Deep Phenotyping in 1p36 Deletion Syndrome

Shim, Youngkyu; Go, Young Jun; Kim, Soo Yeon; Kim, Hunmin; Choi, Jieun; Lim, Byung Chan; Kim, Ki Joong; Chae, Jong Hee

doi:10.26815/acn.2020.00108

Cited by 4 publications

(13 citation statements)

References 16 publications

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“…Additionally, they found expressive language to be absent in about 75% of patients, limited to a few isolated words in 17%, and at the level of two word phrases in 8% [3]. Similarly, poor expressive language has been reported by other studies [9,10]. Overall, speech/language development seems to be significantly more impaired than motor development [9].…”

Section: Introductionmentioning

confidence: 53%

Psychiatric Comorbidities in 1p36 Deletion Syndrome and Their Treatment—A Case Report

Briegel

2021

IJERPH

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1p36 deletion syndrome represents the most common terminal deletion observed in humans. Major clinical findings comprise developmental delay/intellectual disability, poor or absent expressive language, congenital central muscular hypotonia, brain anomalies, brachydactyly/camptodactyly, short feet, and characteristic facial features like straight eyebrows, deep-set eyes, and midface hypoplasia. So far, there is very limited knowledge about comorbid psychiatric disorders and their effective treatment in this special population. To fill this gap, this case report presents an initially four-year-old girl with 1p36.33–1p36.32 deletion, moderate intellectual disability, insomnia, oppositional-defiant disorder and attention deficit/hyperactivity disorder covering a period of time of about 1.5 years comprising initial psychological/psychiatric assessment, subsequent day clinic/outpatient treatment (amongst others including off-label use of melatonin and methylphenidate as well as parent-child interaction therapy) and follow-up assessment. Follow-up results indicated good efficacy of melatonin and methylphenidate medication without any adverse effects. Multidisciplinarity in diagnosis and treatment are mandatory to meet needs of patients with complex genetic disorders like 1p36 deletion syndrome. Off-label use of melatonin (for insomnia) and methylphenidate (for attention deficit/hyperactivity disorder) should be considered in young children with 1p36 deletion syndrome if behavioral interventions are not sufficient.

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Section: Introductionmentioning

confidence: 53%

Psychiatric Comorbidities in 1p36 Deletion Syndrome and Their Treatment—A Case Report

Briegel

2021

IJERPH

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“…Craniofacial malformation is a prominent phenotype in those with the 1p36 deletion. 18 The 15q duplication was the most common duplication in our IESS cohort. In a study of 83 patients with 15q duplication, 63% were reported to have epilepsy, 42% of whom diagnosed with infantile spasms.…”

Section: Cnvsmentioning

confidence: 84%

“…In our study, 6 patients with IESS also had other seizure types, including focal seizures, tonic seizures, and myoclonic seizures. Craniofacial malformation is a prominent phenotype in those with the 1p36 deletion 18 . Bahi‐Buisson et al reported 53 epilepsy patients with 1p36 deletion, and about one‐third of the patients (19/53) developed refractory epilepsy 19 .…”

Section: Discussionmentioning

confidence: 99%

Novel copy number variations and phenotypes of infantile epileptic spasms syndrome

Cheng,

Bai,

Yang

et al. 2024

Clinical Genetics

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We summarize the copy number variations (CNVs) and phenotype spectrum of infantile epileptic spasms syndrome (IESS) in a Chinese cohort. The CNVs were identified by genomic copy number variation sequencing. The CNVs and clinical data were analyzed. 74 IESS children with CNVs were enrolled. 35 kinds of CNVs were identified. There were 11 deletions and 5 duplications not reported previously in IESS, including 2 CNVs not reported in epilepsy. 87.8% were de novo, 9.5% were inherited from mother and 2.7% from father. Mosaicism occurred in one patient with Xq21.31q25 duplication. 16.2% (12/74) were 1p36 deletion, and 20.3% (15/74) were 15q11‐q13 duplication. The age of seizure onset ranged from 17 days to 24 months. Seizure types included epileptic spasms, focal seizures, tonic seizures, and myoclonic seizures. All patients displayed developmental delay. Additional features included craniofacial anomaly, microcephaly, congenital heart defects, and hemangioma. 29.7% of patients were seizure‐free for more than 12 months, and 70.3% still had seizures after trying 2 or more anti‐seizure medications. In conclusion, CNVs is a prominent etiology of IESS. 1p36 deletion and 15q duplication occurred most frequently. CNV detection should be performed in patients with IESS of unknown causes, especially in children with craniofacial anomalies and microcephaly.

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“…Deep phenotyping, or "the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described" 7 , is a fundamental component of precision medicine that requires timely synthesis of multiple types of patient data 19,20 . Deep phenotyping has been successfully applied to rare disease and genetic disorders [21][22][23][24][25][26][27][28][29][30][31][32][33] , cancer [34][35][36][37][38][39][40] , and pregnancy [41][42][43] using a variety of clinical and -omic data. Despite large-scale biobanking efforts and resources like the UK Biobank (https://www.ukbiobank.ac.uk) and the All of Us (AoU) Research Program (https://www.researchallofus.org), most EHRs do not systematically integrate nor have the infrastructure to integrate patient-level genomic data or other forms of external knowledge (e.g., scientific literature) with clinical data [44][45][46] .…”

Section: Introductionmentioning

confidence: 99%

Ontologizing health systems data at scale: making translational discovery a reality

et al. 2023

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Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

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Deep Phenotyping in 1p36 Deletion Syndrome

Cited by 4 publications

References 16 publications

Psychiatric Comorbidities in 1p36 Deletion Syndrome and Their Treatment—A Case Report

Psychiatric Comorbidities in 1p36 Deletion Syndrome and Their Treatment—A Case Report

Novel copy number variations and phenotypes of infantile epileptic spasms syndrome

Ontologizing health systems data at scale: making translational discovery a reality

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