The scientific process of analysis and deduction is frequently, often subconsciously, used by physicians to develop a differential diagnosis based on patients’ symptoms. Common disorders are most frequently diagnosed in general practice. Rare diseases are uncommon and frequently remain undiagnosed for many years. Cognitive errors in clinical judgment delay definitive diagnosis. Whole-exome sequencing has helped identify the cause of undiagnosed or rare diseases in up to 40% of children. This article provides experiences with an undiagnosed or rare disease program, where detailed data accumulation and a multifaceted analytical approach assisted in diagnosing atypical presentations of common disorders.
Key points
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Patients who have been misdiagnosed or who remain undiagnosed may experience continued suffering or a progression in their disease, leading to potential disabilities and even preventable life-threatening complications.
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Misdiagnosis or lack of a specific diagnosis leads to unnecessary diagnostic testing and invasive procedures, which, in addition to increasing patient suffering and risking complications, add major costs to the health care system.
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Whole-exome sequencing (WES) is the diagnostic test of choice for children with undiagnosed or rare diseases (URDs) after traditional laboratory and imaging studies have not yielded a diagnosis.
Medicine is a science of uncertainty and an art of probability.
Defining rare and undiagnosed diseases
A rare disease is defined in the United States as one affecting fewer than 200,000 patients; however, there are more individual rare diseases than there are common diseases, cumulatively affecting more than 25 million people. Nonetheless, health care providers are more likely to see patients within the narrower spectrum of highly prevalent common diseases than they are to encounter patients with a much less prevalent individual rare disease. Although some rare diseases, such as Huntington chorea, may have characteristic findings that facilitate diagnosis, the presenting manifestations of rare diseases are often nonspecific, such as weight loss, weakness, fatigue, or fever. When signs and symptoms are nonspecific, initial diagnostic impressions may favor diseases seen commonly within the scope of a practice, leading many rare diseases to be initially misdiagnosed or to remain undiagnosed.
Many but not all patients with an undiagnosed disease have a rare disease. Both common and rare diseases may present atypically and remain undiagnosed for weeks to decades despite multiple subspecialist consultations and extensive laboratory and imaging studies. Given that both common and rare diseases may remain undiagnosed despite these evaluations, classifying a disease as “undiagnosed” is challenging. Time is an imperfect criterion, because symptoms may remain incomplete and static or may evolve over a prolonged period. Furthermore, nonspecific signs or symptoms of a rare disease may truncate the evaluation process if they leave a health care provider with the impression of a more common disease. The perpetuation of incomplete or inaccurate diagnostic labels may lead to an inability to alter the course of a diagnostic evaluation and to significant delays in appropriate diagnosis and therapy. Complexity is an imperfect criterion as well, because some undiagnosed diseases may be restricted to a single symptom or organ system, whereas others may have systemic manifestations necessitating evaluation and management by multiple specialties. Undiagnosed diseases may be analogous to the definition historically applied to patients with fever of unknown origin, which requires both the passage of a certain period of time as well as a progression from basic to more aggressive or even invasive diagnostic procedures. Some undiagnosed diseases may be as simple as an adolescent with 6 months of headache, eventually diagnosed with pseudotumor cerebri, or as complex as a child originally thought to have treatment-refractory chronic autoimmune demyelinating polyneuropathy, who was found 10 years after initial presentation to have a rare form of riboflavin transporter deficiency ( Table 1 ).
| Initial Diagnosis/Manifestation | Final Diagnosis |
|---|---|
| Neurologic | |
| Cardiomyopathy delayed myopathy | Myofibrillar myopathy |
| Late-onset autistic regression | Kleefstra syndrome |
| Autoimmune polyneuropathy | Riboflavin transporter deficiency |
| Laryngitis | Miller Fisher variant Guillain-Barré syndrome with vocal cord paralysis |
| Hypotonia | Nemeline myopathy |
| Siblings with neurodegenerative disorder | NDUF10A (mitochondrial complex 1) |
| Microcephaly, absent speech | NDUFV3 mutation |
| Hypotonia | LAMA dystroglycanopathy |
| Seizures | SCN2B mutation |
| Inflammatory, immune, infectious, infiltrative | |
| IBD | XIAP |
| IBD | IPEX |
| Obstructive hydrocephalus | fHLH |
| Congenital infection | fHLH |
| Nonimmune hydrops | fHLH |
| Nonimmune hydrops | Congenital neuroblastoma |
| CRMO | LCH |
| Orbital cellulitis | LCH |
| Neonate with urticaria | NOMID |
| Rule out sepsis | Dengue fever |
| Rule out sepsis | Rat-bite fever |
| Pneumonia with effusion | Lymphoma |
| Recurrent lymphadenitis | ALPS |
| Evans syndrome | ALPS |
| Viral meningitis | Tuberculous meningitis |
| Pulmonary alveolar proteinosis | CD40 ligand deficiency |
| Arthritis | Hyper-IgD syndrome |
| Central nervous system vasculitis | ADA-2 deficiency |
| Interstitial lung disease | CGD |
| CVID | CTLA4 deficiency |
| Neutropenia | GATA2 deficiency |
| Other | |
| Chronic fatigue syndrome | Addison disease |
| Hepatic failure | Citrin deficiency |
| Intestinal pseudo-obstruction | Intestinal leiomyositis |
| Anorexia nervosa | Celiac disease |
| Growing pains | Scurvy |
| Lymphedema, microphthalmia | Oculo-facial-digital syndrome |
| Cardiomyopathy | Semialdehyde dehydrogenase deficiency |
| Atypical HUS | DGKE mutation |
| Failure to thrive, increased respiratory effort | Marshall-Smith syndrome ( NFIX ) |
| SCID | HDAC8 -associated Cornelia de Lange |
| Microphthalmia, high myopia, pigmentary choroidopathy | EFTUD2 mutation |
| Intrauterine fetal demise | Coffin-Siris syndrome ( ARID1B ) |
| Hypermobility EDS | Noonan syndrome ( KRAS ) |
| Scoliosis, renal disease | Coffin-Siris syndrome ( ARID1B ) |
| Myopathy, hypotonia | Arterial toruosity syndrome |
Defining rare and undiagnosed diseases
A rare disease is defined in the United States as one affecting fewer than 200,000 patients; however, there are more individual rare diseases than there are common diseases, cumulatively affecting more than 25 million people. Nonetheless, health care providers are more likely to see patients within the narrower spectrum of highly prevalent common diseases than they are to encounter patients with a much less prevalent individual rare disease. Although some rare diseases, such as Huntington chorea, may have characteristic findings that facilitate diagnosis, the presenting manifestations of rare diseases are often nonspecific, such as weight loss, weakness, fatigue, or fever. When signs and symptoms are nonspecific, initial diagnostic impressions may favor diseases seen commonly within the scope of a practice, leading many rare diseases to be initially misdiagnosed or to remain undiagnosed.
Many but not all patients with an undiagnosed disease have a rare disease. Both common and rare diseases may present atypically and remain undiagnosed for weeks to decades despite multiple subspecialist consultations and extensive laboratory and imaging studies. Given that both common and rare diseases may remain undiagnosed despite these evaluations, classifying a disease as “undiagnosed” is challenging. Time is an imperfect criterion, because symptoms may remain incomplete and static or may evolve over a prolonged period. Furthermore, nonspecific signs or symptoms of a rare disease may truncate the evaluation process if they leave a health care provider with the impression of a more common disease. The perpetuation of incomplete or inaccurate diagnostic labels may lead to an inability to alter the course of a diagnostic evaluation and to significant delays in appropriate diagnosis and therapy. Complexity is an imperfect criterion as well, because some undiagnosed diseases may be restricted to a single symptom or organ system, whereas others may have systemic manifestations necessitating evaluation and management by multiple specialties. Undiagnosed diseases may be analogous to the definition historically applied to patients with fever of unknown origin, which requires both the passage of a certain period of time as well as a progression from basic to more aggressive or even invasive diagnostic procedures. Some undiagnosed diseases may be as simple as an adolescent with 6 months of headache, eventually diagnosed with pseudotumor cerebri, or as complex as a child originally thought to have treatment-refractory chronic autoimmune demyelinating polyneuropathy, who was found 10 years after initial presentation to have a rare form of riboflavin transporter deficiency ( Table 1 ).
| Initial Diagnosis/Manifestation | Final Diagnosis |
|---|---|
| Neurologic | |
| Cardiomyopathy delayed myopathy | Myofibrillar myopathy |
| Late-onset autistic regression | Kleefstra syndrome |
| Autoimmune polyneuropathy | Riboflavin transporter deficiency |
| Laryngitis | Miller Fisher variant Guillain-Barré syndrome with vocal cord paralysis |
| Hypotonia | Nemeline myopathy |
| Siblings with neurodegenerative disorder | NDUF10A (mitochondrial complex 1) |
| Microcephaly, absent speech | NDUFV3 mutation |
| Hypotonia | LAMA dystroglycanopathy |
| Seizures | SCN2B mutation |
| Inflammatory, immune, infectious, infiltrative | |
| IBD | XIAP |
| IBD | IPEX |
| Obstructive hydrocephalus | fHLH |
| Congenital infection | fHLH |
| Nonimmune hydrops | fHLH |
| Nonimmune hydrops | Congenital neuroblastoma |
| CRMO | LCH |
| Orbital cellulitis | LCH |
| Neonate with urticaria | NOMID |
| Rule out sepsis | Dengue fever |
| Rule out sepsis | Rat-bite fever |
| Pneumonia with effusion | Lymphoma |
| Recurrent lymphadenitis | ALPS |
| Evans syndrome | ALPS |
| Viral meningitis | Tuberculous meningitis |
| Pulmonary alveolar proteinosis | CD40 ligand deficiency |
| Arthritis | Hyper-IgD syndrome |
| Central nervous system vasculitis | ADA-2 deficiency |
| Interstitial lung disease | CGD |
| CVID | CTLA4 deficiency |
| Neutropenia | GATA2 deficiency |
| Other | |
| Chronic fatigue syndrome | Addison disease |
| Hepatic failure | Citrin deficiency |
| Intestinal pseudo-obstruction | Intestinal leiomyositis |
| Anorexia nervosa | Celiac disease |
| Growing pains | Scurvy |
| Lymphedema, microphthalmia | Oculo-facial-digital syndrome |
| Cardiomyopathy | Semialdehyde dehydrogenase deficiency |
| Atypical HUS | DGKE mutation |
| Failure to thrive, increased respiratory effort | Marshall-Smith syndrome ( NFIX ) |
| SCID | HDAC8 -associated Cornelia de Lange |
| Microphthalmia, high myopia, pigmentary choroidopathy | EFTUD2 mutation |
| Intrauterine fetal demise | Coffin-Siris syndrome ( ARID1B ) |
| Hypermobility EDS | Noonan syndrome ( KRAS ) |
| Scoliosis, renal disease | Coffin-Siris syndrome ( ARID1B ) |
| Myopathy, hypotonia | Arterial toruosity syndrome |
The challenges of evaluating undiagnosed or rare diseases
Children with URDs have often been evaluated by individual subspecialists in medical centers across the country and have been on a diagnostic odyssey for many years or even decades. Delays in diagnosis are often multifactorial, although they may be categorized broadly as either inherent to the disease process or related to pitfalls in the diagnostic evaluation. Diagnostic pitfalls may be further classified as patient-specific, physician-specific, or related to limitations in various diagnostic modalities. In many ways, the structure of the health system promotes these diagnostic pitfalls, because individual expertise and practice are promoted. The cognitive process of an experienced clinician often relies on experience and gut instincts or on disease pattern recognition to formulate a diagnosis. Thus, despite adherence to a rigid scientific methodology of data collection, analysis, and deductive inference, the prioritization and interpretation of data ultimately rely on that individual expert opinion and are subject to individual bias or error. The development of a URD program, in which a core of experienced clinicians collaborate with relevant subspecialists, mitigates many of these individual biases and ensures a more rigorous application of the scientific method when analyzing available data.
Disease-specific Factors
One reason for delayed diagnosis is the all-too-true aphorism, “diseases do not read the textbook.” For example, patients with endocarditis rarely have all or any of the classic physical findings associated with this disease. Some patients with periodic fever syndromes or other autoinflammatory diseases may not have fever, individuals with hyper–immunoglobulin D (IgD) syndrome may have normal levels of IgD, and hyperkalemia may be present in the classic hypokalemic form of Bartter syndrome. The great masqueraders of the past century—lupus, tuberculosis, and syphilis—still exist but have been joined by others, including hemophagocytic syndromes, periodic fever/autoinflammatory syndromes, neuroimmunologic diseases, and other autoimmune and immunodeficiency syndromes. In addition to having patients whose disease evolution and diagnostic evaluation have persisted for a prolonged time period, most large pediatric hospitals have cared for patients with URDs who have evaded a specific diagnosis in the early phase of their disease and who present acutely with a serious or catastrophic illness. In the authors’ experience, these acutely ill patients represent approximately 15% to 20% of patients; they require immediate consultation as well as aggressive and rapid diagnostic evaluation.
Patient-specific Factors
Families of children with URD may be viewed with certain negative biases. They are often anxious from the persistence of their child’s chronic undiagnosed medical illness. These families have often shared the diagnostic odyssey with multiple physicians and have reached a point where they are over-reporting the minutest details in hopes of discovering the clue or clues that will lead to a diagnosis. This may result in a diagnostician presented with an overwhelming amount of information, all of it seemingly equally important to the family, making it difficult to form an accurate representation of the child’s signs and symptoms. There may be some suspicion on the part of health care providers that the information is even factitious and an effort to force further diagnostic testing. Parents and families may be perceived as doctor-shopping as part of their effort to find answers to their questions. In addition, because of unsatisfactory previous interactions with the health care system, these families may not always speak well of their past experiences. An attribution error from this negative stereotype may lead to an inappropriate diagnosis of Munchausen syndrome by proxy (also known as medical child abuse or factitious disorder by proxy). Although it is essential to be aware of this possibility, the diagnosis of Munchausen syndrome by proxy in a child with a URD should be considered and made in a manner identical to all other diagnoses considered: after careful review of all available information; consideration of the specific pattern and details of the signs, symptoms, laboratory, imaging, and other data; and deliberate and thoughtful conversations with the patient, family members, and all involved health care providers. This diagnosis should not be made prematurely or simply because nothing else fits.
Physician-specific Factors: Issues in Clinical Judgment
Two important maxims in the evaluation of children with URDs are to expect the unexpected and to never say never. During the evaluation of many patients, well-intended and often senior experts in their field have made statements like, “I have never seen this symptom in the proposed disease,” “It cannot be this,” and, even mistakenly, “It must be this.” This appeal to authority often results in avoidable diagnostic errors. Despite evidence of convincing geographic clustering and the development of a preceding unusual rash in a majority of patients, the originally described patients with Lyme arthritis were most frequently misdiagnosed as having juvenile rheumatoid arthritis. Statements like, “In my experience” or “We see this,” are more authoritative than evidence based and eventually lead to a diagnostic momentum that excludes consideration of other disorders. Once a diagnosis is fixed in a medical record, in particularly a multiyear record, it is most often perpetuated, assumed to be correct, and difficult to question or rethink.
Appeals to authority can increase the tendency toward confirmation bias, in which the clinician seeks out only information that affirms a diagnosis and excludes facts that contradict the initial diagnosis. Atypical or new clinical findings may be a clue to the real diagnosis and should not be ignored. Overcoming confirmation bias is particularly problematic if a physician advocating for a particular diagnosis is a senior subspecialist recognized as an expert in the field, because it often prevents the entire team from considering other possible diseases. Even independent of appeals to authority, confirmation bias is detrimental to the diagnostic process because many URDs are atypical or uncommon manifestations of a common disease or are unrecognized manifestations of a rare disease. Always maintain a broad differential diagnosis and do not eliminate disorders from consideration solely because they initially do not seem to fit. On a busy hospital service or in a clinic setting, there may be a tendency to rule out a diagnosis too quickly. Once a diagnosis is incorrectly considered ruled out, it is difficult to rethink that diagnosis even in spite of evidence suggesting the excluded disease. Published clinical descriptions of diseases—in particular newly described diseases—tend to be biased in favor of the most commonly recognized manifestations and should be interpreted with caution. The true breadth of clinical manifestations of a specific disease may be much more extensive than suggested by descriptions in textbooks or in the literature. Recently, genomic testing has provided molecular evidence that many disorders exhibit greater clinical heterogeneity than previously appreciated. Always ask, “Do any of the features match what we know regarding a specific disease?” and “Could this be a condition I have seen before, but with a new or different clinical pattern?”
An attribution error in URDs occurs when minimizing signs, symptoms, or laboratory data. This is typified by the use of slight or slightly before describing an abnormality. Classically used by medical students who are unsure whether they hear a cardiac murmur or see a rash, when used by more experienced health care workers, the term, slight , may deemphasize an actual critical finding. Slight tachycardia should be stated as tachycardia if the heart rate is elevated above a normal range; the same is true for abnormal laboratory data. A sodium level of 150 mEq/L is elevated and abnormal; it may suggest a specific condition. These types of findings should not be overlooked in the child with an undiagnosed disease. Every symptom, every finding on the physical examination, and every discovery on laboratory testing and imaging should be considered potentially important clues that lead to a correct diagnosis.
Some children with URDs may appear seemingly healthy. Because many of the complaints of URDs may be vague or vexing, and because there is frequently considerable family anxiety regarding the lack of a diagnosis, the significance of the illness may not be appreciated or the parents may be thought of as over-reacting. This type of benign thinking is a type of affective error, where emotions may interfere with diagnostic judgment. “This child looks too well” or “Hoping for the good” or expecting that “Nothing really bad could be wrong with this child” clouds diagnostic decision making. Because most practitioners see common disorders on a day-to-day basis, they may miss the zebra among the horses. Because common diseases are common, a neutropenia may be assumed the result of viral suppression or drug induced, when a patient in fact has leukemia; a child presenting with tachypnea and fever initially diagnosed with pneumonia may have salicylate toxicity; or an athlete with prolonged knee pain initially diagnosed as a sprain may have osteogenic sarcoma. Conversely, significant family anxiety may lead to malignant thinking, another affective error in which a health care provider favors potential diagnoses with higher acuity or an increased risk for morbidity or mortality, simply as a function of that anxiety. Diagnosticians need to be self-aware of the tendency for these types of errors and to maintain the same impartial and broad differential diagnosis for a given set of signs and symptoms, even when a child appears generally well or in the context of significant family anxiety.
Perpetuating a diagnosis over time, whether due to appeals to authority, confirmation bias, attribution errors, benign thinking, or other affective errors, should be a cause to go back to the beginning of the illness and review all information available. Adolescent-onset behavioral and neurologic regression in a child originally diagnosed with autism may actually be a metabolic or neurodegenerative disorder. Recurrent episodes of swelling initially thought to be allergic reactions may eventually be diagnosed as episodes of hereditary angioedema or as nephrotic syndrome if the swelling is predominantly periorbital. Abdominal pain attributed to constipation but persisting despite evidence of normal stool output may in fact be porphyria, familial Mediterranean fever, lupus, or even malrotation with intermittent volvulus. Skin lesions that may appear eczematous or psoriasiform, when present in an unusual distribution restricted over the small joints of the hands, may be correctly diagnosed as associated with dermatomyositis.
Limitations in Diagnostic Testing
When evaluating children with URDs, it is important to recognize the limitations of diagnostic testing. Rarely is a diagnostic test 100% sensitive or specific, and as such, the positive and negative predictive values are often not ideal. Test results should not be considered dichotomously as ruling a particular condition either “in” or “out” but rather as increasing or decreasing the post-test probability of that condition in accordance with the positive or negative predictive value of that test as well as any other findings or results from laboratory or imaging studies. Laboratory error should be considered as well. There may be a tendency to believe the hard data of a particular test result more than believing eyes, ears, and hands and to trust that test results are more accurate and definitive than information gathered from history and physical examination. Finally, the absence of a positive laboratory test does not always disprove a diagnosis. For example, most but not all patients with lupus have a positive antinuclear antibody test; fewer have positive anti–double-stranded DNA titers. Only 80% to 90% of patients with endocarditis have positive blood cultures. The long QT syndrome (LQTS) has traditionally been diagnosed based on an age-specific length of the QT interval. There are more than 1000 genetic variants that account for approximately 80% of patients with LQTS. Nonetheless, 30% of patients with a gene mutation and resultant risk for arrhythmias do not demonstrate an abnormal QT interval on standard ECG testing.
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