Session Two: Evaluation and Testing Decisions
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Session Two: Evaluation and Testing Decisions






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  • Facilitator Script: [ See supplementary information for example introduction.]
  • Key Point: There are three essential skills in family history assessment for genetic risk. Facilitator Script: Before we get started in this session about genomic evaluation, let’s briefly recap the three essential skills in family history assessment for genetic risk. In the last session, we learned how to distinguish genetic from non-genetic disease using clues from the family history by: Interviewing for sufficient detail, including family structure and manifestations of disease Recognizing features suggestive of underlying genetic mechanisms, such as early age of onset Assessing relationships between affected family members to guess at inheritance patterns In the interest of time, we won’t be practicing these skills in the clinical examples we discuss today. For each example we discuss, you can assume these initial steps have been performed. In fact, as you will see, the information you obtain during risk assessment is critical to forming a genetic testing strategy, so we are building on those risk assessment skills. Today we will discuss how risk assessment information can inform your evaluation plan and testing decisions.
  • Key Point: There are a number of decisions to make between risk assessment and ordering genetic testing. Facilitator Script: To bridge the gap between risk assessment and genetic testing, you need a thoughtful evaluation plan. We will use the clinical and family history to focus evaluations and narrow the differential. We’ll also discuss strategies that maximize utility and cost-effectiveness of genetic testing.
  • Facilitator Script: In this workshop, we will cover these topics
  • Key Point: Evaluation and testing decisions do not necessarily involve discreet steps that can be generalized from case to case. Facilitator script: As a clinician, you must juggle several pieces of information during your evaluation. Although we will be discussing each piece one-by-one for educational purposes, in the clinic you may be synthesizing this information all at once, or in a different order than we present.
  • Key Point: Cost-effective evaluation is informed by the data you gather in risk assessment Facilitator script: In the following clinical examples, we’ll discuss how to: Use clinical and family history to narrow the differential Identify the most likely causative variants and sequence first and second tier tests Develop a strategy for the most cost-effective testing using family history information Again, although we are presenting these steps sequentially, test selection and strategy do not necessarily need to happen in a particular order, and may even occur simultaneously.
  • Facilitator script: Our first step in genetic testing decisions is to narrow the differential.
  • -TRANSITION- Facilitator Script Let’ s walk through this with a model case. Here is Tim, a ten-year-old male referred by his pediatrician for developmental evaluation. Upon starting preschool, he was noted to be clumsy in comparison to his peers. Tim’s clumsiness has increased to the point where he is having several falls a day, some with injury
  • Facilitator Script: Upon intake, you collect the following information. There is little of note except the family history of movement problems. We’ll come back to this soon.
  • Facilitator Script: On exam, you note the following: Major and minor structural anomalies are absent Intellectual ability appears to be normal Normal muscle strength Abnormalities of speech, arm movements, and gait Evidence of abnormal reflexes, cranial nerve responses, and vibration sense
  • -INSTRUCTIONS- Large group discussion to assess learners’ prior understanding of a differential for movement disorders Jot down ideas generated by participants on white board/iPad/paper easel. Elicit both genetic and non-genetic diagnoses Facilitator Script : Given the information you have now, what causes/conditions would you want to explore for this patient? Additional prompts What symptoms are you concerned about? Are there non-genetic/treatable causes of the symptoms this patient presents? Do you suspect a genetic ataxia? Why? Do you know of specific genetic conditions that could be associated with these findings?
  • Key Point: The initial differential may be broad and general. -INSTRUCTIONS- Debrief for the large group discussion, reinforcing evidence to support certain diagnoses, and filling in gaps for diagnoses that were not brought up. Facilitator Script: Your initial differential should include non-genetic causes that can be easily ruled-out. The initial list may include specific genetic ataxias if there are strong signs, but at this point it is enough to recognize the possibility of a genetic cause. Evidence to support a genetic ataxia come from red flags and patterns, and may include: Family history of movement disorders A specific constellation of neurologic findings Constellations of non-neuro findings (not evident in this case: ie. dysmorphic features, behavioral profiles) Early age of onset Note : If people suggest specific genetic ataxias, note them and then refocus on the broader differential. For example: “We’re going to come back to these genetic ataxias, but right now let’s focus on the non-genetic candidates.”
  • Key point: First rule out non-genetic and treatable causes of ataxia Facilitator script: The first step is to rule out non-genetic causes of ataxia which may be treatable, such as checking vitamin E levels. You can see by the labs that were done on the right side of the slide, that we can cross of many things on our list We’ve listed some of the more common and well-known ataxias here, but as you will see, the genetic differential may be more complex. More detail: MRI is normal, r/o structural abnormalities MRI in cerebellar ataxia is non-specific and will not distinguish the types or the conditions, with some rare exceptions. In this age group toxins, such as heavy metals and alcohol, are less likely.
  • Key Point: A number of web-based tools are available for developing and refining your genetic differential. Instructions: OPTIONAL INTERACTION: If time allows, begin by asking audience if they have experience with any of these tools. Were they helpful? Any other tools they use that are not shown here? Concentrate on this slide on using tools to form the initial genetic differential. Don’t get bogged down in the relative strengths, limits and best uses of each of these tools. Refer class to handout. We’ll discuss refining/prioritizing in the next few slides. We’ll discuss using tools for refining differential in the next few slides. Facilitator script: The next step can be to use tools to identify potential genetic diagnoses. There are a number of web-based tools are available for developing and refining your genetic differential. Each of these tools can be useful to identify an initial list of candidate conditions for a given clinical presentation. GeneTests, OMIM and published guidelines are oriented around the overarching disease or primary finding, such as “ataxia” or “developmental delay” SimulConsult can be searched by the primary finding too, but is also useful for identifying a differential based on collections of findings. You may find that you will need to use more than one tool to capture the best disease candidates. GeneTests, SimulConsult and OMIM are linked and each can be accessed from the other. More detail: GeneReviews is a free medical genetics information resource that contains expert-authored and peer-reviewed genetic disease descriptions. It is most useful after you have formulated an initial differential diagnosis. You can search for specific conditions and learn more about their distinguishing features to refine and prioritize the differential. A few summaries of general disease categories exist; for example there is a general summary of genetic ataxias. Summaries include a differential diagnosis. SimulConsult is a free decision-support software that helps build and refine a differential. You can search based on a primary finding, or enter a collection of findings. The tool will suggest additional findings and labs to consider. The National Guideline Clearinghouse is an online database of published disease-specific guidelines for diagnosis and management. These publications often suggest evaluations and diagnoses to consider. OMIM is an online catalog of genetic syndromes and gene associations. You can search for specific diseases to learn about defining features, or you can enter clinical features to get a differential. Other tools not shown here include: London Dysmorphology Database UpToDate Handout: Differential Diagnosis POC tool
  • Key Point: We need a way to filter and prioritize the initial differential. Instructions: Don’t focus on details or read off the lists in the slides. Use this slide to demonstrate the large number of genetic conditions that might be associated with a general feature like “ataxia” OPTIONAL DEMONSTRATION: When time and technology allow, use the links below for a live demonstration of an initial search for differential on GeneTests, OMIM, or SimulConsult. Consider also showing how GeneTests is linked to SimulConsult. Facilitator script: As you can see, a search for “ataxia” in these tools produces quite a long list of candidates to consider. (Left: GeneReviews; Center: SimulConsult; Right: OMIM) For the non-geneticist, it may be difficult to know where to start. Let’s talk about strategies for refining these lists. Right now the top genetic ataxia candidates are: Ataxia-telangiectasia Friedreich ataxia Spinocerebellar ataxia Links for live demonstrations:
  • Key Point: Identifying distinctive patient features can help you rank your differential in order of probability. Facilitator script: Depending on the length and complexity of your initial differential, you may use different tools to refine the list. The process starts with identifying distinctive patient features and then comparing these to disease descriptions When your differential is short, GeneReviews can be helpful to learn about key findings for each condition. (Left: Summary of disease presentation, natural history, and differential with distinctive features in GeneReviews) When your differential is long, SimulConsult can help match your patient’s features to the most likely candidates. (Right: screen capture of the SimulConsult input fields. Can be filtered by features relevant to specific conditions, or by body system)
  • -INSTRUCTIONS- Large group discussion Facilitator Script : What stands out to you the most? What is most distinctive? Note : If people mention family history and inheritance patterns, refocus on the personal history. For example: “We’re going to come back to the family history in a minute, but right now let’s focus on the clinical features.”
  • INSTRUCTIONS Animated slide, use arrow keys to step through to reveal each point. Key Point: Both presence and absence of distinctive features can inform your differential, so be sure to note both. Facilitator Script: Clinical features may point toward underlying disease in a particular system, structure, or pathway. That may in turn point to a specific gene or set of genes. In general, distinctive features may include labs, characteristic physical features or anomalies, or even distinct cognitive and behavioral phenotypes. In this particular case, unique features are neurological, pointing toward a cerebellar ataxia. Evidence is lacking for an ataxia with non-neurologic findings, such as ataxia-telangiectasia, which involves skin findings and abnormal AFP and immunoglobin Evidence is lacking for a metabolic or muscle disease More details Dysmetria in upper extremities, ataxic gait, and speech abnormalities suggest cerebellar disease. Slow horizontal saccades indicate cranial nerve involvement. Decreased vibration sense suggests posterior column involvement. deep tendon reflexes are absent
  • Key Point: Use the distinctive features you’ve identified to rank your differential by probability. Facilitator script: Use the distinctive features you’ve identified to rank your differential by probability. The tools we’ve discussed can help you do this: Use GeneReviews disease summaries to prioritize a short list. Use SimulConsult when you have a broad/long differential and lots of clinical information. This slide shows a screen capture of an example output that one might obtain when developing a differential for ataxia The software compares the clinical features you have entered to a database of known genetic and neurological conditions. It then generates a differential ranked by relative probability, which is dynamic and updates in real time as you add more information. Note that AT, FA, and SCA are in the top 5 More detail: Clicking on a condition on the differential will reveal common clinical findings specific to that condition. You can then indicate if those findings are also present in your patient, and the program will update the probability of that diagnosis
  • Key Point: We can shorten our list of probable diagnoses significantly by looking at distinctive features. INSTRUCTIONS: Animated interactive slide. Optional group discussion to assess what audience knows already about each condition and their assessment of the likelihood. Use arrows to fill in each field. Facilitator script: Let’s look at some of the most common conditions you might identify using SimulConsult or GeneReviews. Now that we’ve looked more closely at the distinctive features in this patient, we want to determine how well the patient matches these common forms of genetic ataxia. INTERACTION: What do you know about the defining features of (disease name) ? How likely do you think it is that Tim has (disease name) ? Note : If people mention family history and inheritance patterns, refocus on the personal history. For example: “We’re going to come back to the family history in a minute, but right now let’s focus on what the clinical features tell us.” Handout: Summary of each syndrome More detail: Ataxia telangiectasia Ataxia Telangiectasia (AT) is a rare inherited disorder that affects the nervous, immune, and other body systems. Individuals with AT have progressive difficulty with coordinating movements (ataxia) beginning in early childhood, usually before age 5. Affected children typically develop difficulty walking, problems with balance and hand coordination, chorea, myoclonus, and neuropathy. Most children require a wheelchair by adolescence. People with AT also have slurred speech and oculomotor apraxia. Telangiectases often occur in the eyes and on the surface of the skin and are often present in early childhood. People with AT often have a weakened immune system, and many develop chronic lung infections. They are also at an increased risk of developing cancer, particularly leukemia and lymphoma. Affected individuals are very sensitive to the effects of radiation exposure, including medical x-rays. Although people with AT usually live into adulthood, their life expectancy is reduced. AT inherited in an autosomal recessive pattern. Carriers of an AT gene mutation are also at increased risk to develop some cancers, especially breast and leukemia. Friedreich’s ataxia Friedreich’s ataxia (FA) is characterized by slowly progressive ataxia with mean onset between age ten and 15 years and usually before age 25 years. FA is typically associated with dysarthria, muscle weakness, spasticity in the lower limbs, scoliosis, bladder dysfunction, absent lower limb reflexes, and loss of position and vibration sense. Approximately two-thirds of individuals have cardiomyopathy; up to 30% have diabetes mellitus; and approximately 25% have an "atypical" presentation with later onset or retained tendon reflexes. Neiman Pick type C Niemann-Pick disease type C is a lipid storage disease that can present in infants, children, or adults. Neonates can present with ascites and severe liver disease from infiltration of the liver and/or respiratory failure from infiltration of the lungs. Other infants, without liver or pulmonary disease, have hypotonia and developmental delay. The classic presentation occurs in mid-to-late childhood with the insidious onset of ataxia, vertical supranuclear gaze palsy, and dementia. Dystonia and seizures are common. Dysarthria and dysphagia eventually become disabling, making oral feeding impossible; death usually occurs in the late second or third decade from aspiration pneumonia. Adults are more likely to present with dementia or psychiatric symptoms. Spinocerebellar ataxia The hereditary ataxias are a group of genetic disorders characterized by slowly progressive incoordination of gait and are often associated with poor coordination of hands, speech, and eye movements. Frequently, atrophy of the cerebellum occurs. There are upwards of 35 different spinocerebellar ataxia (SCA) syndromes and it is often difficult to distinguish from one another. Inherited (genetic) forms of ataxia must be distinguished from the many acquired (non-genetic) causes of ataxia. The genetic forms of ataxia are diagnosed by family history, physical examination, neuroimaging, and molecular genetic testing. [Adapted from GeneTests reference]
  • Key Point: Family history patterns can be critical to refining your differential. Facilitator script: Now let’s return to the family history and see how that contributes to our differential. Again, the tools we’ve discussed can help you incorporate family history into your refinement process. You can consult GeneReviews or OMIM and compare your patient’s family patterns to the inheritance of each disease. As illustrated on this slide, SimulConsult will also take family history information into account when prioritizing the differential.
  • INSTRUCTIONS: Group discussion Facilitator script: Do you think the movement disorders in the family are related? Why or why not? If so, what is the most likely pattern of inheritance? What else do you notice about how movement disorders are presenting in this family?
  • Key Point: Though we need to confirm family diagnoses with records, this is a suspicious family history. Facilitator script: This is a suspicious family history for an autosomal dominant condition. It is likely that the father’s and grandfather’s findings are related to a cerebellar ataxia When possible, we should confirm family diagnoses with records in order to be confident about an inheritance pattern Older relatives could have coincidental, common but unrelated age-related movement disorders, such as Parkinson disease Family could have coincidental non-genetic/treatable conditions that mimic genetic ataxia, like a toxicity. It is also possible that family reports are inaccurate. Of special note, the onset of the condition seems to be earlier with each generation. This is called “anticipation” and is sometimes accompanied by an increase in severity of symptoms Anticipation is most often associated with “ trinucleotide repeat ” variants, which are unstable and can expand in size from generation to generation, changing age of onset and severity.
  • Key Point: Inheritance patterns can rapidly narrow your differential when the family history is distinctive. INSTRUCTIONS: Animated interactive slide. Group discussion to assess what audience knows already about each condition and their assessment of the likelihood. Use arrows to fill in each field. Facilitator script: Let’s look again at that list of common ataxias we identified before. INTERACTION: What do you know about the inheritance pattern of (disease name) ? How likely do you think it is that Tim has (disease name)? After reveal: Most of the genetic ataxias are autosomal recessive. When dominant ataxia is suspected, the spinocerebellar ataxias are a likely candidate. Anticipation in the family history is also suggestive of SCA, which is frequently associated with a triplet repeat variant. Looking at inheritance patterns first may have saved us time distinguishing features of the conditions on the differential. Again, in real clinical time, you will probably be assessing clinical features and family history simultaneously. And, in reality, the differential diagnosis may not be so clear-cut. Your next step will depend on your level of confidence in the clinical evidence and your assessment of the most likely diagnosis. Options are: Take more time to confirm family diagnoses and research candidate conditions Involve a genetics specialist (we’ll talk more about consultation and referral later) Research the testing options, which we will discuss next. Handout: Summary of each syndrome
  • Key Point: The SCAs are a group of primarily dominant cerebellar ataxias with different genetic causes and overlapping features. Facilitator script: The SCAs are a group of disorders characterized by progressive incoordination of gait, hands, speech, and eyes. Atrophy of the cerebellum may also occur. Anticipation may make prognosis for SCAs challenging. Family members who have earlier onset disease may also have more severe symptoms and faster progression. Thus, we cannot predict that Tim’s disease course will be similar to his father or grandfather. Though we’ve narrowed our differential to spinocerebellar ataxia, note that there are multiple subtypes of the disease with different genetic causes. This genetic diversity will be significant in our next step: selecting appropriate tests. (transition)
  • Facilitator script: Let’s continue with our patient Tim and look at how we make decisions about appropriate genetic testing.
  • Key Point: Tools are available to identify genes associated with a condition. Facilitator script: We can utilize the same tools we’ve discussed before to identify the genes associated with a given condition. Illustrated here is an abbreviated list of genes associated with the various subtypes of SCA, generated by a search on GeneTests. As you see, there are 36 subtypes, each associated with a different gene. (Genetic heterogeneity discussed further on next slide)
  • Key Point: A disease may be associated with just a single gene, or with any one of a multiple number of genes. Facilitator script: SCA is an example of a condition that demonstrates “genetic heterogeneity”. You do not need to memorize the term genetic heterogeneity, but it is the concept that a single disorder can be caused by any one of a multiple number of variants independently associated with the disease. (These variants are not acting together in one individual, but have been seen in different individuals with the disease. “Or” not “and”) This is in contrast to a condition like Huntington disease, which is associated with just one gene. Genetic heterogeneity means we have to make a decision about whether to target a single gene, or try to capture all possible genes on a single test. Let’s talk about how to do that in the following slides. (transition)
  • Key Point: Use gene frequency and phenotype data to identify the most likely candidates Facilitator script: Genetic heterogeneity means we have to make a decision about whether to target a single gene, or try to capture all possible genes on a single test. Our first task is to determine whether there is evidence that subtypes of a condition, like a specific SCA, can be clearly distinguished from each other based on clinical features. Next, we want to determine whether there is evidence that certain subtypes are more common, and therefore more likely in our patient (This will be practiced on the next slide) More details: Use tools like GeneReviews and OMIM to compare the different subtypes and genes associated with the condition. Inheritance patterns and published diagnostic criteria can also be useful evidence for this step.
  • Instructions: Interactive slide. After describing the evidence on this slide, generate discussion about whether testing could reasonably be targeted. Facilitator script: From GeneReviews we learn that reduced saccadic velocity is most common in SCA type 2 (71-92%), while we see that feature in 50% of SCA1, and less than 10% of the other subtypes. Dystonia and pyramidal involvement also differ somewhat from subtype to sybtype. We also learn that three subtypes (2, 3, and 6) account for the majority of SCA. Those three subtypes have roughly the same frequency. INTERACTION: Given this evidence, how confident are you that you could distinguish between the subtypes based on clinical features? Would you choose to target testing, or try to capture multiple SCA genes? Which genes would you target or include on a panel? Figure 1. From GeneReviews: Worldwide distribution of SCA subtypes [Schöls et al 1997, Moseley et al 1998, Saleem et al 2000, Storey et al 2000, Tang et al 2000, Maruyama et al 2002, Silveira et al 2002, van de Warrenburg et al 2002, Dryer et al 2003, Brusco et al 2004, Schöls et al 2004, Shimizu et al 2004, Zortea et al 2004, Jiang et al 2005].
  • Key Point: When subtypes are equally common and can’t be distinguished clinically, use a multi-gene panel. Facilitator script: The SCAs are difficult to distinguish clinically, and a step-wise protocol is typically used, starting with a multi-gene panel of the 6 most common genes, followed by a panel of 6 less common genes. When in doubt ask the lab for assistance. Lab specialists can often tell you what types of tests exist and which one is most appropriate for your patient. (Case where single gene testing is better discussed on next slide)
  • Key Point: Consider detection rate, limitations, and costs of available technologies. Facilitator script: Though multi-gene panels can be useful in patients like Tim, becoming over-reliant on panels drives up the cost of care. For example, if our patient Tim had lacked a family history, and involved muscle weakness and scoliosis, the recessive condition Friedreich ataxia would have been more likely. Diagnostic criteria exist for FA, and can identify up to 75% without genetic testing. Confirmatory genetic testing targeted at the single gene associated with FA is more cost-effective than a general ataxia panel. More details: Testing targeted to a single gene may be more cost-effective when: One gene accounts for the vast majority of cases (low genetic heterogeneity) Subtypes can be clearly distinguished by clinical features Subtypes can be clearly distinguished by inheritance pattern Remember that all genetic tests have limitations. Even whole genome sequencing cannot detect certain types of variants, such as triplet repeat variants like those common in SCA and Friedreich ataxia.
  • Key Point: Support is available to improve your evaluation and testing decisions. Facilitator script: To summarize, prioritizing a differential diagnosis requires due-diligence involving: Confirming family history with records Comparing features of overlapping conditions Investigating population prevalence of various conditions Familiarity with genetic testing criteria Everyone has a different comfort level with the genetic differential and test selection, and genetic conditions vary widely in their complexity. Consider referral or consultation with a genetics specialist when you lack the time or evidence to support a specific diagnosis and testing strategy. More detail: Genetic counselor/geneticists can help: Contact family Dig up records Do literature search and review Provide patient advocacy and support information Help arrange testing and facilitate insurance submission Lab specialists can help: suggesting multi-gene testing panels, step-wise tests based on frequency Identifying clinical features that suggest you can target testing to a single gene Facilitate insurance submission
  • Facilitator script: Once we’ve determined WHAT we will be testing for, it is important to identify WHO in the family to test. Often testing can start with the patient, but we will also talk about situations where testing the patient isn’t the best first step. We also need to determine who else in the family is at risk and can benefit from testing, and facilitate family communication about this. Let’s return to our patient Tim to explore these ideas. (Illustrated algorithm is just an example. The specific order of testing varies based on the clinical details.)
  • INSTRUCTIONS: Interactive slide. Generate discussion about inheritance patterns and risk for relatives.
  • Key Point: You can quickly estimate risk to first and second degree relatives for an autosomal dominant condition. Facilitator script: Generally speaking, risk for autosomal dominant conditions is halved for each generation away from the last confirmed diagnosis. For example, the aunt is a first-degree relative of the grandfather, and so has a 50% risk. Her son has half her risk, or 25%. If the aunt is diagnosed, then her son’s risk becomes 50%. More details: “ Cascade testing” is an approach to family testing in which all first-degree relatives of each newly diagnosed individual are offered testing. For conditions like SCA which have a typical age of onset, genetic specialists can help refine risk with statistical calculations based on whether symptoms have developed at a given age. The risk for autosomal recessive conditions depends on the carrier status of the parents, which is related to both family history and population carrier rates.
  • Key Point: A negative is uninformative in at-risk relatives if the family’s causative variant is unknown. INSTRUCTIONS: Animated interactive slide. Use arrow key to introduce an alternate scenario, indicate test results and reveal answer. Generate discussion about testing strategy. Use arrow key again to reveal answer. Facilitator script: For the scenario we’ve presented, you would typically test your patient Tim, since he has symptoms. Alternatively, you could start testing in Tim’s father or grandfather, then confirm in Tim. (ARROW KEY) However, imagine a scenario where the aunt or cousin are your patient, and no prior family testing has been done. (Perhaps Tim and his father declined testing, the cousin was brought to you first because of the family history, or the cousin presented for other indications, and this family history was incidentally discovered). INTERACTION: (ARROW KEY) What would a negative result in the cousin mean if no prior family testing has been done? REVEAL: (ARROW KEY) We can’t predict disease status if we don’t know the causative result in the family. Ideally you should start testing in an affected individual. More detail: A negative in an asymptomatic individual could mean: The patient did not inherit the causative family variant The causative variant was not included on the test (the family has a rare variant not included on the panel)
  • Key Point: For the most cost-effective approach, target testing when the family mutation is known. Facilitator script: When the causative mutation or alteration is known in a family, test at-risk relatives for that specific mutation. This is the most time and cost effective approach.
  • Key Point: Communicate with the family about risk, test decisions and strategies, and next steps INSTRUCTIONS: This slide wraps up the large group discussion of Tim’s case. It is not a header/ introduction to the subsequent small group. Facilitator Script: The patient and family may not need to understand all the details of the differential and how you eliminated candidate diagnoses However, a general understanding of risks to the family will put the purpose of testing in context Why you suspect a particular diagnosis Whether there is any doubt about the testing plan How well a test can confirm or rule-out a diagnosis What your next steps will be Who else may be at risk and whether they can be tested Encourage the family to communicate this information to their relatives. We’ll be discussing critical elements of pre-test counseling and informed consent for genetic testing in more detail in the next work shop
  • -INSTRUCTIONS- Signal of transition to small group practice. Make sure everyone has the toolkit and patient handout to complete the activity. Facilitator Script Now, you all will have an opportunity to practice a differential and testing decision for another patient. Break into groups of 3 – 5 and work together on the case for about 10 minutes. Read through the patient history and then work through the discussion questions with your group. Use the information provided to practice refining your differential and selecting a test OR, if WiFi is available, use the toolkit and web resources to narrow the differential and test options Identify one person to be spokesperson for the group. After you discuss as a small group we will reconvene and discuss your findings with the larger group. -Facilitator INSTRUCTIONS- Small group work for about 10 min, or as your time allows. Walk around the room to hear what the groups are saying. This will help you determine where there is confusion and what they already know that may need less explaining. In handout: 1. Provide history, exam, labs 2. Provide list of differential dx to use with online tools OR provide 1 paragraph descriptions of features and genetics for each condition (in lieu of WiFi access) Smith Lemli-Opitz PKU Angelman Creatine transporter deficiency 3. Provide fact sheet on testing options Methylation of chromosome 15, SNRPN region Sequencing of UBE3A gene 7-dehydrocholesterol Serum and urine creatine guadinoacetate Serum amino acids with phenylalanine Chromosomal microarray analysis 5. Provide DD/ID workup and CMA testing guidelines? 6. Discussion questions: What unique features might help narrow the differential? What is the most likely diagnosis? What evidence suggests that diagnosis? What evidence led you away from the other diagnoses? Which of the following tests do you recommend? Results of the first analysis were normal. What is your next step?
  • Instructions: Engage large group in discussion about the case. Encourage volunteers from each small group to share their approach to the case. If the dx comes out, explore the thinking and evidence leading to it. Facilitator script: What evidence pointed toward a specific diagnosis? What evidence pointed away from other diagnoses?
  • Key Point: Behavioral and motor features stand out, and lack of abnormal labs and imaging reduces likelihood of some diagnoses. Facilitator script: In general, distinctive features may include labs, characteristic physical features or anomalies, and even distinct cognitive and behavioral phenotypes. Remember to assess both what is present, and what is absent. In this case our biggest clue is the behavioral phenotype.
  • Instructions: Summarize the findings discussed with the previous question, and ask the group to commit to a particular diagnosis. Skip this slide if the diagnosis already came out in the previous discussion. Facilitator script: Based on the findings we just discussed, what did you decide is the most likely diagnosis?
  • Key Point: Angelman syndrome involves a unique behavioral phenotype Instructions: Don’t cover genetic mechanism and testing here. This will be discussed in the subsequent Q&A slides. Picture reference: GeneReviews
  • INSTRUCTIONS: Ask for volunteers to share their approach to the case. Encourage discussion about how they came to their decisions. Facilitator script: Based on your understanding of Angelman syndrome from the handout, Which testing option would you choose? Why? What specific gene, chromosome region, or biochemical/metabolic testing would you perform?
  • Key Point: DNA sequencing is not always the most efficient first line test for Angelman syndrome Facilitator script: Most cases of Angelman syndrome can be attributed to a disruption of a critical region on the maternally inherited copy of chromosome 15. In unaffected individuals, the maternal chromosome 15 is methylated, or imprinted, while the paternal chromosome is not. Several mechanisms may lead to the absence of the maternal, methylated critical region. Methylation analysis can identify abnormal methylation patterns, though it can’t differentiate between the various causes. (Note: sequence changes will be discussed in a subsequent slide) Images from:
  • Instructions: Ask for volunteers to discuss whether and why they considered CMA testing. Facilitator script: How many thought CMA testing was the best approach? Why? One of the causes of an abnormal methylation pattern associated with Angelman is a microdeletion of the chromosome region. What might be the down-side of doing CMA testing vs. methylation analysis?
  • Key point: Currently, CMA testing is most cost-effective when a specific syndrome is NOT evident Facilitator script: Currently CMA testing is more costly than targeted analysis for specific syndromes (like FISH or methylation studies). This may change in the future. Because CMA is genome-wide, it also has risks of uncertain and uninterpretable results, as well as incidental findings. This risk is lower with targeted testing. However, for patients with ID/autism who lack signs of a specific syndrome, CMA is a more powerful diagnostic test than traditional chromosome analysis, and is now recommended as a first tier test in this population. More detail: Angelman methylation costs $350 (through Greenwood Genetics as of June 2013)
  • Facilitator script: If your first tier testing is negative, what is your next step? Have you ruled out Angelman syndrome? Do you move on to other potential diagnoses in the differential, or test further for Angelman syndrome? Given what you’ve learned about the genetic causes of Angelman syndrome from your handout, what second tier testing would you recommend?
  • Key Point: Remember, when a single condition has multiple possible genetic causes, you may need to plan for a step-wise testing protocol. Facilitator script: Remember, when a single condition has multiple possible genetic causes, you may need to plan for a step-wise testing protocol. An initial negative test may not rule out the condition if it is associated with more than one variant. Sequence variants are the second most common cause of Angelman syndrome (11%), and are not detected by methylation analysis. A step-wise protocol, following methylation analysis with UBE3A sequencing, will identify over 80% of cases. Consultation with a geneticist is recommended if these tests are negative and Angelman syndrome is highly suspected. Recent findings have identified other genes for which testing may be available, that are associated with an Angelman-like phenotype.
  • Facilitator Script: In summary, we have explored these key points in this workshop on evaluation and decision-making

Session Two: Evaluation and Testing Decisions Session Two: Evaluation and Testing Decisions Presentation Transcript

  • Genomics for the Child Neurologist: Evaluation & Testing Decisions
  • Facilitator(s) Name • Expertise • Credentials • Titles
  • Re-Cap: Genomic Risk Assessment Ask the right questions Identify red flags Identify patterns
  • Workshop Two: Genetics Evaluation & Testing Decisions Risk Assessment Genetic Testing Differential Diagnosis Evaluation bridges the gap
  • Evaluation & Testing Decisions Learning Objectives 1. Use family and clinical histories to narrow the differential 2. Select the appropriate single-gene test, panel, or step-wise protocol 3. Develop a family testing strategy to maximize cost- effectiveness
  • Family Labs Exam Imaging Elements of Evaluation History
  • Narrow the differential Select appropriate tests Develop a family testing strategy Genomic evaluation and testing decisions build on risk assessment
  • Narrow the Differential
  • 10 yo male History of clumsiness Recent increase Some falls with injury Clinical Scenario: Tim
  • Clinical History Birth History: •Normal Developmental History: •Normal Past Medical History: •Minor infections Review of Systems: •Unremarkable Social History: •Tim lives with his parents and his younger sister Family History: •Intake form indicates movement/muscle problems in Tim’s father and paternal grandfather
  • Exam Physical Exam: •No dysmorphic features •Normal arches •General exam is normal Neurological Exam: •Mental status: alert •Speech is dysarthric and scanning •Cranial nerves: slow horizontal saccades •Normal muscle tone, bulk and strength •Reaches with dysmetria •Deep tendon reflexes absent •Decreased vibration sense •Ataxic gait
  • What is your initial differential diagnosis? • Speech is dysarthric and scanning • Cranial nerves: slow horizontal saccades • Normal muscle tone, bulk and strength • Reaches with dysmetria • Deep tendon reflexes absent • Decreased vibration sense • Ataxic gait
  • Initial Differential Diagnosis • Vitamin deficiencies (E, B vitamins) • Toxicity (heavy metals, alcohol) • Structural abnormalities • Traumatic tissue damage • Genetic ataxias
  • Step 1: Rule out non-genetic causes Neuroimaging: •MRI normal Laboratory Tests: •E and B vitamins within normal limits •AFP & immunoglobulin normal •Lactose and gluten challenge normal •Other routine studies within normal limits
  • Step 2: Use tools to identify potential genetic diagnoses
  • Genetic differentials can be overwhelming
  • Step 3: Refine the differential with distinctive patient features
  • Which of Tim’s features might help differentiate diagnosis? • Normal MRI, general exam, routine labs, cognitive status • Motor: Normal tone, bulk and strength • Speech is dysarthric and scanning • Slow horizontal saccades • Reaches with dysmetria, ataxic gait • Absent deep tendon reflexes, decreased vibration sense
  • Signs of cerebellar disease with normal labs and imaging Distinctive findings PRESENT: •Evidence of cerebellar disease •Evidence of posterior column involvement •Absent deep tendon reflexes Distinctive findings ABSENT: •Dysmorphology and skin findings •Abnormal AFP and immunoglobulin •Evidence of metabolic or muscle disease
  • Prioritize your differential based on your clinical evidence
  • Refined differential based on clinical features Condition Defining Features Likelihood Ataxia telangiectasia Friedreich’s ataxia Neiman Pick type C Spinocerebellar ataxia Skin findings, abnormal AFP and immunoglobulin Dysarthria, spasticity, loss of position and vibration sense, absent lower limb reflexes Usually accompanied by hepatosplenomegaly and loss of vertical saccades Progressive incoordination of gait, hands, speech and eyes Less Likely Possible Less Likely Possible
  • Step 4: Use family history patterns to narrow the differential
  • What features of Tim’s family history might narrow the differential?
  • Possible autosomal dominant with evidence of anticipation Movement disorder in multiple generations Early age of onset
  • Refined differential based on inheritance patterns Condition Inheritance Likelihood Ataxia telangiectasia Friedreich’s ataxia Neiman Pick type C Spinocerebellar ataxia Family history assessment can save you time! Autosomal Recessive Autosomal Recessive Autosomal Recessive Most Autosomal Dominant Less Likely Less Likely Most Likely Less Likely
  • SCA Overview Features: •Progressive incoordination of gait •Poor coordination of hands, speech and eye movements •Atrophy of the cerebellum Genetics •Over 35 subtypes with different genetic causes and overlapping features •6 genes account for 65% of cases •SCA3 (ATXN3 gene) is the most common form •Most variants are trinucleotide repeat expansions and demonstrate anticipation •Usually autosomal dominant inheritance Management •Primarily supportive
  • Select appropriate tests
  • Step 1: Use tools to determine associated genes and available testing …
  • Test choice is complicated by multiple genetic causes GENE 1 GENE 1 OR OR GENE 2 GENE 2 GENE 1 GENE 1 GENE 3 GENE 3 Huntington Disease SCA
  • Step 2: Determine whether there is sufficient evidence to target a single gene Phenotype Prevalence by Subtype Gene Frequency Gene1 Gene2 Gene3 Gene4
  • Would you target testing, or use a panel capturing multiple genes? Phenotype Prevalence by Subtype Gene Frequency From GeneReviews
  • When in doubt, ask the lab if panels or step-wise protocols are recommended AND AND GENE 2 GENE 2 GENE 1 GENE 1 GENE 3 GENE 3
  • HOWEVER, there are cases where targeted testing is the clear choice Test Cost Detection Single gene (FXN) analysis $840 % Recessive ataxia panel $6,345 %% Comprehensive ataxia panel $18,760 %%% Alternate example: Freidreich ataxia
  • Consider referral or consult for refining differential and targeting testing When to consult/refer: •Large and overlapping genetic differential •Complex family history is difficult to interpret •There are many candidate genes/variants and multiple testing options are available
  • Develop a Family Testing Strategy Proband First Test Parents Test Sibs Test Relatives Identify Gene
  • Who else in the family is at risk?
  • First degree relatives of individuals with AD conditions are at 50% risk 50% 50%25%
  • Start testing in an affected individual, or risk uninformative results Never Tested: Causative variant unknown Your Patient SCA panel: No Mutation Found Can’t predict disease status
  • Once a mutation is found, target testing in relatives at lower cost Step-wise multi-gene panels: ATXN2 mutation found $ 13,330 Targeted ATXN2 analysis: $ 790
  • Facilitate the testing plan through family communication Key points to discuss: •Distinctive clinical features and family patterns •Uncertainty about the diagnostic route •How well a test can confirm or rule-out a diagnosis •Next steps based on positive or negative results •Who else is at risk Stay tuned for Workshop 3!
  • Small Group Practice
  • What evidence helped you refine the differential?
  • Critical evaluations • Jerky, tremulous movements • Hand flapping • Normal growth makes SLO unlikely • Normal newborn screen makes PKU unlikely • Normal MRS makes Creatine transporter deficiency unlikely Unique features
  • Which condition is the most likely in Nico?
  • Angelman syndrome is the best fit • Global delay • Autistic-like features • Generalized epilepsy • Jerky, tremulous movements • Hand flapping • Disruption of imprinting of UBE3A gene
  • Which test is the appropriate first step? A. Methylation analysis of a specific chromosome region B. Sequencing of a specific gene C. Serum and urine amino acids D. Other specific metabolic/biochemical testing E. Chromosomal microarray analysis
  • Methylation analysis of the critical chr 15 region detects most cases = Unmethylated = Methylated 68% 7% 3% © 2008 Angel Syndrome Foundation, Inc.
  • Why not order chromosomal microarray analysis?
  • Features were sufficient to justify single gene analysis ACMG recommends CMA as first- line test for ID/autism in the absence of defining features suggestive of a specific syndrome
  • Methylation analysis was negative. What is your next step?
  • UBE3A sequencing is the next step 11%
  • Summary: Genomic Evaluation and Testing Decisions • Use tools, unique features and inheritance patterns to narrow your differential. • Consider genetic heterogeneity when selecting from single-gene, multi-gene panels, or step-wise tests • Start testing with an affected individual • Target testing for known causative familial variants in at- risk family members • Consider referral or consultation with complicated differentials and testing options
  • Next steps • Refer or consult with genetics • Pre-test counseling and informed consent • Order testing • Interpret and apply results To be discussed in workshop 3
  • Homework/Practice • Watch two 5 minute demonstration videos on SimulConsult • Practice using clinical information and tools to refine the differential diagnosis and testing strategy (Developmental regression)
  • Thank you!