Genetic Testing

Essentials

• It is advisable to centralize genetic diagnostics to specialized centres with adequate expertise.
• Carrier status of patients' relatives is best examined in units specializing in genetics.
• Nowadays, genetic testing is rarely useful in the diagnosis and treatment planning of common chronic diseases.
• Due to their variable quality, gene tests ordered from the internet should not be recommended for patients.
• If a patient has already bought such a test, the physician can react to the reported highly significant genetic risks of common diseases as he or she would to a highly significant family history.

Therapeutic indications

• Diagnosis of disease
• Detection of disease gene carriership
• Preparing for possible future diseases
• Detection of susceptibility to disease
• Detection of disease genes in an embryo or fetus
• Investigation of changes in cancer tissue
• Genetic tests are used to look for answers to a few fundamentally different kinds of questions that will be discussed under separate headings below.

Confirming the diagnosis of a rare disease by genetic testing

• Genetic testing can be used to examine whether a patient has, for example, a disease belonging to a rare local disease heritage.
  • For example, a diagnosis of congenital nephrosis of the Finnish type (CNF) can be confirmed by testing for the major mutations of the NPHS1 gene in Finland, i.e. deletion of two bases c.121_122del (p.Leu41fs*50) or the clearly rarer point mutation c.3325C>T (p.Arg1109Ter). These two mutations together cover more than 90% of the mutations causing congenital nephrosis in Finland.
  • If a patient's symptoms are clearly suggestive of this disease but the said mutations are not found in the sample, sequencing of the whole NPHS1 gene, i.e. reading the whole coding section of the gene, could be considered in order to, perhaps, find rarer mutations of the gene explaining the disease.
• In cases in which the diagnosis of a disease is considered clinically (nearly) confirmed, an accurately targeted genetic test (for specific mutations or for sequencing of specific genes) can be done to confirm the diagnosis and to offer a tool for testing for carriership in family members or for fetal diagnosis in any subsequent pregnancies.
• There are no particular problems involved in targeted genetic tests. They are a part of the continuum of diagnosis of rare diseases. At best, they provide an accurate diagnosis easily and at relatively low cost, and diagnostic techniques that are more expensive and place a greater burden on the patient, such as biopsies or imaging, can be avoided.

Use of multi-gene panel tests to search for an accurate diagnosis in patients with rare symptomatology

• If symptoms and findings suggest a certain group of rare diseases, it may be difficult or impossible to deduce the specific genes in which mutations might produce the symptoms.
• In multi-gene panel testing a group of genes associated with similar symptoms is sequenced in order to seek the disease causing the symptoms.
• As next-generation sequencing (NGS) has reduced the price of genetic sequencing, panels may now even include genes that very improbably cause the symptoms.
  • Multi-gene panels for retinal diseases, for example, may in some laboratories include even hundreds of genes that are studied per a single referral, whereas some other laboratories request the clinician to focus the referral in more detail so that smaller test panels, tailored for specific symptoms, can be used.
• In most cases, multi-gene panels save both time and money compared to the use of several individual genetic tests.
• Problems associated with multi-gene panel testing
  • Comparing available multi-gene panels may be difficult because the laboratories update their panels constantly as more knowledge becomes available.
  • Assistance can be obtained from the genetics laboratory or the clinical genetics unit of the nearest university hospital and these may provide assistance even when the test is not performed in the laboratory of one's own hospital. When selecting a test, a laboratory considers, among other things, the suitability of the test, the laboratory accreditation and the quality assurance of the test.
  • If genetic testing is considered, the patient may also be referred, as necessary, to a clinical genetics unit.
  • The results of gene testing may be surprising even if the genes chosen for the panel are associated with certain symptoms.
    • For example, in a large gene test panel performed to diagnose a retinal disease, a progressive neurological disease starting with eye symptoms, such as juvenile neuronal ceroid lipofuscinosis http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=11290, may be found.
  • When considering a test, the patient should be told that wide multi-gene panel tests may reveal something unexpected about the heredity or prognosis of the disease.

Identifying an unknown cause of symptoms by (almost) genome-wide testing

• If the cause of symptoms is hard to define, examination of all protein-coding genes in the genome (whole exome sequencing, WES) or of the whole genome (whole genome sequencing, WGS) may be used to support the diagnostics.
  • Exome sequencing is possibly the most practical approach in situations where the patient's clinical picture does not suggest the involvement of any particular gene and doesn't even seem to fit any disease group that can be diagnosed with a specific gene panel.
  • Use of ES as the primary gene testing method is on the increase, but using WGS in clinical diagnostics is still rare.
• When the whole exome or genome is read, the interpretation is more difficult than with genetic panels: several variations in genetic scripting are always found and many of them are hard to interpret.
  • Definite mutations may be found in genes known to cause quite different diseases. For example, a baby in intensive care might be found to have a mutation causing cancer in adulthood or leading to dementia in middle age.
  • Laboratories have developed methods to search the genome-wide genetic testing data only for changes that could potentially cause the patient's symptoms. Even if all the patient's genes are covered, the results often include only changes in genes that are considered to be relevant to the symptom pattern.
  • In addition, many laboratories offer the option of including a few dozen clinically relevant disease genes in the comprehensive genome-wide genetic testing and reporting the results to the subject if he or she so wishes. This could help to prevent diseases in certain rare situations, such as in hereditary predisposition to cancer. If this is done, a thorough discussion should be conducted and a formal agreement process carried out with the test subjects before performing such test.

Interpreting the results of genetic testing

• Laboratories classify the variants found in tests into 5 different categories, employing perhaps somewhat different criteria, but the same principles.
  • Pathogenic (P): a well-known mutation that is known to cause a specific disease.
  • Likely pathogenic (LP): a well-known variant that has several characteristics suggesting that it causes a specific disease, but there is no certainty about this.
  • Variant of uncertain significance (VUS): a variant that usually has not been found earlier (not available in publications or variant databases), and although some of its characteristics suggest that it might cause a specific type of disease, its role therefore remains unclear.
  • Two further categories, Likely benign and (certainly) Benign; variants belonging to these groups are not reported by laboratories in their results.
• A clinician is left with the difficult task to consider what to do about VUS variants and how to explain the results to the test subjects. In these kinds of situations the expertise available within a clinical genetics unit is useful. Testing other family members for the change can sometimes help to interpret its significance, but often the situation remains uncertain. It is likely that the significance of such a change will be better understood after some years as knowledge accumulates.
• Even if it is posssible to conclude that a patient's disease is genetic, it is far from always possible to identify a genetic defect that would match the situation.

Genetic testing of cancer tissue

• The development of a cancer tumour is always associated with a number of local genetic changes in the tumour itself.
• These can be investigated by genetic testing of tumour tissue in cancer types where the range of mutations in the tumour influences treatment choices.
• The discovery of mutations in a cancer tumour does not usually mean that the cancer is associated with a hereditary predisposition. This possibility is assessed separately.

Genetic testing and genetic counselling

Genetic testing and data protection

• From the point of view of health care, results of genetic testing are as sensitive personal information as other entries in patient records.
• It should be agreed with the patient whether it is allowable to use the information for the benefit of their close relatives, and this agreement should be entered in the patient record.
• Patients may express their concern about the results of genetic testing getting into the wrong hands from the laboratory, health care or research environment, such as into the hands of the police or an insurance company. This theoretical risk does exist particularly in genome-wide tests which theoretically identify the individual tested.
• A theoretical risk of information getting into the wrong hands cannot be denied but the issue can be brought into perspective by reminding patients that each blood sample or tuft of hair contains the individual's whole genetic information and could thus theoretically be used inappropriately.

The primary care physician and genetic testing

• Diagnosis of rare diseases is typically the responsibility of specialized care and in most cases dedicated special units. Possible genetic tests and counselling are often provided by clinical genetics units.
• However, health centres do use some genetic tests, such as the test for lactose intolerance Lactose Intolerance.
• Pharmacogenetic tests will probably become more common within the next few years and become a part of the array of tests used at health centres.
• A general practitioner may be confronted with the issue of genetic testing when relatives of patients with genetic diseases wish to have their own situation clarified. Such cases most often concern hereditary susceptibility to cancer, sometimes progressive neurological diseases of adulthood or carriership of disease genes in association with family planning. Such testing should be done at clinical genetics units of university hospitals but as genetic testing becomes more common, the task allocation may need to be reconsidered.
• Many common diseases result from the combination of inherited predisposition and external conditions. Genetic testing is very rarely used in their diagnosis and treatment planning; family history and consideration of lifestyle usually provide sufficient hints on the risk of disease.
• People buy also genetic tests marketed directly to consumers. Such tests may be bought for examining descent but also for medical reasons.
• Extensive test packages marketed to consumers on the internet aim to predict the risk of developing ordinary chronic diseases. They can give some indication of the risks of future diseases, but do not reveal who will actually develop a disease and who will not. Typically, they provide results stating that the risk is only slightly different compared to the general risk in the population.
  • Such tests should not be recommended for patients; it is quite justified to say that the health care system will adopt genetic tests for susceptibility to various diseases as the reliability of such tests improves and is scientifically proved.
  • Another reason for not recommending such tests is the wide variety of their sources; health centre physicians cannot be expected to study the whole array and be able to pick out reliable sources for their patients.
  • Consumers should also understand that the results are related to today's knowledge and that the prognosis may not be accurate in a year's time, given the rapid development of genetic knowledge.
  • Some operators may also use methods which provide information not only on susceptibility genes but also on mutations causing a high risk of disease, i.e. information that the subject may not have anticipated.
• If a person bringing up this issue has already bought such a test and does not quite know what to do about the results, the physician can read the report and react to any highly significant risk of disease as he would to a highly significant family history. No attention should be paid to slightly increased or reduced risks because results change as more research data is collected.