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Genetic testing

Genetic testing
Authors:
Wendy Kohlmann, MS, CGC
Anne Slavotinek, MBBS, PhD
Section Editor:
Benjamin A Raby, MD, MPH
Deputy Editor:
Jennifer S Tirnauer, MD
Literature review current through: Oct 2022. | This topic last updated: Oct 07, 2022.

INTRODUCTION — Genetic testing can uncover a diagnosis that allows tailored interventions to prevent or treat disease or disease complications. Appropriate use of genetic testing, including understanding the limitations and challenges of available testing approaches, is crucial to the successful use of genetic testing in improving health and quality of life.

This topic reviews principles of clinical genetic testing, including testing methods, indications for testing, ethical considerations, and practical issues.

Additional discussions are provided on the following:

Genetic counseling – (See "Genetic counseling: Family history interpretation and risk assessment".)

Personalized medicine, including direct-to-consumer (DTC) testing – (See "Personalized medicine".)

Disclosure of incidental findings from genetic testing – (See "Secondary findings from genetic testing".)

BASIC PRINCIPLES

Terminology — The genotype can be defined as the deoxyribonucleic acid (DNA) blueprint that is associated with the clinical manifestations of a trait, phenotype, or disease. This and other commonly used terms in genetic testing are summarized in the table (table 1). An extensive glossary of genetic terms is provided separately. (See "Genetics: Glossary of terms".)

Genetic testing can refer to any type of testing that helps determine an individual's genotype. It can be determined for the germline (cells arising from the germ cells and applicable to the vast majority of cells in the body) or for selected somatic cells such as tumor cells.

The term "genotyping" is used differently in two different contexts:

Determining the genotype.

Referring to a certain type of microarray or testing method that determines the genotype for a subset of selected nucleotide variants.

The terminology used to describe the results of clinical genetic testing is shifting, based on guidance from the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published in 2015 [1]. This guidance seeks to avoid nonspecific, pejorative, or confusing terms such as mutation or polymorphism, which refer to genetic variation but do not specify whether the variation is associated with disease. (See "Genetics: Glossary of terms", section on 'Polymorphism'.)

The ACMG guidance uses the term "variant," which refers to variation from a reference sequence; for clinical testing, variants are classified into one of five categories of pathogenicity [1]:

Pathogenic

Likely pathogenic (at least 90 percent confidence in pathogenicity)

Variant of uncertain (or unknown) significance (VUS)

Likely benign (at least 90 percent confidence in benign status)

Benign

Generally, variants classified as pathogenic or likely pathogenic are considered appropriate for incorporating into clinical care. In this document, the term pathogenic will be used to refer to both pathogenic and likely pathogenic variants. These designations indicate the degree of confidence that a variant is associated with the disease phenotype, but they do not specify the likelihood of developing disease. Disease likelihood depends on the presence of specific genetic variants as well as other factors such as the inheritance pattern (recessive or dominant), penetrance and expressivity, the individual's age, and other contributory genetic and environmental factors. (See 'Likelihood of disease' below.)

The assignment of a variant to a category of pathogenicity is based on available data that include family studies (testing of additional first-degree relatives, such as parents, can determine if the variant segregates with the disease), epidemiologic data, and laboratory testing that can involve functional studies that demonstrate altered protein function in cells or animals [1]. Additional discussion of these categories and the criteria used to assign them is presented separately. (See "Secondary findings from genetic testing", section on 'Definitions and classification of variants'.)

The term "mutation" is still sometimes used in several circumstances such as when discussing certain known mutations, disease pathogenesis, and laboratory techniques. However, use of this term in a clinical setting should be avoided whenever possible.

Single nucleotide polymorphism (SNP) has been used to refer to single base pair substitutions that are present in a large portion of the typical, or healthy, population. The frequency of SNPs has traditionally been defined as >1 percent. However, this term can be vague when used in reference to genetic testing. SNP is also sometimes used to refer to a type of panel testing that can evaluate the presence of a subset of nucleotide changes (as in "SNP array"). (See "Basic genetics concepts: DNA regulation and gene expression", section on 'Sequence variants' and "Tools for genetics and genomics: Cytogenetics and molecular genetics", section on 'Genotyping microarrays'.)

Extent of DNA analysis — The extent of genetic testing can range from analyzing a single variant (such as the variant for factor V Leiden) to the entire genome. The appropriate test depends on the indication or presenting feature(s), the tests available for the suspected condition(s), and the available information regarding the genetic cause(s) of the condition or presenting features.

Selected variants versus entire gene — For every gene, it is possible to evaluate selected variants (certain nucleotide substitutions or other changes) or the entire gene (every coding nucleotide and the nucleotides near the splice sites in the coding region of the gene). The approach used depends on the purpose of the testing and the current state of knowledge about the variants that can cause disease in that gene.

As examples:

Selected variants – For some genes, only one or two variants are known to be associated with a particular condition. Examples include:

Factor V Leiden

The p.Cys282Tyr (p.C282Y) variant in HFE associated with most cases of hereditary hemochromatosis

In these cases, testing for the specific variant alone is reasonable and introduces less extraneous information. Testing is typically performed by sequencing.

Genotyping of individual variants is also used for at-risk relatives of individuals confirmed to carry a pathogenic variant in a specific gene. For example, siblings and offspring of a carrier of a pathogenic BRCA1 variant can be tested for the familial pathogenic variant alone rather than all known pathogenic BRCA1 variants.

Some gene panels that are bundled as direct-to-consumer (DTC) genetic tests include variants that have been associated with common, complex diseases such as type 2 diabetes, autoimmune disease, and metabolic traits. Due to the inherent genetic complexities of these disorders, the effects conferred by each variant alone are often relatively small (odds ratios of <1.5 for risk variants) and can be inconsistent across different ethnic populations. Therefore, the predictive accuracy of these tests is highly variable, and most of the panels have not been comprehensively validated. (See "Personalized medicine", section on 'Direct-to-consumer testing'.)

As noted below, there are several methods that can be used to determine variation at selected nucleotide positions. (See 'Methods' below.)

Entire gene – For many genetic disorders, the disease gene is very sensitive to variation at many locations, with large numbers of pathogenic variants known to cause disease. Examples include the breast and ovarian cancer genes, BRCA1 and BRCA2, and the cystic fibrosis gene, CFTR. There are different approaches to testing in these cases.

Single-nucleotide genotyping panels – When the majority of cases of a disease are caused by a limited number of variants, one approach is to genotype for the most common pathogenic variants first, followed by reflex to more comprehensive testing of all potential variants (using sequencing) if the initial testing is negative but concern for the disease remains high. This practice is used frequently for screening in cystic fibrosis, where a panel of 25 variants in the CFTR gene will correctly classify more than 90 percent of patients of European ancestry. This approach is less expensive, and the turnaround time is typically faster than more comprehensive approaches. However, additional testing should be considered in patients of non-European ancestry, as rarer, ancestry-specific variants may not be well represented on these panels.

Sequencing – The more comprehensive approach of sequencing consists of evaluating all nucleotides across the gene to identify all possible pathogenic or likely pathogenic variants. The two main advantages of sequencing are that all positions in the gene are tested and that rare variants that would not be included on genotyping panels can be identified. Examples in which initial gene sequencing is useful include the F9 gene associated with hemophilia B. Sequencing can be limited to one gene, to a set of genes implicated in a group of related disorders (so-called "gene sequencing panels"). Massively parallel sequencing can also be performed for extended, genome-wide testing. This type of genomic testing can be limited to the coding regions of all genes, called whole exome sequencing (WES), or it can include coding and noncoding regions, termed whole genome sequencing (WGS). (See "Genetics of hemophilia A and B", section on 'F9 gene (hemophilia B)' and "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Diagnosis of complex diseases'.)

Copy number variation – In addition to screening for single base-pair changes, detection of deletions or duplications of exons or entire genes is often necessary as part of clinical testing. This is particularly important for genes where duplications or deletions are frequently observed (for example, PMP22 in Charcot-Marie-Tooth neuropathies). Copy number variants (CNVs) are also referred to as deletion/duplications (del/dups) and can be of varying sizes. CNV testing is often included as part of the standard evaluation of genes by many clinical laboratories in gene panels, and CNV analysis can also be performed on exome sequencing data. CNVs can be identified using microarray technologies that rely on hybridization of patient and control DNA to probes on the array. (See "Genomic disorders: An overview", section on 'Detection of genomic disorders'.)

Entire chromosome – Some disorders, such as Down syndrome (trisomy 21), are associated with chromosome aneuploidy. Segmental chromosomal gains or losses, also resulting from CNVs, unbalanced chromosome translocations, or other structural cytogenetic rearrangements, can also be associated with genetic conditions.

This form of genetic variation often occurs on a much larger scale compared to nucleotide substitutions. Methods such as high-resolution karyotyping, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (array CGH), or SNP arrays can be used. (See 'Cytogenetic testing and FISH' below.)

For prenatal detection of chromosome abnormalities, noninvasive prenatal screening (NIPS) using cell-free DNA is increasingly used instead of (or prior to) invasive testing such as amniocentesis or chorionic villus sampling. (See 'Clinical applications' below and "Prenatal screening for common aneuploidies using cell-free DNA".)

One gene versus many genes

Single gene – Some disorders are clearly linked to a single gene. Examples include conditions such as cystic fibrosis, which is associated with variants in the CFTR gene; hemophilia B, caused by variants in the F9 gene; or adult-onset hereditary hemochromatosis, associated with variants in the iron regulatory gene HFE.

When a single gene is implicated, testing that gene alone is generally appropriate, with additional genetic testing reserved for individuals for whom the initial testing was uninformative.

Panel of selected genes – Some disorders are genetically heterogeneous, caused by pathogenic variants in one of several genes. Examples include hereditary cancer syndromes or hereditary platelet function disorders. In such cases, gene panel testing for the known genes associated with the disorder is usually considered more efficient and cost-effective.

However, different institutions and different testing laboratories may select different genes (and different variants in those genes) to include in their panel. Thus, it is important to review the genes listed on the panel to ensure that testing includes all of the gene(s) of interest.

All genes – If the clinical presentation does not suggest a particular gene or group of genes, an individual may undergo sequencing of all of the known genes as part of WES or WGS. WES or WGS is now a standard tool for gene discovery studies where a large number of patients (or ideally, large kindreds) with similar disease manifestations are available for study. Their utility in the clinical setting, however, is largely dependent on the availability of practitioners with expertise in interpretation of such sequence data.

Genetic counselors and/or clinical geneticists should consult with patients prior to WES or WGS to assist with both pre-test and post-test counseling. Given the frequency of disease-causing variants, WES and WGS will often result in the identification of variants of unknown significance (VUSs). Moreover, the unexpected finding of one or more pathogenic variants in genes that cause genetic disorders different from the condition being investigated (referred to as incidental or secondary findings) is not uncommon. Most studies find a prevalence of secondary findings of at least 1 percent. The return of such findings to unprepared patients can have deleterious consequences, including negative psychologic impacts, and there may be implications for obtaining life insurance and disability insurance. Genetic counselors and/or clinical geneticists can address these issues prior to testing and advise patients and providers accordingly. (See "Secondary findings from genetic testing".)

Methods — Many clinical laboratories use capillary-based Sanger sequencing for evaluating specific variants in one gene, whereas most multiplex genotyping platforms are microarray-based. (See 'Microarrays' below.)

Whole gene, whole exome, or whole genome assays typically rely on next-generation sequencing (NGS) technologies, although whole gene sequencing is also performed. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications".)

The methods discussed in the following sections represent some of the commonly used methods but are not comprehensive. Some of the other methods including methylation studies, array comparative genomic hybridization (array CGH), fluorescence in situ hybridization (FISH), and multiple ligation dependent probe amplification (MLPA) are discussed in separate topic reviews. (See "Principles of epigenetics" and "Genomic disorders: An overview", section on 'Detection of genomic disorders'.)

In the majority of applications, these methods all depend on an amplification step in which the patient's DNA sample is copied a number of times to create sufficient material for the assay. Often this amplification step is based on polymerase chain reaction (PCR), but occasionally non-PCR-based isothermal methods can be used. (See "Tools for genetics and genomics: Polymerase chain reaction".)

Microarrays — Microarrays for genetic testing consist of a glass surface (or other matrix) coated with paired sets of oligonucleotide probes (short DNA sequences) that code for a target reference sequence and for the alternate, disease-associated variants. An individual's DNA sample is hybridized to the DNA on the slide, and probes labeled with fluorescent dyes corresponding to the reference and alternate variants are used to detect the patient's DNA sample. This approach is also referred to as allele-specific oligonucleotide hybridization. (See "Tools for genetics and genomics: Cytogenetics and molecular genetics", section on 'Allele specific oligonucleotide hybridization'.)

Microarrays can be used to identify DNA changes of varying size, such as at the level of a single nucleotide, larger portions of one or more genes, or larger regions of one or more chromosomes (CNVs). Most microarrays are SNP microarrays used for CNV detection. Arrays used to identify SNPs are called SNP arrays, genotyping arrays, or genotyping panels. Genotyping panel can also be used to refer to sequencing a group of genes. (See 'Terminology' above.)

Advantages of microarrays for detecting SNPs are the ability to evaluate a large number of variants (including variants involving multiple genes) in a single test. This testing can be more cost-effective than sequencing in some cases, especially when the specific variants being evaluated cause the majority of disease cases (eg, the common CFTR genotyping panels for cystic fibrosis).

A disadvantage of microarray testing for detecting SNPs is that it can only identify changes for which probes have been created and placed on the array. As a result, this method may not detect certain rare, yet clinically important, variants. Additionally, the variants on the array may differ from panel to panel, although there is usually a fair amount of overlap for the best-characterized variants.

Microarrays are frequently used in genome-wide association studies (GWAS), a research application that is sometimes used to associate genetic variation with a disease or trait or to help design genotyping panels. (See "Genetic association and GWAS studies: Principles and applications".)

Sequencing — Sequencing determines the identity of each nucleotide along a region of DNA. Sequencing can be performed using traditional methods (Sanger sequencing) or next-generation sequencing (NGS) methods. NGS uses massively parallel sequencing in a high-throughput format. As a result, it can generate a large amount of sequence data, or almost the entire exome or genome, orders of magnitude more rapidly than would be possible using traditional methods. In many cases, specific NGS results, such as an identified pathogenic variant in a gene, are confirmed by Sanger sequencing as quality control prior to the return of results to patients. NGS technology is discussed in more detail separately. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Terminology and evolution of technologies'.)

Advantages of NGS are the ability to provide information regarding numerous sequence variants and to query a broad group of genes. This is especially useful if the clinical picture does not provide enough information to identify a single gene or small group of genes likely to be responsible for the disease phenotype.

Limitations of NGS include identification of many variants for which the significance is uncertain (VUS), as well as identification of unexpected pathogenic variants unrelated to the original reason for testing, referred to as secondary findings. Decisions regarding which findings to disclose to the patient are an area of active research; typically, only "medically actionable" secondary findings that are designated as pathogenic or likely pathogenic are disclosed to patients and families. Counseling individuals about these limitations prior to testing, and provision of an "opt-out" option if the individual prefers not to receive certain information, is an important component of informed consent for NGS. (See "Secondary findings from genetic testing" and "Genetic counseling: Family history interpretation and risk assessment".)

As NGS sequencing technology is increasingly adopted and costs decrease, the method is becoming more widely used in settings that previously used array technology, such as genotyping panels. The laboratory may continue to report only a subset of variants identified by sequencing, despite having additional information about other variants. This potentially avoids the concerns noted above about how to handle information regarding VUSs.

In some cases, future research may allow additional interpretation of findings and greater predictive accuracy than was available at the time the testing was performed or than information gained from genotyping panels. This increases the potential promise of NGS but also increases the need for extensive data storage capacity and means for reinterpretation and recontacting the tested individual.

With new data or reinterpretation of existing data, a VUS may be reclassified as pathogenic or benign at a future date. Many factors impact the rate of variant classifications. Research consortia and methodologic advances are accelerating the classification of variants in some genes. Analysis of a large dataset of hereditary cancer multigene panel testing found that 7 percent of VUS were reclassified, after finding that the variants were present in multiple individuals [2]. Ultimately, one-fourth of the tested population had a reclassified variant. The majority (90 percent) of VUS were downgraded to benign or likely benign.

Laboratory policies have not been standardized for noting VUSs on reports, reclassifying variants, and notifying patients or ordering clinicians that a variant has been reclassified, and clinicians should be aware of the policies when ordering a test [3]. Many laboratories have protocols for systematically reviewing VUSs and providing amended reports to ordering providers. In situations in which a laboratory reports VUSs but does not provide reclassification information, the burden for tracking that variant can fall on the clinician.

Laboratories that do not report VUSs may reduce the need to counsel and re-contact patients when classifications change. However, up to 10 percent of VUSs will be upgraded to actionable pathogenic variants, and if VUSs are not reported, those diagnoses will be missed [2,3].

Cytogenetic testing and FISH — Cytogenetic testing and fluorescence in situ hybridization (FISH) are used to determine chromosomal changes at the level of larger regions of the genome such as an entire chromosome or chromosome segment, rather than a single gene. Examples include detection of aneuploidies (chromosome gains [trisomies] or losses); chromosomal translocations or inversions; and copy number variants (CNVs; gains or losses within a region of a chromosome).

Typical uses for these methods include prenatal diagnosis of fetal aneuploidies and oncology testing (eg, classification of hematologic malignancies). As cytogenetic testing and FISH require many cells for analysis, and in the prenatal setting this requires invasive procedures such as amniocentesis or chorionic villus sampling, prenatal testing is moving towards the use of noninvasive methods that evaluate small fragments of circulating fetal DNA in the maternal blood.

Some cytogenetic testing, such as karyotyping and metaphase FISH, requires dividing cells from which individual chromosomes can be isolated. Interphase FISH does not require dividing cells.

Advantages of cytogenetic testing and FISH include the ability to obtain a global view of chromosome number and structure and to monitor genetic changes in an entire tumor over time.

Limitations of cytogenetic testing and FISH include the labor and expertise required to perform the analysis, which are not always available. These methods are not as useful for monitoring certain specific changes over time, such as development of a new mutation responsible for reduced efficacy of chemotherapy (acquired resistance mutations).

Technical considerations and additional information about these tests are discussed separately. (See "Tools for genetics and genomics: Cytogenetics and molecular genetics".)

Likelihood of disease — The purpose of genetic testing is to determine the likelihood that an individual has or will develop a certain condition or disease phenotype, and in some cases, to predict which therapies will be more effective for treatment. Disease likelihood depends on a number of technical and biologic factors.

Accuracy of testing – Studies have demonstrated that there can be variation in the consistency of genetic test results, especially for testing performed in a laboratory that has not been certified by the Clinical Laboratory Improvement Amendments (CLIA). (See "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Accuracy' and "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Limitations' and "Personalized medicine", section on 'Concerns about value, accuracy, and interpretation'.)

Pathogenicity interpretation – As noted above (see 'Terminology' above), the pathogenicity of variants identified from genetic testing is determined using a combination of epidemiologic, clinical, and research data that provide information about the association of the variant with disease. Different CLIA-certified or noncertified laboratories may sometimes produce different interpretations of the pathogenicity classification of the same genetic variant, and as previously discussed, classification may change over time as more information becomes available.

Greater certainty that a variant is pathogenic or benign is useful for determining whether an individual is at risk for the disease, but it typically does not mean that development of the disease is inevitable.

Inheritance pattern – Some conditions are monogenic (caused by a pathogenic variant in a single gene), with a Mendelian inheritance pattern. Examples include certain cancer syndromes or metabolic disorders. Other conditions are multigenic (caused by pathogenic variants in more than one gene). Diseases can also be multifactorial (due to a combination of genetic and environmental factors).

For monogenic disorders, the inheritance pattern (autosomal or sex-linked; recessive or dominant) determines whether heterozygosity is likely or sufficient to confer increased risk of disease or whether homozygosity or compound heterozygosity is necessary for the disease to manifest. (See "Inheritance patterns of monogenic disorders (Mendelian and non-Mendelian)", section on 'Mendelian inheritance patterns'.)

Penetrance and expressivity – Penetrance refers to the likelihood that an individual with the disease genotype will actually manifest one or more of the clinical features associated with the disease. Highly penetrant conditions are those in which disease is invariably present in individuals with the disease genotype; an example of a highly penetrant condition is Huntington disease in individuals who have a pathogenic trinucleotide expansion in the HTT gene.

Disease variants causing cancer can initially be identified from kindreds with high-disease penetrance. In many cases, subsequent studies in the general population reveal a lower penetrance rate for the same variant (ie, ascertainment bias for high penetrance from the high-risk families). This may be the case with certain cancer genes such as the breast cancer genes BRCA1 and BRCA2 or Lynch syndrome genes [4,5]. Further research is needed to provide patients and families with more individualized risk estimates. (See "Genetic testing and management of individuals at risk of hereditary breast and ovarian cancer syndromes" and "Li-Fraumeni syndrome", section on 'Spectrum of malignancies and age at onset'.)

Variable expressivity refers to clinical differences in the way a disease is expressed. As an example, some individuals with CFTR variants manifest classic manifestations of cystic fibrosis, whereas others may have an isolated finding such as congenital absence of the vas deferens. These concepts and other factors that affect the strength of association between genotype and phenotype are discussed separately. (See "Inheritance patterns of monogenic disorders (Mendelian and non-Mendelian)", section on 'Penetrance and expressivity'.)

It may help to discuss these considerations with the individual before testing is performed, as part of the informed consent process. If the testing has already been performed, these considerations and a plan for further evaluation (if needed) can be addressed at the time results are provided. (See 'Coordinating testing with counseling' below and "Genetic counseling: Family history interpretation and risk assessment", section on 'Content of genetic counseling'.)

CLINICAL APPLICATIONS — Testing can be performed at different times during a patient's life and for different purposes (diagnosing a disease, predicting disease risk, or determining carrier status). Testing to determine germline genotype (present at birth) can be performed on blood, saliva, or buccal (cheek) cells, all of which contain the individual's germline DNA. Testing on tissues such as tumors can be used to identify additional acquired genetic changes.

Preimplantation testing — Preimplantation testing is performed on embryos resulting from in vitro fertilization for couples at high risk for genetic conditions for which the disease-causing variant(s) has already been identified. Determining the genotype of the embryo from a single cell allows selection of unaffected embryos to implant. (See "Preimplantation genetic testing".)

Prenatal screening and testing

Screening – Prenatal screening can be done using maternal blood to analyze fetal DNA (cell-free DNA [cfDNA]); this is increasingly being used to assess for chromosome aneuploidies and genetic conditions [6]. This type of noninvasive prenatal screening (NIPS) is primarily used for individuals at higher risk of carrying a fetus with a chromosomal abnormality or congenital anomaly, but several professional organizations recommend that doctors discuss all screening options, including NIPS, with all pregnant individuals [7,8]. NIPS has the advantage of limiting risks associated with invasive procedures [9].There is a crucial difference between screening and diagnostic testing. Those who screen positive should be offered diagnostic testing (eg, by amniocentesis). (See "Prenatal screening for common aneuploidies using cell-free DNA".)

Testing – Prenatal testing determines whether a variant is present in a fetus. Typically, this is used for genes that are inherited in Mendelian patterns (autosomal dominant, autosomal recessive, or X-linked) or for chromosomal abnormalities. Prenatal testing can also be performed to follow up an abnormal screen for fetal aneuploidy. Specimens for analysis traditionally have been obtained by chorionic villus sampling or amniocentesis. (See "Chorionic villus sampling" and "Diagnostic amniocentesis" and "Prenatal screening for common aneuploidies using cell-free DNA".)

Prenatal testing can provide reassurance or guide decisions regarding options as to whether to continue or terminate a pregnancy with an affected fetus. Prenatal testing for a condition such as Huntington disease, which is fully penetrant and has no specific or life-extending treatment, or for conditions that are lethal in childhood, carries different implications from testing for a condition that confers an increased risk of developing a disease for which preventive therapies are available, such as colon cancer.

Testing in children — Genetic testing is incorporated into pediatric care when the findings will provide a diagnosis or affect timely management during childhood. Predictive testing for adult-onset conditions is not generally pursued until adulthood, when the individual can make their own decision regarding testing. However, due to the complex overlapping phenotypes of many pediatric genetic conditions, whole exome sequencing (WES) may be considered to be an efficient approach for making a diagnosis in childhood, particularly when the child's health status is critical [10-12]. The use of WES in children is expected to increase the detection of genetic factors related to adult-onset conditions. (See 'Testing children' below and "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Indications for NGS'.)

Testing in adults — Genetic testing for adult-onset conditions can be used to predict disease risk (presymptomatic testing) or to establish or confirm a diagnosis (diagnostic testing).

Testing can be conceptualized according to its purpose:

Predictive testing – Used to predict disease risk (presymptomatic testing). Predictive testing is a method of risk assessment for unaffected individuals who are at risk for developing conditions with a hereditable component. Knowledge of an increased risk for a particular disease may lead to interventions to decrease the risk. The value of a test is influenced by the disease penetrance and whether there are effective prevention or early treatment strategies to impact its clinical course.

Examples include increased monitoring or prophylactic surgery for variants associated with hereditary cancer syndromes, or additional testing or interventions for variants associated with hypertrophic cardiomyopathy. (See "Cancer risks and management of BRCA1/2 carriers without cancer" and "Familial adenomatous polyposis: Screening and management of patients and families" and "Hypertrophic cardiomyopathy: Gene mutations and clinical genetic testing".)

Some companies are marketing genetic testing directly to healthy people in the general population, referred to as direct-to-consumer (DTC) testing. This subject is discussed separately. (See "Personalized medicine", section on 'Direct-to-consumer testing'.)

Diagnostic testing – Used to make or confirm the clinical diagnosis of a disorder. For hereditary cancer syndromes, diagnostic testing may be a useful tool for identifying the most appropriate treatment strategies. Examples include more extensive or less extensive cancer surgeries or use of targeted chemotherapy or biologic therapy known to be effective or ineffective in tumors with certain genotypes.

Carrier testing – Used to determine if an individual of reproductive age is heterozygous for a disease variant associated with an autosomal recessive disorder (a disorder that only manifests in homozygotes or compound heterozygotes for a pathogenic variant [or for X-linked disorders, a disorder that more typically manifests only in males]).

Carrier testing can be performed in families with a family history for a specific genetic condition or in particular populations in which pathogenic variants for a certain condition have a relatively high prevalence, such as Tay Sachs disease among individuals with Ashkenazi Jewish ancestry. (See "Preconception and prenatal carrier screening for genetic disease more common in people of Ashkenazi Jewish descent and others with a family history of these disorders".)

Pharmacogenetic testing – Used to guide drug dosing or drug avoidance in individuals with variants that affect drug metabolism or toxicities. The results may have no effect on health, but their identification may be critical for administration of certain drugs. (See "Overview of pharmacogenomics".)

QUESTIONS TO CONSIDER BEFORE TESTING

Is genetic testing indicated? — Ideally, patients should be counseled by a clinical geneticist, genetic counselor, or a clinician with expertise in the specific disease prior to genetic testing, to help answer questions about the usefulness and potential implications of the results. (See 'Coordinating testing with counseling' below and "Genetic counseling: Family history interpretation and risk assessment".)

The clinical utility is the likelihood that a test will prompt an intervention to improve health; the clinical utility of a genetic test depends on the impact of the results on clinical care. As an example, while the genetic test for Huntington disease has high clinical validity (predictive value), the clinical utility is limited because of few treatment or intervention options available for those who test positive. However, family members at risk for this disease may choose to undergo genetic testing to make reproductive plans or for the psychologic benefit in relieving uncertainty and facilitating future planning [13]. In other cases, the information from genetic testing raises more questions for the patient than it answers, sometimes at considerable expense and with the potential for harm (eg, from invasive diagnostic procedures).

Before initiating genetic testing, it is important to determine whether an alternative testing approach would be more useful, such as iron studies in an individual with suspected hereditary hemochromatosis or lipid panel in an individual with suspected familial hypercholesterolemia. These questions can be challenging to answer and may require consultation with a specialist in the specific disorder or with a genetic counselor or clinical geneticist.

At what age should testing be performed? — Genetic testing can be performed across the lifespan. (See 'Clinical applications' above.)

In general, testing in childhood is appropriate for diseases that manifest in childhood, and deferral to adulthood (or a few years before disease manifestations are expected) is reasonable for adult-onset conditions. Deferral to adulthood in these cases allows proper informed consent and ensures that the most current testing methods and interpretation of the clinical implications are available to the patient's current clinician(s). (See 'Obtaining informed consent' below.)

Which test is best? — As noted above, testing can analyze different numbers of genes and different numbers of variants within those genes. (See 'Extent of DNA analysis' above.)

It is worthwhile considering what extent of testing and what testing method will provide the most useful information with the least cost and burden to the patient.

Single gene or single variant testing is appropriate when a single gene disorder is suspected or a familial disease variant has been identified and there is value in determining whether an individual carries that variant. Transthyretin amyloidosis is an example. (See "Overview of amyloidosis", section on 'Heritable amyloidoses' and "Genetic factors in the amyloid diseases", section on 'Transthyretin'.)

Multigene panels are particularly helpful for settings in which variants in several possible genes may be relevant. Examples include:

Breast cancer – (See "Prognostic and predictive factors in early, non-metastatic breast cancer", section on 'Gene expression-based prognostic profiles'.)

Preconception testing – (See "Preconception and prenatal carrier screening for genetic disease more common in people of Ashkenazi Jewish descent and others with a family history of these disorders".)

Gene panels for heterogeneous conditions such as hearing loss

More extensive testing such as whole genome sequencing (WGS) can generally be reserved for complex disorders for which a clear panel of implicated genes is not available. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Diagnosis of complex diseases'.)

This subject is discussed in more detail separately. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Whole genome, exome, or gene panel'.)

Coordinating testing with counseling — Genetic testing should be coordinated with appropriate genetic counseling to help patients understand the consent process and the implications of a positive or a negative result for themselves and their relatives. Patients should also be counseled about the possibility of receiving a result that they have a variant (or variants) of uncertain significance (VUS), if relevant. Targeting genetic counseling to the patient is vital to the successful use of genetic testing.

Health care providers should consider the need for pretest genetic counseling services before offering genetic testing. These services may include obtaining family history including a three-generation family pedigree, discussing the objectives of testing, clarifying the limitations of testing, and outlining the myriad potential implications of test results, including secondary findings, VUS, and the potential implications of findings for other family members. (See "Genetic counseling: Family history interpretation and risk assessment" and "Secondary findings from genetic testing".)

For certain common disorders for which genetic testing is used, it may be impractical to involve a genetic counselor or clinical geneticist prior to testing. As an example, individuals with iron overload are frequently tested for a pathogenic variant in the HFE gene associated with hereditary hemochromatosis. Practitioners who will be confronted with such testing on an ongoing basis should become familiar with and routinely apply the principles of genetic counseling as they relate to the specific disorder.

ETHICAL, LEGAL, AND PSYCHOSOCIAL ISSUES — A number of ethical and psychosocial issues apply to genetic testing, including the consequences for the family, issues related to testing children who are unaffected, and concerns about genetic discrimination. Clinicians and patients must consider the benefits and risks of genetic testing, including the possibility of false-positive and false-negative results. Genetic information may have unique risks based upon the meaning attributed to the diagnosed disorder and the value of the information for family members [14].

Psychosocial consequences of testing — Because of the familial nature of genetics, the results of testing may impact the patient as well as other family members. The family dynamics and the family support system may determine how the results impact the tested individual and their family. Many genetics professionals use the family history intake to assess the family dynamics and to understand outside influences that impact the social support of the patient [15,16]. (See "Genetic counseling: Family history interpretation and risk assessment", section on 'Family history'.)

Less commonly, family dynamics may be affected by results of genetic testing. As examples, individuals who test negative may have the following reactions [17,18]:

Some may experience a sense of relief.

Some may experience "survivor guilt" if other family members are found to have the variant.

Some may feel alienated from affected family members with whom they no longer share the same risk status.

This phenomenon has some similarities to that seen in the setting of bereavement. (See "Bereavement and grief in adults: Clinical features", section on 'Loss of attachment'.)

Disclosure to family members — The patient should be encouraged to inform family members of genetic risk that may affect their care. Genetic counselors and clinical geneticists include a discussion about information sharing when providing the test result, and they often provide the patient with a copy of the test result or a model letter for family members to use for this purpose. If a genetic counselor is not involved in the testing process, the provider who orders the test should assume that responsibility.

Most patients are willing to provide consent for such disclosure or to readily disclose the information themselves [19,20]. For some, their express purpose for genetic testing is to make information available to family members.

However, the rare situation in which a patient refuses to voluntarily disclose information about a genetic risk to family members raises a conflict between two competing ethical obligations: the duty to protect patient privacy and autonomy versus the duty to disclose information for the purpose of preventing future harm. Sometimes, if the primary care provider is caring for multiple members of the same family, that person is in a position to further explore reasons for the refusal and potentially help the patient understand the impact of sharing.

Legal opinions vary regarding the clinician's duty to warn at-risk family members about a familial genetic condition:

There does not appear to be a legal obligation to inform family members in the United States, although legal opinions may vary [21]. Some genetics providers obtain consent for disclosure and family member contact information at the time of testing; others highly encourage the patient to share the information obtained from their genetic testing with family members.

Despite numerous guidelines and policy papers, there is no clear consensus or set of legal guidelines available in most countries. As an example, in 2017, the high court in the United Kingdom ruled on appeal that health care practitioners may be liable for failing to disclose a patient's Huntington gene status, if affected, to offspring [22,23].

Until clear legal obligations are defined, it is important to document conversations about disclosure, and in some cases, clinicians may wish to consult with medical geneticists, genetic counselors, or bioethicists in the event that patients do not provide consent to share information.

It is also strongly advised that pretest counseling and consent discussions include informing the patient of the potential implications of genetic test results for other family members, and, if appropriate, these discussions should emphasize that in situations where others' lives are at risk, although maintenance of patient confidentiality is a paramount concern, the practitioner may deem that the risks to relatives of not disclosing results would outweigh any potential harm to the patient by disclosure.

Testing children — Genetic testing of children and adolescents raises additional caveats, especially in cases when establishing a genetic diagnosis would have no immediate impact on the child's clinical care or prognosis. In such situations, it is frequently recommended that testing be postponed until the child is old enough to decide if they themselves will consent to testing and would like to undergo the test, as discussed above. (See 'Clinical applications' above.)

However, a broad sequencing approach with whole exome sequencing (WES) or whole genome sequencing (WGS) may identify numerous variants of potential future clinical significance that might manifest during adulthood but would be of no use to the patient during their youth, and the patient and relatives may be burdened rather than empowered by the information. This must be balanced by the greater diagnostic yield of broad sequencing approaches in some clinical situations.

A position statement by the American Society of Human Genetics (ASHG) addressing the issue of testing children was published in 2015 [24]. In addition to discussing issues of consent and assent (ie, agreement by a person not legally able to give consent) that are specific to genetic tests, this document provides recommendations regarding a variety of issues.

We agree with the ASHG recommendations, which include the following guidance [24]:

Parents or caregivers should be encouraged to defer their child's testing until adulthood so that the individual concerned can evaluate the risks and benefits of testing, unless there is a clinical intervention appropriate for childhood.

When genetic testing is indicated and the diagnosis is apparent from clinical examination or other investigations, initial testing should be limited to targeted gene panels or single gene testing based on the clinical presentation, and WES or WGS generally should be reserved for patients for whom initial testing has been unrevealing or in whom a diagnosis or condition is not obvious. This approach reduces the possibility of identifying secondary (incidental) findings unrelated to the testing indication.

Adolescents should be provided with the opportunity to discuss genetic testing and concerns related to genetic disorders. A comprehensive discussion that includes other aspects of informed consent in adolescent health care is presented separately. (See "Consent in adolescent health care".)

Although controversial, discovery of misattribution of parentage from genetic testing is not routinely disclosed unless there is a clear medical benefit that outweighs potential harms.

Additional information is available in the ASHG document and elsewhere in UpToDate. (See "Genetic counseling: Family history interpretation and risk assessment".)

Racial disparities — Racial disparities in obtaining appropriate genetic testing persist and require attention. (See "Society guideline links: Diversity, equity, and inclusivity in medicine".)

These disparities were illustrated in series of case presentations that highlighted the following reasons for disparities in genetic evaluation [25]:

Doctors, nurses, genetics professionals – Lack of familiarity with typical presentations in individuals with non-European backgrounds, racial bias (implicit or explicit)

Health care system – Reduced access to health care, limited availability of educational materials, bias in gene panels (more likely to include variants seen in White individuals), racial makeup of the health care team does not match that of the patient, racial bias (implicit or explicit)

Patient – Lack of trust in health care provider or health care system

Ongoing attention to mitigating health care disparities is needed.

Genetic discrimination — A common concern about genetic testing is the potential for inadequate privacy protections and the potential negative impact of genetic testing on employment and medical and life insurance coverage. The concern about genetic discrimination affects not only the individual undergoing genetic testing but also can extend to their unaffected family members [26,27]. Fear of genetic discrimination or broad data sharing is a common reason for declining genetic testing [28].

The following protections are available in the United States:

ADA – Individuals who are disabled by a genetic disorder are protected from discrimination by the Americans with Disabilities Act (ADA). (See "Disability assessment and determination in the United States".)

GINA – Legal protection against the use of genetic information by group health insurance plans and employers is available at the federal level through the Genetic Information Nondiscrimination Act (GINA) [29]. Enacted in 2008, GINA prohibits discrimination by health insurers and employers on the basis of genetic information. GINA prohibits the use of genetic information to determine insurance eligibility, coverage, underwriting, or premium charges. GINA also prohibits health insurers and employers from asking or requiring a person to take a genetic test [30,31].

GINA has the following limitations [32]:

It does not address the use of genetic information in other insurance markets (eg, long-term care, life, and disability insurance) [33]. The regulation of insurance markets outside of health insurance is determined at the state level [34].

It does not apply to employers with fewer than 15 employees, the United States military (and the TRICARE military health system), the Indian Health Service, the Veterans Health Administration, or the Federal Employees Health Benefits Program [33].

Since its enactment in 2008, there have been few challenges to GINA. However, the majority of individuals remain unaware of the legislation, and those who are aware of it have several misconceptions about the specific protections and limitations associated with it [32]. An online survey of 1479 people conducted in 2014 revealed that 79 percent of respondents were not familiar with GINA, and of those who claimed to be familiar with it, only a minority could correctly describe the protections afforded by the legislation [32].

In addition to GINA, most states within the United States also have additional legislation protecting against the use of genetic information by health insurers and employers [14,35,36].

ACA – The United States Affordable Care Act (ACA) prohibits variations in health insurance premiums based on health status and genetic information [37].

Outside the United States, legislation and policies regarding the use of genetic information in insurance and employment varies considerably by country [38,39].

United Kingdom – Although the potential for genetic discrimination in health care is considerably less in nations with government-sponsored health care systems, the British government issued a moratorium prohibiting insurers from using genetic test results to set premiums for certain life insurance, long-term care, and income protection policies [40,41]. In general, notification of insurers is required for medical diagnoses but not for the results of genetic testing, which is considered predictive rather than diagnostic [42].

Europe – In 1997, the Council of Europe established the European Convention on Human Rights and Biomedicine (also known as the Oviedo Convention), which prohibits discrimination based on an individual's genetic background.

Europe/Australia/Canada – Over 30 European countries, Australia, and Canada have also implemented some form of anti-discrimination legislation or moratorium or signed on to abide by the standards of the Oviedo Convention [43].

Other countries – Legal protection against genetic discrimination is lacking in other areas of the world, and fear of stigmatization in these countries may significantly hinder access to genetic services and research [44].

Undisclosed familial relationships — Disclosure of unexpected family relationships, such as a finding of nonpaternity, has been publicized as an outcome of direct-to-consumer ancestry tests. (See "Personalized medicine", section on 'Direct-to-consumer testing'.)

However, information about familial relationships cannot be determined by all clinical genetic tests. Testing of a single individual or family variant testing would not generally provide enough information to reveal an unexpected relationship.

When clinical genetic analysis involves comprehensive testing of family members, such as testing parent-child trios to maximize interpretation of whole exome or whole genome sequencing results, it is possible to identify previously undisclosed or unknown relationships such as undisclosed adoption or misattributed paternity. Discussion of this possibility should be included as part of the consent process when this is possible based on the testing method and family members involved [45].

PRACTICAL ISSUES

Which relatives should be tested? — Whenever possible, initial genetic testing should be performed on an affected individual. Once a disease variant has been identified, testing of first-degree relatives is technically straightforward, and they are usually tested for the specific variant. Cascade testing to the first-degree relatives of individuals who test positive can then be performed. Relatives who have inherited the variant may be candidates for enhanced screening or risk reduction strategies, while those who have not inherited the alteration can be spared unnecessary procedures. (See 'Management and follow-up' below.)

This strategy can reduce the number of tests performed on unaffected individuals and simplifies interpretation, which in turn reduces cost and the possibility of identifying variants of uncertain significance.

While it is possible to begin the genetic testing process in an unaffected individual, there is a greater chance that these results will be uninformative. As an example, if an unaffected person does not have a pathogenic variant in a particular gene, it may be impossible to know whether there is no identifiable familial variant or whether a familial variant is present in the kindred but not in the tested individual (a true negative).

In some cases, however, the affected relatives may have died or may be unable or unwilling to be tested. Genetic counseling in these situations should evaluate the optimal testing approach, facilitate communication among relatives, and explain the limitations of genetic testing when it cannot be performed on an affected individual. (See "Genetic counseling: Family history interpretation and risk assessment", section on 'Family history'.)

Who should order the test? — Genetic evaluation can be performed in the context of a genetic counseling appointment with a genetic counselor or clinical geneticist, by a primary care provider, or by a disease specialist. What is most important is that individuals ordering genetic testing are able to determine the appropriate test and methodology, address the logistic issues of test ordering, prepare patients for psychosocial outcomes and implications for family members, interpret results, and incorporate test findings into management. (See 'Management and follow-up' below.)

The use of genetic testing has increased, and the increase in clinical indications for genetic testing has caused the number of patients needing this service to outpace the availability of genetic specialists. Strategies for delivering genetic services will need to be developed to ensure appropriate use and equitable access to testing. This may involve technologies such as telephone and telemedicine to increase access to genetic specialists, group counseling, and non-genetics health care providers developing expertise in the role of genetic testing within their specific specialties [46].

Collaborative service delivery models in which health care providers are working with the support of genetics specialists should also be considered as a strategy for ensuring all aspects of genetic counseling process are addressed [47]. Other models such as the use of pretest educational aids (eg, videos) and partnerships between genetic counselors and other health care providers are being implemented to meet this growing need [47-49].

Obtaining informed consent — Informed consent, a tenet of patient-centered medicine, is a foundation for the voluntary nature of genetic testing.

Informed consent means that the patient fully understands and agrees to the procedure. Consent involves more than just the signing of a document; consent requires discussion that includes the details of the testing and its risks, benefits, and limitations, including the sensitivity and specificity of different genetic tests (if available). When offering genetic testing, especially to unaffected individuals, most clinicians follow language from the United States Department of Health, Education, and Welfare, which encourages the patient to voluntarily exercise free power of choice, without any element of force, fraud, deceit, duress, over-reaching, or other ulterior form of constraint or coercion [50]. (See "Informed procedural consent".)

These issues and other aspects of informed consent for genetic testing are discussed in more detail separately. (See "Genetic counseling: Family history interpretation and risk assessment", section on 'Informed consent for genetic testing'.)

Submitting the proper samples (source of DNA) — Genetic testing for germline variants can be conducted on virtually any tissue. Most laboratories prefer blood specimens, although cheek (buccal) swabs and saliva samples may be an option for certain types of genetic testing. Germline testing of individuals with active hematologic malignancies often requires isolating DNA from skin or other tissue samples.

Testing for acquired (somatic) mutations requires the appropriate tissue (eg, tumor, bone marrow). DNA can be obtained from essentially any nucleated cell type, whereas classical cytogenetic analysis, such as karyotyping, requires dividing cells. (See 'Cytogenetic testing and FISH' above.)

Cost and insurance reimbursement — Costs of genetic tests vary widely, from USD $100 to $300 for common and routine tests to over USD $4000, or significantly higher, for large gene panels or whole genome testing involving multiple family members. Comprehensive multigene panels for hereditary cancers and/or cardiovascular disease are available self-pay for $250 to $350.

Factors to consider in comparing costs among testing laboratories include:

Thoroughness of testing and whether the methods used include optimal approaches for sequence analysis as well as evaluations for large deletions and duplications.

Approaches for classifying genetic variants and notifying providers about changes in classification.

Programs for facilitating cascade testing for other family members that may benefit from genetic testing if a causative variant is found for the patient.

The use of robotics and standardized primers for gene amplification have helped to lower the costs of genetic testing. However, the costs of interpreting the results of DNA testing can be expensive, especially if the interpretation of pathogenicity is uncertain. Including samples from other affected relatives or biological parents may help with the interpretation. Public databases can be helpful in the interpretation process by establishing the frequency of a variant in different populations within that database.

In the United States, insurance reimbursement is becoming more common for genetic testing as testing becomes a more routine part of clinical care. Coverage of genetic testing by insurance will vary depending on the type of test, whether it is being done to make a diagnosis in an affected person or to predict risk in an unaffected individual, and on the patient's specific type of insurance coverage.

In a pre-authorization letter, a clear indication of the purpose of the test and the manner in which it will change management is more effective than a vague form letter. A study that reported on findings of whole exome sequencing (WES) for 250 patients (mostly children with neurologic phenotypes, all of whom had undergone prior genetic testing) found that insurance coverage for the costs was similar to other genetic testing and provided reimbursement for the majority of tests [51].

Genetic testing (especially single gene testing) and perinatal genetic screening are commonplace in many countries with nationalized public health care systems.

Where to test/resources for testing — Genetic testing is available for thousands of conditions [52]. Some genetic tests for common variants such as factor V Leiden are offered through many laboratories, while other genetic tests are more specialized and may only be available from one or two clinical laboratories. It is important to select a testing laboratory with well-curated clinical and molecular genetic information on the genes being tested.

Several online resources for obtaining genetic testing are available. As examples:

Genetic Testing Registry (www.ncbi.nlm.nih.gov/gtr/) – Directories of genetic clinics and laboratories.

GeneReviews (www.ncbi.nlm.nih.gov/books/NBK1116/) – Overviews and disease-specific discussions of counseling, diagnosis, and management for individuals and families with inherited disorders.

National Cancer Institute (www.cancer.gov/about-cancer) – Genetic components of cancer including evidence-based overview to clinical genetics (PDQ).

The Human Genome Epidemiology Network (HuGE Net) (www.cdc.gov/genomics/hugenet/default.htm) – Epidemiology and public health aspects of genetics.

Resources for genetic counseling are listed separately (see "Genetic counseling: Family history interpretation and risk assessment", section on 'Use of family history to assess genetic risk'), and disease-specific testing resources are also described in individual disease topic reviews in UpToDate.

For some rare conditions, testing is only available in a research setting. Most research laboratories are not Clinical Laboratory Improvement Amendments certified and thus not authorized to provide results to the patient for the purpose of clinical decision making. Therefore, when pursuing testing through a research study, it is important to clarify with the investigator the exact testing that will be done on the sample, if and how results might become available, and the expected turnaround time.

MANAGEMENT AND FOLLOW-UP

Acting on the results of testing — There are typically three possible outcomes from genetic testing:

A pathogenic or likely pathogenic variant associated with the patient's disorder is identified that confirms a diagnosis or a disease risk, facilitates additional testing or interventions tailored to the genetic test result, and allows genetic testing to be offered to at-risk family members when appropriate. (See "Personalized medicine".)

No variant is identified. Failure to identify a pathogenic variant does not eliminate the possibility of a causative genetic variant or an inherited risk. A negative result may mean that a genetic alteration still exists in the gene(s) tested but cannot be identified with available technologies, a genetic alteration exists in a known gene that was not tested, or a genetic alteration exists in a currently unknown or undescribed gene.

A variant of uncertain significance (VUS) is identified. The uncertainty refers to the available data regarding disease risk from clinical and research studies, not the accuracy of testing or the likelihood of disease (see 'Likelihood of disease' above). VUS may be more common in populations that are under-represented in the reference genomes included in public databases. (See "Secondary findings from genetic testing", section on 'Underrepresented ethnicities'.)

When a VUS is identified, risk estimates can sometimes be made on the basis of the family history, taking into account information from the laboratory report. It is also important to let the family know that most laboratories continue to research the significance of these variants and the variant can be reclassified at a later time. Having a plan in place to communicate and follow-up with the individual or family can be important. Additional discussion of variant classifications is presented separately. (See "Secondary findings from genetic testing", section on 'Definitions and classification of variants'.)

Repeat testing — Generally, germline genetic testing does not need to be repeated for a specific gene as long as the results are obtained from a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory and are considered to be accurate, since germline DNA sequence does not change. However, more extensive testing or re-analysis of previous sequence data may be appropriate when new information about pathogenicity of certain genes becomes available, and (as for any clinical test) re-testing for a specific gene(s) may be reasonable if there is a basis for questioning the initial results (eg, strong family history of breast and ovarian cancer with BRCA mutations identified in other family members but not the patient) or any technological advancement that may detect pathogenic variants previously missed (eg, initial testing only included sequencing, and testing to evaluate for large deletions and genomic rearrangements becomes available).

Repeat testing on tumor or blood samples may be appropriate when evaluating for new genetic changes (eg, a mutation that confers resistance to therapy) or for residual disease following potentially curative treatment.

Saving genetic material for future use — For conditions in which genes have not yet been identified or there is a lack of evidence of an effective intervention, preservation of genetic material from the affected individual by DNA banking for future genetic testing can be a reasonable option. This involves the storage of DNA (usually extracted from blood, occasionally from tissue samples) for future testing should it become desired. In the United States, most insurance companies will not pay for testing of affected family members whom they do not insure. This includes testing of banked DNA from a deceased individual to determine appropriate testing for an unaffected family member.

INFORMATION FOR PATIENTS — UpToDate offers two types of patient education materials, "The Basics" and "Beyond the Basics." The Basics patient education pieces are written in plain language, at the 5th to 6th grade reading level, and they answer the four or five key questions a patient might have about a given condition. These articles are best for patients who want a general overview and who prefer short, easy-to-read materials. Beyond the Basics patient education pieces are longer, more sophisticated, and more detailed. These articles are written at the 10th to 12th grade reading level and are best for patients who want in-depth information and are comfortable with some medical jargon.

Here are the patient education articles that are relevant to this topic. We encourage you to print or e-mail these topics to your patients. (You can also locate patient education articles on a variety of subjects by searching on "patient info" and the keyword(s) of interest.)

Basics topics (see "Patient education: Genetic testing (The Basics)")

SUMMARY AND RECOMMENDATIONS

Terminology – Genetic testing is any type of testing that helps determine the genotype (DNA blueprint) in the germline or somatic cells. Terminology is shifting to avoid nonspecific, pejorative, or confusing terms such as mutation or polymorphism and instead to use the "variant," which refers to a difference from a reference sequence, along with a qualifier about pathogenicity (table 1). (See 'Terminology' above.)

Methods – Testing can involve a single gene, panel of genes, or the entire exome or genome. For each gene, it is possible to analyze a single variant, a panel of variants, or the entire coding sequence. Methods include Sanger sequencing, microarrays, next-generation sequencing, cytogenetics, and fluorescence in situ hybridization (FISH); cytogenetics and FISH assess alterations in chromosome number or structure. The laboratory generally determines which method to use. (See 'Extent of DNA analysis' above and 'Methods' above.)

Purpose – The purpose of genetic testing is to determine the likelihood or presence of a condition or disease, and in some cases the likely response to treatment. Disease likelihood can also depend on other factors, both genetic (inheritance pattern, penetrance, and expressivity) and environmental, not all of which are well-characterized. (See 'Likelihood of disease' above.)

Applications – Clinical applications cover the lifespan, from fetal testing to oncology and pharmacogenomics. (See 'Clinical applications' above.)

Pretest considerations – Determine whether the test is indicated, the ideal age at which to test, and which test provides useful information with the least cost and burden. These considerations can be discussed during pretest genetic counseling, which can help patients understand the implications of a positive or a negative result. (See 'Questions to consider before testing' above.)

Ethical and psychosocial – Ethical and psychosocial concerns related to genetic testing include potential consequences for at-risk relatives, inability to obtain informed consent from children, and fears about genetic discrimination. Racial disparities exist and should be addressed. In the United States, legal protection is available at the federal level through the Genetic Information Nondiscrimination Act (GINA); however, these protections do not apply to long-term care, life insurance, or disability insurance. Other countries have enacted privacy and nondiscrimination legislation as well. (See 'Ethical, legal, and psychosocial issues' above.)

How to order – Initial testing should be performed on an affected individual when possible; future testing can be tailored for at-risk relatives. Testing can be ordered by any clinician involved in the individual's care who address the appropriate test and methodology, logistics of test ordering, counseling, and use of results in clinical care. This may include a clinical geneticist, genetic counselor, primary care provider, or disease specialist. Informed consent is a foundation for the voluntary nature of genetic testing. The Genetic Testing Registry and other resources are available. (See 'Practical issues' above.)

Follow-up – Management may involve additional testing or interventions tailored to disease or disease risk. If testing is negative or reveals a variant of uncertain significance, management depends on the estimated likelihood of disease. Positive results from germline testing generally do not need to be repeated if the results are obtained from a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory and are considered to be accurate, since germline DNA sequence does not change. More extensive testing, re-analysis of sequence data, or review of new information about pathogenicity may be appropriate. (See 'Management and follow-up' above.)

Genetic counseling and personalized medicine – (See "Genetic counseling: Family history interpretation and risk assessment" and "Genetics: Glossary of terms" and "Personalized medicine" and "Secondary findings from genetic testing".)

ACKNOWLEDGMENTS — The UpToDate editorial staff acknowledges Vickie Venne, MS, CGC, and Deborah Hartzfeld, MS, CGC, who contributed to earlier versions of this topic review.

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