SNP Genotyping at HPCGG

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SNP Genotyping at HPCGG
Alison Brown Lab Manager and Technical
Director Harvard Partners Center for Genomics and
Genetics 65 Landsdowne Street Cambridge, MA
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A brief history..

• In 2001, HPCGG was established with Dr Raju
  Kucherlapati as Scientific Director
• Genotyping Core Facility was set up at BWH and
  HSPH in Boston, using Sequenom MassARRAY and
  Taqman as Genotyping Platforms
• Future - further technologies to be introduced
• ABI SNPlex
• Illumina BeadArray

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Our requirements in 2001

• High throughput
• High accuracy
• High completion rates
• Low per genotype cost
• Automatic allele calling..with manual editing
• Low use of DNA per reaction

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Sequenom MassARRAY BiFlex
MALDI-TOF Mass Spectrometer Analyzer
Automated Liquid Handler Microdispenser
Miniaturized Biochip SpectroCHIP
SpectroPOINT
Automated Analysis SpectroTYPER-RT
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Getting Started

• Customers
• Staff and Automation
• Bioinformatics support

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Customers

• Channing Laboratory
• Variety of cohort sizes
• Large amount of SNP genotyping projects
• Close working partnership
• Harvard Medical School Partners Healthcare
• External Customers

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Staff and Automation

• Staff
• Experienced in General Mol Biol
• Troubleshooting
• Customer liaison
• Automation
• Pre-PCR
• Link to LIMS

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Bioinformatics Support

• Channing Laboratory Bioinformatics Division
  Director, Brent Richter
• LIMS
• sample tracking
• storage of data
• QC of Genotyping data
• QA of automatic allele calling

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Bioinformatics Support - LIMS
Samples
Assays
5-CGGGATAAATATCGACTC-3
5-GGTATGATGCATGCA/GTTTTTAGAAACCCC...-3
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Bioinformatics Support - Data
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Bioinformatics Support - QC
(Developed by The Channing Laboratory
Bioinformatics Division, Brent Richter Director)
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Bioinformatics Support - QA
(Developed by The Channing Laboratory
Bioinformatics Division, Brent Richter Director)
Sequenom SpectroTYPER version 3.1
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Our requirements in 2005

• Improve/supplement/replace current system
• Higher throughput
• Higher accuracy
• Higher completion rates
• MUCH lower per genotype cost
• Automation of allele calling
• Low use of DNA per reaction

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Adaptability of the Platform

• Sequenom SpectroTYPER version 3.1
• SNP Genotyping
• Allelotyping
• Allele specific expression
• Gene expression
• Oligonucleotide Checking

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HPCGG Sequenom Genotyping Facility

• Director Dr David Kwiatkowski, MD PhD.
• Lab Manager Alison Brown
• Technical Staff
• Maura Regan Human Genotyping
• Andrew Bolton Mouse Genotyping
• Bioinformatics
• Brent Richter
• YongDong Zhou