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Integration of Molecular Diagnostics
Integration of Molecular Diagnostics
Key Words: Personalized medicine; Molecular diagnostics; Pharmacogenomics; Pharmacogenetics; Toxicogenomics; Cancer predisposition;
Productivity
DOI: 10.1092/VMLL66Y5KHQ35KUE
❚Table 1❚
Estimated Worldwide Molecular Diagnostics Markets*
By diagnostic technique
DNA probes 240 400 850
Polymerase chain reaction–based 1,450 2,200 4,350
Fluorescence in situ hybridization 600 850 2,350
Arrays 400 1,300 3,300
Others 450 750 1,150
Total 3,140 5,500 12,000
By clinical setting
Infections 2,080 2,920 5,100
Cancer 337 900 1,900
Genetic tests 320 792 2,007
Food supply testing 110 198 400
Others 293 690 1,593
Total 3,140 5,500 11,000
* Modified from Jain KK. Molecular Diagnostics: Technologies, Markets, Companies. Basel, Switzerland: Jain PharmaBiotech Publications; 2002. Data are given in millions of
US dollars.
❚Table 3❚
Genetically Prescribed Medications
APOE-4, apolipoprotein E, epsilon 4; BRCA, breast cancer; CETP, cholesteryl ester transfer protein; HMG-CoA, 3-hydroxy-3-methylglutaryl coenzyme A; TPMT, thiopurine S-
methyltransferase.
more effective health care for all individuals whether well Disease outcome
Disease Management
y
or in the early or late stages of illness.
og
Symptom Severity
ol
Genetic variants can be used to predict the predisposi- Monitoring
th
ar
Pharmacogenomic
ul
cancer ❚Table 4❚. Preventive therapies currently in use for a
ec
ol
Clinical
M
variety of diseases include selective estrogen receptor modu- Prognostic
symptoms
lators for patients at risk for breast cancer 18 and
Normal Screening Subclinical
osteoporosis19 and statins for people at risk for developing
health disease process
coronary artery disease.20 Predisposition
Time
❚Table 4❚
Cancer Predisposition and Tumor Suppressor Genes
for complex diseases such as asthma, diabetes mellitus, Prediction of Drug Efficacy
atherosclerosis, and psychiatric disorders. In oncology, SNP The application of genotyping strategies to predict anti-
technology has focused on detecting the predisposition for cancer drug efficacy has emerged in a variety of clinical
cancer, predicting toxic responses to drugs, and selecting the settings.35-39 Genotype resistance testing of HIV isolates has
best individual and combination anticancer drugs. demonstrable clinical usefulness and provides a way to assist
therapeutic decision making for patients whose HIV RNA
Cancer Predisposition Testing levels are rising.40 In colorectal cancer, pretreatment geno-
SNP genotyping and gene sequencing (see “Predisposi- typing on peripheral blood samples is being used to select
tion, Screening, and Early Diagnosis of Disease”) have therapy based on the prediction of resistance associated with
revealed a variety of familiar cancer predisposition certain genetic polymorphisms.39
syndromes (Table 4) based on single and multiple gene vari-
ants.24-27 Genotyping has been introduced widely for the
detection of familial cancers of the breast, ovary, and colon;
Pharmacogenomics
melanoma; and multiple endocrine neoplasia.26,28-30
Pharmacogenomics can best be defined as the applica-
Prediction of Drug Toxicity tion of whole genome technologies (eg, gene and protein
One of the earliest applications of SNP genotyping in expression data) for the prediction of the sensitivity or
cancer management was the discovery of variations in drug resistance of an individual’s disease to a single drug or
metabolism associated with genomic variations in drug- group of drugs.41,42
metabolizing enzymes such as the cytochrome system.31-33
Other detoxification pathways associated with SNP-based Transcriptional Profiling and Genomic Microarrays
variations in drug metabolism have been described,32-34 but, The development of printed and spotted genomic
in comparison with the cytochrome gene system, these microarrays has permitted the rapid accumulation of new
markers have not achieved substantial clinical usefulness. information about gene mutation and expression in human
The potential clinical value of the pharmacogenetics malignant neoplasms.43-50 Microarrays can be used to deter-
approach for predicting drug toxicity will be revealed as mine gene mutations and SNPs and to provide rapid
more candidate polymorphisms are discovered. screening information about messenger RNA expression. In
transcriptional profiling, the relative expression levels of of anticancer drugs has been used as a guide to anticancer
messenger RNA of both characterized and novel genes drug therapy. 50-56 By using cDNA microarrays, several
from a tumor can be compared with the gene expression groups have reported their success at discovering gene
status of a reference sample. Reference samples can expression that can be linked to resistance and responsive-
include cell lines, normal tissues, and cancer precursor ness to standard-of-care chemotherapy.57,58 During the next
lesions. 43-50 Transcriptional profiling has the ability to several years, the ability of this approach to personalize the
generate hundreds of thousands of data points, and it treatment of newly diagnosed cancer patients with individu-
requires sophisticated and complex information systems for alized selection and dosage of chemotherapeutic agents will
accurate and useful data analysis. Complementary DNA be tested on a large scale.
(cDNA) microarrays were introduced during the mid-
1990s51 and have achieved widespread use for the expres-
sion profiling of human clinical samples and in drug and
Pharmacodynamics
biomarker target discovery. The microarray technique has
generated a wealth of new information in the fields of In addition to the pharmacogenetic and pharmacoge-
leukemia and lymphoma and solid tumor classification, nomic tests, a series of bioassays, gene expression profiles,
drug and biomarker target discovery, and pharmacoge- and tissue-based biomarkers have emerged to guide the
nomic drug efficacy testing43-50 ❚Image 1❚. Oligonucleotide dosage, timing, and route of administration for novel thera-
❚Image 1❚ Breast cancer complementary DNA (cDNA) microarray results evaluated by hierarchical gene cluster analysis for defining
specific gene expression signatures. Hierarchical clustering algorithm permits the clustering of individual tumor profiles on the
basis of their similarities to their coexpression with the estrogen receptor alpha gene. Each row represents a tumor and each
column a single gene. Red indicates up-regulation; green, down-regulation; and black, no change in relative gene expression.
A B
130
predisposition,28-30,88 to screen for malignant and nonmalig- 110
nant diseases,89-92 and to facilitate diagnosis of early and 90
70
recurrent disease ❚Figure 2❚ and ❚Image 3❚ when therapy can 50
be most effective.93,94 High-throughput proteomic profiling 30
10
has emerged as a potential breakthrough in early disease –10
–30
detection and therapy monitoring.95-98 A recent serum-based – 50
1 5 10 15 20 25 30 35 40
study using the surface-enhanced laser desorption ionization
CT Number of PCR Cycles
technique combined with self-learning, computer pattern
recognition software successfully detected early stage
ovarian cancer with high sensitivity and specificity. 99 ❚Figure 2❚ Micrometastasis detection of breast cancer in a
Biomedical and function imaging including computed sentinel axillary lymph node biopsy specimen. Real-time
tomography, magnetic resonance imaging, and positron polymerase chain reaction (PCR; TaqMan, Applied
emission tomography scanning also have contributed major Biosystems, Foster City, CA) detection of cytokeratin 19
advances in the early detection of disease ❚Image 4❚ and in messenger RNA after 25 cycles of amplification (red)
the monitoring of therapeutic response.100 normalized to internal control dye (blue).
A B
❚Image 3❚ Micrometastasis detection of breast cancer in a sentinel axillary lymph node biopsy specimen. A, Section of half of a
❚Image 4❚ Metastatic prostate cancer in cervical lymph nodes. Radiolabeled indium scan using the J591 monoclonal antibody,
which detects the external domain of prostate-specific membrane antigen. The scan confirms that the initial clinical finding of a
neck mass was a cervical metastasis from prostate cancer. This patient subsequently had a significant (>50%) reduction in
serum prostate-specific antigen level in response to a single dose of yttrium 90 cytotoxic radio-conjugate of J591.
Acknowledgments: We are indebted to F. Symmans, MD, and 18. Jordan VC. Progress in the prevention of breast cancer:
L. Pustzai, MD, M.D. Anderson Cancer Center, Houston, TX; and concept to reality. J Steroid Biochem Mol Biol. 2000;74:269-277.
N. Bander, MD, New York Presbyterian Hospital, New York, NY, 19. Doren M, Samsioe G. Prevention of postmenopausal
for their collaborative efforts. osteoporosis with oestrogen replacement therapy and
associated compounds: update on clinical trials since 1995.
Hum Reprod Update. 2000;6:419-426.
20. Crouch MA. Effective use of statins to prevent coronary heart
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