Genetic Testing

A genetic test examines the genetic information contained inside a person's cells, called DNA, to determine if that person has or will develop a certain disease or could pass a disease to his or her offspring. Genetic tests also determine whether or not couples are at a higher risk than the general population for having a child affected with a genetic disorder.

Purpose

Some families or ethnic groups have a higher incidence of a certain disease than does the population as a whole. For example, individuals from Eastern European, Ashkenazi Jewish descent are at higher risk for carrying genes for rare conditions that occur much less frequently in populations from other parts of the world. Before having a child, a couple from such a family or ethnic group may want to know if their child would be at risk of having that disease. Genetic testing for this type of purpose is called genetic screening.

During pregnancy, the baby's cells can be studied for certain genetic disorders or chromosomal problems such as Down syndrome. Chromosome testing is most commonly offered when the mother is 35 years or older at the time of delivery. When there is a family medical history of a genetic disease or there are individuals in a family affected with developmental and physical delays, genetic testing may also be offered during pregnancy. Genetic testing during pregnancy is called prenatal diagnosis.

Prior to becoming pregnant, couples who are having difficulty conceiving a child or who have suffered multiple miscarriages may be tested to see if a genetic cause can be identified.

A genetic disease may be diagnosed at birth by doing a physical evaluation of the baby and observing characteristics of the disorder. Genetic testing can help to confirm the diagnosis made by the physical evaluation. In addition, genetic testing is used routinely on all newborns to screen for certain genetic diseases which can affect a newborn baby's health shortly after birth.

There are several genetic diseases and conditions in which the symptoms do not occur until adulthood. One such example is Huntington's disease. This is a serious disorder affecting the way in which individuals walk, talk and function on a daily basis. Genetic testing may be able to determine if someone at risk for the disease will in fact develop the disease.

Some genetic defects may make a person more susceptible to certain types of cancer. Testing for these defects can help predict a person's risk. Other types of genetic tests help diagnose and predict and monitor the course of certain kinds of cancer, particularly leukemia and lymphoma.

Precautions

Because genetic testing is not always accurate and because there are many concerns surrounding insurance and employment discrimination for the individual receiving a genetic test, genetic counseling should always be performed prior to genetic testing. A genetic counselor is an individual with a master's degree in genetic counseling. A medical geneticist is a physician specializing and board certified in genetics.

A genetic counselor reviews the person's family history and medical records and the reason for the test. The counselor explains the likelihood that the test will detect all possible causes of the disease in question (known as the sensitivity of the test), and the likelihood that the disease will develop if the test is positive (known as the positive predictive value of the test).

Learning about the disease in question, the benefits and risks of both a positive and a negative result, and what treatment choices are available if the result is positive, will help prepare the person undergoing testing. During the genetic counseling session, the individual interested in genetic testing will be asked to consider how the test results will affect his or her life, family, and future decisions.

After this discussion, the person should have the opportunity to indicate in writing that he or she gave informed consent to have the test performed, verifying that the counselor provided complete and understandable information.

Description

Genes and chromosomes

Deoxyribonucleic acid (DNA) is a long molecule made up of two strands of genetic material coiled around each other in a unique double helix structure. This structure was discovered in 1953 by Francis Crick and James Watson.

DNA is found in the nucleus, or center, of most cells (Some cells, such as a red blood cell, don't have a nucleus). Each person's DNA is a unique blueprint, giving instructions for a person's physical traits, such as eye color, hair texture, height, and susceptibility to disease. DNA is organized into structures called chromosomes.

The instructions are contained in DNA's long strands as a code spelled out by pairs of bases, which are four chemicals that make up DNA. The bases occur as pairs because a base on one strand lines up with and is bound to a corresponding base on the other strand. The order of these bases form DNA's code. The order of the bases on a DNA strand is important to ensuring that we are not affected with any genetic diseases. When the bases are out of order, or missing, then often times, our cells do not produce important proteins which can lead to a genetic disorder. While our genes are found in every cell of our body, not every gene is functioning all of the time. Some genes are turned on during critical points in development and then remain silent for the rest of our lives. While other genes remain active all of our lives so that our cells can produce important proteins that help us digest food properly or fight off the common cold.

The specific order of the base pairs on a strand of DNA is important in order for the correct protein to be produced. A grouping of three base pairs on the DNA strand is called a codon. Each codon, or three base pairs, comes together to spell a word. A string of many codons together can be thought of as a series of words all coming together to make a sentence. This sentence is what instructs our cells to make a protein that helps our bodies function properly.

Our DNA strands containing a hundred to several thousand copies of genes are found on structures called chromosomes. Each cell typically has 46 chromosomes arranged into 23 pairs. Each parent contributes one chromosome to each pair. The first 22 pairs are called autosomal chromosomes, or non-sex chromosomes and are assigned a number from 1–22. The last pair are the sex chromosomes and include the X and the Y chromosomes. If a child receives an X chromosome from each parent, the child is female. If a child receives an X from the mother, and a Y from the father, the child is male.

Just as each parent contributes one chromosome to each pair, so each parent contributes one gene from each chromosome. The pair of genes produces a specific trait in the child. In autosomal dominant conditions, it takes only one copy of a gene to influence a specific trait. The stronger gene is called dominant; the weaker gene, recessive. Two copies of a recessive gene are needed to control a trait while only one copy of a dominant gene is needed. Our sex chromosomes, the X and the Y also contain important genes. Some genetic diseases are caused by missing, or altered genes on one of the sex chromosomes. Males are most often affected by sex chromosome diseases when they inherit an X chromosome with missing or mutated genes from their mother.

TYPES OF GENETIC MUTATIONS. Genetic disease results from a change, or mutation, in a chromosome or in one or several base pairs on a gene. Some of us inherit these mutations from our parents, called hereditary or germline mutations, while other mutations can occur spontaneously, or for the first time in an affected child. For many of the adult on-set diseases, genetic mutations

A scientist examines a DNA sequencing autoradiogram on a light box. (Photo Researchers, Inc. Reproduced by permission.)

can occur over the lifetime of the individual. This is called acquired or somatic mutations and these occur while the cells are making copies of themselves or dividing in two. There may be some environmental effects, such as radiation or other chemicals, which can contribute to these types of mutations as well.

There are a variety of different types of mutations that can occur in our genetic code to cause a disease. And for each genetic disease, there may be more than one type of mutation to cause the disease. For some genetic diseases, the same mutation occurs in every individual affected with the disease. For example, the most common form of dwarfism, called achondroplasia, occurs because of a single base pair substitution. This same mutation occurs in all individuals affected with the disease. Other genetic diseases are caused by different types of genetic mutations that may occur anywhere along the length of a gene. For example, cystic fibrosis, the most common genetic disease in the caucasian population is caused by over hundreds of different mutations along the gene. Individual families may carry the same mutation as each other, but not as the rest of the population affected with the same genetic disease.

Some genetic diseases occur as a result of a larger mutation which can occur when the chromosome itself is either rearranged or altered or when a baby is born with more than the expected number of chromosomes. There are only a few types of chromosome rearrangements which are possibly hereditary, or passed on from the mother or the father. The majority of chromosome alterations where the baby is born with too many chromosomes or missing a chromosome, occurs sporadically or for the first time with a new baby.

The type of mutation that causes a genetic disease will determine the type of genetic test to be performed. In some situations, more than one type of genetic test will be performed to arrive at a diagnosis. The cost of genetic tests vary: chromosome studies can cost hundreds of dollars and certain gene studies, thousands. Insurance coverage also varies with the company and the policy. It may take several days or several weeks to complete a test. Research testing where the exact location of a gene has not yet been identified, can take several months to years for results.

Types of Genetic Testing

Direct DNA mutation analysis

Direct DNA sequencing examines the direct base pair sequence of a gene for specific gene mutations. Some genes contain more than 100,000 bases and a mutation of any one base can make the gene nonfunctional and cause disease. The more mutations possible, the less likely it is for a test to detect all of them. This test is usually done on white blood cells from a person's blood but can also be performed on other tissues. There are different ways in which to perform direct DNA mutation analysis. When the specific genetic mutation is known, it is possible to perform a complete analysis of the genetic code, also called direct sequencing. There are several different lab techniques used to test for a direct mutation. One common approach begins by using chemicals to separate DNA from the rest of the cell. Next, the two strands of DNA are separated by heating. Special enzymes (called restriction enzymes) are added to the single strands of DNA and then act like scissors and cut the strands in specific places. The DNA fragments are then sorted by size through a process called electrophoresis. A special piece of DNA, called a probe, is added to the fragments. The probe is designed to bind to specific mutated portions of the gene. When bound to the probe, the mutated portions appear on x-ray film with a distinct banding pattern.

Indirect DNA Testing

Family linkage studies are done to study a disease when the exact type and location of the genetic alteration is not known, but the general location on the chromosome has been identified. These studies are possible when a chromosome marker has been found associated with a disease. Chromosomes contain certain regions that vary in appearance between individuals. These regions are called polymorphisms and do not cause a genetic disease to occur. If a polymorphism is always present in family members with the same genetic disease, and absent in family members without the disease, it is likely that the gene responsible for the disease is near that polymorphism. The gene mutation can be indirectly detected in family members by looking for the polymorphism.

To look for the polymorphism, DNA is isolated from cells in the same way it is for direct DNA mutation analysis. A probe is added that will detect the large polymorphism on the chromosome. When bound to the probe, this region will appear on x-ray film with a distinct banding pattern. The pattern of banding of a person being tested for the disease is compared to the pattern from a family member affected by the disease.

Linkage studies have disadvantages not found in direct DNA mutation analysis. These studies require multiple family members to participate in the testing. If key family members choose not to participate, the incomplete family history may make testing other members useless. The indirect method of detecting a mutated gene also causes more opportunity for error.

Chromosome analysis

Various genetic syndromes are caused by structural chromosome abnormalities. To analyze a person's chromosomes, his or her cells are allowed to grow and multiply in the laboratory until they reach a certain stage of growth. The length of growing time varies with the type of cells. Cells from blood and bone marrow take one to two days; fetal cells from amniotic fluid take seven to 10 days.

When the cells are ready, they are placed on a microscope slide using a technique to make them burst open, spreading their chromosomes. The slides are stained: the stain creates a banding pattern unique to each chromosome. Under a microscope, the chromosomes are counted, identified, and analyzed based on their size, shape, and stained appearance.

A karyotype is the final step in the chromosome analysis. After the chromosomes are counted, a photograph is taken of the chromosomes from one or more cells as seen through the microscope. Then the chromosomes are cut out and arranged side-by-side with their partner in ascending numerical order, from largest to smallest. The karyotype is done either manually or using a computer attached to the microscope. Chromosome analysis is also called cytogenetics.

Applications for Genetic Testing

Newborn screening

Genetic testing is used most often for newborn screening. Every year, millions of newborn babies have their blood samples tested for potentially serious genetic diseases.

Carrier testing

An individual who has a gene associated with a disease but never exhibits any symptoms of the disease is called a carrier. A carrier is a person who is not affected by the mutated gene he or she possesses, but can pass the gene to an offspring. Genetic tests have been developed that tell prospective parents whether or not they are carriers of certain diseases. If one or both parents are a carrier, the risk of passing the disease to a child can be predicted.

To predict the risk, it is necessary to know if the gene in question is autosomal or sex-linked. If the gene is carried on any one of chromosomes 1–22, the resulting disease is called an autosomal disease. If the gene is carried on the X or Y chromosome, it is called a sex-linked disease.

Sex-linked diseases, such as the bleeding condition hemophilia, are usually carried on the X chromosome. A woman who carries a disease-associated mutated gene on one of her X chromosomes, has a 50% chance of passing that gene to her son. A son who inherits that gene will develop the disease because he does not have another normal copy of the gene on a second X chromosome to compensate for the mutated copy. A daughter who inherits the disease associated mutated gene from her mother, on one of her X chromosomes will be at risk for having a son affected with the disease.

The risk of passing an autosomal disease to a child depends on whether the gene is dominant or recessive. A prospective parent carrying a dominant gene, has a 50% chance of passing the gene to a child. A child needs to receive only one copy of the mutated gene to be affected by the disease.

If the gene is recessive, a child needs to receive two copies of the mutated gene, one from each parent, to be affected by the disease. When both prospective parents are carriers, their child has a 25% chance of inheriting two copies of the mutated gene and being affected by the disease; a 50% chance of inheriting one copy of the mutated gene, and being a carrier of the disease but not affected; and a 25% chance of inheriting two normal genes. When only one prospective parent is a carrier, a child has a 50% chance of inheriting one mutated gene and being an unaffected carrier of the disease, and a 50% chance of inheriting two normal genes.

Cystic fibrosis is a disease that affects the lungs and pancreas and is discovered in early childhood. It is the most common autosomal recessive genetic disease found in the caucasian population: one in 25 people of Northern European ancestry are carriers of a mutated cystic fibrosis gene. The gene, located on chromosome 7, was identified in 1989.

The gene mutation for cystic fibrosis is detected by a direct DNA test. Over 600 mutations of the cystic fibrosis gene have been found; each of these mutations cause the same disease. Tests are available for the most common mutations. Tests that check for the 86 of the most common mutations in the Caucasian population will detect 90% of carriers for cystic fibrosis. (The percentage of mutations detected varies according to the individual's ethnic background). If a person tests negative, it is likely, but not guaranteed that he or she does not have the gene. Both prospective parents must be carriers of the gene to have a child with cystic fibrosis.

Tay-Sachs disease, also autosomal recessive, affects children primarily of Ashkenazi Jewish descent. Children with this disease die between the ages of two and five. This disease was previously detected by looking for a missing enzyme. The mutated gene has now been identified and can be detected using direct DNA mutation analysis.

Presymptomatic testing

Not all genetic diseases show their effect immediately at birth or early in childhood. Although the gene mutation is present at birth, some diseases do-not appear until adulthood. If a specific mutated gene responsible for a late-onset disease has been identified, a person from an affected family can be tested before symptoms appear.

Huntington's disease is one example of a late-onset autosomal dominant disease. Its symptoms of mental confusion and abnormal body movements do not appear until middle to late adulthood. The chromosome location of the gene responsible for Huntington's chorea was located in 1983 after studying the DNA from a large Venezuelan family affected by the disease. Ten years later the gene was identified. A test is now available to detect the presence of the expanded base pair sequence responsible for causing the disease. The presence of this expanded sequence means the person will develop the disease.

Another late onset disease, Alzheimer's does not have as well a understood genetic cause as Huntington's disease. The specific genetic cause of Alzheimer's disease is not as clear. Although many cases appear to be inherited in an autosomal dominant pattern, many cases exist as single incidents in a family. Like Huntington's, symptoms of mental deterioration first appear in adulthood. Genetic research has found an association between this disease and genes on four different chromosomes. The validity of looking for these genes in a person without symptoms or without family history of the disease is still being studied.

CANCER SUSCEPTIBILITY TESTING. Cancer can result from an inherited (germline) mutated gene or a gene that mutated sometime during a person's lifetime (acquired mutation). Some genes, called tumor suppressor genes, produce proteins that protect the body from cancer. If one of these genes develops a mutation, it is unable to produce the protective protein. If the second copy of the gene is normal, its action may be sufficient to continue production, but if that gene later also develops a mutation, the person is vulnerable to cancer. Other genes, called oncogenes, are involved in the normal growth of cells. A mutation in an oncogene can cause too much growth, the beginning of cancer.

Direct DNA tests are currently available to look for gene mutations identified and linked to several kinds of cancer. People with a family history of these cancers are those most likely to be tested. If one of these mutated genes is found, the person is more susceptible to developing the cancer. The likelihood that the person will develop the cancer, even with the mutated gene, is not always known because other genetic and environmental factors are also involved in the development of cancer.

Cancer susceptibility tests are most useful when a positive test result can be followed with clear treatment options. In families with familial polyposis of the colon, testing a child for a mutated APC gene can reveal whether or not the child needs frequent monitoring for the disease. In families with potentially fatal familial medullary thyroid cancer or multiple endocrine neoplasia type 2, finding a mutated RET gene in a child provides the opportunity for that child to have preventive removal of the thyroid gland. In the same way, MSH1 and MSH2 mutations can reveal which members in an affected family are vulnerable to familiar colorectal cancer and would benefit from aggressive monitoring.

In 1994, a mutation linked to early-onset familial breast and ovarian cancer was identified. BRCA1 is located on chromosome 17. Women with a mutated form of this gene have an increased risk of developing breast and ovarian cancer. A second related gene, BRCA2, was later discovered. Located on chromosome 13, it also carries increased risk of breast and ovarian cancer. Although both genes are rare in the general population, they are slightly more common in women of Ashkenazi Jewish descent.

When a woman is found to have a mutation of one of these genes, the likelihood that she will get breast or ovarian cancer increases, but not to 100%. Other genetic and environmental factors influence the outcome.

Testing for these genes is most valuable in families where a mutation has already been found. BRCA1 and BRCA2 are large genes; BRCA1 includes 100,000 bases. More than 120 mutations to this gene have been discovered, but a mutation could occur in any one of the bases. Studies show tests for these genes may miss 30% of existing mutations. The rate of missed mutations, the unknown disease likelihood in spite of a positive result, and the lack of a clear preventive response to a positive result, make the value of this test for the general population uncertain.

Prenatal and postnatal chromosome analysis

Chromosome analysis can be done on fetal cells primarily when the mother is age 35 or older at the time of delivery, experienced multiple miscarriages, or reports a family history of a genetic abnormality. Prenatal testing is done on the fetal cells from a chorionic villi sampling (from the baby's developing placenta) at 9–12 weeks or from the amniotic fluid (the fluid surrounding the baby) at 15–22 weeks of pregnancy. Cells from amniotic fluid grow for seven to 10 days before they are ready to be analyzed. Chorionic villi cells have the potential to grow faster and can be analyzed sooner.

Chromosome analysis using blood cells is done on a child who is born with or later develops signs of mental retardation or physical malformation. In the older child, chromosome analysis may be done to investigate developmental delays.

Extra or missing chromosomes cause mental and physical abnormalities. A child born with an extra chromosome 21 (trisomy 21) has Down syndrome. An extra chromosome 13 or 18 also produce well known syndromes. A missing X chromosome causes Turner syndrome and an extra X in a male causes Klinefelter syndrome. Other abnormalities are caused by extra or missing pieces of chromosomes. Fragile X syndrome is a sex-linked disease, causing mental retardation in males.

Chromosome material may also be rearranged, such as the end of chromosome 1 moved to the end of chromosome 3.This is called a chromosomal translocation. If no material is added or deleted in the exchange, the person may not be affected. Such an exchange, however, can cause infertility or abnormalities if passed to children.

Evaluation of a man and woman's infertility or repeated miscarriages will include blood studies of both to check for a chromosome translocation. Many chromosome abnormalities are incompatible with life; babies with these abnormalities often miscarrry during the first trimester. Cells from a baby that died before birth can be studied to look for chromosome abnormalities that may have caused the death.

Cancer diagnosis and prognosis

Certain cancers, particularly leukemia and lymphoma, are associated with changes in chromosomes: extra or missing complete chromosomes, extra or missing portions of chromosomes, or exchanges of material (translocations) between chromosomes. Studies show that the locations of the chromosome breaks are at locations of tumor suppressor genes or oncogenes.

Chromosome analysis on cells from blood, bone marrow, or solid tumor helps diagnose certain kinds of leukemia and lymphoma and often helps predict how well the person will respond to treatment. After treatment has begun, periodic monitoring of these chromosome changes in the blood and bone marrow gives the physician information as to the effectiveness of the treatment.

A well-known chromosome rearrangement is found in chronic myelogenous leukemia. This leukemia is associated with an exchange of material between chromosomes 9 and 22. The resulting smaller chromosome 22 is called the Philadelphia chromosome.

Preparation

Most tests for genetic diseases of children and adults are done on blood. To collect the 5–10 mL of blood needed, a healthcare worker draws blood from a vein in the inner elbow region. Collection of the sample takes only a few minutes.

Prenatal testing is done either on amniotic fluid or a chorionic villus sampling. To collect amniotic fluid, a physician performs a procedure called amniocentesis. An ultrasound is done to find the baby's position and an area filled with amniotic fluid. The physician inserts a needle through the woman's skin and the wall of her uterus and withdraws 5–10 mL of amniotic fluid. Placental tissue for a chorionic villus sampling is taken through the cervix. Each procedures take approximately 30 minutes.

Bone marrow is used for chromosome analysis in a person with leukemia or lymphoma. The person is given local anesthesia. Then the physician inserts a needle through the skin and into the bone (usually the sternum or hip bone). One-half to 2 mL of bone marrow is withdrawn. This procedure takes approximately 30 minutes.

Aftercare

After blood collection the person can feel discomfort or bruising at the puncture site or may become dizzy or faint. Pressure to the puncture site until the bleeding stops reduces bruising. Warm packs to the puncture site relieve discomfort.

The chorionic villi sampling, amniocentesis and bone marrow procedures are all done under a physician's supervision. The person is asked to rest after the procedure and is watched for weakness and signs of bleeding.

Risks

Collection of amniotic fluid and chorionic villi sampling, have the risk of miscarriage, infection, and bleeding; the risks are higher for the chorionic villi sampling. Because of the potential risks for miscarriage, 0.5% following the amniocentesis and 1% following the chorionic villi sampling procedure, both of these prenatal tests are offered to couples, but not required. A woman should tell her physician immediately if she has cramping, bleeding, fluid loss, an increased temperature, or a change in the baby's movement following either of these procedures.

After bone marrow collection, the puncture site may become tender and the person's temperature may rise. These are signs of a possible infection.

Genetic testing involves other nonphysical risks. Many people fear the possible loss of privacy about personal health information. Results of genetic tests may be reported to insurance companies and affect a person's insurability. Some people pay out-of-pocket for genetic tests to avoid this possibility. Laws have been proposed to deal with this problem. Other family members may be affected by the results of a person's genetic test. Privacy of the person tested and the family members affected is a consideration when deciding to have a test and to share the results.

A positive result carries a psychological burden, especially if the test indicates the person will develop a disease, such as Huntington's chorea. The news that a person may be susceptible to a specific kind of cancer, while it may encourage positive preventive measures, may also negatively shadow many decisions and activities.

A genetic test result may also be inconclusive meaning no definitive result can be given to the individual or family. This may cause the individual to feel more anxious and frustrated and experience psychological difficulties.

Prior to undergoing genetic testing, individuals need to learn from the genetic counselor the likelihood that the test could miss a mutation or abnormality.

Normal results

A normal result for chromosome analysis is 46, XX or 46, XY. This means there are 46 chromosomes (including two X chromosomes for a female or one X and one Y for a male) with no structural abnormalities. A normal result for a direct DNA mutation analysis or linkage study is no gene mutation found.

There can be some benefits from genetic testing when the individual tested is not found to carry a genetic mutation. Those who learn with great certainty they are no longer at risk for a genetic disease, may choose not to undergo prophylactic therapies and may feel less anxious and relieved.

Abnormal results

An abnormal chromosome analysis report will include the total number of chromosomes and will identify the abnormality found. Tests for gene mutations will report the mutations found.

There are many ethical issues to consider with an abnormal prenatal test result. Many of the diseases tested for during a pregnancy, cannot be treated or cured. In addition, some diseases tested for during pregnancy, may have a late-onset of symptoms or have minimal effects on the affected individual.

Before making decisions based on an abnormal test result, the person should meet again with a genetic counselor to fully understand the meaning of the results, learn what options are available based on the test result, and what are the risks and benefits of each of those options.