organisation - the Instituto Gulbenkian de Ciência

GENOMICS
UNIT
Carlos Penha Gonçalves Head
PhD in Immunology, University of Umea, 1999
PI of Disease Genetics Group
Head of Facility since 2003
The Unit provides technological support and expertise for research at the genome
scale and is composed by the Sequencing and Genotyping Services.
The Sequencing Service offers DNA sequencing and fragment analysis using
multicapillary with automatic sequencer ABI 3130XL. Taqman® Technology in
a 384-well format is also available to users both for SNP genotyping and Real-
Time PCR gene expression with 7900 HT Fast Real-Time PCR System.
FACILITY STAFF
Maria Isabel Marques (Senior Laboratory Manager)
João Costa (Genotyping Research Assistant)
Susana Ladeiro (Sequencing Research Assistant)
The Genotyping Service offers the Sequenom iPLEX technology, allowing rapid
SNP genotyping assays with up to forty SNPs assayed simultaneously. The facility
collaborates with researchers on: SNP choice and SNP Assay Design, Sequenom
Procedure and Data Management for Genetic Studies, providing access to
the BC/GENE interface software.
MAJOR PROJECTS AND ACCOMPLISHMENTS
GROUPS USING THE SEQUENCING SERVICE
• DNA Sequencing: Thirty in-house, five IGC associated groups and one non
IGC-associated groups used the ABI 3130XL Sequencing Service, with a total
of 11,880 samples sequenced between January and December 2011;
• Fragment Analysis/MIRUS: Four in-house groups used the ABI 3130XL Sequencing
Service with a total of 4,476 samples;
• Fast Real-Time PCR System: Twelve in-house, two IGC associated and three
non IGC-associated groups used 7900 HT on a regular basis (a total of
1,062 hours), to detect gene expression of several genes, on 20 different
projects.
GROUPS USING THE GENOTYPING SERVICE
Eleven internal, two IGC associated groups and seven non IGC-associated
groups used the Genotyping Service in 2011.
A total number of 1,282,560 SNP genotypes were produced between January
2010 and January 2011.
EQUIPMENT AND INFRASTRUCTURE
THE UNIT IS EQUIPPED WITH
• 2 robotic pipetting devices, robot PlateMate 2x2 (Matrix);
• 5 thermocycling machines - ABI 9700 equipped with 2x384 blocks;
• 1 Chip spotting robot (MassARRAY, Nanodispenser);
• 1 SNP detection, MALDI-TOF technology - MassARRAY Compact (Sequenom);
• 1 ABI 3130XL;
• 1 7900 HT Fast Real-Time PCR.
Funding Fundação para a Ciência e a Tecnologia, Portugal
External
26%
Internal
52%
IGC External
26%
Use of genotyping facility in 2011.
IGC ANNUAL REPORT ‘11
FACILITIES AND SERVICES
91