derived
Implants Storage
Aliquots
Mouse
Measurements XENOPATIENTS
EXPERIMENTS
Next Generation Sequecing Molecular Experiments Images

8. LAS data tracking system
Storage Xeno
Integrative
Sample Mice
analyses Containers
BIOLOGICAL
DATA
Surgical
Specimens
LAS LAS Facilities
ALIQUOTs XENOs
LAS
ALIQUOTs
TRANSFORMATION EXPANSION
Biobank
EVENTS EVENTS MOLECULAR
DATA

9. LAS facts&numbers
LAS manages (starting April 2012):
• 622 surgical samples collection
• 7158 mice
• 6895 implanted xenografts
• 4790 explanted xenografts
• 18537 measures (digital caliper)
• 1656 mice treated with 44 different
protocols&schedules
• 51131 archived aliquots
• 3530 derivation events (eg DNA extraction)

10. LAS modules
Integrative analysis module
Account and Privilege Manager
Integrative Public data Clinical data General facilities STATUS
query module miner miner manager working
advanced
development
intermediate
development
Biobank uArray Animal early
Xeno management
management management imaging development
scheduled
Storage Cell lines SangerSeq
Microscopy
management management management
Animal Animal RT-PCR FACS &
Pathology
models facility management Beaming

11. Current Functionalities
Biobank Storage
• Sample collection tracking • Management of containers
• Aliquots Exchange/Split/Usage tracking • Tracking archive process
• Support to derivation processes Query
(protocols, QC/QA)
• Definition of complex queries
• Consumables stock usage (Kits)
• Integration of heterogeneous data
Xenopatients • Exploration of genealogy trees
• Mice life cycle tracking
Analysis
• Surgery practices tracking
• Data mining analyses
• Tumor growth tracking
• Computation of aggregated data
• Treatment protocols
• Plot of data statistics
• Support to decision making process for
experiments

12. People
• IRCC (contributors&users) • POLITO (developers)
• Eugenia Zanella staff
• Giorgia Migliardi • Alessandro Fiori (coordinator)
• Francesca Cottino • Alberto Grand
• Francesco Galimi • Piero Alberto
• Michela Buscarino • Emanuele Geda
• Carlo Zanon students
• Gabriele Picco • Marco Alaimo
• Roberta Porporato • Francesco Brundu
• Daniela Cantarella • Maria Cabiati
• Tommaso Renzulli • Stefania Mellai
• Enzo Medico • Raffaele Passanati
• Domenico Schioppa

13. Milestones
The project is implemented through three steps:
Phase I - Biobanking & Xenopatients management
• Storage
• Aliquots (tissues & derivatives)
• Transformation processes
• Mice
• In Vivo experiments
Phase II - General facilities management
• uArrays
• Sanger sequencing
• RT-PCR
• FACS
• Animal Facility (?)
Phase III - General purpose data management
• In vitro experiments
• Imaging
• Analytical tools
• NextGenSeq data management (in collaboration with informatics)
• Mouse models
• Clinical data integration

14. Biobanking Module

15. Xenografts Module

16. Query Module