May 2007 | Back to Table of Contents
Clinical and Health Affairs
Genetic Tests Physicians Should Know
By Kara Mensink, M.S., and Matthew Ferber, Ph.D.
Abstract
Seven years after completion of the human genome draft sequence, significant advances have been made in genetic testing. This article highlights some of the newest and most important genetic diagnostic and screening tests to come to market in recent years. Application of these tests to clinical practice is also discussed.
With the June 2000 announcement that the human genome draft sequence had been completed, the medical profession eagerly anticipated a revolution in medicine whereby many common disorders could be diagnosed with a simple and inexpensive “gene” test. Nearly 7 years after this landmark discovery, advancements continue to be made, expanding physicians’ ability to diagnose and treat common and esoteric disorders.
In an effort to provide the best patient care and embrace the trend toward individualized medicine, many laboratories, both academic and commercial, have expanded their genetic testing menus. For busy practitioners, keeping up with each of these new tests can be daunting. To respond to their needs, laboratories, including Mayo Medical Laboratories, employ laboratory directors and genetic counselors who are knowledgeable about both the clinical and technical aspects of genetic testing.
In addition to the staff at testing facilities, the Internet has become a valuable tool for finding information about genetic testing. A government-sponsored website, www.genetests.org, allows providers to search for specific genetic disorders and read a comprehensive review of each disease. They can then search for laboratories that test for such disorders and compare their testing methodologies. The site also provides links to the individual labs so users can find out how to order tests.
Although much of the practical impact of genetic testing on clinical practice remains to be seen, changes in the approach to patient diagnosis and management are already underway. In this article, we list some of the newest and most clinically relevant genetic screening and diagnostic tests. Their use affects a broad spectrum of medical specialists, from clinical geneticists to general practitioners.
Newborn Screening
The introduction and application of tandem mass spectrometry technology has increased the number of disorders for which newborns are screened from only a handful in the 1990s to 30, or even 40, in some states today. Consequently, many more newborns are being diagnosed with heritable disorders and disease outcomes have significantly improved. States around the country are mobilizing their resources to ensure that the parents of infants with positive newborn screens are connected with knowledgeable health care providers so appropriate diagnostic testing and follow-up measures can be taken. Specific guidelines in the form of algorithms describe appropriate short-term steps for the follow-up care of infants who screen positive for any of the disorders included in the newborn screen. Those algorithms are available on the American College of Medical Genetics website, www.acmg.net/resources/policies/ACT/condition-analyte-links.htm. The Minnesota Department of Health has teamed with the Mayo Biochemical Genetics Laboratory to screen all newborns in the state for more than 40 genetic disorders.
Cancer Screening
Between 5% and 10% of cancers are caused by an individual having inherited a gene that imposes an increased risk for cancer. However, all cancers, both inherited and acquired, are ultimately the result of genetic mutations. Thus, genetic testing is used to evaluate individuals who have cancer or are at risk for the disease. The following tests have been developed for assistance with screening and diagnosis, establishing an accurate prognosis, and individualizing the treatment of patients with acquired (noninherited) cancers and germline (inherited) cancer syndromes.
♦ Acquired Cancers
HER-2/neu Amplification Associated with Breast Cancer. HER-2/neu is an oncogene on the long arm of chromosome 17 that is amplified in approximately 25% to 30% of breast cancers. This test is useful for determining the prognosis for and management of patients with ductal breast cancers, as amplification or overexpression of HER-2/neu is associated with shorter disease-free survival in patients who are node-negative and poorer overall survival of those who are node-positive. In addition, patients with HER-2/neu gene amplification or overexpression appear to respond better to cyclophosphamide/doxorubicin/5-fluorouracil (CAF) chemotherapy than patients whose tumors do not exhibit HER-2/neu amplification or overexpression and are candidates for treatment with the drug Herceptin.
Imatinib (Gleevec) Responsive Genes. Several clinical studies have demonstrated that malignancies displaying overexpression of ABL, ARG, PDGFRA, and PDGFRB are often responsive to treatment with imatinib mesylate (Gleevec), a drug that specifically targets overexpression of these tyrosine kinases. This test is helpful for establishing prognosis and monitoring treatment of many myeloid malignancies associated with these aberrantly expressed genes including acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), hypereosinophilic syndrome/systemic mast cell disease, and atypical chronic myeloproliferative disorders.
JAK2 V617F Evaluation. Testing for this mutation in the JAK2 gene assists in diagnosing many chronic myeloproliferative disorders (CMPD), including polycythemia vera, essential thrombocythemia, and chronic idiopathic myelofibrosis. JAK2 mutation testing allows clinicians to distinguish reactive conditions from non-CML CMPDs. However, the significance of JAK2 mutation analysis as a prognostic tool for patients with CMPD remains
unclear.
Thiopurine Methyltransferase (TPMT) Deficiency. Children with TPMT deficiency are at risk for life-
threatening immunosuppression associated with the use of Azathioprine (Imuran) and 6-mercaptopurine (6-MP), drugs commonly used for the treatment of acute lymphoblastic leukemia (ALL). Children with ALL should be screened for such deficiency before being prescribed a treatment regimen.
Uridine diphosphate-glycuronosyl transferase 1A1 (UGT1A1) Gene Sequencing. Results of this test are useful for the management of patients with certain solid tumors for which irinotecan is being considered as a possible therapy. The UGT1A1 protein is involved in the metabolism of irinotecan, a chemotherapeutic agent commonly used to treat solid tumors of the colon, rectum, and lung. Individuals with impaired UGT1A1 activity are at risk for life-threatening side effects, including severe diarrhea and neutropenia, if they receive irinotecan.
♦ Inherited Cancers
Familial Adenomatous Polyposis (FAP) Diagnostic Testing by APC Gene Sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). APC gene sequencing and MLPA are estimated to detect the causative mutation in 90% to 95% of individuals affected with classic FAP. Detection of a disease-causing mutation in the APC gene can be used to confirm a diagnosis of FAP in an affected individual and to determine carrier status for at-risk family members. Patients diagnosed with FAP benefit from genetic counseling, prophylactic surgery, and cancer surveillance. For individuals who are at risk, molecular genetic studies can help refine risk estimates and determine an appropriate cancer surveillance regimen.
Hereditary Nonpolyposis Colorectal Cancer (HNPCC) Screening and Diagnostic Testing. Approximately 2% of all colon cancers are caused by germline mutations involving genes associated with HNPCC. Identification of affected individuals allows for presymptomatic testing of family members who may be at risk and provides management guidance for individuals who are affected. For example, if a woman is found to have HNPCC after being diagnosed with colon cancer, she should undergo screening for other HNPCC-related cancers.
Several tests are available for screening and diagnosing HNPCC. To maximize the benefits of testing in the most cost-efficient manner, the tumor from an affected individual should first be screened for features consistent with HNPCC. These tests include immunohistochemical staining for mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2), microsatellite instability testing, BRAF V600E mutation testing, and hypermethylation of the hMLH1 gene promoter.
Depending on the results of tumor screening, appropriate germline testing by DNA sequencing and MLPA can be performed. If a causative germline mutation is identified, the diagnosis of HNPCC is confirmed, and appropriate medical management can be initiated. Additionally, asymptomatic at-risk family members can then be tested to more accurately assess their risk for HNPCC.
Carrier Screening
Certain autosomal recessive disorders are known to be more prevalent in specific ethnic populations. As a result, carrier screening for these disorders had been developed for the purposes of identifying couples and pregnancies at risk for developing these diseases. The American College of Obstetrics and Gynecology (ACOG) has published recommendations to assist providers in determining who should be offered carrier screening for certain disorders.
Cystic Fibrosis. ACOG practice guidelines (Number 325, December 2005) state that all Caucasian women, including those who are Ashkenazi Jews, should be offered carrier screening prior to conception for mutations within CFTR, the gene associated with cystic fibrosis. Detection rates by current molecular population screening techniques are ethnic-specific. Laboratories performing this testing offer residual risk calculations based on the patient’s reported ethnicity and family
history.
Carrier Screening for Disorders among Ashkenazi Jews. ACOG practice guidelines (Numbers 298, August 2004, and 318, October 2005) state that all Ashkenazi Jewish couples should be offered carrier screening for Tay-Sachs disease, Canavan disease, cystic fibrosis, and familial dysautonomia. The guidelines also suggest that all Ashkenazi Jewish couples should be made aware that carrier screening is available for mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia group C, Bloom syndrome, and Gaucher disease. Laboratories offer tests for a variety of combinations of diseases and provide reports that give physicians the necessary information to accurately counsel couples about the risk for such disorders to a pregnancy.
Screening for Endocrine Disorders
Calcium-sensing receptor (CASR) gene mutation screening is useful for proper diagnosis and treatment of disorders of abnormal serum calcium regulation such as familial hypocalciuric hypercalcemia, neonatal severe primary hyperparathyroidism, autosomal dominant hypoparathyroidism, idiopathic hypoparathyroidism, and Bartter’s syndrome.
Testing for Coagulation Defects
Factor V Leiden (R506Q) mutation testing is recommended for medical management of patients with Factor V Leiden deficiency. The presence of this common factor V Leiden mutation poses a risk for venous thromboembolism (VTE), deep-vein thrombosis, and pulmonary embolism and may be a risk factor for complications of pregnancy. In addition, management recommendations for duration of anticoagulation therapy may be influenced by the presence of the R506Q mutation in patients with a history of VTE.
Von Willebrand disease Type 2 N (Normandy) mutation testing allows for proper diagnosis, genetic counseling, and medical management of individuals with mild reduction in factor VIII activity. It is especially useful for distinguishing persons with mild hemophilia A from those with von Willebrand disease. As many as 5% of patients diagnosed with mild hemophilia A are actually found to have a genetic mutation consistent with von Willebrand disease.
Pharmacogenomic Testing
Pharmacogenomic testing allows for the identification of genetic risk factors associated with drug metabolism. It does not assist providers with establishing a specific diagnosis; rather it assists by guiding management and treatment decisions.
CYP2D6 testing helps predict the way a patient metabolizes drugs that are modified by the CYP2D6 enzyme. Such drugs include many antidepressants and tamoxifen, an adjuvent medication commonly prescribed for women with estrogen-receptor positive breast cancer.
CYP2C9 testing can provide information about a person’s ability to metabolize drugs that are modified by CYP2C9. Such drugs include, but are not limited to, fluoxetine, oral hypoglycemic agents and sulfonylureas, NSAIDS, warfarin, and antiepileptic drugs.
CYP2C19 testing is useful for predicting a patient’s ability to metabolize drugs that are modified by CYP2C19. Such drugs include, but are not limited to, anti-ulcer drugs such as omeprazole, anti-seizure drugs such as mephenytoin, the anti-malarial proguanil, the anxiolytic diazepam, the beta-blocker propranolol, and the antidepressants fluvoxamine and fluoxetine.
Conclusion
Most providers agree that genetic testing is the pathway to individualized medicine. However, the swift pace of clinical research, test development, and clinical practice is constantly challenging their ability to stay informed. As research and development continue to move forward, translation to clinical practice will become easier, yielding a system that is adept at implementing the newest discoveries in a relatively short time. Although the past 7 years have been fruitful, the coming years promise to be even more productive. MM
Kara Mensink is a board-certified genetic counselor in the Molecular Genetics Laboratory and Multidisciplinary Neurofibromatosis Clinic. Matthew Ferber is co-director of the Molecular Genetics Laboratory at Mayo Clinic.