Next generation sequencing (NGS) to improve the diagnosis and management of patients with disorders of sex development (DSD)

Disorders of sex development (DSDs) are a diverse group of conditions where the chromosomal, gonadal or anatomical sex can be atypical. The highly heterogeneous nature of this group of conditions often makes determining a genetic diagnosis challenging. Prior to next generation sequencing (NGS) technologies, genetic diagnostic tests were only available for a few of the many DSD-associated genes, which consequently had to be tested sequentially. Genetic testing is key in establishing the diagnosis, allowing for personalised management of these patients. Pinpointing the molecular cause of a patient's DSD can significantly impact patient management by informing future development needs, altering management strategies and identifying correct inheritance pattern when counselling family members. We have developed a 30-gene NGS panel, designed to be used as a frontline test for all suspected cases of DSD (both 46,XX and 46,XY cases). We have confirmed a diagnosis in 25 of the 80 patients tested to date. Confirmed diagnoses were linked to mutations in AMH, AMHR2, AR, HSD17B3, HSD3B2, MAMLD1, NR5A1, SRD5A2 and WT1 which have resulted in changes to patient management. The minimum diagnostic yield for patients with 46,XY DSD is 25/73. In 34/80 patients, only benign or likely benign variants were identified, and in 21/80 patients only variants of uncertain significance (VOUS) were identified, resulting in a diagnosis not being confirmed in these individuals. Our data support previous studies that an NGS panel approach is a clinically useful and cost-effective frontline test for patients with DSDs.

Gonadal function in adult male patients with congenital adrenal hyperplasia

CONTEXT

Current knowledge on gonadal function in congenital adrenal hyperplasia (CAH) is mostly limited to single-center/country studies enrolling small patient numbers. Overall data indicate that gonadal function can be compromised in men with CAH.

OBJECTIVE

To determine gonadal function in men with CAH within the European 'dsd-LIFE' cohort.

DESIGN

Cross-sectional clinical outcome study, including retrospective data from medical records.

METHODS

Fourteen academic hospitals included 121 men with CAH aged 16-68 years. Main outcome measures were serum hormone concentrations, semen parameters and imaging data of the testes.

RESULTS

At the time of assessment, 14/69 patients had a serum testosterone concentration below the reference range; 7 of those were hypogonadotropic, 6 normogonadotropic and 1 hypergonadotropic. In contrast, among the patients with normal serum testosterone (55/69), 4 were hypogonadotropic, 44 normogonadotropic and 7 hypergonadotropic. The association of decreased testosterone with reduced gonadotropin concentrations (odds ratio (OR) = 12.8 (2.9-57.3)) was weaker than the association between serum androstenedione/testosterone ratio ≥1 and reduced gonadotropin concentrations (OR = 39.3 (2.1-732.4)). Evaluation of sperm quality revealed decreased sperm concentrations (15/39), motility (13/37) and abnormal morphology (4/28). Testicular adrenal rest tumor (TART)s were present in 39/80 patients, with a higher prevalence in patients with the most severe genotype (14/18) and in patients with increased current 17-hydroxyprogesterone 20/35) or androstenedione (12/18) serum concentrations. Forty-three children were fathered by 26/113 patients.

CONCLUSIONS

Men with CAH have a high risk of developing hypothalamic-pituitary-gonadal disturbances and spermatogenic abnormalities. Regular assessment of endocrine gonadal function and imaging for TART development are recommended, in addition to measures for fertility protection.

The role of the sonic hedgehog signalling pathway in patients with midline defects and congenital hypopituitarism

INTRODUCTION

The Gli family of zinc finger (GLI) transcription factors mediates the sonic hedgehog signalling pathway (HH) essential for CNS, early pituitary and ventral forebrain development in mice. Human mutations in this pathway have been described in patients with holoprosencephaly (HPE), isolated congenital hypopituitarism (CH) and cranial/midline facial abnormalities. Mutations in Sonic hedgehog (SHH) have been associated with HPE but not CH, despite murine studies indicating involvement in pituitary development.

OBJECTIVES/METHODS

We aimed to establish the role of the HH pathway in the aetiology of hypothalamo-pituitary disorders by screening our cohort of patients with midline defects and/or CH for mutations in SHH, GLI2, Shh brain enhancer 2 (SBE2) and growth-arrest specific 1 (GAS1).

RESULTS

Two variants and a deletion of GLI2 were identified in three patients. A novel variant at a highly conserved residue in the zinc finger DNA-binding domain, c.1552G > A [pE518K], was identified in a patient with growth hormone deficiency and low normal free T4. A nonsynonymous variant, c.2159G > A [p.R720H], was identified in a patient with a short neck, cleft palate and hypogonadotrophic hypogonadism. A 26·6 Mb deletion, 2q12·3-q21·3, encompassing GLI2 and 77 other genes, was identified in a patient with short stature and impaired growth. Human embryonic expression studies and molecular characterisation of the GLI2 mutant p.E518K support the potential pathogenicity of GLI2 mutations. No mutations were identified in GAS1 or SBE2. A novel SHH variant, c.1295T>A [p.I432N], was identified in two siblings with variable midline defects but normal pituitary function.

CONCLUSIONS

Our data suggest that mutations in SHH, GAS1 and SBE2 are not associated with hypopituitarism, although GLI2 is an important candidate for CH.

Improving postgraduate clinical assessment tools: the introduction of video recordings to assess decision making

BACKGROUND

Competency in the management of acutely unwell patients has not previously been formally assessed as part of an objective structured clinical examination (OSCE).

AIM

The reliability of the paediatric postgraduate OSCE was calculated. An objective structured video examination was designed to assess candidates' clinical decision making ability when managing acutely unwell children.

METHODS

The performance of 3522 postgraduate paediatric trainees was assessed (2006-2008). OSCE reliability was determined using Cronbach's alpha and mean inter-item correlation. Performance in the video station was compared with overall performance (not including video station; Mann-Whitney U) and video station scores correlated with individual station scores (Spearman's Rho correlation coefficient).

RESULTS

Clinical examination pass rates for the 684 UK graduates, 1608 overseas candidates training in the UK and 1104 overseas candidates training overseas were 69.7%, 28% and 22.3%, respectively (graduation information not available for 126 candidates). Cronbach's alpha was 0.62. Mean inter-item correlation was 0.15. Candidates who passed the OSCE overall had significantly higher scores on the video station (t(3520) = 14.48); p < 0.001). There was significant positive correlation between scores on the video station, individual stations and overall total score (r's = 0.300; p = 0.001).

CONCLUSIONS

The postgraduate paediatric OSCE provides a sound and valid means of assessing clinical skills at the postgraduate level. The video station provides an important new method of assessment. Its use in other postgraduate clinical examinations should be explored.

Rest-activity disturbances in children with septo-optic dysplasia characterized by actigraphy and 24-hour plasma melatonin profiles

INTRODUCTION

A trial of melatonin treatment in children with septo-optic dysplasia (SOD) and sleep disruption is accepted clinical practice in many centers. However, no objective measurements of sleep/activity patterns with 24-h melatonin profiles have been published for these individuals, and the pathophysiological basis underlying sleep disorders in SOD remains largely unknown.

METHODS

We studied six children with rest-activity disturbances and SOD. All wore an Actiwatch-Mini (a noninvasive method of detecting and recording movement intensity) for 2 wk and were admitted to hospital for a 24-h period during which hourly measurements of serum melatonin were taken. Sleep data were analyzed in conjunction with a detailed sleep diary. Ethical approval was obtained for these studies.

RESULTS

Two children produced virtually no melatonin throughout the 24-h period of measurement and had fragmented sleep patterns with no evidence of a non-24-h sleep-wake disorder or delayed sleep-phase disorder. One child had a normal melatonin profile despite actigraphy showing an arrhythmic sleep pattern. The remaining three children had fragmented sleep, with two having normal melatonin profiles and one having a modest increase in daytime melatonin concentrations, making the timing of dim-light melatonin onset difficult to discern.

CONCLUSIONS

There is considerable variation in timing and amount of melatonin secretion in these children. Surprisingly, none of the children had either actigraphic or melatonin profile evidence of a non-24-h sleep-wake disorder or delayed sleep-phase disorder. Understanding the heterogeneous nature of underlying sleep disorders in this group of children is important and has implications for their management.

Diagnosis of growth hormone deficiency

The diagnosis of growth hormone deficiency (GHD) was essentially a clinical one prior to the advent of radioimmunoassay in the mid-1960s. From this point on both clinical and biochemical serum GH responses to a variety of provocation tests were used to define the condition. The definition of an adequate GH response to stimulation has changed over time, initially being <3 microg/l and gradually increasing to 10 microg/l. Over this period, GH assays became more sensitive and specific, and assays for IGF-1 and IGFBP-3 were developed. Detailed neuroimaging also became widely available and genetic aetiologies for GHD identified. Apart from a number of clear genetic causes for GHD, the diagnostic gold standard remains elusive. However, making the correct diagnosis has significant benefits to the child, guiding both future investigations and management. In this chapter we discuss the importance of taking into account all available evidence when making the diagnosis of GHD including clinical examination, detailed auxological measurements, bone age, molecular analysis, biochemical measures and neuroradiological assessment.

High prevalence of Mycobacterium tuberculosis infection and disease in children and adolescents with type 1 diabetes mellitus

SETTING

Western Cape Province, South Africa.

OBJECTIVES

To describe the prevalence of tuberculosis (TB) infection and disease in children with type 1 diabetes and to investigate the association between glycaemic control and prevalence of TB infection and disease.

DESIGN

Cross-sectional hospital-based study conducted at two public referral hospitals. All children and adolescents (aged <21 years) with type 1 diabetes underwent a Mantoux tuberculin skin test (>or=10 mm classified as Mycobacterium tuberculosis infection), measurement of glycosylated haemoglobin and a chest radiograph. Patients with symptoms suggestive of TB were investigated using mycobacterial culture. Radiologically and/or bacteriologically confirmed disease was classified as TB disease.

RESULTS

Of 291 eligible patients, 258 (88.7%) were included (58% female). The prevalence of M. tuberculosis infection was 29.8% (95%CI 24.2-35.4); nine patients were diagnosed with prevalent TB disease (point prevalence disease 3488 per 100,000 population). Poor glycaemic control (hazard ratio 1.39, 95%CI 1.18-1.63 per unit increase in glycated haemoglobin [HbA1c]) and contact with a TB source case (P = 0.0011) was associated with prevalent TB disease.

CONCLUSIONS

There is a high prevalence of TB disease in diabetic children and adolescents in this setting. Routine TB screening of children with type 1 diabetes may be indicated in settings highly endemic for TB. Preventive treatment should be considered for diabetic children with proof of TB exposure and/or infection.

Estimation of secular trends in adult height, and childhood socioeconomic circumstances in three Eastern European populations

The objective of these analyses was to estimate the strength and direction of secular trends in adult height and childhood socioeconomic circumstances in eight towns in three Eastern European countries in the mid-20th century, and to assess the extent to which childhood conditions might explain the height differences. We used cross-sectional data from the baseline survey of the Health, Alcohol and Psychosocial factors in Eastern Europe (HAPIEE) study, conducted in 2002-2005. The study examined 24,012 men and women born between 1933 and 1957, randomly selected from the general populations of Novosibirsk (Russia), Krakow (Poland) and six towns of the Czech Republic. To allow for age-related height loss we estimated maximum attained height. Parental education and household item ownership at age 10 were used as markers of childhood socioeconomic conditions. In all 5-year birth cohorts, Novosibirsk men and women were shortest. There were positive and statistically significant secular trends in childhood conditions and in maximum adult height. Adjustment for childhood conditions explained about one third of the trend in height. There appeared to be a small reduction in height of persons born during the Second World War which was, however, only significant in Novosibirsk. These results suggest that secular trends in height mirror, but are not wholly explained by, trends in socioeconomic circumstances in early life.

Phosphonate utilization by the globally important marine diazotroph Trichodesmium

The factors that control the growth and nitrogen fixation rates of marine diazotrophs such as Trichodesmium have been intensively studied because of the role that these processes have in the global cycling of carbon and nitrogen, and in the sequestration of carbon to the deep sea. Because the phosphate concentrations of many ocean gyres are low, the bioavailability of the larger, chemically heterogeneous pool of dissolved organic phosphorus could markedly influence Trichodesmium physiology. Here we describe the induction, by phosphorus stress, of genes from the Trichodesmium erythraeum IMS101 genome that are predicted to encode proteins associated with the high-affinity transport and hydrolysis of phosphonate compounds by a carbon-phosphorus lyase pathway. We show the importance of these genes through expression analyses with T. erythraeum from the Sargasso Sea. Phosphonates are known to be present in oligotrophic marine systems, but have not previously been considered to be bioavailable to marine diazotrophs. The apparent absence of genes encoding a carbon-phosphorus lyase pathway in the other marine cyanobacterial genomes suggests that, relative to other phytoplankton, Trichodesmium is uniquely adapted for scavenging phosphorus from organic sources. This adaptation may help to explain the prevalence of Trichodesmium in low phosphate, oligotrophic systems.

The genome of a motile marine Synechococcus

Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria.

Antibody responses to HPV6b E polyproteins and production of monoclonal antibodies

A range of fusion constructs (expressed in Escherichia coli) were produced that contained two or more HPV6b E proteins, producing a single continuous amino acid sequence corresponding to the sequences of the individual E proteins. The constructs also included a C-terminal hexahistidine tag fused in-frame to aid purification. The fusion proteins (polyproteins) were semipurified by Ni(++) metal affinity chromatography under denaturing conditions. Immunization of BALB/c mice with these polyproteins resulted in the production of specific E protein antibodies. The draining lymph nodes from these mice were used to produce monoclonal antibodies (MAbs). The specificity of the polyclonal and MAbs was confirmed by immunoblotting and by screening for reaction with a series of synthetic peptides of E proteins. HPV E polyproteins were found to be immunogenic and immunization with the polyproteins resulted in specific antibody responses to the component E proteins.

Characterization of Trichodesmium spp. by genetic techniques

The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus TRICHODESMIUM: The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of KATAGNYMENE: Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.

Iron stress in open-ocean cyanobacteria (Synechococcus, Trichodesmium, and Crocosphaera spp.): identification of the IdiA protein

Cyanobacteria are prominent constituents of the marine biosphere that account for a significant percentage of oceanic primary productivity. In an effort to resolve how open-ocean cyanobacteria persist in regions where the Fe concentration is thought to be limiting their productivity, we performed a number of Fe stress experiments on axenic cultures of marine Synechococcus spp., Crocosphaera sp., and Trichodesmium sp. Through this work, we determined that all of these marine cyanobacteria mount adaptive responses to Fe stress, which resulted in the induction and/or repression of several proteins. We have identified one of the Fe stress-induced proteins as an IdiA homologue. Genomic observations and laboratory data presented herein from open-ocean Synechococcus spp. are consistent with IdiA having a role in cellular Fe scavenging. Our data indicate that IdiA may make an excellent marker for Fe stress in open-ocean cyanobacterial field populations. By determining how these microorganisms respond to Fe stress, we will gain insight into how and when this important trace element can limit their growth in situ. This knowledge will greatly increase our understanding of how marine Fe cycling impacts oceanic processes, such as carbon and nitrogen fixation.

Overexpression, purification, and refolding of a Porphyromonas gingivalis cysteine protease from Escherichia coli

This paper describes the overexpression of the Rgp-1 (arginine) protease domain from Porphyromonas gingivalis. This protease and the related Kgp (lysine) protease, both of which display trypsin-like specificity, have been implicated as major virulence factors and may play a significant role in the etiology of periodontal disease. Both Rgp-1 and Kgp are initially translated as polyproteins, each containing a protease domain and multiple adhesin domains. The Rgp-1 protease domain was expressed in E. coli, purified, refolded, and assayed for activity. These expression studies demonstrated that prior to the formation of inclusion bodies in the E. coli cytoplasm, the protease was proteolytically active and could hydrolyze a specific synthetic substrate. When the Rgp-1 protease domain was purified from inclusion bodies and refolded, it was found to be autolytically active and displayed specific catalytic activity. This is the first report on the expression and purification of active Rgp-1 from E. coli. Polyclonal antisera raised against recombinant protein recognized the native form of the protease in the P. gingivalis strain W50, indicating that the recombinant protein contained some of the antigenic determinants of the native protease.