Certain
SNP's correlate with the toxicity conferred by chemotherapeutic
agents. The Geneblitz® genotyping service is pleased to offer
genetic testing for the following genes, with their cognate chemotherapeutic.
| Gene |
Drug |
| Dihydro
pyrimidine dehydrogenase (DPD) |
5-Flurouracil
(5-FU) |
| Thymidylate
synthase (TS) |
5-Flurouracil
(5-FU) |
|
Methylene tetrahydrofolate reductase (MTHFR) |
Methotrexate (MTX) |
| Thiopurine
methyl transferase (TPMT) |
6-Mercaptopurine
(6-MP) |
DPD and 5-FU
Upon
administration, 5-FU is normally metabolised by DPD. Polymorphisms
in DPD, most notably the splice site SNP IVS14+1G>A can reduce
the activity of this enzyme.
Between
80 and 90% of the drug is degraded by DPD and if present in reduced
amounts, e.g. due to polymorphism then lowered levels of DPD can
have two effects:
a)
a decrease in 5-FU clearance and a consequential increase in exposure
to the drug results in toxicity
b) an increase in the efficiency of 5-FU in the tumour.
We offer a genotyping assay for the splice site SNP in DPD as
indicated above.
TS
and 5-FU
If
not metabolised by DPD, 5-FU is converted to 5-flurodeoxuridine,
an inhibitor of TS. Certain repeat sequences in the promoter region
of the TS gene correlate with clinical outcome, with fewer repeats
resulting in decreased expression of TS. As before, this will
increase the toxicity due to 5-FU and will increase the efficacy
of the drug in the tumour issue.
We
offer a genotyping assay for the number of repeats in the TS promoter.
MTHFR
and MTX
MTX
toxicity occurs in patients with a homozygous polymorphism (C677T)
in MTHFR gene. This polymorphism occurs in around 10 to 12% of
the population and reduces the activity of the MTHFR enzyme which
in turn increases the potency of MTX. Genotype data may allow
the use of reduced doses of antifolates and hence reduce toxicity.
We
offer a genotyping assay for the C677T polymorphism in MTX.
TPMT
and 6-MP
The
anti leukaemia 6-MP is activated in vivo to 6 thioguanosine in
part using a pathway involving TPMT. Polymorphisms in TPMT correlate
with reduced TPMT activity, increased 6-MP levels and 6-MP induced
toxicity. When genotype data is applied to dosing regimens, reduced
dosing allows TPMT deficient patients to tolerate 6-MP therapy
without toxicity.
We
offer genotyping assays for the following spectrum of TPMT SNP's:
| TPMT
designation |
Nucleotide |
Protein |
| *2 |
238
G to C |
Ala
80 Pro |
| *3A |
460
G to A |
Ala
154 Thr |
| |
719
A to G |
Tyr 240 Cys |
| *3B |
460 G to A |
Ala 154 Thr |
| *3C
|
710
A to G |
Tyr
240 Cys |
| *4 |
IVS9AS
G to A -1 |
No effect |
| *8 |
644
G to A |
Arg
15 His |
Transcriptional profiling of tumour issue
The
intratumour levels of DPD, TS and Thymidine phosphorylase (TP)
can be used to predict responsiveness to treatment with 5-FU/leukovorin.
Using
our Taqman® System for analysis of gene expression, we profile
a service to determine the levels of these particular mRNA's.
Freshly excised and frozen (liquid nitrogen) samples will be required.
| Low
intratumoral mRNA levels of: |
%
Response rate |
| TS |
57 |
| TS
and TP |
79 |
| TS
and DPD |
92 |
| TS,
TP and DPD |
100 |
Other
cancer associated genes
For
tumour analysis we offer a range of SNP genotyping assays (including
for example p53, Ha-, Ki-, N-ras), assays for other polymorphisms
(e.g. LOH, if we can use a microsatellite based PCR reaction to
distinguish the maternal and paternal alleles) and gene amplifications
(including for example c-myc and N-myc). For example, in the case
of p53 we offer the following series of genotyping assays:
Allelic
Variants of p53
| Nucleotide |
Protein |
Association
(where known) |
Nucleotide |
Protein |
Association
(where known) |
| C
to T |
Arg 248 Trp |
|
A
to T |
Lys
120 Ter |
Osteosarcoma |
| G
to A |
Glu
258 Lys |
|
C
to T |
Arg
282 Trp |
Osteosarcoma |
| G
to T |
Gly
245 Lys |
|
G
to A |
Gly
245 Ser |
Osteosarcoma |
| T
to C |
Leu
252 Pro |
|
G to A |
Arg
273 His |
Thyroid Carcinoma |
| C
to G |
Pro
72 Arg |
|
G
to T |
Gly
325 Val |
|
| G
to T |
Arg
249 Ser |
Hepatocellular
Carcinoma |
C
to T |
Arg
282 Trp |
Osteosarcoma |
| G
to T |
Val
157 Phe |
Hepatocellular
Carcinoma |
G
to A |
Arg
181 His |
Breast
cancer |
| G
to A |
Cys
242 Tyr |
|
G
to C |
Arg
280 Thr |
Nasopharyngeal
Carcinoma |
| G
to A |
Gly
245 Asp |
|
C
to A |
Pro
151 Thr |
Breast
cancer |
| G
to A |
Arg
248 Gln |
Osteosarcoma |
C
to T |
Pro
151 Ser |
Breast
cancer |
| T
to C |
Met
133 Thr |
|
G
to T |
Leu
35 Phe |
Pancreatic
cancer |
| G
to T |
Val
272 Teu |
|
T
to A |
Leu
257 Gln |
Multiple
malignancy |
| |
Ser
241 Phe |
Osteosarcoma |
G
to A |
Arg
175 His |
|
| Insert
C |
1BPIns,151C |
|
T
to C |
Leu
344 Pro |
|
| Del
2 bases |
2 BP Del, 209-210 |
Histiocytoma |
G
to C |
Ala
138 Pro |
|
| |
1
BP Ins |
Osteosarcoma
|
|
|
|
| |
Codon
71-72 |
|
|
|
|
We
undertake projects which require investigation of associated oncogenes,
polymorphisms and SNP's and analyse these in any number of your
samples, clinical or otherwise. Together with our transcription
profiling service, this represents a comprehensive set of tests
whereby you can rapidly obtain tumour genotyping and expression
data.
We also offer
services such as Residual
DNA Testing, Genotyping,
Forensic
Testing, Gene
Expression and various
other services. Please click
here
to contact us with your requirements.
We
are reliable,
responsive and cost effective.
