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Beltina.org Genetics and Molecular Medicine Genetic Testing - methods and proceduresGenetic Testing - methods and proceduresGenetic Testing - methods and procedures to determine the presence of a genetic disorder. Diagnostic genetic testing can identify the cause of symptoms resulting from GENE mutations and CHROMOSOMAL DISORDERS. Even when the outcome is certain, the knowledge of the genetic disorder may have little therapeutic value yet create distress for the individual. Genes make all the proteins and enzymes that work in cells and tissues throughout the body, for example, to digest fat or to make energy available to muscle. Southern blot testing determines the presence or absence of a specific nucleotide sequence within different sized fragments of DNA. Direct gene testing can be performed when scientists know exactly where a gene is located on a chromosome and what changes in the gene cause a specific disease.
Clinical Pearl: In general, conditions with common mutations and high penetrance, and whose diagnosis results in a change in management are the best candidates for testing. Diagnostic testing is used to confirm or rule out a known or suspected genetic disorder in a symptomatic individual. DNA testing may yield diagnostic information at a lower cost and with less risk than other procedures.
Diagnostic testing of an individual may have reproductive or psychosocial implications for other family members as well.
Predictive testing is offered to asymptomatic individuals with a family history of a genetic disorder.
Predictive testing is MEDICALLY INDICATED if early diagnosis allows interventions which reduce morbidity or mortality. Even in the absence of medical indications, predictive testing can influence life planning decisions. Because predictive testing can have psychological ramifications, careful patient assessment, counseling, and follow-up are important. Many laboratories will not proceed with predictive testing without proof of informed consent and genetic counseling. Identification of the specific gene mutation in an affected relative or establishment of linkage within the family should precede predictive testing. Predictive testing of asymptomatic children at risk for adult onset disorders is strongly discouraged when no medical intervention is available (ACMG Policy Statement).
Carrier testing is performed to identify individuals who have a gene mutation for a disorder inherited in an autosomal recessive or X-linked recessive manner. Genetic counseling and education should accompany carrier testing because of the potential for personal and social concerns.
Molecular genetic testing of an affected family member may be required to determine the disease-causing mutation(s) present in the family . Carrier testing can improve risk assessment for members of racial and ethnic groups more likely to be carriers for certain genetic conditions. A laboratory that performs the disease-specific test of interest must be identified before any prenatal diagnostic test procedure is offered.
All prenatal diagnostic test procedures have an associated risk to the fetus and the pregnancy; therefore, informed consent is required, most often in conjunction with genetic counseling.
In most cases, before prenatal diagnosis using molecular genetic testing can be offered, specific gene mutation(s) must be identified in an affected relative or carrier parent(s).
Preimplantation testing is performed on early embryos resulting from in vitro fertilization in order to decrease the chance of a particular genetic condition occurring in the fetus.
Preimplantation testing is only performed at a few centers and is only available for a limited number of disorders. Preimplantation testing is not possible in some cases due to difficulty in obtaining eggs or early embryos and problems with DNA analysis procedures. Due to possible errors in preimplantation diagnosis, traditional prenatal diagnostic methods are recommended to monitor these pregnancies. Newborn screening identifies individuals who have an increased chance of having a specific genetic disorder so that treatment can be started as soon as possible. Newborn screening is performed routinely at birth, unless specifically refused by the parents in writing. Screening tests are not designed to be diagnostic, but to identify individuals who may be candidates for further diagnostic tests. Many parents do not realize that newborn screening has been done (or which tests were included), even if they signed a consent form when their child was born. Education is necessary with positive screening results in order to avoid misunderstandings, anxiety and discrimination.
The practical application of genetic test information depends on some mitigating factors, such as genetic heterogeneity, penetrance, and variable expressivity.
Genetic heterogeneity: Simply put, this means that different mutations can cause the same disease. Mutations also can be in the same or in different genes, and some may act in a dominant fashion, or others recessive. Gene Penetrance: 100% penetrance means that every person with a mutation will have the disease.


Variable Expressivity: Severity can vary widely for some diseases, even among affected individuals in the same family.
Sensitivity – the proportion of people with a clinically significant disease (or who will get a disease) that are correctly identified by the test. Both events underscore the increasing importance of data to the business of personalized medicine. Either way, in securing another massive round of financing and lowering its price to $99, the last company standing of the direct-to-consumer (DTC) genetic testing pioneers appears unlikely to be joining deCODE, Navigenics and others in abandoning its consumer-facing approach any time soon.
Last week, personal genetics company 23andMe announced that it had formally delivered the first round of documentation to the U.S.
I sat down last week with The Burrill Report to discuss 23andMe’s recent activities and their implications for the future of DTC genetic testing and personalized medicine.
Last month three direct-to-consumer (DTC) genetic testing companies opened their mailboxes to find a slightly ominous but entirely expected letter from the FDA.
Later today I will join several colleagues here in Chicago, IL at the American Society of Clinical Oncology (ASCO) annual meeting for a panel discussion on Direct-to-Consumer Genetic Testing for Cancer: What Physicians Need to Know (pdf). This will, I believe, mark direct-to-consumer (DTC) genetic testing’s formal debut at ASCO. In advance of ASCO, here are several items of interest from the past few weeks in DTC genetic testing. Last month, the National Institute on Aging and the Alzheimer’s Association issued new diagnostic guidelines that divide Alzheimer’s disease into three distinct stages, reflecting recent evidence that the disease begins to affect the brain years before symptoms become evident. At least for the moment, the new guidelines are intended to be used only with patients enrolled in clinical trials, making them more of a work in progress and not a standardized method of determining disease onset in Alzheimer’s patients. Social media – including Facebook, Twitter and other social networking platforms – are widely credited with fundamentally altering the nature of political discourse and, in some instances, credited as catalysts of political revolution.
The study’s findings are valuable for ALS patients, who frequently experiment with unproven treatments in an attempt to slow progression of the degenerative disease for which there is not yet an effective therapy.
With so many developments at the intersection of genomics and the law, there are often a variety of interesting stories that, for one reason or another, don’t find their way into a full-length posting on the Genomics Law Report.
Nevertheless, it seems increasingly clear that federal science funding is unlikely to increase from its fiscal year 2010 levels, and funding almost certainly will not meet the targets President Obama set in his FY 2012 budget proposal. Earlier this month an FDA advisory panel met for two days to consider a range of issues pertaining to clinical direct-to-consumer (DTC) genetic testing. In response, the FDA agreed to reopen the public docket in order to receive additional public input on scientific issues concerning DTC genetic tests. For those with an interest in the FDA’s oversight of DTC genetic testing, this is the first of several opportunities to be heard.
Beginning this week, we are unveiling a new format for the Genomics Law Report’s regular Twitter Roundup. John Conley is Kenan Professor of Law at the University of North Carolina and of counsel to Robinson, Bradshaw & Hinson, where he specializes in intellectual property and biotechnology.
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 Unported License. The KARYOTYPE, which uses microphotographs to examine and depict an individual’s chromosomes, is one of the more common methods of genetic testing. This knowledge can be helpful when there are treatments and treatment choices for the resulting conditions, and in FAMILY PLANNING decisions. This is currently a significant issue with genetic testing for HUNTINGTON’S DISEASE, for example, a fatal neurodegenerative disorder for which there is no treatment or cure. If that sequence is present in a patient’s sample, the probe will bind to it and light up under a fluorescent microscope. Biochemical testing can be used to look for the presence (or absence) of proteins or enzymes, their quantity (extra, sufficient, reduced, absent), or their structure (normal vs. Indirect testing requires blood from several family members, including those that are known to be carriers or affected with a specific condition. Prenatal diagnostic tests are offered when there is an increased risk of having a child with a genetic condition due to maternal age, family history, ethnicity, or suggestive multiple marker screen or fetal ultrasound examination. Individuals seeking prenatal diagnosis for these conditions should be referred to a professional trained in genetic counseling for a complete discussion of the issues (ACMG Policy Statement). It is generally offered to couples with a high chance of having a child with a serious disorder. For example, there are dominant, recessive, and X-linked forms of Charcot Marie Tooth disease. Huntington’s disease (a fatal, adult-onset neurodegenerative disorder) and achondroplasia (the most common form of dwarfism) are examples of conditions with complete penetrance. For example, current cystic fibrosis tests pick up about 90% or mutations in white, 50% in African Americans and Hispanics, and on 30% in Asian Americans. Coverage of the deal is everywhere, including a typically excellent overview from Matthew Herper of Forbes.
That transaction left plenty of deCODE shareholders out in the cold, and those shareholders aren’t likely to be feeling any better about things this winter. Food and Drug Administration (FDA) in an attempt to receive 510(k) clearance for its consumer product.


Genomes Unzipped received 12 free kits from Lumigenix for review purposes, and Dan Vorhaus has provided legal advice to the company. It should also serve as another reminder that, despite its relatively small numbers (both in terms of dollars and customers), DTC genetic testing continues to exert an outsized influence when it comes to conversations about the future of genomic medicine. This reflects current thinking that Alzheimer’s begins creating distinct and measurable changes in the brains of affected people years, perhaps decades, before memory and thinking symptoms are noticeable. But social media’s ability to affect change need not be limited to politics, as recent developments in the arena of personalized medicine and consumer genomics continue to demonstrate. Last month, PatientsLikeMe, an online patient community, made headlines with a study published in Nature Biotechnology in which the company analyzed self-reported data from nearly 600 patients to demonstrate that the use of lithium had no effect on the progression of amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig’s disease). But the long-term impact of the study’s methodological approach, which suggests “that data reported by patients over the internet may be useful for accelerating clinical discovery and evaluating the effectiveness of drugs already in use,” should be felt far beyond the ALS community.
At least for the moment, the two houses of Congress appear, finally, to be edging toward a budget compromise that would bridge the $51 billion gap between the House bill (which passed at the beginning of March) and the most recent Senate proposal. The non-voting advisory panel’s discussion (pdf), including whether certain genetic tests or categories of tests should be made available only through qualified healthcare professionals, sparked considerable controversy (see here for a collection of links) and confusion. Other methods include cytogenic analysis, AMNIOCENTESIS, and CHORIONIC VILLI SAMPLING (CVS).
The matter of genetic testing to screen for the presence of GENETIC DISORDERS, particularly in people who do not have symptoms or apparent increased risk for conditions of genetic origin, remains an issue of intense ethical debate.
People who carry the gene MUTATION for Huntington’s disease are certain to develop the disease in midlife. FISH also can be used to detect chromosome rearrangements, marker chromosomes (extra pieces of unidentified chromosomal material), and duplications or deletions of large pieces of DNA.
Bands on the film indicate the presence of a DNA piece of interest, and the length of the DNA fragment where it resides.
The American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics (ACMG) recommend that CF carrier screening be offered to all couples when at least one member of the couple is Caucasian and pregnant or considering pregnancy.
Because DNA contains pieces, called markers, that are unique to individuals and families, laboratories can find the markers unique to a family with a genetic disease. Carrier testing is offered to individuals who have family members with a genetic condition, family members of an identified carrier, and individuals in ethnic or racial groups known to have a higher carrier rate for a particular condition. Routine prenatal diagnostic test procedures are amniocentesis and chorionic villus sampling (CVS). Preimplantation testing provides an alternative to prenatal diagnosis and termination of affected pregnancies. There are more than 1,000 mutations in the CFTR gene that are known to cause disease, but most tests look for around 100 of the most common mutations.
In diseases with multiple modes of inheritance, the family history provides invaluable information that will lead you to the correct diagnostic test. Even though we know that three copies of chromosome 21 will result in Down syndrome, we can’t make reliable predictions about how severely any one individual patient may be affected. This is particularly true when the discussion turns to appropriate policy and regulatory oversight. That’s a good thing, given that the current continuing resolution is set to expire on April 8. Both CDRH director Jeffrey Shuren and OIVD Director Alberto Gutierrez are scheduled to participate in a public question-and-answer session on May 5th in Orlando, FL.  An additional town hall discussion is slated for San Francisco, CA later in the year. Some genetic testing methods are highly sophisticated and require specialized equipment and knowledge available only in research centers. Some such practices, such as testing for PHENYLKETONURIA (PKU) in newborns, have become standard in the United States. Southern blotting is often used to determine the size of trinucleotide repeat expansions or large scale deletions. More specialized procedures include placental biopsy, periumbilical blood sampling (PUBS), and fetoscopy with fetal skin biopsy. Therefore, a negative test result does not mean that a patient’s risk status has changed. The breast cancer susceptibility genes, BRCA1 and BRCA2, for example, show incomplete penetrance.
The Genomics Law Report will post additional details for that meeting as they are made available.
Others, such as those for the so-called CANCER genes (BRCA-1, BRCA-2, CA-125, and others), often raise more questions than answers because the consequence of having such genes remains uncertain. It is further recommended by ACOG and ACMG that CF screening be made available to individuals of other racial and ethnic groups.



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