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.

INSIG1 influences obesity-related hypertriglyceridemia in humans

In our analysis of a quantitative trait locus (QTL) for plasma triglyceride (TG) levels [logarithm of odds (LOD) = 3.7] on human chromosome 7q36, we examined 29 single nucleotide polymorphisms (SNPs) across INSIG1, a biological candidate gene in the region. Insulin-induced genes (INSIGs) are feedback mediators of cholesterol and fatty acid synthesis in animals, but their role in human lipid regulation is unclear. In our cohort, the INSIG1 promoter SNP rs2721 was associated with TG levels (P = 2 x 10(-3) in 1,560 individuals of the original linkage cohort, P = 8 x 10(-4) in 920 unrelated individuals of the replication cohort, combined P = 9.9 x 10(-6)). Individuals homozygous for the T allele had 9% higher TG levels and 2-fold lower expression of INSIG1 in surgical liver biopsy samples when compared with individuals homozygous for the G allele. Also, the T allele showed additional binding of nuclear proteins from HepG2 liver cells in gel shift assays. Finally, the variant rs7566605 in INSIG2, the only homolog of INSIG1, enhances the effect of rs2721 (P = 0.00117). The variant rs2721 alone explains 5.4% of the observed linkage in our cohort, suggesting that additional, yet-undiscovered genes and sequence variants in the QTL interval also contribute to alterations in TG levels in humans.

Thromboembolic disease and air travel in pregnancy: a survey of advice given by obstetricians

The objective of this study was to document the awareness of risk and the nature of advice given by obstetricians to pregnant women who intend to travel by air and to compare the results with the advice given in an opinion paper of the Royal College of Obstetricians and Gynaecologists. The results were based on a self-completed questionnaire. All registered members of the Royal College of Obstetricians and Gynaecologists comprising 1349 individuals, obtained from a list provided by the RCOG, were invited to participate. An anonymous postal questionnaire was completed by the individuals before publication of the opinion paper of the RCOG. A total of 862 (62%) questionnaires returned, and 690 (51%) were available for analysis; 67% of obstetricians regard flying as being safe throughout pregnancy, 33% only in the 2nd and 3rd trimester. Nearly all obstetricians advised on simple prophylactic measures such as mobilisation, fluid intake and leg exercise. Fifty-three per cent would advise the use of prophylactic aspirin (75 mg), 49% the use of compression stockings; 4% recommended heparinisation; 44% believed this advice to be applicable only for the 2nd and 3rd trimester, while the RCOG emphasises that the risk of developing venous thromboembolism begins in the 1st trimester. Obstetricians as well as other health professionals need to be made aware that advice on air travel in pregnancy needs to start in the 1st trimester. Further research is needed to explore the relevance of the duration of flight when considering the application of thromboprophylactic measures as well as the value and choice of pharmacological treatment such as aspirin and heparin.

The enhancement and scale up of the extraction of anti-oxidants from Rosmarinus officinalis using ultrasound

The aim of this study was to examine the effect of ultrasound on the solvent extraction of anti-oxidants from the rosemary herb and to scale up the ultrasonic extraction process. The anti-oxidants of interest were identified using HPLC. Results indicated that, compared with conventional solvent extraction, the use of ultrasound gives a more effective extraction at lower temperatures with less dependence on the extraction solvent employed and that scale up of the process is possible.

Characterization of a multiple ligand-gated ion channel cellular membrane affinity chromatography column and identification of endogenously expressed receptors in astrocytoma cell lines

Cellular membranes obtained from the 1321N1 and A172 astrocytoma cell lines were immobilized on a chromatographic phase to create cellular membrane affinity chromatography (CMAC) columns, CMAC(1321N1) and CMAC(A172). The columns were characterized using frontal affinity chromatography with [(3)H]-epibatidine as the marker ligand and epibatidine, nicotine, and methyllycaconitine as the displacers. The results indicated that the columns contained homomeric alpha7 nicotinic acetylcholine receptors (alpha7 nAChR) and heteromeric nicotinic acetylcholine receptors (alpha(x)beta(y) nAChRs), which was confirmed by the addition of subtype-specific inhibitors, alpha-bungarotoxin (alpha7 nAChR) and kappa-bungarotoxin (alpha(x)beta(y) nAChR) to the mobile phase. The presence of two additional ligand-gated ion channels (LGICs), gamma-aminobutyric acid (GABA(A)) and N-methyl-D-aspartic acid (NMDA), was established using frontal affinity chromatography with flunitrazepam and diazepam (GABA(A) receptor) and MK-801 and NMDA (NMDA receptor). The presence of the four LGICs was confirmed using confocal microscopy and flow cytometry. The results indicate that the CMAC(1321N1) and CMAC(A172) columns contain four independently functioning LGICs, that the columns can be used to characterize binding affinities of small molecules to each of the receptors, and that the CMAC approach can be used to probe the expression of endogenous membrane receptors.

Corlett loop for microvascular reconstruction in a neck depleted of vessels

Free tissue transfer has revolutionised reconstruction of the head and neck and there are currently few local factors that preclude its use. These include a lack of suitable recipient vessels in the area for microvascular anastomosis. We describe the use of a Corlett loop in which a temporary arteriovenous fistula (AVF) is created with a transposed cephalic vein to enable reconstruction of a mandibular defect with a fibular free flap.

Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern European descent

The International HapMap Consortium has determined the linkage disequilibrium (LD) patterns of four major human populations. The aim of our investigation was to compare the LD patterns of the HapMap CEPH (Centre d'Etude du Polymorphisme Humain) samples with a family-based cohort of similar ancestry to determine its usefulness as a reference population for disease association studies. We examined four genomic regions on chromosomes 7q, 12p, and 14q totaling 14.3 Mb, initially identified in our linkage study of obesity and the metabolic syndrome. Near identical patterns of LD were detected in both populations. Furthermore, tagSNPs selected based on the HapMap CEPH cohort data capture over 98% of the variants at an r2 > 0.8 in the disease cohort. This confirms the usefulness of the CEPH cohort of the HapMap as a reference sample for further investigations into the genomic variation of populations of Northern European descent.

Idiopathic eruptive macular pigmentation: a case of 21 years' duration

Idiopathic eruptive macular pigmentation is a rare condition characterized by asymptomatic pigmented macules involving the neck, trunk, and proximal portions of the extremities. Age at onset usually varies from 1 to 20 years. The lesions usually appear abruptly and remit spontaneously over months to years. An unusual case of a 24-year-old woman with idiopathic eruptive macular pigmentation lasting 21 years was characterized by several periods of spontaneous resolution followed by recurrences.

Child maltreatment and the early onset of problem behaviors: can a program of nurse home visitation break the link?

This study investigated the relationship between child maltreatment and the early onset of problem behaviors in the Elmira Nurse Home Visitation Program. Participants were predominantly low-income and unmarried mothers and their first-born children who were randomized either to receive over 2 years of home-visitation services by nurses or to be placed in a comparison group. Data were drawn from a follow-up study that took place when the children were 15 years of age. Results demonstrated that, in the comparison group. child maltreatment was associated with significant increases in the number of early onset problem behaviors reported by the youth. For the youth in the nurse-visited group there was no relationship between maltreatment and early onset problem behaviors. We suggest that this finding was due to the effects of the intervention in reducing the number as well as the developmental timing of the maltreatment incidents. Results suggest that prenatal and infancy home visiting by nurses can moderate the risk of child maltreatment as a predictor of conduct problems and antisocial behavior among children and youth born into at-risk families.

Characterization and evolution of a myrosinase from the cabbage aphid Brevicoryne brassicae

The aphid myrosinase gene has been elucidated using Rapid Amplification of cDNA Ends-PCR. Sequencing has shown that aphid myrosinase has significant sequence similarity (35%) to plant myrosinases and other members of glycosyl hydrolase family 1 (GHF1). The residues acting as proton donor and nucleophile, in the hydrolysis of glucosinolates by aphid myrosinase, are identified as Glu 167 and Glu 374 respectively. The equivalent residues in plant myrosinase are Gln 187 and Glu 409 and for the cyanogenic beta-glucosidase Glu 183 and Glu 397. Thus it would appear that the absence of a proton donor is not necessary for the hydrolysis of glucosinolates as was thought to be the case for the plant myrosinases. Aphid myrosinase appears to be more similar to animal beta-O-glucosidases than to plant myrosinases, as assessed by sequence similarity and phylogenetic techniques. These results strongly suggest that myrosinase activity has twice arisen from beta-O-glucosidases in plants and animals. Comparison of aphid myrosinase with plant myrosinase has highlighted Lys 173 and Arg 312 as possibly playing a crucial role in the hydrolysis of glucosinolates by aphid myrosinase.

Purification and characterisation of a non-plant myrosinase from the cabbage aphid Brevicoryne brassicae (L.)

Plant myrosinases and glucosinolates constitute a defence system in cruciferous plants towards pests and diseases. We have purified for the first time a non-plant myrosinase from the cabbage aphid Brevicoryne brassicae (L.) to homogeneity. The protein was N-terminally blocked and protease (trypsin and lys c) degradation gave peptides of which five were sequenced. The protein is a dimer with subunits of mass 54 kDa+/-500 Da. Western blot analysis with an anti-aphid myrosinase antibody showed a strong cross reaction with a protein extract from the Brassica specialist, B. brassicae. The anti-aphid myrosinase antibody does not cross react with plant myrosinase neither does an anti-plant myrosinase antibody cross react with aphid myrosinase.