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The
Genomic Facility
'To facilitate large
scale genomic analyses'
Publications
Personnel
Introduction
The
Wales Gene Park Genomic Facility has been set up to help researchers
with large scale genomic projects. We are funded by the Welsh Assembly,
through a grant from WORD. The Genomic Facility offers a SNP
detection service using DHPLC machines as the primary SNP detection
platform. The group also provides robotic PCR setup for diagnostic
and research purposes.
Services
- We provide a full SNP detection service.
Helping with study design, optimising and setting up PCR reactions,
screening for the presence of heteroduplexes and sequence characterisation
of variants. These larger projects are done on a collaborative
basis.
- We provide researchers with the means
of carrying out large scale PCR on our robotic workstation in
both 96 and 384-well plate format. PCR methods can be written
that are tailored to the researchers
needs and requirements.
- No charges are made for equipment use
or man hours.
Equipment
PCR
setup
is carried out in an amplicon free environment on a Beckman Biomek
FX platform. Following amplification on our MJ Tetrads, the products
are analysed on the Idaho LightScanner or 3 HT Transgenomic
Wave platforms which incorporate the latest Navigator Software.
This includes automated pattern recognition software for the identification
of heteroduplexes. SNP verification is carried out through sequencing
of PCR
product
on an ABI
3100
DNA
Sequencer. Automated software is then used to analyse the chromatograms.
| PCR
set-up
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Dual Arm Liquid Handling Robot;
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Contaminant free environment;
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8 span disposable tip, dispensing head;
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96 disposable tip, dispensing head;
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Over 9000 PCR reactions set up per
day. |
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PCR
amplification
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3 x 4-bay high-throughput
thermal cyclers;
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Real-time monitoring of cycling
temperatures;
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PCR
amplification carried out on 1152 samples simultaneously.
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Analysis
of amplified PCR products
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Three Transgenomic HT wave systems;
- Detection of known and unknown genetic variation over the
length of
amplified product;
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SNP detection on 864 PCR products per day;
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Navigator software™ enables
automated profile analysis. |
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Characterisations
of SNPs
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ABI 3100 sequencer, automated from sample loading to analysis;
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16 capilllaries running in
parallel enables over 300 sequence reactions per day;
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Multiple sequence trace alignments on Gene Codes 'Sequencer'
software™
with heterozygote detection facility. |
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| Publications |
- Azzopardi D, Dallosso A R, Eliason
K, Hendrickson B C, Jones N, Rawstorne E, Colley J, Moskvina
V, Frye C, Sampson J R, Wenstrup R, Scholl T, Cheadle J
P. (2008)
Multiple rare nonsynonymous variants in the adenomatous
polyposis
coli gene predispose to colorectal adenomas
Cancer Res. Jan 15;68(2):358-63
- Dallosso A R, Dolwani S, Jones N,
Jones S, Colley J, Maynard J, Idziaszcyk S, Humphreys V,
Arnold J, Donaldson A, Eccles D, Ellis A, Evans D G, Frayling
I M, Hes F J, Houlston R S, Maher E R, Nielsen M, Parry
S, Tyler E, Moskvina V, Cheadle J P, Sampson, J R
(2008)
Inherited disposition to colorectal
adenomas caused by multiple rare allelles of
MUTYH but not OGG1, NUDT1, NTH1 or NEIL 1, 2 or 3.
Gut
Sept;57(9):1252-5.
- Wilson, C., Idziaszczyk, S., Colley,
J., Humphreys, V., Guy, C., Maynard, J., Sampson, J.R.,
Cheadle, J.P. (2005)
Induction of renal tumorigenesis with
elevated levels of somatic loss of heterozygosity in Tsc1+/-
mice on a Blm-deficient background.
Cancer Res. 15;65(22):10179-82. Link
to Pubmeb
- Wilson C, Bonnet C, Guy C, Idziaszczyk
S, Colley J, Humphreys V, Maynard J, Sampson JR, Cheadle
JP.(2006)
Tsc1 Haploinsufficiency
without Mammalian Target of Rapamycin Activation Is Sufficient
for Renal Cyst Formation in Tsc1+/- Mice.
Cancer Res. 66(16):7934-8.
Link
to Pubmed
- Archer HL, Evans JC, Edwards
S, Colley J, Newbury-Ecob R, O'callaghan F, Huyton M, O'
Regan M, Tolmie J, Sampson J, Clarke AJ, Osborne J. (2006)
CDKL5 mutations cause infantile spasms,
early onset seizures and severe mental retardation in female
patients.
J Med Genet. 2006 Apr 12. Link
to Pubmed
- Colley,
J., Jones, S., Dallosso A.R., Maynard, J.H., Humphreys,
V., Dolwani, S., Sampson, J.R. & Cheadle, J.P. (2005)
Rapid recognition of aberrant
dHPLC elution profiles using the Transgenomic NavigatorTM
software.
Human Mutation 26(2):165. Link
to Pubmed
- Evans, J.C., Archer, H.L., Colley,
J.P., Ravn, K., 3 , Bieber Nielsen, J. , Kerr, A., Williams,
E., Christodoulou, J., Gécz, J., Jardine, P.E., Wright
M.J., Pilz, D.T. , Lazarou, L., 1 , Cooper, D.N. , Sampson,
J.R., Butler, R., Whatley, S., Clarke. A.J. (2005)
Early onset seizures and
Rett-like features associated with mutations in CDKL5.
European Journal
of Human Genetics , 13(10):1113-20. Link
to Pubmed
- Ridley, A.J., Colley, J., Wynford-Thomas,
& Jones, C.J. (2005).
Characterisation of novel
mutations in Cockayne syndrome type A and xeroderma pigmentosum
group C subjects.
Journal of Human Genetics 50(3):151-154. Link
to Pubmed
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| Genomic
Facility Personnel |
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James Colley – Genomic
Facility Manager
Tel: (029) 2074 4008
E-mail: GenomicsWGP@cardiff.ac.uk
Vikki Humphreys- Genomic Research Officer
Julie Maynard- Genomic Research Officer
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| Further Information |
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| For details on the facility
and cost estimates please contact James
Colley. |
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