Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilms tumour susceptibility gene

BACKGROUND

Localisation of the breakpoints of chromosomal translocations has aided the discovery of several disease genes but has traditionally required laborious investigation of chromosomes by fluorescent in situ hybridisation approaches. Here, a strategy that utilises genome-wide paired-end massively parallel DNA sequencing to rapidly map translocation breakpoints is reported. This method was used to fine map a de novo t(5;6)(q21;q21) translocation in a child with bilateral, young-onset Wilms tumour.

METHODS AND RESULTS

Genome-wide paired-end sequencing was performed for approximately 6 million randomly generated approximately 3 kb fragments from constitutional DNA containing the translocation, and six fragments in which one end mapped to chromosome 5 and the other to chromosome 6 were identified. This mapped the translocation breakpoints to within 1.7 kb. Then, PCR assays that amplified across the rearrangement junction were designed to characterise the breakpoints at sequence-level resolution. The 6q21 breakpoint transects and truncates HACE1, an E3 ubiquitin-protein ligase that has been implicated as a somatically inactivated target in Wilms tumourigenesis. To evaluate the contribution of HACE1 to Wilms tumour predisposition, the gene was mutationally screened in 450 individuals with Wilms tumour. One child with unilateral Wilms tumour and a truncating HACE1 mutation was identified.

CONCLUSIONS

These data indicate that constitutional disruption of HACE1 likely predisposes to Wilms tumour. However, HACE1 mutations are rare and therefore can only make a small contribution to Wilms tumour incidence. More broadly, this study demonstrates the utility of genome-wide paired-end sequencing in the delineation of apparently balanced chromosomal translocations, for which it is likely to become the method of choice.

Chain of evidence in sexual assault cases

Chain of evidence (COE) sampling is a legal concept demonstrating the journey of a sample from origin to court. Positive sexually transmitted infection (STI) results may have importance in criminal proceedings and require a demonstrated COE for them to be used as admissible evidence. A retrospective case-notes review of female sexual assault patients was carried out to review COE sampling in two clinics. Three hundred and eighteen patients underwent sexual health screening and COE sampling was indicated in 58 (18%). COE sampling was carried out in 44 (92%) of 48 indicated cases at the Haven (a dedicated sexual assault centre) and five (50%) of 10 at the Ambrose King Centre (a sexual health clinic). COE protocols should be in place in both sexual assault referral centres and sexual health clinics. In specialist clinics, with well-established guidelines and trained dedicated staff, COE sampling standards can be achieved.

Duodenal atresia: associated anomalies, prenatal diagnosis and outcome

BACKGROUND

The diagnosis of duodenal atresia is commonly made prenatally, either as an isolated lesion or due to its association with other chromosomal abnormalities (Robertson et al. in Semin Perinatol 18:182-195, 1994; Hemming and Rankin in J Prenat Diagn 27:1205-1211, 2007). The aim of this study was to describe the prevalence of associated anomalies, prenatal diagnostic accuracy and survival of cases of congenital duodenal atresia in our institution.

METHODS

All cases of duodenal atresia registered with our local congenital anomaly register over a 10-year period, 1995-2004 inclusive, were studied, including those resulting in termination of pregnancies, stillbirths, intrauterine deaths and neonatal deaths. To ensure high-case ascertainment, data were cross checked with prenatal ultrasound, cytogenetic laboratory, pathology department and neonatal surgical data base. Data were analysed for associated anomalies, accuracy of prenatal diagnosis and neonatal outcomes.

RESULTS

A total of 65 patients were initially diagnosed as having duodenal atresia, of these 4 were subsequently excluded (1 postnatal normal bowel and 3 high jejunal atresias). In the remaining 61 cases, 35 (57%) had an association with other congenital abnormalities and 26 (43%) were isolated anomalies. Thirty-five were male and 26 female (M:F = 1.4:1). Twenty-one out of 29 (72%) patients prenatally diagnosed, compared with 14 out of 32 (44%) patients diagnosed postnatally had associated anomalies. Duodenal atresia was suspected on routine prenatal ultrasonography at 20-week gestation in 33 cases and confirmed in 29 (48%) cases with 4 false-positive diagnoses (1 normal bowel and 3 high jejunal atresias). No prenatal diagnosis was made in 32 (52%) babies. Of the 61 cases, 53 were live births with 2 early neonatal deaths (1 cardiac and 1 VACTERL), 5 terminations, 2 intrauterine deaths and 1 stillbirth (Fig. 3). Overall neonatal survival was 96% (51 cases). Mortality in the group diagnosed prenatally was 34 % (10 cases).

CONCLUSION

This study shows an overall increased association of duodenal atresia with Down's syndrome. In the group diagnosed prenatally, mortality as well as the association with other congenital anomalies was found to be higher. We have demonstrated a greater prenatal diagnostic accuracy, but confirm postnatal outcomes similar to previous studies.

Patent processus vaginalis: a window to the abdomen

A patent processus vaginalis (PPV) allows a communication between the peritoneum and scrotum. Hydrocoele is the usual presentation of a PPV in children. However, with intraabdominal pathology the patent PPV may provide the first clue to the mischief within the abdomen. We present here two unusual cases associated with a PPV and migration of intraabdominal contents from the abdomen to the scrotum.

Comparison between open and thoracoscopic resection of congenital lung lesions

PURPOSE

This study compares the outcome between thoracoscopic and thoracotomy resection of congenital lung lesions.

METHODS

From November 2005 to August 2007, 14 consecutive cases of video-assisted thoracoscopic (VATS) lung resections have been performed in our institution. A retrospective review comparing these cases to the previous open thoracotomies for lung resection was performed. Intraoperative and early postoperative results were compared.

RESULTS

The mean age for VATS resection was 10 months compared with 7 months for thoracotomy. There were no major intraoperative complications. One case was converted from thoracoscopy to thoracotomy, and there was one anesthetic failed attempt of VATS resection, which was then performed open. Seven VATS resections and 6 thoracotomies were for congenital cystic adenomatous malformations. Intraoperative chest drains were used for all VATS resections but only 10 of the 14 thoracotomies, one of which developed a tension pneumothorax within hours of discharge. Perioperative outcomes including time to removal of chest drain, length of postoperative intravenous opioid requirement, and hospital stay were similar for both groups. Three had postoperative complications. Operative time was significantly lower in the thoracotomy group (124 minutes compared with 170 minutes, P < .05). The subgroup of congenital lobar emphysema had a particularly prolonged VATS resection time of 220 vs 155 minutes (P < .05). The thoracotomy group was more likely to receive adjuvant regional anesthesia (12 of 14 compared with 5 of 14).

CONCLUSIONS

Thoracoscopic resection of lung lesions results in longer operative time but is a safe and feasible alternative to open thoracotomy. Congenital lobar emphysema is a subgroup more challenging thoracoscopically, and it is recommended that these should be preselected for open surgery.

Integrated community-based sexual health services for young people in urban areas: are we meeting the needs of the local community?

Community-based sexual health services (SHS) are intended to improve access for people who may have difficulty attending traditional genitourinary medicine clinics. The objective of this study was to review uptake of sexually transmitted infection (STI) testing in an outreach clinic for those under 25 in an area where Black and minority ethnic groups comprise the majority of the local population. A retrospective case-notes review was undertaken of those attending. Standards were that Fraser guidelines should be completed in all under 16-year-old and all clients should be offered STI testing, HIV testing and contraception (if applicable) in accordance with local standards. One hundred and seventeen clients attended. Ten percent self-reported ethnicity was Asian. Thirty-six (31%) clients tested for chlamydia. Thirty (26%) had an HIV test. Five (14% of those tested) had a positive nucleic acid amplification test for chlamydia. Five (13%) of those requesting long term contraception had STI testing. This service has successfully improved access to STI screening. However, there may have been missed opportunities to offer tests in those requesting contraception. Under-representation of those of non-white ethnicity suggests access to SHS may be a particular problem and further work is required to improve the sexual health of the local community.

Partial pressure of oxygen in arterial blood in normal pregnant women in Dhaka city

In the present study the partial pressure of oxygen in arterial blood (PaO2) was estimated in 32 women in Dhaka city. For this purpose a total 32 women subjects with age ranged from 25 years to 35 years without any recent history of respiratory diseases were selected and divided into 8 healthy non-pregnant women as control and 24 normal pregnant women as experimental group. Experimental group was further divided into 8 first trimester, 8 second trimester & 8 third trimester of pregnant women. The PaO2 was estimated by using "Easy Blood Gas Auto Analyzer". The PaO2 was estimated during the 1st, 2nd, 3rd trimesters of pregnant women and non-pregnant women. The mean of measured values of PaO2 were analyzed statistically in relation to 1st, 2nd, 3rd trimesters of pregnant women & non-pregnant women. The PaO2 was significantly higher in 1st trimester, 2nd trimester & 3rd trimester of pregnant women than that of non-pregnant women. There were no statistically significant difference of PaO2 between the 1st trimester and 2nd trimester; between the 1st trimester and 3rd trimester; and between the 2nd trimester and 3rd trimester of pregnant women. It may be concluded that the causes of progressively increased PaO2 throughout the pregnancy were most likely to be due to effect of progesterone causing hyperventilation.

Evaluation of objective structured practical examination and traditional practical examination

To evaluate the competency of Objective Structured Practical Examination (OSPE) as an assessment technique compared to Traditional Practical Examination (TDPE) in assessment of laboratory component of physiology, the results of Physiology practical examination of 400 students from 4 Medical Colleges, two Government and two non Government (Dhaka Medical College, Mymensingh Medical College, Bangladesh Medical College, Uttara Women's Medical College) under Dhaka University were studied. Students' performance in OSPE and TDPE was compared. Mean score obtained in OSPE was 77.72+/-0.66 and found significantly higher than that for TDPE (64.44+/-0.61). Again mean scores achieved in OSPE were compared among different Medical Colleges and significant difference was noted. In OSPE, male students achieved significantly higher score than that of female students, especially in responding question station. The outcome of the present study thus indicates that OSPE is a better choice as an assessment technique over the Traditional method measuring wide range of practical skill. It may be concluded that it is important for competency based performance discrimination and it also helps improving students performance quality in laboratory exercise.

Performance of laser bonded glass/polyimide microjoints in cerebrospinal fluid

In this paper, laser bonded microjoints between glass and polyimide is considered to examine their potential applicability in encapsulating neural implants. To facilitate bonding between polyimide and glass, a thin titanium film with a thickness of 2 microm was deposited on borosilicate glass plates by a physical vapor deposition (PVD) process. Titanium coated glass was then joined with polyimide by using a cw fiber laser emitting at a wavelength of 1.1 microm (1.0 W) to prepare several tensile samples. Some of the samples were exposed to artificial cerebrospinal fluid (aCSF) at 37 degrees C for two weeks to assess long-term integrity of the joints. Both the as-received and aCSF soaked samples were subjected to uniaxial tensile loads for bond strengths measurements. The bond strengths for the as-received and aCSF soaked samples were measured to be 7.31 and 5.33 N/mm, respectively. Although the long-term exposure of the microjoints to aCSF has resulted in 26% reduction of bond strength, the samples still retain considerably high strength as compared with the titanium-polyimide samples. The failed glass/polyimide samples were also analyzed using optical microscopy, and failure mechanisms are discussed. In addition, a two dimensional finite element analysis (FEA) was conducted to understand the stress distribution within the substrate materials while the samples are in tension. The FEA results match reasonably well with the experimental load-displacement curves for as-received samples. Detailed discussion on various stress contours is presented in the paper, and the failure mechanisms observed from the experiment are shown in good agreement with the FEA predicted ones.

Surveillance for Wilms tumour in at-risk children: pragmatic recommendations for best practice

BACKGROUND

Most Wilms tumours occur in otherwise healthy children, but a small proportion occur in children with genetic syndromes associated with increased risks of Wilms tumour. Surveillance for Wilms tumour has become widespread, despite a lack of clarity about which children are at increased risk of these tumours and limited evidence of the efficacy of screening or guidance as to how screening should be implemented.

METHODS

The available literature was reviewed.

RESULTS

The potential risks and benefits of Wilms tumour surveillance are finely balanced and there is no clear evidence that screening reduces mortality or morbidity. Prospective evidence-based data on the efficacy of Wilms tumour screening would be difficult and costly to generate and are unlikely to become available in the foreseeable future.

CONCLUSIONS

The following pragmatic recommendations have been formulated for Wilms tumour surveillance in children at risk, based on our review: (1) Surveillance should be offered to children at >5% risk of Wilms tumour. (2) Surveillance should only be offered after review by a clinical geneticist. (3) Surveillance should be carried out by renal ultrasonography every 3-4 months. (4) Surveillance should continue until 5 years of age in all conditions except Beckwith-Wiedemann syndrome, Simpson-Golabi-Behmel syndrome and some familial Wilms tumour pedigrees where it should continue until 7 years. (5) Surveillance can be undertaken at a local centre, but should be carried out by someone with experience in paediatric ultrasonography. (6) Screen-detected lesions should be managed at a specialist centre.

ATM and breast cancer susceptibility

ATM was originally identified by positional cloning as the gene that underlies the autosomal recessive condition ataxia-telangiectasia. The encoded protein plays a central role in the complex processes that repair DNA double-strand breaks. Nearly 20 years ago, epidemiological surveys of relatives of ataxia-telangiectasia cases suggested that female relatives were at modestly increased risk of breast cancer. Subsequently, many studies have tried to clarify the role of ATM in breast cancer susceptibility, but have produced inconclusive and/or inconsistent results. Recently, large epidemiological and molecular studies have finally provided conclusive evidence that ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles.

Syndromes and constitutional chromosomal abnormalities associated with Wilms tumour

Wilms tumour has been reported in association with over 50 different clinical conditions and several abnormal constitutional karyotypes. Conclusive evidence of an increased risk of Wilms tumour exists for only a minority of these conditions, including WT1 associated syndromes, familial Wilms tumour, and certain overgrowth conditions such as Beckwith-Wiedemann syndrome. In many reported conditions the rare co-occurrence of Wilms tumour is probably due to chance. However, for several conditions the available evidence cannot either confirm or exclude an increased risk, usually because of the rarity of the syndrome. In addition, emerging evidence suggests that an increased risk of Wilms tumour occurs only in a subset of individuals for some syndromes. The complex clinical and molecular heterogeneity of disorders associated with Wilms tumour, together with the apparent absence of functional links between most of the known predisposition genes, suggests that abrogation of a variety of pathways can promote Wilms tumorigenesis.

Multiple mechanisms are implicated in the generation of 5q35 microdeletions in Sotos syndrome

BACKGROUND

Sotos syndrome is characterised by learning difficulties, overgrowth, and a typical facial appearance. Microdeletions at 5q35.3, encompassing NSD1, are responsible for approximately 10% of non-Japanese cases of Sotos. In contrast, a recurrent approximately 2 Mb microdeletion has been reported as responsible for approximately 50% of Japanese cases of Sotos.

METHODS

We screened 471 cases for NSD1 mutations and deletions and identified 23 with 5q35 microdeletions. We investigated the deletion size, parent of origin, and mechanism of generation in these and a further 10 cases identified from published reports. We used "in silico" analyses to investigate whether repetitive elements that could generate microdeletions flank NSD1.

RESULTS

Three repetitive elements flanking NSD1, designated REPcen, REPmid, and REPtel, were identified. Up to 18 cases may have the same sized deletion, but at least eight unique deletion sizes were identified, ranging from 0.4 to 5 Mb. In most instances, the microdeletion arose through interchromosomal rearrangements of the paternally inherited chromosome.

CONCLUSIONS

Frequency, size, and mechanism of generation of 5q35 microdeletions differ between Japanese and non-Japanese cases of Sotos. Our microdeletions were identified from a large case series with a broad range of phenotypes, suggesting that sample selection variability is unlikely as a sole explanation for these differences and that variation in genomic architecture might be a contributory factor. Non-allelic homologous recombination between REPcen and REPtel may have generated up to 18 microdeletion cases in our series. However, at least 15 cannot be mediated by these repeats, including at least seven deletions of different sizes, implicating multiple mechanisms in the generation of 5q35 microdeletions.

Partial NSD1 deletions cause 5% of Sotos syndrome and are readily identifiable by multiplex ligation dependent probe amplification

BACKGROUND

Most cases of Sotos syndrome are caused by intragenic NSD1 mutations or 5q35 microdeletions. It is uncertain whether allelic or genetic heterogeneity underlies the residual cases and it has been proposed that other mechanisms, such as 11p15 defects, might be responsible for Sotos cases without NSD1 mutations or 5q35 microdeletions.

OBJECTIVE

To develop a multiplex ligation dependent probe amplification (MLPA) assay to screen NSD1 for exonic deletions/duplications.

METHODS

Analysis was undertaken of 18 classic Sotos syndrome cases in which NSD1 mutations and 5q35 microdeletions were excluded. Long range polymerase chain reaction (PCR) was used to characterise the mechanism of generation of the partial NSD1 deletions.

RESULTS

Eight unique partial NSD1 deletions were identified: exons 1-2 (n = 4), exons 3-5, exons 9-13, exons 19-21, and exon 22. Using long range PCR six of the deletions were confirmed and the precise breakpoints in five cases characterised. This showed that three had arisen through Alu-Alu recombination and two from non-homologous end joining.

CONCLUSIONS

MLPA is a robust, inexpensive, simple technique that reliably detects both 5q35 microdeletions and partial NSD1 deletions that together account for approximately 15% of Sotos syndrome.

Initial-rate method for the determination of pantoprazole in pharmaceutical formulations using 1-fluoro 2,4-dinitrobenzene

A simple and selective kinetic spectrophotometric method for the determination of pantoprazole in pharmaceutical preparations is described. The procedure is based upon a kinetic investigation of the reaction of the drug with 1-fluoro-2,4-dinitrobenzene in DMSO at room temperature. The absorbance of the coloured product was measured at 420 nm. The plot of the logarithm of the initial rate of the reaction vs. the logarithm of molar concentration of pantoprazole is linear over the range 10-20 microg x ml(-1). The procedure retains its accuracy in the presence of a large excess of its degradate, sulfenic acid, which is prepared by degradating the pure drug in borate buffer of pH 8 at room temperature for seven days. The results are validated statistically and through recovery studies. The method has been successfully applied to the determination of pantoprazole in commercial tablets. Statistical comparison of the results with the reference method shows excellent agreement and indicates no significant difference in accuracy and precision.

Laser bonded microjoints between titanium and polyimide for applications in medical implants

Bioencapsulation of medical implant devices, and neural implant devices in particular, requires development of reliable hermetic joints between packaging materials that are often dissimilar. Titanium-polyimide is one of the biocompatible material systems, which are of interest to our research groups at Wayne State University and Fraunhofer USA. We have found processing conditions for successful joining of titanium with polyimide using near-infrared diode lasers or fiber lasers along transmission bonding lines with widths ranging from 200 to 300 microm. Laser powers of 2.2 and 3.8 W were used to create these joints. Laser-joined samples were tested in a microtester under tensile loading to determine joint strengths. In addition, finite element analysis (FEA) was conducted to understand the stress distribution within the bond area under tensile loading. The FEA model provides a full-field stress distribution in and around the joint that cause eventual failure. Results from the investigation provide an initial approach to characterize laser-fabricated microjoints between dissimilar materials that can be potentially used in optimization of bio-encapsulation design.

The prevalence of glaucoma in Bangladesh: a population based survey in Dhaka division

BACKGROUND/AIM

Few studies have reported on the epidemiology and clinical characteristics of glaucoma in south Asia. This project aimed to determine the prevalence of glaucoma of Dhaka, Bangladesh.

METHOD

A multistage, stratified, clustered sample was drawn from Dhaka Division, Bangladesh, using systematic sampling to identify individual subjects aged 35 years and older. Examination of all subjects included Snellen visual acuity, slit lamp examination (including gonioscopy and applanation tonometry) and a stereoscopic assessment of the vertical cup:disc ratio (CDR). In selected subjects, a threshold visual field examination was performed. Glaucoma was diagnosed on the basis of statistical abnormality of the vertical CDR combined with an abnormal visual field test, or in subjects with advanced glaucoma who could not complete field testing, a grossly abnormal CDR. If it was not possible to examine the optic discs and the subject was blind, glaucoma was diagnosed on the basis of a raised intraocular pressure.

RESULTS

Of 3562 eligible subjects, 2347 were examined (66%). Among people aged 40 years and older, the prevalence of definite glaucoma was 2.1% (95% confidence interval: 1.5 to 2.9; 39 people). The prevalence of definite and probable glaucoma was 3.1% (95% CI: 2.4 to 4.0; 58 people) in subjects of the same age. Primary open angle glaucoma was the most common form of glaucoma, accounting for 75% of the total. Among cases of blindness not attributable to refractive error, 5% were caused by glaucoma. Glaucoma prevalence was higher in men than women, but did not show the typical increase with age.

CONCLUSION

Glaucoma prevalence is relatively high in Bangladesh, although it accounts for only a small proportion of blindness in the community. It is estimated that there are approximately 586 000 people 40 years and older with definite or probable glaucoma in Bangladesh.