What Can the New Gene Tests Tell Us?

Some Currently  
Available DNA-Based 
Gene Tests      

Gene tests for the disorders listed below were available as of 1996 from clinical genetics laboratories approved by New York State. Test names and a description of the diseases or symptoms thereof appear in parentheses. Susceptibility tests are noted by an asterisk and provide only an estimated risk for developing the disorder.      

• Alpha-1-antitrypsin deficiency (AAT; emphysema and liver disease) 
• Amyotrophic lateral sclerosis (ALS; Lou Gehrig's Disease; progressive motor function loss leading to paralysis and death) 
• Alzheimer's disease* (APOE; late onset variety of senile dementia) 
• Ataxia telangiectasia (AT; progressive brain disorder resulting in loss of muscle control and cancers) 
• Gaucher disease (GD; enlarged liver and spleen, bone degeneration) 
• Inherited breast and ovarian cancer* (BRCA 1 and 2; early onset tumors of breasts and ovaries) 
• Hereditary nonpolyposis colon cancer* (CA; early onset tumors of colon and sometimes other organs) 
• Charcot-Marie-Tooth (CMT; loss of feeling in ends of limbs) 
• Congenital adrenal hyperplasia (CAH; hormone deficiency; ambiguous genitalia and male pseudohermaphroditism) 
• Cystic fibrosis (CF; disease of lung and pancreas resulting in thick mucous accumulations and chronic infections) 
• Duchenne muscular dystrophy/Becker muscular dystrophy (DMD; severe/mild muscle wasting, deterioration, weakness) 
• Dystonia (DYT; muscle rigidity, repetitive twisting movements) 
• Fanconi anemia, group C (FA; anemia, leukemia, skeletal deformities) 
• Factor V-Leiden (FVL; bleeding disorder) 
• Fragile X syndrome (FRAX; leading cause of inherited mental retardation) 
• Hemophilia A and B (HEMA and HEMB; bleeding disorders) 
• Huntington disease (HD; usually midlife onset; progressive, lethal, degenerative neurological disease) 
• Myotonic dystrophy (MD; progressive muscle weakness; most common form of adult muscular dystrophy) 
• Neurofibromatosis type 1 (NF1; multiple benign nervous system tumors that can be disfiguring; cancers) 
• Phenylketonuria (PKU; progressive mental retardation due to missing enzyme; correctable by diet) 
• Adult Polycystic Kidney Disease (APKD; kidney failure and liver disease) 
• Prader Willi/Angelman syndromes (PW/A; decreased motor skills, cognitive impairment, early death) 
• Sickle cell disease (SS; blood cell disorder; chronic pain and infections) 
• Spinocerebellar ataxia, type 1 (SCA1; involuntary muscle movements, reflex disorders, explosive speech) 
• Spinal muscular atrophy (SMA; severe, usually lethal progressive muscle wasting disorder in children) 
• Thalassemias (THAL; anemias - reduced red blood cell levels) 
• Tay-Sachs Disease (TS; fatal neurological disease of early childhood; seizures, paralysis) 

Lately we have learned a lot about our genetic legacy. We now know that, in fact, all diseases have a genetic component, whether inherited or resulting from the body's response to environmental stresses like viruses or toxins. The successes of the Human Genome Project (HGP) have even enabled researchers to pinpoint errors in genes--the smallest units of heredity--that cause or contribute to disease.   

The ultimate goal is to use this information to develop new ways to treat, cure, or even prevent the thousands of diseases that afflict humankind. But the road from gene identification to effective treatments is long and fraught with challenges. In the meantime, biotechnology companies are racing ahead with commercialization by designing diagnostic tests to detect errant genes in people suspected of having particular diseases or at risk for developing them.   

An increasing number of gene tests are becoming available commercially (SEE BOX: Some Currently Available DNA-Based Gene Tests), although the scientific community continues to debate the best way to deliver them to a public and medical community that are unaware of their scientific and social implications. While some of these tests have greatly improved and even saved lives, scientists remain unsure of how to interpret many of them. Also, patients taking the tests face significant risks of jeopardizing their employment and/or insurance status. And because genetic information is shared, these risks can extend beyond them to their family members as well.   

Even so, many more tests are in the works as dozens of new biotechnology companies vie to spin genetic data into gold. In the United States alone over four hundred laboratory programs aim to develop gene tests for disorders ranging from arthritis to obesity, and the list grows daily. The technology continues to advance rapidly, and future versions will allow simultaneous testing for hundreds of different genetic mistakes. The volume of available personal genetic data is on the brink of exploding, increasing the urgency of addressing ethical, legal, and social implications thereof. This was not unexpected. From its start over six years ago, HGP planners have dedicated at least 3 percent of the budget to grappling with just these issues.   

Beginning with a short introduction to ground the reader in the DNA science underlying gene tests, this article explains some of the tests, their limitations, and the extraordinary potential of DNA medicine for the twenty-first century.   

A GENETIC SCIENCE PRIMER   
A gene is simply a piece of DNA, the chemical responsible for storing and transferring all hereditary information in a cell. Genes accomplish this by containing recipes for making proteins, the true workhorses of all our trillions of cells. All living organisms are made up largely of proteins, which provide the structural components of all our cells and tissues as well as specialized enzymes for all essential chemical reactions. Through these proteins, our genes determine how well we process foods, detoxify poisons, and respond to infections. Although our cells have the same genes, not all genes are active in all cells. Heart cells synthesize proteins required for that organ's structure and function, liver cells make liver proteins, and so on.   

In humans and other higher organisms, a DNA molecule consists of two ribbon-like strands that wrap around each other, resembling a twisted ladder. The ladder rungs are made up of chemicals called bases, abbreviated A, T, C, and G. Each rung consists of a pair of bases, either A and T or C and G. We have three billion base pairs (six billion bases) of DNA in most of our cells; this is our genome. With the exception of identical twins, the sequence of the bases--the order of As, Ts, Cs, and Gs--is different for everyone, which is what makes each of us unique. Variation in base sequence, along with environmental factors, accounts for all our diversity, including disease.   

The DNA making up our genome is divided into tightly coiled packets called chromosomes, which reside in the nucleus of each cell. Each chromosome is a single DNA molecule, and lengths range from 50 million to 250 million bases. Scientists can distinguish the chromosomes by size, distinctive staining patterns, and other characteristics.   

Most cells have 46 chromosomes, 23 from each parent. A set of 23 contains 22 numbered chromosomes (1-22) plus either an X or Y sex-determining chromosome. Females receive an X from each parent, and males get one X and one Y. Sperm and egg cells only have 23 chromosomes, and mature red blood cells have none.   

Chromosomes are not continuous strings of genes. Genes are interspersed among millions of bases of DNA that do not code for proteins (noncoding DNA) and whose functions are largely unknown. In fact, genes constitute only a tiny fraction of the human genome, a mere 3 percent. Scientists estimate that we have about 60,000 to 80,000 genes, whose sizes range from fewer than one thousand to several million bases. We have two copies of every gene, one from each of our parents.  

 
FROM DIVERSITY TO DISEASE 
For all our outward variation, we are surprisingly alike at the DNA level. Differences account for only one tenth of 1 percent of our DNA (about three million base pairs). Yet DNA base sequence variations are responsible for all our physical differences and influence many of our other characteristics as well. Sequence variation can occur in our genes, and the resulting different forms of the same gene are called alleles. People can have two identical or two different alleles for a particular gene. Variation also occurs outside the genes in the noncoding part of our DNA.   

Mutations. While most DNA variation is normal, harmful sequence changes sometimes occur in our DNA that cause or contribute to disease. All DNA sequence changes--called mutations--are either passed down from parent to child (in the sperm or egg cells) or acquired during a person's lifetime. The vast majority of diseases are due to acquired changes, known as sporadic mutations. These mutations can arise spontaneously during normal functions, as when a cell divides, or in response to environmental stresses such as toxins, radiation, hormones, and perhaps even diet. Nature provides us with a system of finely tuned repair enzymes that find and fix most DNA errors. But as we age, our repair systems may become less efficient and allow us to accumulate uncorrected mutations. This can result in diseases such as cancer.   

Depending on where in our genome they occur, mutations can have devastating effects or none at all. If they are small and fall in the vast sea of noncoding sequences, no one might be the wiser. Changes within genes, however, can result in faulty proteins that function at less-than-normal levels or those that are completely nonfunctional, causing disease. (For a list of some of the most commonly inherited disorders, SEE BOX: Some of the Most Common Inherited Disorders).   

Sometimes only a tiny change in DNA sequence will lead to a serious disease. The substitution of just a single base, for example, leads to sickle cell anemia. Other diseases are caused by deletions or additions of single or multiple bases. Too many repetitions of a particular sequence of three DNA bases can doom a person to Huntington's disease, a fatal neurological disorder; Fragile X syndrome, the most common form of inherited mental retardation; or myotonic dystrophy, a muscle-wasting disease. Other diseases can result from large rearrangements of DNA.   

Some of the Most Common Inherited Disorders    

• Congenital heart defects (encompasses a variety of malformations) 
• Familial adenomatous polyposis (colon cancer) 
• Polycystic kidney disease 
• Hemochromatosis (iron storage disease) 
• Neural tube defects 
• Hypercholesterolemia 
• Diabetes, type 1 
• Breast and ovarian cancer 
• Cleft lip and palate 
• Down Syndrome 
• Fragile-X mental retardation 
• Sickle cell anemia 
• Cystic fibrosis 
• Duchenne Muscular Dystrophy 
• Hemophilia A 
• Marfan Syndrome 

For most diseases the causes are much more complex. The common scourges afflicting Western civilization are thought to be due to a variety of gene mutations, perhaps acting together, or to a combination of genes and environmental factors. Heart disease, diabetes, hypertension, cancers, Alzheimer's disease (AD), schizophrenia, and manic depression are all examples of complex diseases.   

Except for rare forms of these disorders that are inherited in some families, single mutated genes associated with complex diseases are not considered causative. Rather, they confer a susceptibility to their bearers and, given the right combinations of genes and environmental factors, will allow a disease to develop. Untangling the genetic and environmental contributions to complex disease will be one of the greatest challenges for medical researchers in the next century.   

Finding Disease Genes. To find a gene that is a likely candidate for involvement in disease, scientists must search for DNA changes that are linked only with people who have a particular disease. Searching randomly through three billion base pairs of DNA for tiny changes that may be linked with disease is no easy task. Scientists labored through 10 years of tedious, painstaking work to find the genes for both Huntington's disease and cystic fibrosis. Thanks to the HGP, researchers now have some guidance from chromosome maps. Generated within the last two years, these maps specify thousands of unique DNA regions that act as mile markers along the chromosomal highways. These types of markers, which form a grid of known locations across every chromosome, are especially informative to researchers searching for small differences in DNA sequence among the members of large families. The high-quality maps have dramatically sped up the discovery of disease genes, reducing the hunt from years (at a cost of several million dollars) to months in some cases.   

Luck plays an important part in any gene hunt. Researchers studying large families with several cases of an inherited disease scan the genomes of all family members for any changes in marker DNA sequence that correlate with the presence of disease. How long it takes to find a disease gene this way depends in large part on the particular markers chosen.   

In fall 1996, a region on chromosome 1 was found to be associated with a form of prostate cancer that runs in families. Researchers examined over 300 DNA marker regions in the genomes of some 100 families and compared the DNA sequences of affected individuals with healthy ones. The location of the implicated region containing the mutation was made available to the entire research community via the Internet. This region is now the focus of an intensive search for the causative gene by many groups around the world. Although the type of prostate cancer studied in these families is rare, researchers expect it will lead to insights into how the more common forms arise.   

Once the disease genes themselves or their approximate chromosomal regions are finally identified, academic and commercial laboratories often translate these findings into gene tests that can detect the particular mutations associated with a disease. 

Cheating the Fates: Making Healthy Babies Through Science    

 Several in vitro fertilization (IVF) clinics offer prospective parents who are at high risk for some genetic diseases (such as Tay Sachs and Huntington's disease) a way to ensure that they will not pass on the defective gene to their children. The clinics also offer them the option of remaining ignorant of their own genetic status, which many choose. After fertilization of the egg outside the mother's body, scientists test resulting embryos for gene mutations associated with a particular disease, and embryos without the mutation are selected preferentially for uterine implantation. Peace of mind does not come cheap, though. One company estimates that parents can expect to pay about $25,000 for one child conceived this way. 

• carrier screening, which involves identifying unaffected individuals who carry one copy of a gene for a disease that requires two copies for the disease to be expressed; 
• prenatal diagnostic testing; 
• newborn screening; 
• presymptomatic testing for predicting adult-onset disorders such as Huntington's disease; 
• presymptomatic testing for estimating a risk for developing adult-onset cancers and Alzheimer's disease; 
• confirmational diagnosis of a symptomatic individual; and 
• forensic/identity testing. 

Gene testing already has dramatically improved lives. Some tests are used to clarify a diagnosis and direct a physician toward appropriate treatments, while others allow families to avoid having children with devastating diseases (SEE BOX: Cheating the Fates) or identify people at high risk for conditions that may be preventable. Aggressive monitoring for and removal of colon growths in those inheriting a gene for familial adenomatous polyposis, for example, has saved many lives. On the horizon is a gene test that will provide doctors with a simple diagnostic test for a common iron storage disease, transforming it from a usually fatal condition to a treatable one.(SEE BOX: A Twenty-first Century Diagnostic Meets a Dark Ages Treatment). 

A Twenty-first Century Diagnostic Meets a Dark Ages Treatment   
 
In the summer of 1996, researchers reported finding a gene flaw associated with hemochromatosis, a common hereditary disorder characterized by excess iron storage. Hemochromatosis appears in midlife, when the iron that has accumulated in various organs begins to wreak damage resulting in a range of problems from diabetes and cirrhosis to liver cancer and cardiac dysfunction. A simple and effective treatment has been available for centuries: excess iron is depleted through bloodletting, or phlebotomy. But diagnosis is difficult, and if the condition is left untreated, an early death will ensue. Yet when the disease is identified at an early stage, life expectancy can be normal.    

Because it is one of the most common inherited diseases, and easily treated if diagnosed early (or even prevented in siblings and children of those affected), this disease stands as a model of the great potential of gene-based diagnostics. 

A limitation of all medical testing is the possibility for laboratory errors. These might be due to sample misidentification, errors resulting from contamination of the chemicals used for testing, or other sources.   

Many in the medical establishment feel that uncertainties surrounding test interpretation, current lack of available medical options for these diseases, their potential for provoking anxiety, and risks for discrimination and social stigmatization could outweigh the benefits of testing. Some complexities of current gene tests are outlined below in discussions of tests for Huntington's disease and cystic fibrosis, two disorders caused by single-gene defects, and the tests that may detect predispositions to the more complex Alzheimer's disease and breast cancer.   

Huntington's Disease (HD). The test for HD costs about $275 not including the costs for doctor and genetic counseling appointments, which can run several thousand dollars. It predicts with chilling certainty the future development of this devastating neurological condition that strikes in midlife, causing progressive and unrelenting physical and mental deterioration. While taking the genetic test would help high-risk people--those with an affected parent--better plan their lives, the great majority choose not to be tested when they understand all the implications. These include the psychological impact of knowing that they will (or will not) get the disease, the absence of preventive treatments, and the risk of affecting insurance and employment status.   

Cystic Fibrosis (CF). Although CF is also a single-gene disease, the issues involved in testing for mutations in this large gene are much more complex than those for HD. An astounding six hundred mutations have been found, and few correlations have been made between specific mutations and disease severity. In its most severe form, CF causes an accumulation of thick mucus in the lungs, creating an ideal breeding ground for bacteria, and damage to the gastrointestinal and reproductive systems. Someone with a mild form might have a tendency toward bronchitis.   

Interpretation of a positive test is difficult, as it usually cannot predict the severity of the disease. Sometimes the disease is diagnosed in people who had no previous clue that they were "genetically ill." Another limitation of current CF gene tests is that they probe for only the most common mutations. (An example is one DNA testing company that tests for 70 CF mutations for $150.) A negative test, therefore, could not rule out CF. These limitations pose difficult quandaries for people making reproductive decisions. They gain little information in return for the costs, including social risks, involved in testing.   

Early this year an independent consensus panel sponsored by the National Institutes of Health recommended that testing for CF gene mutations be offered as an option to pregnant couples and to those planning a pregnancy, as well as to those individuals with a family history of CF and partners of people with CF. The panel did not, however, advocate testing of newborns or those in the general population. Education, counseling, and informed consent were emphasized.   

Alzheimer's Disease (AD). Information available from the current susceptibility test for AD is even less informative. AD is a progressive brain disorder usually striking in mid- to late life and causing devastating memory loss and impaired thinking. There are two forms of AD. A rare, early-onset, simply inherited type (occurring between 35 to 60 years) accounts for about 5 percent of all cases. The much more common form of AD (sporadic AD), the subject of a controversial gene test, is a complex disease characterized by a later onset (around 70 to 80 years). Scientists believe it is caused by a combination of genes and environmental factors. The most common form of mental impairment of old age, sporadic AD now affects some four million people in the United States, and predictions are for fourteen million cases by 2040.   

Researchers have found three different forms (alleles) of a gene called ApoE that appears to modify the risk of developing sporadic AD. The ApoE gene codes for a protein, called apolipoprotein E, that appears to be involved with transporting cholesterol in the blood. People with the ApoE2 allele appear to be at lowest risk of AD, those with ApoE3 have an intermediate risk, and those with ApoE4 have the highest risk.   

A gene test for the ApoE alleles has been marketed to doctors since 1995 for $195. As a predictive test on healthy people, no definitive information can be gained because AD is known to develop without ApoE4, some people with ApoE4 never develop the disease, it cannot be used to predict age of onset or severity, and no current treatments or preventive methods are available. People being tested run the usual social risks concerning family and psychological issues, as well as insurance and employment discrimination. For these reasons, use of this test to predict a predisposition to AD has been discouraged by professional genetics groups.   

Breast Cancer. Predisposition tests for people at high risk for a rare, inherited form of breast cancer have been marketed to doctors and patients since 1996. Only about 10 percent of breast cancer cases are inherited (familial). The majority are sporadic, occurring in women with no family history of the disease. This year some 185,000 U.S. women will be diagnosed with breast cancer and 44,000 will die of it. The estimated lifetime risk of breast cancer for all U.S. women (without regard to family medical history) is 12 percent by age 65. No gene tests yet exist for diagnosing or determining a susceptibility to sporadic breast cancer, but at least 50 genes have been suggested for involvement in the disease.   

Mutations in two genes, called BRCA1 and BRCA2 (for BReast CAncer), have been implicated in the rare familial breast cancer. Research has suggested that women with a strong family history of the disease who carry these mutations run an increased risk of developing breast cancer, although just how much is the subject of continuing controversy. Some women with the mutations never develop breast cancer. Women with BRCA1 mutations also face a high risk of ovarian cancer compared with those in the general population. Men with BRCA1 mutations show no increased risk of breast cancer but a slightly increased risk of prostate cancer. Men with BRCA2 mutations have a slightly higher risk of breast cancer.   

Over two hundred mutations have been found in the BRCA1 and BRCA2 genes, and each family typically carries its own characteristic mutation.   

The tests for BRCA1 and BRCA2 run as high as $2,400 and can involve examination of more than 16,000 DNA base pairs for mutations. Researchers say interpreting the results is very difficult, as nothing is known about the risk associated with each mutation. Also, no proven preventive or management strategies exist, so doctors do not know what follow-up to recommend. Increased surveillance, including frequent mammograms, is a possibility, but studies have not shown their usefulness in women under 50. Some women opt to remove healthy breasts (or ovaries) as a preventive measure, although there can be no assurance that all tissue has been removed. Women taking the gene tests run the usual psychological and social risks already mentioned, and these risks will very likely reach their daughters as well.   

Because of profound uncertainties surrounding the breast cancer tests, their use outside the research laboratory has been discouraged by the American Society for Human Genetics and the National Breast Cancer Coalition, among others. In an editorial in The New England Journal of Medicine this spring, former NIH director Bernadine Healy noted that the use of the test in everyday clinical practice "violates a common-sense rule of medicine: don't order a test if you lack the facts to know how to interpret the result."   

On a more optimistic note for the future, researchers are now conducting clinical trials on advanced breast, ovarian, and prostate cancer patients using the normal version of the BRCA1 gene (SEE BOX: Using Genes to Treat Disease). While this research is at a very early stage, the hope is that this and other similar trials will pave the way to completely new ways of treating previously intractable diseases and usher in an age of gene-based therapies. 

Using Genes to 
Treat Disease    

Researchers have taken an intriguing step toward developing new treatments for breast, ovarian, and prostate cancers. Last year, reports demonstrated that injecting a normal version of the BRCA1 gene could stop unwanted cell growth and inhibit tumor growth when introduced into human tumors grafted onto lab mice. Researchers are now testing the effects of injecting a normal BRCA1 gene into women with advanced breast and ovarian cancer and men with prostate cancer; this type of treatment is called gene therapy.

The goal of these and most current gene-therapy studies is not yet therapeutic; their primary objectives are to demonstrate safety of the procedure, not its efficacy. 

The potential for using genes themselves to treat disease--known as gene therapy--is the most exciting application of DNA science, and has captured the imaginations of the public as well as the biomedical community for good reason. This rapidly developing field holds great potential for treating or even curing genetic and acquired diseases, using normal genes to replace or supplement a defective gene or to bolster immunity to disease (e.g., by adding a gene that suppresses tumor growth). Over 150 clinical gene therapy trials are now in progress in the United States, most for different kinds of cancers. Performed on patients in advanced stages of disease, the goal of most current studies is establishing the safety of gene therapy rather than its effectiveness. The technology itself still faces many obstacles before it can become a practical approach for treating disease.   

The atlas of human biology generated by the HGP will provide an enormous store of genes for studying, and ultimately preventing, the ills that beset us. As the factors underlying the maladies and vagaries of the human condition slowly come to light, the challenge will be to use the information responsibly.