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Cores and Resources on Campus

Human Genetic Resources Core

The purpose of the core is to facilitate genetic research in human populations campus-wide. It has three components: 1) Cell and DNA Repository for tissue culture, cell banking and DNA isolation and storage); 2) Database Management Systems for laboratory and clinical research information; 3) Data Analysis for the coordination of statistical analysis of genetic data from human studies. In addition to providing cell banking, DNA isolation and storage for research and for the clinical (medical) genetics program.
http://www.cumc.columbia.edu/dept/human-genetics/

Columbia Resources for Genotyping, Sequencing, Mutation Detection

Targeted SNP genotyping Assay Platform
Brenner Lab Taqman assay ABI 7700
Diabetes Center FP-TDI
Pyrosequencing
LJL Biosystems Criterion Analyst AD (PE AcycloPrime-FP SNP Detection Kit)
Clark Lab IPLEX Sequenom
Genome-wide SNP’s

Gene Chip Facility Cancer Center Affymetrix Genechip Affymetrix Genechip genotyping
Mutation detection

Diabetes Center Heteroduplex analysis Transgenomics Wave
Gharavi Lab Heteroduplex analysis Spectrumedix Sequencer
Clark Lab Heteroduplex analysis> Transgenomics Wave
Microsatellite Genotyping
Gharavi lab Spectrumedix Sequencer
Clark Lab

ABI 3700
Allikmets lab PCR ABI 9700


SEQUENCING/GENOTYPING FACILITIES

1. Herbert Irving Cancer Center DNA Analysis and Sequencing Facility
http://www.ccc.columbia.edu/dna_analysis_seq.html
LOCATION:
CONTACT PERSON (phone and email):

DNA sequencing charges:
CancerCenter Members: $7 per template
Non-CancerCenter Members: $9 per template

2. DNA Sequencing Service, Columbia University Protein Core Facility
https://www.dnasequencing.hs.columbia.edu/
LOCATION: P&S 16-432, 630 W. 168th Street, New York, NY 10032
CONTACT PERSON: Changhong Qiao, 212-305-0078, cq19@columbia.edu

 
Columbia
University
Non-profit
Institution
Profit
Company
Regular

$7

$8

$10

Difficult

$10

$12

$15

High Volume

$6

$7

$8

3. Columbia Genome Center (Ju/Russo Laboratory)
http://genome4.cpmc.columbia.edu/researcher/russo.html
http://genome4.cpmc.columbia.edu/researcher/ju.html
https://www.genomecenter.columbia.edu/page.php?pageid=22
LOCATION: 
CONTACT PERSON (phone and email):

Sequencing as part of larger projects (association/linkage studies, genome sequencing, sequencing of libraries (EST, microRNA, SAGE, RDA, full length cDNA, etc.).  The laboratory does not just do sequencing, but will do all upstream (cloning, PCR) and downstream (sequence analysis) as well.  Mostly collaborative arrangements.

Pricing varies depending on what is requested.  As an example, in a SNP analysis by sequencing, we may do everything from primer design, to PCR and PCR cleanup, to bidirectional sequencing, to SNP calling at a cost of about $8.00-10.00 per patient per amplimer.  In most cases, we don't do template sequencing projects like the above two facilities, which are designed for that purpose.

This facility uses two 3730xl sequencers (96-capillary).

Other instruments in Ju/Russo lab that could be useful for genomics projects:
       1. BioTrove Open Array System for Genotyping (this runs intermediate numbers of Genotypes, somewhere between SNPlex (which can be done on the 3730xl sequencers and whole genome genotyping (Illumina, Affymetrix).  The advantage is that it can handle nearly any combination of sample number and SNP number within the range of a few to a few hundred.  Eventually the instrument can also be used for expression.

This instrument uses TaqMan assays (ABI) (as opposed to mass analysis as is used in the Sequenom instrument (see iPLEX approach under Lorraine Clark facility below).  Further details on system capabilities: http://www.biotrove.com/products/open_array/snp/

The charge to develop each open array plate is $450, and I believe you need to order at least 4 replicate plates at once.  TaqMan primers/probes need to be ordered from ABI separately.  Each plate is sufficient for 3,072 assays (e.g., 48 samples 64 SNPs; 12 samples 256 SNPs; etc.).  Cost comes to about 9-16 cents per SNP.  NOTE:  Machine is on loan from company currently.
       2. Real time thermal cycler (ABI 7000).
       3. Spotter for producing slide-based microarrays.
       4. Mass spectrometers (MALDI-TOF and LC-MSD that can be used for assorted SNP assays).

4. Lorraine Clark Laboratory (Department of Pathology)
LOCATION: 
CONTACT PERSON (phone and email):

This Core facility is for medium throughput SNP genotyping based on iPLEX chemistry--for more details of the technology, go to this web site: http://www.sequenom.com/iPLEX/index2.php

As a core facility we are currently charging $1242.64 for genotyping 384 DNAs with -plex level up to 24 SNPs or $0.12/genotype. This includes Assay design, development and optimization, PCR and assay set up and QC analysis of genotype data.

Other instruments in Clark lab that could be useful for genomics projects:

       1. ABI 3700 Genetic Analyzer
       2. Sequenom MassArray SNP Genotyping System
       3. Geneamp PCR system 9700 (2 machines for a total of 4x384 well blocks)
       4. MJ Research Tetrad 96 well PCR machine + MJ Research 384 well PCR machine
       5. Wave Transgenomic DHPLC instrument
       6. Computers and software
       6xPCs and 2xMacs, Genotyper and Genescan (ABI), Sequencher (Genecodes), Mutation surveyor (Softgenetics), MassARRAY software (Sequenom)

The matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) based MassARRAY platform is a medium to high throughput platform that can be used for SNP genotyping, SNP discovery, and allele frequency analysis. Genotype discrimination is based on a limited primer-extension reaction and allele specific termination products are analyzed in a MALDI-TOF mass spectrometer. The mass EXTEND and iPLEX methods allows individual genotyping on a medium throughput scale using 384-multi-well plates, with SNP multiplexing up to 24-plex in each well (individual DNA sample) routinely obtained, with such working assays designed for >95% of confirmed SNPs and >99.7% accuracy.

OTHER FACILITIES (NON-SEQUENCING): 

FACS facility
http://www.ccc.columbia.edu/FCCF/flow_cytometry.html

Commercial resources for Genotyping

Affymetrix GeneChip purchase
Can use for WGA genotyping and array CGH (copy #)
http://www.affymetrix.com/index.affx
deCODE Genetics STR genotyping
(ABI sequencers)
http://www.decode.com/
Illumina SNP genotyping and copy number variation http://www.illumina.com/
ABI SNP genotyping (Taqman Assay)
Cogenics High volume sequencing, SNP genotyping (Sequenom platform) http://www.cogenics.com/
Polymorphic DNA Technologies Resequencing, variant discovery http://www.polymorphicdna.com/index.html
NimbleGen Array CGH
ChIP-chip analysis
http://www.nimblegen.com/
AsperBiotech Custom microarrays for resequencing and genotyping based on APEX technology http://www.Asperbio.com/


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