Mutation analysis and clinical profile of South African patients with Neurofibromatosis type 1 (NF1) phenotype

Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic condition with complete age-dependent penetrance, variable expressivity and a global prevalence of ∼1/3,000. It is characteriszed by numerous café-au-lait macules, skin freckling in the inguinal or axillary regions, Lisch nodules of the iris, optic gliomas, neurofibromas, and tumour predisposition. The diagnostic testing strategy for NF1 includes testing for DNA single nucleotide variants (SNVs), copy number variants (CNVs) as well as RNA analysis for deep intronic and splice variants, which can cumulatively identify the causative variant in 95% of patients. In the present study, NF1 patients were screened using a next-generation sequencing (NGS) assay targeting NF1 exons and intron/exon boundaries for SNV and NF1 multiple ligation-dependent probe amplification (MLPA) analysis for CNV detection. Twenty-six unrelated Southern African patients clinically suspected of having NF1, based on the clinical diagnostic criteria developed by the National Institute of Health (NIH), were included in the current study. A detection rate of 58% (15/26) was obtained, with SNVs identified in 80% (12/15) using a targeted gene panel and NF1 gene deletion in 20% (3/15) identified using MLPA. Ten patients (38%) had no variants identified, although they met NF1 diagnostic criteria. One VUS was identified in this study in a patient that met NF1 diagnostic criteria, however there was no sufficient information to classify variant as pathogenic. The clinical features of Southern African patients with NF1 are similar to that of the known NF1 phenotype, with the exception of a lower frequency of plexiform neurofibromas and a higher frequency of developmental/intellectual disability compared to other cohorts. This is the first clinical and molecular characterisation of a Southern African ancestry NF1 cohort using both next-generation sequencing and MLPA analysis. A significant number of patients remained without a diagnosis following DNA-level testing. The current study offers a potential molecular testing strategy for our low resource environment that could benefit a significant proportion of patients who previously only received a clinical diagnosis without molecular confirmation.

A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments

Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.

Mutation profiling in South African patients with Cornelia de Lange syndrome phenotype

BACKGROUND

Cornelia de Lange Syndrome (CdLS) presents with a variable multi-systemic phenotype and pathogenic variants have been identified in five main genes. This condition has been understudied in African populations with little phenotypic and molecular information available.

METHODS AND RESULTS

We present a cohort of 14 patients with clinical features suggestive of CdLS. Clinical phenotyping was carried out and cases were classified according to the international consensus criteria. According to this criteria, nine patients had classical CdLS, one had non-classical CdLS and four presented with a phenotype that suggested molecular testing for CdLS. Each patient underwent mutation profiling using a targeted next generation sequencing panel of 18 genes comprising known and suspected CdLS causal genes. Of the 14 patients tested, pathogenic and likely pathogenic variants were identified in nine: eight variants in the NIPBL gene and one in the STAG1 gene.

CONCLUSIONS

We present the first molecular data for a cohort of South African patients with CdLS. Eight of the nine variants identified were in the NIPBL gene, the most commonly involved gene in cases of CdLS. This is also the first report of a patient of African ancestry presenting with STAG1-related CdLS.

Williams-Beuren syndrome in diverse populations

Williams-Beuren syndrome (WBS) is a common microdeletion syndrome characterized by a 1.5Mb deletion in 7q11.23. The phenotype of WBS has been well described in populations of European descent with not as much attention given to other ethnicities. In this study, individuals with WBS from diverse populations were assessed clinically and by facial analysis technology. Clinical data and images from 137 individuals with WBS were found in 19 countries with an average age of 11 years and female gender of 45%. The most common clinical phenotype elements were periorbital fullness and intellectual disability which were present in greater than 90% of our cohort. Additionally, 75% or greater of all individuals with WBS had malar flattening, long philtrum, wide mouth, and small jaw. Using facial analysis technology, we compared 286 Asian, African, Caucasian, and Latin American individuals with WBS with 286 gender and age matched controls and found that the accuracy to discriminate between WBS and controls was 0.90 when the entire cohort was evaluated concurrently. The test accuracy of the facial recognition technology increased significantly when the cohort was analyzed by specific ethnic population (P-value < 0.001 for all comparisons), with accuracies for Caucasian, African, Asian, and Latin American groups of 0.92, 0.96, 0.92, and 0.93, respectively. In summary, we present consistent clinical findings from global populations with WBS and demonstrate how facial analysis technology can support clinicians in making accurate WBS diagnoses.

Inspiratory muscle training in severe spinal muscular atrophy: a case report

Background/Aims

Inspiratory muscle training aims to preserve or improve respiratory muscle strength in children with neuromuscular diseases in order to prevent or minimise pulmonary morbidity. The aim of this study was to determine the effect of inspiratory muscle training on clinical outcomes and health-related quality of life in a child with advanced neuromuscular disease and severe pulmonary restriction.

Methods

A one patient pre-test post-test study design was implemented. General function, spirometry, peak expiratory cough flow and health-related quality of life were measured at baseline and after a 6-week inspiratory muscle training programme. Inspiratory muscle strength (maximal inspiratory mouth pressure and sniff nasal inspiratory pressure) was measured every 2 weeks. The patient used a tapered flow threshold inspiratory training device (POWERbreathe K3) at an intensity of ± 30% of maximal inspiratory mouth pressure twice a day, 5 days per week.

Findings

The non-ambulatory 10-year-old girl with type 2 spinal muscular atrophy initially had a forced vital capacity of 18% predicted and peak expiratory cough flow of 60 litres/minute. A substantial improvement was seen in inspiratory muscle strength between baseline and 4 weeks. Patient health-related quality of life improved and patient satisfaction was high, with a score of 9/10. The patient developed a lower respiratory tract infection towards the end of the inspiratory muscle training period. No other adverse events occurred.

Conclusions

Improved inspiratory muscle strength and health-related quality of life was associated with inspiratory muscle training in a child with advanced spinal muscular atrophy. Controlled clinical trials are recommended to determine the safety and efficacy of inspiratory muscle training in children with advanced spinal muscular atrophy and severe respiratory muscle weakness to inform clinical practice.

Cornelia de Lange syndrome in diverse populations

Cornelia de Lange syndrome (CdLS) is a dominant multisystemic malformation syndrome due to mutations in five genes-NIPBL, SMC1A, HDAC8, SMC3, and RAD21. The characteristic facial dysmorphisms include microcephaly, arched eyebrows, synophrys, short nose with depressed bridge and anteverted nares, long philtrum, thin lips, micrognathia, and hypertrichosis. Most affected individuals have intellectual disability, growth deficiency, and upper limb anomalies. This study looked at individuals from diverse populations with both clinical and molecularly confirmed diagnoses of CdLS by facial analysis technology. Clinical data and images from 246 individuals with CdLS were obtained from 15 countries. This cohort included 49% female patients and ages ranged from infancy to 37 years. Individuals were grouped into ancestry categories of African descent, Asian, Latin American, Middle Eastern, and Caucasian. Across these populations, 14 features showed a statistically significant difference. The most common facial features found in all ancestry groups included synophrys, short nose with anteverted nares, and a long philtrum with thin vermillion of the upper lip. Using facial analysis technology we compared 246 individuals with CdLS to 246 gender/age matched controls and found that sensitivity was equal or greater than 95% for all groups. Specificity was equal or greater than 91%. In conclusion, we present consistent clinical findings from global populations with CdLS while demonstrating how facial analysis technology can be a tool to support accurate diagnoses in the clinical setting. This work, along with prior studies in this arena, will assist in earlier detection, recognition, and treatment of CdLS worldwide.

Towards a Treatment for Intolerance of Uncertainty for Autistic Adults: A Single Case Experimental Design Study

Intolerance of uncertainty (IU) is indicated as an important transdiagnostic process variable in a range of anxiety disorders. Anxiety is very common in autistic adults. This study evaluates a manualised treatment programme for autistic adults, which focused on IU. An eight session programme (CUES-A©) was developed and delivered to four autistic adults on an individual basis. A single case experimental design was used to provide a preliminary evaluation of the feasibility, acceptability and preliminary effectiveness of the programme. Data regarding retention, acceptability and feasibility indicate that the participants valued the programme. Analyses of outcome measures indicate that the programme has promise as a treatment option for autistic adults experiencing IU.

Biallelic BRCA2 mutations in two black South African children with Fanconi anaemia

Fanconi anaemia (FA) is a genotypically and phenotypically heterogeneous genetic condition, characterized cytogenetically by chromosomal instability and breakage secondary to impaired DNA repair mechanisms. Affected individuals typically manifest growth restriction and congenital physical abnormalities and most progress to hematological disease including bone marrow aplasia. A rare genetic subtype of FA (FA-D1) is caused by biallelic mutations in the BRCA2 gene. Affected individuals manifest severe congenital anomalies and significant pigmentary changes and are additionally at risk for early onset leukemia and certain solid organ malignancies, including Wilms tumors and brain tumors. Parents of affected individuals are obligate carriers for heterozygous BRCA2 mutations and are thus potentially at risk for adult onset cancers which fall within the hereditary breast and ovarian cancer spectrum. We present two cases of black South African patients with FA diagnosed with biallelic BRCA2 mutations and discuss the phenotypic consequences and implications for them and their families. Recognition of this severe end of the phenotypic spectrum of FA is critical in allowing for confirmation of the diagnosis as well as cascade screening and appropriate care of family members.

A novel mutation in ETFDH manifesting as severe neonatal-onset multiple acyl-CoA dehydrogenase deficiency

Neonatal-onset multiple acyl-CoA dehydrogenase deficiency (MADD type I) is an autosomal recessive disorder of the electron transfer flavoprotein function characterized by a severe clinical and biochemical phenotype, including congenital abnormalities with unresponsiveness to riboflavin treatment as distinguishing features. From a retrospective study, relying mainly on metabolic data, we have identified a novel mutation, c.1067G>A (p.Gly356Glu) in exon 8 of ETFDH, in three South African Caucasian MADD patients with the index patient presenting the hallmark features of type I MADD and two patients with compound heterozygous (c.1067G>A+c.1448C>T) mutations presenting with MADD type III. SDS-PAGE western blot confirmed the significant effect of this mutation on ETFDH structural instability. The identification of this novel mutation in three families originating from the South African Afrikaner population is significant to direct screening and strategies for this disease, which amongst the organic acidemias routinely screened for, is relatively frequently observed in this population group.

Noonan syndrome in diverse populations

Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low-set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world.

Novel Zeb2 gene variation in the Mowat Wilson syndrome (MWS)

BACKGROUND

Mowat Wilson syndrome (MWS) is an uncommon association of Hirschsprung's disease (HSCR). Phenotypic features may develop with time, causing initial difficulties in diagnosis. MWS results from haploinsufficiency of the Zinc finger E-box-binding homeobox 2 (ZEB2) gene, and molecular diagnosis of ZEB2 mutation is required to confirm the diagnosis. We report the first confirmed cases of MWS in three children with the typical facial features, mental retardation, absent corpus callosum, epilepsy, and HSCR and novel Zeb2 variations on DNA analysis.

METHODOLOGY

Clinical features were monitored. DNA extracted from peripheral blood was subjected to bidirectional sequencing analysis following PCR DNA amplification. ZEB2 gene results were compared to the ZEB2 reference sequence (ENS00000169554) for variation. Bioinformatic investigation of novel gene variants was via the "Blastx" program function available via the National Center for Biotechnology Information (http://www.bioinfo.org/NPInter/blast/blast_link.cgi).

RESULTS

Clinical follow-up showed that the phenotypic features were not all present at birth but developed with time in 2 surviving patients. Several Zeb2 variations were detected in the promoter region of the ZEB2 gene of which 2 were novel (-56A/T 1174 11A/12A). In addition, a novel heterozygous single nucleotide insertion in exon 2 of ZEB2 in one patient results in a frameshift causing deletion of the first 8 amino acids of the ZEB2 protein and an alteration of amino acids 9 (G9A), 11 (R11G), and 12 (C12A). In the third patient, a novel single nucleotide deletion exon 8 (1784delC Het) results in a frameshift at amino acid 595 of translated protein. This shortens protein from 1214 to 594 amino acids and affects the functionality of the critical ZEB2 protein.

CONCLUSIONS

MWS is an important link to recognise clinically. It underlines the functionality of the Zeb2 gene in certain syndromic Hirschsprung's disease. These variations probably contribute to the clinical features of the Mowat Wilson phenotype in Hirschsprung's disease but should be confirmed in further research.

Compound heterozygosity in a South African patient with facioscapulohumeral muscular dystrophy

Facioscapulohumeral muscular dystrophy (FSHD) is characterised by weakness and atrophy of the facial and shoulder girdle muscles. The FSHD phenotype segregates as an autosomal dominant trait and is caused by a deletion of an integral number of 3.3 kilobase pair (kb) repeat units on chromosome 4q35. Haplotype and Southern blot analyses of chromosome 4 resulted in the detection of two BlnI resistant deletion fragments, of 24 kb and 34 kb respectively, in a single individual from a South African FSHD family. The patient had moderate facial weakness and marked winging and high-riding of the scapulae with prominent pectoral and proximal arm muscle atrophy and weakness. Quadriceps and anterior tibial muscles were weak and the patient had bilateral foot drop. Although none of his children were symptomatic yet and only two showed very mild clinical signs, one had inherited the 24 kb deletion fragment, while the other two had the 34 kb deletion fragment. Molecular analysis conclusively identified the first compound heterozygous case in the South African FSHD population. However, in accordance with other studies of compound heterozygotes and clinical findings, no direct correlation between the clinical severity of this patient and the number of deletion fragments was observed.

Cost effectiveness of screening for Chlamydia trachomatis: a review of published studies

OBJECTIVE

Screening for Chlamydia trachomatis in the lower genital tract may contribute to the prevention of pelvic inflammatory disease in women. The purpose of this review was to critically appraise, and summarise studies of the cost effectiveness of screening for C trachomatis.

METHODS

A literature search was conducted on Medline and in Health Star from 1990-2000. Keywords were C trachomatis, screening, cost effectiveness. Bibliographies of reviewed articles were also searched. The population studied was asymptomatic sexually active women under 30 years of age in a primary care setting. The intervention assessed was screening for lower genital tract infection with C trachomatis and the outcomes studied were cases of C trachomatis detected, cases of PID prevented, and associated costs. Studies were assessed using the Drummond criteria for economic evaluations. They were assessed qualitatively as they were too heterogeneous to allow quantitative analysis.

RESULTS

10 studies were included. All were modelled scenarios and all found screening to be more cost effective than simply testing symptomatic women, although all were based on probabilities that were assumed. Six of the studies focused on DNA based testing, three of them using urine. The models showed screening to be cost effective at prevalences of 3.1-10.0%, and cost saving (overtesting symptomatic women) at a prevalence as low as 1.1%, if age was used as a selection factor and DNA based tests were used in urine samples.

CONCLUSIONS

At the prevalence of infection expected in the target population, all studies suggest screening is cost effective. However, the assumptions used in the models have been difficult to confirm and there is a need for more data, particularly on the risk of complications in women with asymptomatic lower tract infection.

Prevention of pelvic inflammatory disease by the control of C. trachomatis infection

OBJECTIVES

To determine if there is evidence to indicate that screening for Chlamydia trachomatis (chlamydia) is an effective intervention in the prevention of pelvic inflammatory disease (PID).

METHODS

A systematic review was made of the literature to assess the effectiveness of screening asymptomatic young women for lower genital tract infection with C. trachomatis in the prevention of PID and its major sequelae tubal infertility and ectopic pregnancy.

RESULTS

There is considerable literature describing screening for lower genital tract infection with C. trachomatis, but only two randomized controlled trials, two ecological studies and one case-controlled trial were identified. These studies were graded and the evidence pooled. The suggestion that screening for chlamydia is an effective intervention in the prevention of PID is supported by Grade 2 evidence (level B recommendation). However, there are large gaps in the literature. Only small numbers of women have been studied and the follow-up periods are short. The studies have been conducted using mainly culture of cervical swabs to diagnose chlamydial infection and not the more recent nucleic acid based tests. The risk of a woman developing PID following detection of lower tract infection with C. trachomatis is still uncertain.

CONCLUSIONS

There is evidence to support a level B recommendation that screening for chlamydia using culture is effective in preventing PID in the short term. Further randomized controlled trials are required to assess screening using nucleic acid based tests and involving longer follow-up periods.

A systematic review of the prevalence of Chlamydia trachomatis among European women

The study aim was to establish by systematic review the prevalence of asymptomatic Chlamydia trachomatis infection of the lower female genital tract in Europe and also to assess the extent and effect of screening. The search process was wide ranging, using the electronic databases Medline, Embase and Aidsline and the Internet using the search engines Netscape and Euro-ferret. Studies published in any language during 1980-2000 were included if they unambiguously reported prevalence of C. trachomatis infection in asymptomatic women, and were assessed qualitatively. From >300 papers which quantified C. trachomatis urogenital infection, only 14 studies met the inclusion criteria: four from the UK, two from Sweden, two from The Netherlands, and one each from Bulgaria, France, Finland, Hungary, Italy and Spain. In only one study had screening taken place. The prevalence of C. trachomatis in unscreened asymptomatic women in Europe ranges from 1.7 to 17% depending upon the setting, context and country. The mode was -6% for women seeking contraception, and 4% for women having cervical smears. In conclusion, this review confirms high prevalence rates of C. trachomatis infection among asymptomatic women in many European settings.

Flap repair: an effective strategy for minimising sexual morbidity associated with the surgical management of vulval intra epithelial neoplasia

OBJECTIVE

To assess the sexual function after local excision and flap repair for symptomatic vulval intraepithelial neoplasia (VIN).

STUDY DESIGN

A retrospective analysis of five sexually active women who had persistent, symptomatic VIN diagnosed in a dedicated tertiary referral vulval clinic and treated with local excision and flap repair. Sexual function was assessed using a modified version of the Sabbatsberg Sexual Self-Rating Scoring (SRS) system.

RESULTS

The mean age of the cohort was 32 years (range 30 to 51). Four patients had previously been unsuccessfully treated with local excision. Follow up ranged from 5 to 33 months. The SRS scores were 90, 90, 81, 72 and 25. Endogenous depression may explain this last score. There has been no recurrence of VIN.

CONCLUSION

In sexually active women with symptomatic VIN III, a flap reconstruction should be considered in addition to local excision as the treatment of choice.

AIDS and the inner city: critical issues

AIDS affects people of every race and economic group. The author discusses the psychosocial impact of AIDS on the predominantly poor, ethnic minority populations of the inner city in an effort to dispel misconceptions about the sociological issues these individuals face.