6q16.3q23.3 duplication associated with Prader-Willi-like syndrome

Desch, Laurent; Marle, Nathalie; Mosca-Boidron, Anne-Laure; Faivre, Laurence; Eliade, Marie; Payet, Muriel; Ragon, Clémence; Thévenon, Julien; Aral, Bernard; Ragot, Sylviane; Ardalan, Azarnouche; Dhouibi, Nabila; Bensignor, Candace; Thauvin‐Robinet, Christel; Chehadeh, Salima El; Callier, Patrick

doi:10.1186/s13039-015-0151-6

Cited by 11 publications

(4 citation statements)

References 25 publications

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“…Agilent Array‐CGH 4 × 180 kb and ADM2 Cytogenomics software were performed at the Dijon University Hospital Cytogenetic Laboratory (Desch et al., 2015) with an overall median probe spacing of 13 kb with 114 kb standard deviation (STD). Three consecutive probe deviations was the minimum threshold for a positive result, which failed to detect CNVs smaller than 30 kb.…”

Section: Methodsmentioning

confidence: 99%

Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array‐CGH

Tisserant

Vitobello

Callegarin

et al. 2022

Annals of Human Genetics

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It has been estimated that Copy Number Variants (CNVs) account for 10%–20% of patients affected by Developmental Disorder (DD)/Intellectual Disability (ID). Although array comparative genomic hybridization (array‐CGH) represents the gold‐standard for the detection of genomic imbalances, common Agilent array‐CGH 4 × 180 kb arrays fail to detect CNVs smaller than 30 kb. Whole Exome sequencing (WES) is becoming the reference application for the detection of gene variants and makes it possible also to infer genomic imbalances at single exon resolution. However, the contribution of small CNVs in DD/ID is still underinvestigated. We made use of the eXome Hidden Markov Model (XHMM) software, a tool utilized by the ExAC consortium, to detect CNVs from whole exome sequencing data, in a cohort of 200 unsolved DD/DI patients after array‐CGH and WES‐based single nucleotide/indel variant analyses. In five out of 200 patients (2.5%), we identified pathogenic CNV(s) smaller than 30 kb, ranging from one to six exons. They included two heterozygous deletions in TCF4 and STXBP1 and three homozygous deletions in PPT1, CLCN2, and PIGN. After reverse phenotyping, all variants were reported as causative. This study shows the interest in applying sequencing‐based CNV detection, from available WES data, to reduce the diagnostic odyssey of additional patients unsolved DD/DI patients and compare the CNV‐detection yield of Agilent array‐CGH 4 × 180kb versus whole exome sequencing.

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Section: Methodsmentioning

confidence: 99%

Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array‐CGH

Tisserant

Vitobello

Callegarin

et al. 2022

Annals of Human Genetics

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“…Cases with PWLS provide novel insight into the complex genotypephenotype relationship of PWS. Many chromosomal alterations involving different chromosomes have been described in relation to PWLS [10][11][12]. Several cases of PWLS with a small deletion in the PWS critical region have been described.…”

Section: Requirements Clinical Diagnosis Pws For Adults 8 Points Of Which 5 Points Majormentioning

confidence: 99%

The Diagnostic Journey of a Patient with Prader–Willi-Like Syndrome and a Unique Homozygous SNURF-SNRPN Variant; Bio-Molecular Analysis and Review of the Literature

Pellikaan

Woerden

Kleinendorst

et al. 2021

Genes

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Prader–Willi syndrome (PWS) is a rare genetic condition characterized by hypotonia, intellectual disability, and hypothalamic dysfunction, causing pituitary hormone deficiencies and hyperphagia, ultimately leading to obesity. PWS is most often caused by the loss of expression of a cluster of genes on chromosome 15q11.2-13. Patients with Prader–Willi-like syndrome (PWLS) display features of the PWS phenotype without a classical PWS genetic defect. We describe a 46-year-old patient with PWLS, including hypotonia, intellectual disability, hyperphagia, and pituitary hormone deficiencies. Routine genetic tests for PWS were normal, but a homozygous missense variant NM_003097.3(SNRPN):c.193C>T, p.(Arg65Trp) was identified. Single nucleotide polymorphism array showed several large regions of homozygosity, caused by high-grade consanguinity between the parents. Our functional analysis, the ‘Pipeline for Rapid in silico, in vivo, in vitro Screening of Mutations’ (PRiSM) screen, showed that overexpression of SNRPN-p.Arg65Trp had a dominant negative effect, strongly suggesting pathogenicity. However, it could not be confirmed that the variant was responsible for the phenotype of the patient. In conclusion, we present a unique homozygous missense variant in SNURF-SNRPN in a patient with PWLS. We describe the diagnostic trajectory of this patient and the possible contributors to her phenotype in light of the current literature on the genotype–phenotype relationship in PWS.

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“…Seven patients with 6q duplications were reported in 3 papers (25,38,39), though 2 of them had an additional chromosomal aberration, namely a 10p duplication (38) and a 10p deletion (25). Most patients had obesity (86%), developmental delay/intellectual disability (71%), and speech delay, with articulation defects and little language development (43%).…”

Section: Q Duplicationmentioning

confidence: 99%

The Spectrum of the Prader–Willi-like Pheno- and Genotype: A Review of the Literature

2021

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Prader-Willi syndrome (PWS) is a rare genetic syndrome, caused by the loss of expression of the paternal chromosome 15q11-q13 region. Over the past years, many cases of patients with characteristics similar to PWS, but without a typical genetic aberration of the 15q11-q13 region, have been described. These patients are often labelled as Prader-Willi-like (PWL). PWL is an as-yet poorly defined syndrome, potentially affecting a significant number of children and adults. In the current clinical practice, patients labelled as PWL are mostly left without treatment options. Considering the similarities with PWS, children with PWL might benefit from the same care and treatment as children with PWS. This review gives more insight into the pheno- and genotype of PWL and includes 86 papers, containing 368 cases of patients with a PWL phenotype. We describe mutations and aberrations for consideration when suspicion of PWS remains after negative testing. The most common genetic diagnoses were Temple syndrome (formerly known as maternal uniparental disomy 14), Schaaf-Yang syndrome (truncating mutation in the MAGEL2 gene), 1p36 deletion, 2p deletion, 6q deletion, 6q duplication, 15q deletion,15q duplication, 19p deletion, fragile X syndrome and Xq duplication. We found that the most prevalent symptoms in the entire group were developmental delay/intellectual disability (76%), speech problems (64%), overweight/obesity (57%), hypotonia (56%) and psycho-behavioral problems (53%).In addition, we propose a diagnostic approach to patients with a PWL phenotype for (pediatric) endocrinologists. PWL comprises a complex and diverse group of patients, which calls for multidisciplinary care with an individualized approach.

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6q16.3q23.3 duplication associated with Prader-Willi-like syndrome

Cited by 11 publications

References 25 publications

Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array‐CGH

Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array‐CGH

The Diagnostic Journey of a Patient with Prader–Willi-Like Syndrome and a Unique Homozygous SNURF-SNRPN Variant; Bio-Molecular Analysis and Review of the Literature

The Spectrum of the Prader–Willi-like Pheno- and Genotype: A Review of the Literature

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