The Value of MLPA in Waardenburg Syndrome

Waardenburg Syndrome: The Contribution of Next-Generation Sequencing to the Identification of Novel Causative Variants

Waardenburg syndrome (WS) is characterized by hearing loss and pigmentary abnormalities of the eyes, hair, and skin. The condition is genetically heterogeneous, and is classified into four clinical types differentiated by the presence of dystopia canthorum in type 1 and its absence in type 2. Additionally, limb musculoskeletal abnormalities and Hirschsprung disease differentiate types 3 and 4, respectively. Genes PAX3, MITF, SOX10, KITLG, EDNRB, and EDN3 are already known to be associated with WS. In WS, a certain degree of molecularly undetected patients remains, especially in type 2. This study aims to pinpoint causative variants using different NGS approaches in a cohort of 26 Brazilian probands with possible/probable diagnosis of WS1 (8) or WS2 (18). DNA from the patients was first analyzed by exome sequencing. Seven of these families were submitted to trio analysis. For inconclusive cases, we applied a targeted NGS panel targeting WS/neurocristopathies genes. Causative variants were detected in 20 of the 26 probands analyzed, these being five in PAX3, eight in MITF, two in SOX10, four in EDNRB, and one in ACTG1 (type 2 Baraitser-Winter syndrome, BWS2). In conclusion, in our cohort of patients, the detection rate of the causative variant was 77%, confirming the superior detection power of NGS in genetically heterogeneous diseases.

[Common clinical causes and audiological manifestations of unilateral hearing loss in children]

Objective:To analyze the common clinical causes and audiological manifestations of unilateral hearing loss in children, and to provide a basis for early prevention and intervention. Method:A retrospective analysis of 20 cases of children diagnosed with unilateral hearing loss was conducted. The medical history was collected, followed by audiological and imaging examinations. Result:The audiological performance of 20 children with unilateral hearing loss: 1 case of conductive deafness, whose hearing curve was flat and showed moderate hearing loss. There were 19 cases of sensorineural deafness, of which 1 case was moderate deafness, 16 cases were severe deafness, and 2 cases were extremely severe deafness. The imaging results showed that there were 1 case with transverse fracture of the temporal bone, 1 case with congenital cholesteatoma, 9 cases with dysplasia of the cochlear nerve, and 4 cases with malformation of the inner ear. The history of the two children was collected and there were clear congenital cytomegalovirus infection and mumps virus infection. The causes of the remaining 3 cases were unknown. Conclusion:Unilateral hearing loss in children is a common clinical diseasewith complex and diverse causes. Carefully analysis should be made to find out the causes and symptomatic treatment to provide a basis for early prevention and intervention of children's hearing.

Comprehensive analysis of syndromic hearing loss patients in Japan

More than 400 syndromes associated with hearing loss and other symptoms have been described, corresponding to 30% of cases of hereditary hearing loss. In this study we aimed to clarify the mutation spectrum of syndromic hearing loss patients in Japan by using next-generation sequencing analysis with a multiple syndromic targeted resequencing panel (36 target genes). We analyzed single nucleotide variants, small insertions, deletions and copy number variations in the target genes. We enrolled 140 patients with any of 14 syndromes (BOR syndrome, Waardenburg syndrome, osteogenesis imperfecta, spondyloepiphyseal dysplasia congenita, Stickler syndrome, CHARGE syndrome, Jervell and Lange-Nielsen syndrome, Pendred syndrome, Klippel-Feil syndrome, Alport syndrome, Norrie disease, Treacher-Collins syndrome, Perrault syndrome and auditory neuropathy with optic atrophy) and identified the causative variants in 56% of the patients. This analysis could identify the causative variants in syndromic hearing loss patients in a short time with a high diagnostic rate. In addition, it was useful for the analysis of the cases who only partially fulfilled the diagnostic criteria.

Interstitial Chromosome 3p13p14 Deletions: An Update and Review

Deletions of proximal chromosome 3p13p14 are infrequent chromosomal alterations. Variable sizes and breakpoints have been reported in patients with a wide range of phenotypes that are evolving as additional cases are reported. The routine use of high-density chromosomal microarrays (CMA) has allowed the identification of many more cases of this disorder and clinical phenotyping shows evidence for an emerging profile among patients with overlapping deletions of 3p13p14. Here, we review the currently reported cases, their phenotypes and where available, the genomic intervals delineated by CMA. Surprisingly, we found that a significant number of proximal chromosome 3p deletions involve structural rearrangements, especially insertions, that have been identified in balanced parental chromosome complements. This region is historically known as a common human chromosomal fragile site, although an underlying genomic mechanism related to its architecture has not been identified. We conclude that identification of an interstitial 3p deletion in a proband by CMA should prompt consideration of further structural chromosomal evaluation using more traditional cytogenetic techniques. While the variability in breakpoints does not suggest a unifying underlying mechanism for these alterations, identification of the haploinsufficient genes in each patient's deletion interval and their developmental roles can guide genotype-phenotype correlations and impact clinical management.

Waardenburg syndrome: Novel mutations in a large Brazilian sample

This paper deals with the molecular investigation of Waardenburg syndrome (WS) in a sample of 49 clinically diagnosed probands (most from southeastern Brazil), 24 of them having the type 1 (WS1) variant (10 familial and 14 isolated cases) and 25 being affected by the type 2 (WS2) variant (five familial and 20 isolated cases). Sequential Sanger sequencing of all coding exons of PAX3, MITF, EDN3, EDNRB, SOX10 and SNAI2 genes, followed by CNV detection by MLPA of PAX3, MITF and SOX10 genes in selected cases revealed many novel pathogenic variants. Molecular screening, performed in all patients, revealed 19 causative variants (19/49 = 38.8%), six of them being large whole-exon deletions detected by MLPA, seven (four missense and three nonsense substitutions) resulting from single nucleotide substitutions (SNV), and six representing small indels. A pair of dizygotic affected female twins presented the c.430delC variant in SOX10, but the mutation, imputed to gonadal mosaicism, was not found in their unaffected parents. At least 10 novel causative mutations, described in this paper, were found in this Brazilian sample. Copy-number-variation detected by MLPA identified the causative mutation in 12.2% of our cases, corresponding to 31.6% of all causative mutations. In the majority of cases, the deletions were sporadic, since they were not present in the parents of isolated cases. Our results, as a whole, reinforce the fact that the screening of copy-number-variants by MLPA is a powerful tool to identify the molecular cause in WS patients.

Novel PAX3 mutations causing Waardenburg syndrome type 1 in Tunisian patients

Waardenburg syndrome (WS) is an auditory-pigmentary disease characterized by a clinical and genetic variability. WS is classified into four types depending on the presence or absence of additional symptoms: WS1, WS2, WS3 and WS4. Type 1 and 3 are mostly caused by PAX3 mutations, while type 2 and type 4 are genetically heterogeneous. The aims of this study are to confirm the diagnostic of WS1 by the sequencing of PAX3 gene and to evaluate the genotype phenotype correlation. A clinical classification was established for 14 patients WS, as proposed by the Waardenburg Consortium, and noted a predominance of type 1 and type 2 with 6 patients WS1, 7 patients WS2 and 1 patient WS3. A significant inter and intra-familial clinical heterogeneity was also observed. A sequencing of PAX3 gene in the 6 patients WS1 confirmed the diagnosis in 4 of them by revealing three novel mutations that modify two functional domains of the protein: the c.942delC; the c.933_936dupTTAC and the c.164delTCCGCCACA. These three variations are most likely responsible for the phenotype, however their pathogenic effects need to be confirmed by functional studies. The MLPA analysis of the 2 patients who were sequence negative for PAX3 gene revealed, in one of them, a heterozygous deletion of exons 5 to 9 confirming the WS1 diagnosis. Both clinical and molecular approaches led to the conclusion that there is a lack of genotype-phenotype correlation in WS1, an element that must be taken into account in genetic counseling. The absence of PAX3 mutation in one patient WS1 highlights the fact that the clinical classification is sometimes insufficient to distinguish WS1 from other types WS hence the interest of sequencing the other WS genes in this patient.

A novel mutation in PAX3 associated with Waardenburg syndrome type I in a Chinese family

CONCLUSION

The novel compound heterozygous mutation in PAX3 was the key genetic reason for WS1 in this family, which was useful to the molecular diagnosis of WS1.

PURPOSE

Screening the pathogenic mutations in a four generation Chinese family with Waardenburg syndrome type I (WS1).

METHODS

WS1 was diagnosed in a 4-year-old boy according to the Waardenburg syndrome Consortium criteria. The detailed family history revealed four affected members in the family. Routine clinical, audiological examination, and ophthalmologic evaluation were performed on four affected and 10 healthy members in this family. The genetic analysis was conducted, including the targeted next-generation sequencing of 127 known deafness genes combined with Sanger sequencing, TA clone and bioinformatic analysis.

RESULTS

A novel compound heterozygous mutation c.[169_170insC;172_174delAAG] (p.His57ProfsX55) was identified in PAX3, which was co-segregated with WS1 in the Chinese family. This mutation was absent in the unaffected family members and 200 ethnicity-matched controls. The phylogenetic analysis and three-dimensional (3D) modeling of Pax3 protein further confirmed that the novel compound heterozygous mutation was pathogenic.

A novel mutation in the PAX3 gene causes Waardenburg syndrome type I in an Iranian family

OBJECTIVES

Sensorineural hearing impairment (HI) is one of the most frequent congenital defects, with a prevalence of 1 in 500 among neonates. Although there are over 400 syndromes involving HI, most cases of HI are nonsyndromic (70%), 20% of which follow autosomal dominant mode of inheritance. Waardenburg syndrome (WS) ranks first among autosomal dominant syndromic forms of HI. WS is characterized by sensorineural hearing impairment, pigmentation abnormalities of hair and skin and hypoplastic blue eyes or heterochromia iridis. WS is subdivided into four major types, WS1-WS4. WS1 is diagnosed by the presence of dystopia canthorum and PAX3 is the only gene involved. This study aims to determine the pathogenic mutation in a large Iranian pedigree affected with WS1 in order to further confirm the clinical diagnosis.

METHODS

In the present study, a family segregating HI was ascertained in a genetic counseling center. Upon clinical inspection, white forelock, dystopia canthorum, broad high nasal root and synophrys, characteristic of WS1 were evident. In order to clarify the genetic etiology and confirm the clinical data, primers were designed to amplify exons and exon-intron boundaries of the responsible gene, PAX3 with 10 exons, followed by the Sanger DNA sequencing method.

RESULTS

Genetic analysis of PAX3 revealed a novel mutation in PAX3 (c.1024_1040 del AGCACGATTCCTTCCAA). Our data provide genotype-phenotype correlation for the mutation in PAX3 and WS1 in the studied family, with implications for genetic counseling, which necessitates detailed clinical inspection of HI patients to distinguish syndromic HI from the more common non-syndromic cases.

CONCLUSION

Our results reveal the value of phenotype-directed genetic analysis and could further expand the spectrum of PAX3 mutations.

Molecular and clinical characterization of Waardenburg syndrome type I in an Iranian cohort with two novel PAX3 mutations

Waardenburg syndrome (WS) is a disease of abnormal neural-crest derived melanocyte development characterized by hearing loss and pigmentary disturbances in hair, eyes and skin. WS is subdivided into four major types, WS1-WS4, where WS1 is recognized by the presence of dystopia canthorum, with PAX3 being the only known gene involved. This study aimed at investigating PAX3 mutations and clinical characteristics of WS1 in a group of Iranian patients. A total of 12 WS1 patients from four unrelated Iranian families were enrolled. Waardenburg consortium guidelines were used for WS1 diagnosis. A detailed family history was traced and a thorough clinical examination was performed for all participants. Furthermore, WS1 patients underwent screening for PAX3 mutations using PCR-sequencing. Dystopia canthorum, broad high nasal root and synophrys were observed in all patients. Early graying, hair discoloration, hypoplastic blue eyes (characteristic brilliant blue iris) and hearing loss were the most common features observed, while heterochromia iridis was the least frequently observed sign among the studied Iranian WS1 patients. Genetic analysis of PAX3 revealed four mutations including c.667C>T, c.784C>T, c.951delT and c.451+3A>C. Two of the four mutations reported here (c.951delT and c.451+3A>C) are being reported for the first time in this study. Our data provide insight into genotypic and phenotypic spectrum of WS1 in an Iranian series of patients. Our results expand the spectrum of PAX3 mutations and may have implications for the genetic counseling of WS in Iran.

EPHA4 haploinsufficiency is responsible for the short stature of a patient with 2q35-q36.2 deletion and Waardenburg syndrome

Background

Waardenburg syndrome type I (WS1), an auditory-pigmentary genetic disorder, is caused by heterozygous loss-of-function mutations in PAX3. Abnormal physical signs such as dystopia canthorum, patchy hypopigmentation and sensorineural hearing loss are common, but short stature is not associated with WS1.

Case presentation

We reported a 4-year and 6 month-old boy with a rare combination of WS1 and severe short stature (83.5 cm (−5.8SD)). His facial features include dystopia canthorum, mild synophrys, slightly up-slanted palpebral fissure, posteriorly rotated ears, alae nasi hypoplasia and micrognathia. No heterochromia was noticed. He had a normal intelligence quotient and hearing. Insulin-like growth factor-1 (IGF-1) was 52.7 ng/ml, lower than the normal range (55 ~ 452 ng/ml) and the peak growth hormone level was 7.57 ng/ml at 90 minutes after taking moderate levodopa and pyridostigmine bromide. The patient exhibited a good response to human growth hormone (rhGH) replacement therapy, showing a 9.2 cm/year growth rate and an improvement of 1 standard deviation (SD) of height after one year treatment. CMA test of patient’s DNA revealed a 4.46 Mb de novo deletion at 2q35-q36.2 (hg19; chr2:221,234,146-225,697,363).

Conclusions

PAX3 haploinsufficiency is known to cause Waardenburg syndrome. Examining overlapping deletions in patients led to the conclusion that EPHA4 is a novel short stature gene. The finding is supported by the splotch-retarded and epha4 knockout mouse models which both showed growth retardation. We believe this rare condition is caused by the haploinsufficiency of both PAX3 and EPH4 genes. We further reported a growth response to recombinant human growth hormone treatment in this patient.

Detection of PAX2 deletions and duplications using multiplex ligation-dependent probe amplification

BACKGROUND

Renal coloboma syndrome (RCS) is a rare inherited disorder caused by mutations in the PAX2 gene. Clinical testing is currently performed by bidirectional Sanger sequencing of all 12 coding exons of the PAX2 gene, which detects point mutations or small insertion/deletion mutations. Large genomic deletions of PAX2 have been identified in 3/90 known RCS families, accounting for approximately (3%) of RCS cases. In these cases, the deletion was detected by cytogenetic techniques such as G-banding or array comparative genomic hybridization. While these methods would be sufficient to identify whole gene deletions, they may not be able to identify smaller rearrangements affecting single exons. Similarly, such deletions would not be detected by Sanger sequencing.

AIM

The aim of this study was to determine whether mutation-negative RCS probands harbor a genomic deletion or duplication involving one or more exons of the PAX2 gene. We evaluated this hypothesis in 46 patients with a clinical suspicion of RCS in whom no mutations were identified.

RESULTS

We developed a multiplex ligation-dependent probe amplification assay to detect gene deletion/duplication in all 12 exons of the PAX2 gene. Of the 46 PAX2 mutation-negative samples tested, none demonstrated deletions or duplications in the PAX2 gene. This suggests that deletions or duplications in PAX2 are unlikely to significantly contribute to the pathogenesis of RCS, beyond the known 3% of cases that have been attributed to whole gene deletions. Given these results, we hypothesize that other genes and/or locus control regions regulating PAX2 may be involved in the pathogenesis of PAX2 mutation-negative cases of RCS.

Genetic analysis of PAX3 for diagnosis of Waardenburg syndrome type I

CONCLUSION

PAX3 genetic analysis increased the diagnostic accuracy for Waardenburg syndrome type I (WS1). Analysis of the three-dimensional (3D) structure of PAX3 helped verify the pathogenicity of a missense mutation, and multiple ligation-dependent probe amplification (MLPA) analysis of PAX3 increased the sensitivity of genetic diagnosis in patients with WS1.

OBJECTIVES

Clinical diagnosis of WS1 is often difficult in individual patients with isolated, mild, or non-specific symptoms. The objective of the present study was to facilitate the accurate diagnosis of WS1 through genetic analysis of PAX3 and to expand the spectrum of known PAX3 mutations.

METHODS

In two Japanese families with WS1, we conducted a clinical evaluation of symptoms and genetic analysis, which involved direct sequencing, MLPA analysis, quantitative PCR of PAX3, and analysis of the predicted 3D structure of PAX3. The normal-hearing control group comprised 92 subjects who had normal hearing according to pure tone audiometry.

RESULTS

In one family, direct sequencing of PAX3 identified a heterozygous mutation, p.I59F. Analysis of PAX3 3D structures indicated that this mutation distorted the DNA-binding site of PAX3. In the other family, MLPA analysis and subsequent quantitative PCR detected a large, heterozygous deletion spanning 1759-2554 kb that eliminated 12-18 genes including a whole PAX3 gene.

Inherited hearing loss: molecular genetics and diagnostic testing

BACKGROUND

Hearing loss is a clinically and genetically heterogeneous condition with major medical and social consequences. It affects up to 8% of the general population.

OBJECTIVE

This review recapitulates the principles of auditory physiology and the molecular basis of hearing loss, outlines the main types of non-syndromic and syndromic deafness by mode of inheritance, and provides an overview of current clinically available genetic testing.

METHODS

This paper reviews the literature on auditory physiology and on genes, associated with hearing loss, for which genetic testing is presently offered.

RESULTS/CONCLUSION

The advent of molecular diagnostic assays for hereditary hearing loss permits earlier detection of the underlying causes, facilitates appropriate interventions, and is expected to generate the data necessary for more specific genotype-phenotype correlations.

Cochlear implantation and congenital deafness: perceptive and lexical results in 2 genetically pediatric identified population

OBJECTIVE

To evaluate the perceptive and linguistic results in 2 predefined genetic population of children with implants.

STUDY DESIGN

Retrospective cohort study.

SETTING

Otolaryngology department of a tertiary referral hospital.

PATIENTS

Among 336 children with prelingual deafness who underwent implantation in our department between 1997 and 2007, 85 with GJB2 gene-related (Cx) deafness and 30 patients with Waardenburg syndrome (WaardS) were included. Mean age at implantation was 4.7 years (range, 15 mo to 16.5 yr) in the Cx group and 4.8 years (range, 16 mo to 16 yr) in the WaardS group. The mean follow-up period was 6.5 years (range, 19 mo to 12 yr) in the Cx group and 7.1 years (range, 27 mo to 13.5 yr) in the WaardS group. More than 75% of the families in both groups scored 4 and 5 when using the Mary Pat Moeller rating (p > 0.05). A psychoneurological evaluation was performed in one third of the patients in both groups.

MAIN OUTCOME MEASURES

Patients underwent linguistic and perceptive evaluations at 12, 24, 36, and 48 months: speech perception with closed-set and open-set words, speech production (Level 1 = vocalizations to Level 5 = complex sentences), and lexical comprehension with EVIP/GaelP (Peabody Picture Vocabulary Test) tests that ranged in 5 levels (-2 SD to +2 SD).

RESULTS

Score results for open-set words were 38.5%, 57.5%, 69%, and 75% in the Cx group and 30.5%, 59%, 67.5%, and 78% in the WaardS group (p > 0.05) at 12, 24, 36, and 48 months. The proportion of children in Levels 4 and 5 of speech production was 27%, 42%, 57.5%, and 58% in the Cx group and 23%, 33%, 55%, and 66% in the WaardS group (p > 0.05). Lexical result at Level -2 SD at 1 year was 90% in the Cx group and 85% in the WaardS group and that at 4 years was 70% in the Cx group and 65% in the WaardS group (p > 0.05).

CONCLUSION

Perceptive and linguistic evolutions for both populations were of good quality, but lexical evaluation showed residual language difficulties in both groups.

Novel splice mutation in microthalmia-associated transcription factor in Waardenburg Syndrome

Waardenburg Syndrome (WS) is a syndromic form of hearing loss associated with mutations in six different genes. We identified a large family with WS that had previously undergone clinical testing, with no reported pathogenic mutation. Using linkage analysis, a region on 3p14.1 with an LOD score of 6.6 was identified. Microthalmia-Associated Transcription Factor, a gene known to cause WS, is located within this region of linkage. Sequencing of Microthalmia-Associated Transcription Factor demonstrated a c.1212 G>A synonymous variant that segregated with the WS in the family and was predicted to cause a novel splicing site that was confirmed with expression analysis of the mRNA. This case illustrates the need to computationally analyze novel synonymous sequence variants for possible effects on splicing to maximize the clinical sensitivity of sequence-based genetic testing.

GeneMarker® HID: A reliable software tool for the analysis of forensic STR data

GeneMarker(®) HID was assessed as a software tool for the analysis of forensic short tandem repeat (STR) data and as a resource for analysis of custom STR multiplexes. The software is easy to learn and use, and includes design features that have the potential to reduce user fatigue. To illustrate reliability and accuracy, STR data from both single-source and mixture profiles were analyzed and compared to profiles interpreted with another software package. A total of 1898 STR profiles representing 28,470 loci and more than 42,000 alleles were analyzed with 100% concordance. GeneMarker HID was also used to successfully analyze data generated from a custom STR multiplex, with simplified and rapid implementation. Finally, the impact of the user-friendly design features of the software was assessed through a time scale study. The results suggest that laboratories can reduce the time required for data analysis by at least 25% when using GeneMarker HID.

Sensorineural deafness, distinctive facial features, and abnormal cranial bones: a new variant of Waardenburg syndrome?

The Waardenburg syndromes (WS) account for approximately 2% of congenital sensorineural deafness. This heterogeneous group of diseases currently can be categorized into four major subtypes (WS types 1-4) on the basis of characteristic clinical features. Multiple genes have been implicated in WS, and mutations in some genes can cause more than one WS subtype. In addition to eye, hair, and skin pigmentary abnormalities, dystopia canthorum and broad nasal bridge are seen in WS type 1. Mutations in the PAX3 gene are responsible for the condition in the majority of these patients. In addition, mutations in PAX3 have been found in WS type 3 that is distinguished by musculoskeletal abnormalities, and in a family with a rare subtype of WS, craniofacial-deafness-hand syndrome (CDHS), characterized by dysmorphic facial features, hand abnormalities, and absent or hypoplastic nasal and wrist bones. Here we describe a woman who shares some, but not all features of WS type 3 and CDHS, and who also has abnormal cranial bones. All sinuses were hypoplastic, and the cochlea were small. No sequence alteration in PAX3 was found. These observations broaden the clinical range of WS and suggest there may be genetic heterogeneity even within the CDHS subtype.