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Social disparities in cancer survival have been demonstrated in Australia despite a universal healthcare insurance system. Colorectal cancer is common, and reasons for survival disparities related to socioeconomic status need to be investigated and addressed. The aim is to evaluate the current Australian literature concerning the impact of socioeconomic status on colorectal cancer survival and stage at presentation.A systematic search of PUBMED, EMBASE, SCOPUS and Clarivate Web of Science databases from January 2010 to March 2022 was performed. Studies investigating the impact of socioeconomic status on colorectal stage at presentation or survival in Australia were included. Data were extracted on author, year of publication, state or territory of origin, patient population, other exposure variables, outcomes and findings and adjustments made.Of the 14 articles included, the patient populations examined varied in size from 207 to 100 000+ cases. Evidence that socioeconomic disadvantage was associated with poorer survival was demonstrated in eight of 12 studies. Evidence of effect on late stage at presentation was demonstrated in two of seven studies. Area-level measures were commonly used to assess socioeconomic status, with varying indices utilized.There is limited evidence that socioeconomic status is associated with late-stage at presentation. More studies provide evidence of an association between socioeconomic disadvantage and poorer survival, especially larger studies utilizing less clinically-detailed cancer registry data. Further investigation is required to analyse why socioeconomic disadvantage may be associated with poorer survival.

usc Refereed/Peer-reviewed Purpose: Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). Methods: A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. Results: Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. Conclusion: RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data.

PPP1R13L-associated cardiocutaneous syndrome is an autosomal recessive condition that presents with life-threatening dilated cardiomyopathy in early childhood, with or without features of inflammation on cardiac histology. There is also a variably expressed ectodermal phenotype.

Pathogenic variants in DDX3X have recently been identified to be a relatively common cause of intellectual disability in females. In this study, we describe six female probands, from five unrelated families, with five novel heterozygous variants in DDX3X, and the identification of potential germline mosaicism. Consistent features between this cohort and previously described cases include developmental delay or intellectual disability, growth disturbance and movement disorder. Common facial dysmorphism within the cohort include short palpebral fissures, micrognathia, bulbous nasal tip, protruding ears, high arched palate, thin upper vermillion and smooth philtrum. Novel clinical features identified from this cohort include facial dysmorphisms, perinatal complications, valgus feet deformity, lipoatrophy, dystonic episodes, and cutaneous mastocytosis. This case series attempts to expand the phenotype of the DDX3X syndrome; however, it remains heterogeneous. Description of further cases is required to more accurately identify the significance of novel phenotypes within this cohort.

Spin triplet superconductivity in the Kondo lattice ${\mathrm{UTe}}_{2}$ appears to be associated with spin fluctuations originating from incipient ferromagnetic order. Here we show clear evidence of twofold enhancement of superconductivity under pressure, which discontinuously transitions to magnetic order, likely of ferromagnetic nature, at higher pressures. The application of a magnetic field tunes the system back across a first-order phase boundary. Straddling this phase boundary, we find another example of reentrant superconductivity in ${\mathrm{UTe}}_{2}$. As the superconductivity and magnetism exist on two opposite sides of the first-order phase boundary, our results indicate other microscopic mechanisms may be playing a role in stabilizing spin triplet superconductivity in addition to spin fluctuations associated with magnetism.

Contains fulltext : 220423.pdf (Publisher’s version ) (Closed access) CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.

Nematicity, where rotational symmetry is broken while translational symmetry is conserved, is prevalent in high-temperature superconductors. In particular, nematic quantum critical point has been universally found near the optimum doping of the superconducting dome of several iron-based superconductor families. In such a regime, evidence for strong nematic fluctuations have been observed. As the precursor to this order, nematic fluctuations emerge before nematicity, providing favorable ground to study how nematic order modifies the electronic structure in the absence of structural distortion. Here we use spatially resolved angle-resolved photoemission spectroscopy to investigate the correlation between the onset of nematic fluctuations and electronic structure in an optimally doped ${\mathrm{BaFe}}_{2}{({\mathrm{As}}_{1\ensuremath{-}x}{\mathrm{P}}_{x})}_{2}$ ($x\phantom{\rule{0.222222em}{0ex}}\ensuremath{\sim}\phantom{\rule{0.222222em}{0ex}}0.3$) superconductor. We reveal a strong spatially varying anisotropy of the Fermi surface on a length scale of tens of microns with strong correlation between the changes in the hole and electron Fermi pockets, consistent with the variations expected in the presence of fluctuating nematic order. These results provide direct evidence for spatial nematic fluctuations in the optimal doping regime of iron-based superconductors.

New Zealand has a multiethnic population and a national cardiac inherited disease registry (Cardiac Inherited Disease Registry New Zealand [CIDRNZ]). Ancestry is reflected in the spectrum and prevalence of genetic variants in long QT syndrome (LQTS).The purpose of this study was to study the genetic testing yield and mutation spectrum of CIDRNZ LQTS probands stratified by self-identified ethnicity.A 15-year retrospective review of clinical CIDRNZ LQTS probands with a Schwartz score of ≥2 who had undergone genetic testing was performed.Of the 264 included LQTS probands, 160 (61%) reported as European, 79 (30%) NZ Māori and Pacific peoples (Polynesian), and 25 (9%) Other ethnicities, with comparable clinical characteristics across ethnic groups (cardiac events in 72%; age at presentation 28±19 years; corrected QT interval 512±55 ms). Despite comparable testing (5.3±1.4 LQTS genes), a class III-V LQTS variant was identified in 35% of Polynesian probands as compared with 63% of European and 72% of Other probands (P.0001). Among variant-positive CIDRNZ LQTS probands (n=148), Polynesians were more likely to have non-missense variants (57% vs 39% and 25% in probands of European and Other ethnicity, respectively; P=.005) as well as long QT syndrome type 1-3 variants not reported elsewhere (71% vs European 22% and Other 28%; P.0001). Variants found in multiple probands were more likely to be shared within the same ethnic group; P.01).Genetic testing of Polynesian LQTS probands has a lower diagnostic yield, despite comparable testing and clinical disease severity. Rare LQTS variants are more common in Polynesian LQTS probands. These data emphasize the importance of increasing the knowledge of genetic variation in the Polynesian population.

Background Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder with a population frequency of approximately 1 in 10,000. The most common epigenetic defect in BWS is a loss of methylation (LOM) at the 11p15.5 imprinting centre, KCNQ1OT1 TSS-DMR, and affects 50% of cases. We hypothesised that genetic factors linked to folate metabolism may play a role in BWS predisposition via effects on methylation maintenance at KCNQ1OT1 TSS-DMR. Results Single nucleotide variants (SNVs) in the folate pathway affecting methylenetetrahydrofolate reductase (MTHFR), methionine synthase reductase (MTRR), 5-methyltetrahydrofolate-homocysteine S-methyltransferase (MTR), cystathionine beta-synthase (CBS) and methionine adenosyltransferase (MAT1A) were examined in 55 BWS patients with KCNQ1OT1 TSS-DMR LOM and in 100 unaffected cases. MTHFR rs1801133: C>T was more prevalent in BWS with KCNQ1OT1 TSS-DMR LOM (p T, rs150331990: A>G and rs757460628: G>A encoding NP_001124295 p.Arg136Cys, p.His1118Arg and p.Arg1223His, respectively. These variants have population frequencies of less than 1 in 1000 and were absent from 100 control cases. Functional characterization using a hemimethylated DNA trapping assay revealed a reduced methyltransferase activity relative to wild-type DNMT1 for each variant ranging from 40 to 70% reduction in activity. Conclusions This study is the first to examine folate pathway genetics in BWS and to identify rare DNMT1 missense variants in affected individuals. Our data suggests that reduced DNMT1 activity could affect maintenance of methylation at KCNQ1OT1 TSS-DMR in some cases of BWS, possibly via a maternal effect in the early embryo. Larger cohort studies are warranted to further interrogate the relationship between impaired MTHFR enzymatic activity attributable to MTHFR rs1801133: C>T, dietary folate intake and BWS. Electronic supplementary material The online version of this article (10.1186/s13148-018-0546-4) contains supplementary material, which is available to authorized users.

We report the results of a pilot project for clinical DNA sequencing in New Zealand. This project aimed to estimate the diagnostic yield of next generation sequencing in the New Zealand clinical en...

The phenomenon of T-linear resistivity commonly observed in a number of strange metals has been widely seen as evidence for the breakdown of the quasiparticle picture of metals. This study shows that a recently discovered H/T scaling relationship in the magnetoresistance of the strange metal BaFe_{2}(As_{1-x}P_{x})_{2} is independent of the relative orientations of current and magnetic field. Rather, its magnitude and form depend only on the orientation of the magnetic field with respect to a single crystallographic axis: the direction perpendicular to the magnetic iron layers. This finding suggests that the magnetotransport scaling does not originate from the conventional averaging or orbital velocity of quasiparticles as they traverse a Fermi surface, but rather from dissipation arising from two-dimensional correlations.

We present the strain and temperature dependence of an anomalous nematic phase in optimally doped BaFe_{2}(As,P)_{2}. Polarized ultrafast optical measurements reveal broken fourfold rotational symmetry in a temperature range above T_{c} in which bulk probes do not detect a phase transition. Using ultrafast microscopy, we find that the magnitude and sign of this nematicity vary on a 50-100 μm length scale, and the temperature at which it onsets ranges from 40 K near a domain boundary to 60 K deep within a domain. Scanning Laue microdiffraction maps of local strain at room temperature indicate that the nematic order appears most strongly in regions of weak, isotropic strain. These results indicate that nematic order arises in a genuine phase transition rather than by enhancement of local anisotropy by a strong nematic susceptibility. We interpret our results in the context of a proposed surface nematic phase.

Background To review long QT syndrome molecular autopsy results in sudden unexplained death in young (SUDY) between 2006 and 2013 in New Zealand. Methods Audit of the LQTS molecular autopsy results, cardiac investigations and family screening data from gene-positive families. Results During the study period, 365 SUDY cases were referred for molecular autopsy. 128 cases (35%) underwent LQTS genetic testing. 31 likely pathogenic variants were identified in 27 cases (21%); SCN5A (14/31, 45%), KCNH2 (7/31, 22%), KCNQ1 (4/31, 13%), KCNE2 (3/31, 10%), KCNE1 (2/31, 7%), KCNJ2 (1/31, 3%). Thirteen variants (13/128, 10%) were ultimately classified as pathogenic. Most deaths (63%) occurred during sleep. Gene variant carriage was more likely with a positive medical history (mostly seizures, 63% vs 36%, p = 0.01), amongst females (36% vs 12%, p = 0.001) and whites more than Maori (31% vs 0, p = 0.0009). Children 1–12 years were more likely to be gene-positive (33% vs 14%, p = 0.02). Family screening identified 42 gene-positive relatives, 18 with definitive phenotypic expression of LQTS/Brugada. 76% of the variants were maternally inherited (p = 0.007). Further family investigations and research now support pathogenicity of the variant in 13/27 (48%) of gene-positive cases. Conclusion In New Zealand, variants in SCN5A and KCNH2, with maternal inheritance, predominate. A rare variant in LQTS genes is more likely in whites rather than Maori, females, children 1–12 years and those with a positive personal and family history of seizures, syncope or SUDY. Family screening supported the diagnosis in a third of the cases. The changing classification of variants creates a significant challenge.

Purpose : The craniosynostoses are characterized by premature fusion of one or more cranial sutures. The relative contribution of previously reported genes to craniosynostosis in large cohorts is unclear. Here we report on the use of a massively parallel sequencing panel in individuals with craniosynostosis without a prior molecular diagnosis. Methods : A 20-gene panel was designed based on the genes’ association with craniosynostosis, and clinically validated through retrospective testing of an Australian and New Zealand cohort of 233 individuals with craniosynostosis in whom previous testing had not identified a causative variant within FGFR1-3 hot-spot regions or the TWIST1 gene. An additional 76 individuals were tested prospectively. Results : Pathogenic or likely pathogenic variants in non-FGFR genes were identified in 43 individuals, with diagnostic yields of 14% and 15% in retrospective and prospective cohorts, respectively. Variants were identified most frequently in TCF12 (N = 22) and EFNB1 (N = 8), typically in individuals with nonsyndromic coronal craniosynostosis or TWIST1-negative clinically suspected Saethre–Chotzen syndrome. Clinically significant variants were also identified in ALX4, EFNA4, ERF, and FGF10. Conclusion : These findings support the clinical utility of a massively parallel sequencing panel for craniosynostosis. TCF12 and EFNB1 should be included in genetic testing for nonsyndromic coronal craniosynostosis or clinically suspected Saethre–Chotzen syndrome.

Administrative data are routinely captured for each hospital admission and may serve as an alternative source for populating databases. This study aims to determine the accuracy of administrative data to provide tumour characteristics and short-term post-operative outcomes, after a colorectal cancer (CRC) resection, compared with clinical data.A retrospective study of all CRC resections at a single hospital from 1 January 2008 to 31 December 2013 was conducted. Local administrative data were coded as per ICD-10-AM (International Classification of Diseases, Tenth Revision, Australian Modification) and Australian Classification of Health Interventions. Clinical data for all patients were extracted from the medical charts and compared with administrative data. Code combinations and algorithms were used to improve the accuracy of administrative data.A total of 436 patients were identified. The accuracy of algorithms combining tumour location and type of operation for right colon, left colon and rectum were 93, 89 and 88%, respectively. The accuracy of histological type was 89%, lymph node status 92% and metastasis status 88%. The accuracy of return to theatre and in-hospital mortality was 100%.Administrative data can provide reliable information on tumour details and short-term post-operative outcomes. The potential for administrative data to validate data captured in registries and be used independently for audit and research should be further explored.

Multinucleate cellular syncytial formation is a hallmark of skeletal muscle differentiation. Myomaker, encoded by Mymk (Tmem8c), is a well-conserved plasma membrane protein required for myoblast fusion to form multinucleated myotubes in mouse, chick, and zebrafish. Here, we report that autosomal recessive mutations in MYMK (OMIM 615345) cause Carey-Fineman-Ziter syndrome in humans (CFZS; OMIM 254940) by reducing but not eliminating MYMK function. We characterize MYMK-CFZS as a congenital myopathy with marked facial weakness and additional clinical and pathologic features that distinguish it from other congenital neuromuscular syndromes. We show that a heterologous cell fusion assay in vitro and allelic complementation experiments in mymk knockdown and mymkinsT/insT zebrafish in vivo can differentiate between MYMK wild type, hypomorphic and null alleles. Collectively, these data establish that MYMK activity is necessary for normal muscle development and maintenance in humans, and expand the spectrum of congenital myopathies to include cell-cell fusion deficits., During embryogenesis, the cytoplasmic protein Myomarker (MYMK) mediates muscle fibre formation by fusion of myoblasts. Here, the authors identify autosomal recessive mutations in MYMK that cause Carey-Fineman-Ziter syndrome in humans, and model the disease variants in zebrafish.

To investigate regional variations in the detection of sudden death syndromes across New Zealand by assessing registrations in the national Cardiac Inherited Diseases Registry New Zealand (CIDRNZ).The CIDRNZ has been a national entity since 2009, with a hub in Auckland and locally funded regional coordinators (Midland, Central) linked with multidisciplinary cardiac genetic teams. Registration is consent-based and voluntary, and involves the collection of clinical/genetic information and permits genetic testing and research. Registry data were extracted from the CIDRNZ in October 2015 and results are expressed as registrations per 100,000 people by district health board area.The CIDRNZ has 1,940 registrants from 712 families, 46% of whom are definitely or probably affected by cardiac inherited disease. There are clear regional differences in registration frequencies between regions and between the North and South Islands, both for overall registrations (56/100,000 and 14/100,000, respectively; p0.001) and for long QT syndrome registrations (15/100,000 and 6/100,000, respectively; p0.001). Regions with local coordinators have the highest number of registrations.The detection of sudden death syndromes in New Zealand through a cardiac genetic registry is possible but much work is needed to improve regional variation in the detection/reporting of these conditions across the country.

We study magnetotransport properties of the electron-doped superconductor ${\mathrm{Pr}}_{2\ensuremath{-}x}{\mathrm{Ce}}_{x}{\mathrm{CuO}}_{4\ifmmode\pm\else\textpm\fi{}\ensuremath{\delta}}$ with $x=0.14$ in magnetic fields up to 92 T, and observe Shubnikov-de Haas magnetic quantum oscillations. The oscillations display a single frequency $F=255\ifmmode\pm\else\textpm\fi{}10$ T, indicating a small Fermi pocket that is $\ensuremath{\sim}1%$ of the two-dimensional Brillouin zone and consistent with a Fermi surface reconstructed from the large holelike cylinder predicted for these layered materials. Despite the low nominal doping, all electronic properties including the effective mass and Hall effect are consistent with overdoped compounds. Our study demonstrates that the exceptional chemical control afforded by high quality thin films will enable Fermi surface studies deep into the overdoped cuprate phase diagram.

The linear change in resistance with temperature in high-temperature superconductors is an enduring mystery. And now, the resistance in a magnetic field shows similar scaling, suggesting that physicists have another probe of the linear behaviour. Many exotic metallic systems have a resistivity that varies linearly with temperature, and the physics behind this is thought to be connected to high-temperature superconductivity in the cuprates and iron pnictides1,2,3,4,5,6,7,8,9. Although this phenomenon has attracted considerable attention, it is unclear how the relevant physics manifests in other transport properties, for example their response to an applied magnetic field. We report measurements of the high-field magnetoresistance of the iron pnictide superconductor BaFe2(As1−xPx)2 and find that it obeys an unusual scaling relationship between applied magnetic field and temperature, with a conversion factor given simply by the ratio of the Bohr magneton and the Boltzmann constant. This suggests that magnetic fields probe the same physics that gives rise to the T-linear resistivity, providing a new experimental clue to this long-standing puzzle.

The duplication of chromosome 3q is a rare disorder with varying chromosomal breakpoints and consequently symptoms. Even rarer is the unbalanced outcome from a parental inv(3) resulting in duplicated 3q and a deletion of 3p. Molecular karyotyping should aid in precisely determining the length and breakpoints of the 3q+/3p− so as to better understand a child’s future development and needs. We report a case of an infant male with a 57.5 Mb duplication from 3q23-qter. This patient also has an accompanying 1.7 Mb deletion of 3p26.3. The duplicated segment in this patient encompasses the known critical region of 3q26.3-q27, which is implicated in the previously reported 3q dup syndrome; however, the accompanying 3p26.3 deletion is smaller than the previously reported cases. The clinical phenotype of this patient relates to previously reported cases of 3q+ that may suggest that the accompanying 1.7 Mb heterozygous deletion is not clinically relevant. Taken together, our data has refined the location and extent of the chromosome 3 imbalance, which will aid in better understanding the molecular underpinning of the 3q syndrome.

Multiple self-healing squamous epithelioma (MSSE), also known as Ferguson-Smith disease (FSD), is an autosomal-dominant skin cancer condition characterized by multiple squamous-carcinoma-like locally invasive skin tumors that grow rapidly for a few weeks before spontaneously regressing, leaving scars(1,2). High-throughput genomic sequencing of a conservative estimate (24.2 Mb) of the disease locus on chromosome 9 using exon array capture identified independent mutations in TGFBR1 in three unrelated families. Subsequent dideoxy sequencing of TGFBR1 identified 11 distinct monoallelic mutations in 18 affected families, firmly establishing TGFBR1 as the causative gene. The nature of the sequence variants, which include mutations in the extracellular ligand-binding domain and a series of truncating mutations in the kinase domain, indicates a clear genotype-phenotype correlation between loss-of-function TGFBR1 mutations and MSSE. This distinguishes MSSE from the Marfan syndrome-related disorders in which missense mutations in TGFBR1 lead to developmental defects with vascular involvement but no reported predisposition to cancer

The relatively rare proximal microdeletion of 17q12 (including deletion of the HNF1B gene) is associated with the renal cysts and diabetes syndrome. Recent reports have suggested that there may also be an association between this microdeletion and learning difficulties/autism. This case report describes one of only a few reported families segregating the 17q12 microdeletion, but which highlights the nonpenetrance and variable expressivity of multiple features of this condition.

The absence of a definitive genetic test for the autosomal recessive condition Schinzel-Giedion syndrome is a significant handicap to the recognition of this disorder. Radiological features have been an important aspect of many of the published cases. In a series of six cases, we now establish a consistency among many of the radiological features in affected cases which will be an important diagnostic aid in identifying future cases. This is confirmed by reference to an extensive review of previously published instances of the syndrome. Moreover, the clinical data, including previously unpublished photographs, which we detail from our patients will assist in enhanced diagnosis in the future.

Objectives To assess the opinions of individuals with mucopolysaccharidoses (MPS) and their parents regarding the use of enzyme replacement therapy (ERT). Study design A validated questionnaire, including hypothetical clinical scenarios about ERT for MPS, was distributed to members of MPS support groups in the United States and Australia. Results The questionnaire was completed by 249 MPS support group members. Overall, 92% were in favor of ERT where MPS causes severe physical problems but does not affect intellect, and 69% were in favor of ERT where the physical limitations are mild and intellect is spared. Only 47% were in favor of ERT where severe physical and intellectual problems are well established; however, 77% were in favor of ERT in this situation if treatment begun early prolongs life and improves quality of life. Conclusion Most respondents were in favor of ERT for MPS, even where it would not alter the intellectual deterioration. The medical community has a responsibility to advocate for their patients in situations where ERT is appropriate and recognize the economic burden and "family function burden" ERT can incur.

To date, there have been only a few reports of patients carrying a microdeletion in chromosome 12q14. These patients usually present with pre- and postnatal growth retardation, and developmental delay. Here we report on two additional patients with both genotype and phenotype differences. Similar to previously published cases, one patient has haploinsufficiency of theHMGA2gene and shows severe short stature and developmental delay. The second patient is only one of a handful without the loss of theHMGA2gene and shows a much better growth profile, but with absolute macrocephaly. This patient’s deletion is unique and hence defines a likely macrocephaly locus that contributes to the general phenotype characterising the 12q14 syndrome.

In this report we show that mithramycin considerably increases the direct cytotoxic effect of tumour necrosis factor (TNF) on tumour cells in vitro. Sensitisation to TNF-induced apoptosis was prevented by the broad caspase inhibitor zVAD-fmk, whereas overexpression of Bcl-2 had no effect. Mithramycin also potentiated cell death induced by Fas agonistic antibodies. In contrast, mithramycin reduced the percentage of cells undergoing apoptosis due to factor withdrawal. TNF-induced activation of NF-kappaB (NF-kappaB)-dependent gene expression was not modulated by mithramycin treatment. Concomitantly with the increased sensitivity, the protein level of the short-spliced cFLIP variant was downregulated. These results indicate that mithramycin enhances TNF-induced cell death in an NF-kappaB-independent manner, and suggest that the Fas-associated death domain protein plays a crucial role in the TNF-sensitising effect of mithramycin.

Background— Large gene rearrangements, not detectable by standard molecular genetic sequencing techniques, are present in a minority of patients with long QT syndrome. We aimed to screen for large rearrangements in genes responsible for long QT syndrome as part of the molecular autopsy of a 36-year-old woman who died suddenly and had a negative autopsy. A retrospective analysis of an ECG identified a long QT interval, but sequencing of known LQT genes was uninformative. Methods and Results— Array comparative genomic hybridization was used to screen for deletions and duplications in 101 genes implicated in cardiac disorders and sudden death using a postmortem blood sample. A 542 kb deletion encompassing the entire KCNJ2 gene was identified in the decedent. The mother had electrocardiographic U-wave changes consistent with Andersen–Tawil syndrome and exaggerated by exercise but none of the characteristic noncardiac features. Fluorescence in situ hybridization confirmed the deletion in the decedent and established its presence in the mother. Conclusions— A novel application of array comparative genomic hybridization and fluorescence in situ hybridization has identified that long QT syndrome and sudden cardiac death may occur as a result of a deletion of an entire gene. The case also supports recent research suggesting that noncardiac features of Andersen–Tawil syndrome occur only with missense or minor gene rearrangements in the KCNJ2 gene, resulting in a dominant negative effect on Kir2.x channels.

The increase in eosinophils at the site of antigen challenge has been used as evidence to suggest that this cell type plays a role in the pathophysiology of asthma. Aberrant production of several different cytokines, particularly interleukin (IL)-5, has been shown to result in eosinophilia. IL-5 influences the development and maturation of eosinophils in a number of different ways. Of note is the ability of IL-5 to act as a survival factor for eosinophils specifically inhibiting apoptosis. The precise mechanism by which IL-5 exerts its effect remains obscure. We used microarray technologies to investigate the changes in the messenger RNA expression profile of eosinophils after treatment with IL-5. Using the Affymetrix Hu6800 chip, a total of 80 genes were observed to be regulated by 2-fold or greater. Many of the genes previously identified as regulated by IL-5 were regulated in our microarray experiments. Of the 73 genes found to be upregulated, many were shown to play a role in adhesion, migration, activation, or survival of eosinophils or hematopoietic cells, whereas the function of others was unknown. To facilitate the identification of genes that govern the apoptosis and survivability of eosinophils, we used an alternative cellular model, TF1.8 cells, whose survival was also dependent on IL-5. Comparison of these models identified four genes, Pim-1, DSP-5 (hVH3, B23), CD24, and SLP-76, whose regulation was similarly coordinated in both systems. Identification of Pim-1 and SLP-76 as regulated by IL-5 led us to suggest a direct role for these proteins in the IL-5 signaling pathway in eosinophils. The tissue distribution of these genes demonstrated that Pim-1 and SLP-76 were relatively restricted to the eosinophil compared with their expression in brain, bone marrow, kidney, liver, and lung. By contrast, DSP-5 and CD24 were confirmed as ubiquitous in their expression by microarray.

The difficulties associated with studying molecular mechanisms important in hemopoietic stem cell (HSC) function such as the problems of purifying homogeneous stem cell populations, have prompted us to adapt the murine ES cell system as an in vitro model of HSC generation and function. We now report that careful analysis of the time course of HSC generation in differentiating ES cells allows them to be used as a source of known and novel hemopoietic gene products. We have generated a subtracted library using cDNA from ES cells collected just prior to and just following the emergence of HSCs. Analysis of this library shows it to be a rich source of known hemopoietic and hemopoietic related gene products with 44% of identifiable cDNAs falling into these camps. We have demonstrated the value of this system as a source of novel genes of relevance to HSC function by characterizing a novel membrane protein encoding cDNA that is preferentially expressed in primitive hemopoietic cells. Intriguingly, further analysis of the known components of the subtracted library is suggestive of erythroid preconditioning of the ES cell-derived HSC. We have used dot-blot and in situ analysis to indicate that this erythroid preconditioning is probably restricted to primitive but not definitive HSC.

Contains fulltext : 88081.pdf (Publisher’s version ) (Closed access) Schinzel-Giedion syndrome is characterized by severe mental retardation, distinctive facial features and multiple congenital malformations; most affected individuals die before the age of ten. We sequenced the exomes of four affected individuals (cases) and found heterozygous de novo variants in SETBP1 in all four. We also identified SETBP1 mutations in eight additional cases using Sanger sequencing. All mutations clustered to a highly conserved 11-bp exonic region, suggesting a dominant-negative or gain-of-function effect. 01 juni 2010

Fryns-Aftimos syndrome (MIM 606155) is a rare condition characterised by pachygyria, severe mental retardation, epilepsy and characteristic facies. We report a patient who, unlike previously reported cases, remains seizure free with relatively mild developmental delay and facial phenotype.

We describe two patients who have hypochondroplasia with medial temporal lobe dysgenesis. This association has only been reported once before. Both patients had an FGFR3 mutation: 1620C --> A, resulting in Asn540Lys. FGFR3 is expressed in the brain during development and plays a role in hippocampal formation. We suggest FGFR3 mutations might cause cerebral malformations in hypochondroplasia as well as in thanatophoric dysplasia. Further neuroimaging studies of patients with hypochondroplasia and epilepsy or developmental delay may clarify the proportion of patients with hypochondroplasia who have this pattern of central nervous system abnormalities.

Background Long QT syndrome (LQTS) prevalence is estimated at 4 of 10,000 based on community electrocardiogram (ECG) screening, about which there is disagreement regarding efficacy, accuracy, cost-effectiveness, and practicality. Family studies of autosomal dominant conditions such as LQTS have revealed 8–9gene-positive family members per proband. Objective To evaluate a cardiac/genetic registry and family screening program as a tool to identify LQTS in the community. Methods Possible LQTS probands were referred to the New Zealand Cardiac Inherited Disease service. The registry was first established in the northern region (population 2.03 million), including central Auckland (population 0.46 million). After clinical evaluation, genetic testing and family cascade screening were initiated. Genotype-positive individuals were classified as definite LQTS, and others were classified as definite or probable LQTS by clinical and ECG criteria. Results One hundred twelve probands were identified (presentation: 7 sudden death, 82 cardiac event, 16 ECG abnormality, and 7 sudden death of a family member). Following cascade screening, 309 patients with LQTS were identified (248 definite and 61 probable). Two hundred twenty patients had LQTS-causing mutations identified (120 [55%] LQT1, 78 [35%] LQT2, 19 [9%] LQT3, 1 [0.5%] LQT 5, and 2 [1%] LQT7). Thus far, an average of 2.1 definitely or probably affected family members have been identified per proband. The community detection rate is 1.5 of 10,000 for the whole region and 2.2 of 10,000 in Auckland. Conclusions A high level of community detection of LQTS is possible using a clinical registry. With adequate resourcing, this has the potential to be an effective alternative to community ECG screening.

In this paper we apply an optimal control technique to derive control fields that transfer an electron between ends of a chain of donors or quantum dots. We formulate the transfer as an optimal steering problem, and then derive the dynamics of the optimal control. A numerical algorithm is developed to effectively generate control pulses. We apply this technique to transfer an electron between sites of a triple quantum dot and an ionized chain of phosphorus dopants in silicon. Using the optimal pulses for the spatial shuttling of phosphorus dopants, we then add hyperfine interactions to the Hamiltonian and show that a 500 G magnetic field will transfer the electron spatially as well as transferring the spin components of two of the four hyperfine states of the electron-nuclear spin pair., 9 pages, 3 figures

An amniotic fluid sample from anin vitrofertilized pregnancy was referred for cytogenetic analysis based on a Down syndrome screening risk of 1 : 21. Routine cytogenetic analysis showed a nonmosaic karyotype of 46,XX,r(21)(p11.2q22.3), with partial monosomy for chromosome 21 due to a ring chromosome replacing one of the normal homologues. Detailed ultrasound scanning for the remainder of the pregnancy did not reveal any unusual findings. Parental bloods showed that the mother was mosaic for the ring 21 with a karyotype of 46,XX,r(21)(p11.2q22.3)/46,XX and the father had an unrelated Robertsonian translocation, with a karyotype of 45,XY,rob(13;14)(q10;q10). Microarray analysis of cultured amniocytes determined the extent of the deletion of chromosome 21 material in the ring. The parents were given genetic counselling, and a phenotypically normal female baby was delivered at term. This case highlights the importance of karyotyping as an initial step in the management of couples referred forin vitrofertilization.

The analysis of the human genome has largely been undertaken in a research environment, but recent developments in technology and associated workflow have allowed diagnostic laboratories to interrogate DNA at significantly improved levels of resolution. Principally, whole genome-based analysis of copy number changes using microarrays has led to this method replacing conventional karyotyping as a routine diagnostic workhorse. The resolution offered by microarrays is an improvement of at least an order of magnitude compared to karyotyping, but it comes at a cost in terms of the time spent in data interpretation. Overall, however, the die has been cast and cytogeneticists need to become familiar with the tools used by molecular geneticists and bioinformaticists. The following review provides a brief background to array technology, but uses a series of case studies to illustrate the usefulness and challenges of interpreting array data.

Background Retrospective investigation of sudden unexplained death in the young (SUDY) reveals that a high proportion is due to inherited heart disease. Objective The purpose of this study was to ascertain the diagnostic value of postmortem long QT (LQT) genetic analysis in a prospective study of SUDY victims 1–40 years old. Methods Denaturing high-performance liquid chromatography or direct sequencing of LQT genes 1, 2, 3, 5, and 6 was performed, in a National New Zealand protocol, in SUDY victims aged 1–40 years. Results Over 26 months (2006–2008), DNA was stored at autopsy from 52 victims of sudden unexpected death. Further testing revealed a diagnosis in 19 cases (poisoning 4, dilated cardiomyopathy 3, myocarditis 3, other 9). The remaining 33 cases underwent genetic testing (age at death 18 months–40 years, median 25 years). Eighteen (55%) died during sleep or at rest, and 7 (21%) died during light activity. Rare missense variants in LQT genes were found in 5 (15%) cases (confidence interval 3%–27%): T96R in KCNQ1 (11-year-old male), P968L in KCNH2 (32-year-old female), P2006A in SCN5A (34-year-old female), and R67H and R98W in KCNE1 (17- and 38-year-old females, respectively). Evidence of pathogenicity was provided by in vitro evidence (T96R), family phenotype–genotype co-segregation (R98W, P2006A), and/or previous reports (R67H, P968L, P2006A, R98W). Family cardiac investigation was possible in 23 (70%) families and revealed probable cause of death for 5 (15%) other victims (confidence interval 3%–27%). Conclusion Most community SUDY occurs at rest or during light activity. A diagnostic rate of 15% supports the transition of LQT genetic autopsy, combined with family investigation, into routine medical practice.

We conducted a survey of physician opinions in relation to enzyme replacement therapy (ERT) and extended newborn screening (ENBS) for mucopolysaccharidoses (MPS). A questionnaire consisting of hypothetical clinical scenarios about ERT and ENBS for MPS was posted on metab-L, a list server for the metabolic community. The questionnaire included similar questions to those used in previous studies that sought the views of individuals and families affected by MPS. Our aim was to compare medical professionals’ opinions with that of the individuals and families affected by MPS that they serve. The questionnaire was completed by 35 physicians, most of whom were metabolic physicians. Responses differed significantly between the physician and parent groups when the clinical scenario involved intellectual impairment. In this setting, physicians were significantly less inclined to advocate the use of ERT. Comparison of the responses to the ENBS scenarios revealed that compared to physicians, family of individuals with MPS were more inclined to desire diagnosis at birth, even if no treatment could alter the outcome of the condition. Compared to the family of individuals with MPS, physicians are more likely to advocate the use of ERT and ENBS where there is proven medical benefit to the affected individual.

The traditional understanding of genetic disease, that, with the exception of aneuploidy, it is due primarily to single base pair changes or small deletions and duplications has been challenged over the last decade. This challenge has been spearheaded by increasing evidence of the frequency and significance of larger genomic rearrangements. It now appears that a substantial proportion of Mendelian conditions are caused by deletions and duplications that involve the copy number of one or more contiguous genes. It is becoming apparent too that de novo chromosomal events are much more frequent than spontaneous point mutations and that chromosomal rearrangement is likely to account for the vast majority of sporadic disease.

Background: There has been an exponential increase in the number of genes implicated in inherited retinal disease over the last decade, but the genetic and phenotypic heterogeneity limited mutation detection. The high cost of sequencing and long turn around times meant that gene testing was not a viable option, particularly in New Zealand. Recently, advancements including development of micro-array-based mutation analysis and non-for-profit laboratories have resulted in affordable and time-efficient testing. This has enabled genetic diagnostics to become an integral component of the work-up for inherited retinal disease. Methods: Genetic testing for inherited retinal disorders was initiated via the Ocular Genetic Clinic in Auckland 2 years ago. A retrospective audit of genetic testing over this period was carried out. The results of these tests and outcomes are discussed. Results: Thirty-five probands have undergone genetic testing for retinal disorders. This has included X-Linked Retinoschisis, Leber Congenital Amaurosis, Retinitis Pigmentosa, Albinism, Achromatopsia, Usher syndrome, Stargardt disease and Mitochondrial disease. Of these, 54% of tests (19/35) showed a rare variant or pathogenic mutation. Three couples have proceeded to investigate the options of prenatal diagnosis and/or pre-implantation genetic diagnosis. Conclusion: The introduction of genetic testing, largely via disease arrays, has been highly successful at clarifying disease genotype in our cohort. It is now a timely and cost-effective investigation that should be elemental to the assessment of inherited retinal disease. Genetic testing in an opportune fashion permits genetic counselling, enables families to make reproductive choices and might allow the possibility of gene therapy interventions.