Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases.


PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the noncoding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity, and magnetic resonance image changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, probably missed owing to failure of alignment.ConclusionThese cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses.





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Publication Info

Pena, Loren DM, Yong-Hui Jiang, Kelly Schoch, Rebecca C Spillmann, Nicole Walley, Nicholas Stong, Sarah Rapisardo Horn, Jennifer A Sullivan, et al. (2018). Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. Genetics in medicine : official journal of the American College of Medical Genetics, 20(4). pp. 464–469. 10.1038/gim.2017.128 Retrieved from https://hdl.handle.net/10161/17166.

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Allyn McConkie-Rosell

Professor in Pediatrics

Undiagnosed disorders are often not amenable to the traditional diagnostic approaches and the lack of a diagnosis leads to repeated clinical consultations and laboratory testing, causing substantial personal and familial emotional and financial stress.  For parents of children with undiagnosed diseases, the extensive search for a diagnosis and inherent uncertainty surrounding their child’s health can result in stress, frustration and worries about worsening of symptoms and delays in treatment or inappropriate treatment.  As genetic testing becomes more advanced so do the expectations, associated uncertainty, and if diagnosed, an increased the frequency of a diagnosis of an ultra-rare disorder.  Thus, it is important to describe the complex emotional experience and the relationship to health care engagement and to follow this process in real time with parents as they are experiencing the diagnostic process in order to better understand their needs and to develop strategies to improve outcomes.  Challenges posed by WES for clinicians are largely by virtue of variation in the clinical relevance of results. For instance, many cases require clinical follow-up of variants of uncertain significance and secondary/incidental findings, and it has become necessary communicate effectively with patients/families at multiple stages to both educate and address expectations (pre-test counseling) and relay uncertain or less understood results (post-test counseling). Likewise, parents of children with rare disorders may be challenged to understand the process, the outcome, the certainty of the diagnosis; effectively communicate information to family members and providers; and use the new information to the benefit their of families.  Responsive to these shifting clinical needs, my research is focused on exploring how families manage genetic information with the goal of identifying genetic counseling strategies to facilitate their positive adaptation, coping, and use of information.  


Sujay Mansukhlal Kansagra

Professor of Pediatrics

Sujay Kansagra, MD is a professor at Duke and the director the Pediatric Neurology Sleep Medicine Program. He is an active clinician and researcher.  He specializes in treating a variety of sleep disorders, including sleep apnea, insomnia, narcolepsy and parasomnias. His prior clinical research involves sleep pathology in rare conditions such as alternating hemiplegia of childhood and infantile Pompe disease. He has also served as the Duke PI on mult-centered pharmacologic trials involving migraine and narcolepsy.  Dr. Kansagra is the author of numerous peer-reviewed research publications and 5 books. He is currently doing research on novel technology that helps with behavioral insomnia of childhood.

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