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Background and Objectives: \ud Gastrectomy for gastric cancer is associated with significant infective postoperative complications. C-reactive protein (CRP) is a useful biomarker in the early detection of infective complications following major abdominal surgery. This single-centre retrospective study aimed to determine the relationship between postoperative CRP levels and development of postoperative infective complications after gastrectomy.\ud \ud Methods: \ud Daily postoperative CRP levels were analyzed to determine a CRP threshold associated with infective complications. ROC curve analysis was used to determine which postoperative day (POD) gave the optimal cutoff. Multivariate analysis was performed to determine significant factors associated with complications.\ud \ud Results: \ud One hundred and forty-four patients were included. A total of 61 patients (42%) had at least one infective complication. A CRP level of 220 mg/L was associated with the highest AUC (0.765) with a sensitivity of 70% and specificity of 76% (positive predictive value, 67%; negative predictive value, 78%). More patients with a CRP > 220 mg/L on POD 3 developed infective complications (67% vs. 21%, p

Graphical abstract, Highlights • Large GGGGCC repeat expansions within BAC vectors are highly unstable. • CRISPR-Cas9 screening of BAC vector clones to determine repeat length. • CRISPR-Cas9 cloning of GGGGCC repeat expansion regions into the linear pJazz vector. • pJazz dramatically stabilizes GGGGCC repeat expansions over 4 kb in length., Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such repeats in bacterial vectors, especially with large repeat expansions. Designing constructs for more precise genome engineering projects, such as engineering knock-in mice, proves a greater challenge still, since these unstable repeats require numerous cloning steps in order to introduce homology arms or selection cassettes. Here, we report our efforts to clone a large hexanucleotide repeat in the C9orf72 gene, originating from within a BAC construct, derived from a C9orf72-ALS patient. We provide detailed methods for efficient repeat sizing and growth conditions in bacteria to facilitate repeat retention during growth and sub-culturing. We report that sub-cloning into a linear vector dramatically improves stability, but is dependent on the relative orientation of DNA replication through the repeat, consistent with previous studies. We envisage the findings presented here provide a relatively straightforward route to maintaining large-range microsatellite repeat-expansions, for efficient cloning into vectors.

Autosomal ring chromosomes are rare cytogenetic findings that arise from breakage and fusion of the chromosome ends. Rings are mitotically unstable, usually sporadic and associated with a 'ring syndrome', characterized by a variable phenotype: growth retardation, no significant dysmorphisms and normal to moderately disabled intelligence. We describe the clinical features and molecular characterization of two sisters with ring chromosome 4. Karyotype analysis was performed on both sisters and parents. Chromosome microarray was performed on both sisters to delineate the breakpoint imbalance. Both sisters had a large ring 4 chromosome in the majority of cells analyzed on karyotype. Microarray results were identical in the sisters, showing a 55.8 kb duplication on the terminal 4p arm and a 1.5 Mb deletion on the terminal 4q arm. No genes of interest were identified in these regions. Parental karyotypes on lymphocytes and fibroblasts were normal, with no finding of mosaicism for the ring 4 chromosome. Polymorphic marker analysis revealed the maternal origin of the ring. To our knowledge, this is the first reported instance of a ring 4 chromosome recurring in siblings after extensive parental testing, which suggests this was due to maternal gonadal mosaicism.

SUMMARYAmyotrophic lateral sclerosis - frontotemporal dementia spectrum disorder (ALS/FTD) is a complex neurodegenerative disease; up to 10% of cases are familial, usually arising from single dominant mutations in >30 causative genes. Transgenic mouse models that overexpress human ALS/FTD causative genes have been the preferred organism for in vivo modelling. However, while conferring human protein biochemistry, these overexpression models are not ideal for dosage-sensitive proteins such as TDP-43 or FUS.We have created three next-generation genomically humanised knock-in mouse models for ALS/FTD research, by replacing the entire mouse coding region of Sod1, Tardbp (TDP-43) and Fus, with their human orthologues to preserve human protein biochemistry, with exons and introns intact to enable future modelling of coding or non-coding mutations and variants and to preserve human splice variants. In generating these mice, we have established a new-standard of quality control: we demonstrate the utility of indirect capture for enrichment of a region of interest followed by Oxford Nanopore sequencing for robustly characterising large knock-in alleles. This approach confirmed that targeting occurred at the correct locus and to map homologous recombination events. Furthermore, extensive expression data from the three lines shows that homozygous humanised animals only express human protein, at endogenous levels. Characterisation of humanised FUS animals showed that they are phenotypically normal compared to wildtype littermates throughout their lifespan.These humanised mouse strains are critically needed for preclinical assessment of interventions, such as antisense oligonucleotides (ASOs), to modulate expression levels in patients, and will serve as templates for the addition of human ALS/FTD mutations to dissect disease pathomechanisms.

Design has the potential to significantly improve safety and well being, reduce risk and save lives either during the design phase or through targeted design interventions towards urban infrastructure, systems and services. The broad user-centred skills and technical knowledge base of designers allows the potential for clear problem definition using ethnographic discovery processes, creative design and innovative design resolution in a socio-technical context. Safeness by Design, an initiative emerging from RMIT University’s School of Design, aims to enhance health, wellbeing and social values by using design to achieve actual and evident safeness across a broad range of environment and contexts. Addressing urban safeness in early studio collaborations with the City of Melbourne and the Ajuntament de Barcelona, the initiative has resulted in design interventions that embrace holistic and multidisciplinary approaches to the issues of safeness on personal, social, spatial and technological levels. Student project outcomes have been exhibited in 2020 at both Melbourne and Barcelona Design Weeks. Is this a new design paradigm? As designers transition from product dependant (and market driven) outcomes to those less tangible activities, increasingly the role of design as an enabler of societel wellbeing, capable of making a greater contribution to communities and lifestyles opens up new practice foci. Whilst design has always considered safety, and in many istances have been required to address safety from a compliance and/or product liability perspective, safeness by design aims to apply a specific lens to design practice. Aspirational in its intent, it seeks to operate outside of safety compliance frameworks; utlising human centred design, experience and interaction design, social design and service design approaches, rather risk management methodologies, to achieve actual or perceived safeness. Rather than a design specialisation, it proposes a generalist and multidisciplinary approach that activates all of the designers toolkit, and operates within a social framework that is qualitative and less measurable or tangible. This is not Failure Modes Effects Analysis (FMEA), rather it is design using its understanding of user behaviour and situational contexts to identify and respond to safeness concerns through targeted design activities and interventions. This paper introduces Safeness by Design as a new design paradigm, examining the contribution of early works to safer urban contexts, and proposes a safeness-led approach to design practice.

Objective Trisomy of the long arm of chromosome 1 is a very rare cytogenetic anomaly that is difficult to diagnose because of tissue-limited mosaicism. This study aimed to further characterize the prenatal and post-natal findings associated with this anomaly, including the first reported chromosomal microarray finding. Method This is a retrospective study of six cases of mos 46,X,der(Y)t(Y;1)(q12;q21)/46,XY, diagnosed both prenatally and post-natally. Detailed clinical features and pregnancy outcome were documented. Results Recurrent prenatal and post-natal features of our case series, as well as the previously reported cases, were described, suggesting a Fryns-like phenotype. A diagnosis of mosaic trisomy 1q is difficult to confirm post-natally in some cases because of the tissue provided for analysis, emphasizing the need to study multiple tissue types in cases of fetal loss with a suspected underlying chromosomal imbalance. Conclusion The overlap of clinical features between mosaic trisomy 1q and Fryns syndrome emphasizes the need to obtain appropriate samples for genetic analysis. The present cases and a review of the literature suggest that partial trisomy of the long arm of chromosome 1 is a distinct de novo clinical entity with low recurrence risk. © 2017 John Wiley & Sons, Ltd.

Recently, Alazami and colleagues identified 33 putative candidate disease genes for neurogenetic disorders. One such gene was DPH1, in which a homozygous missense mutation was associated with a 3C syndrome-like phenotype in four patients from a single extended family. Here we report a second homozygous missense variant in DPH1, seen in four members of a founder population, and associated with a phenotype initially reminiscent of Sensenbrenner syndrome. This post-publication ‘match’ validates DPH1 as a gene underlying syndromic intellectual disability with short stature and craniofacial and ectodermal anomalies, reminiscent of, but distinct from, 3C and Sensenbrenner syndromes. This validation took several years after the independent discoveries due to the absence of effective methods for sharing both candidate phenotype and genotype data between investigators. Sharing of data via web-based anonymous data exchange servers will play an increasingly important role towards more efficient identification of the molecular basis for rare Mendelian disorders.

Inherited dental malformations constitute a clinically and genetically heterogeneous group of disorders. Here, we report on four families, three of them consanguineous, with an identical phenotype, characterized by significant short stature with brachyolmia and hypoplastic amelogenesis imperfecta (AI) with almost absent enamel. This phenotype was first described in 1996 by Verloes et al. as an autosomal recessive form of brachyolmia associated with AI. Whole-exome sequencing resulted in the identification of recessive hypomorphic mutations including deletion, nonsense and splice mutations, in the LTBP3 gene, which is involved in the TGF-beta signaling pathway. We further investigated gene expression during mouse development and tooth formation. Differentiated ameloblasts synthesizing enamel matrix proteins and odontoblasts expressed the gene. Study of an available knockout mouse model showed that the mutant mice displayed very thin to absent enamel in both incisors and molars, hereby recapitulating the AI phenotype in the human disorder.

The aim of this study was to calculate the cost of a range of needle and syringe program (NSP) models to contribute to planning for effective NSP delivery. Existing health service data was used to estimate the cost per needle distributed across four modes of service delivery (Primary NSP, including one model of Primary NSP providing primary health care; Secondary NSP; Vending Machine and Outreach) over three years. Costs were primarily affected by the ratio of the volume of equipment distributed to staff costs. The average cost per unit for Primary, Secondary and Outreach modes was approximately $1.00. The cost for Vending Machine provision (accounting for income from service users) was the cheapest option at $0.30–0.40 per unit. When income from services users are not included in calculations, other considerations may be more important than cost when making decisions about providing access to NSP services to a marginalized client group with diverse needs.

Background & objectives: To support recent political commitments to end tuberculosis (TB) in the World Health Organization South-East Asian Region (SEAR), there is a need to understand by what measures, and with what investment, these goals could be reached. These questions were addressed by using mathematical models of TB transmission by doing the analysis on a country-by-country basis in SEAR. Methods: A dynamical model of TB transmission was developed, in consultation with each of the 11 countries in the SEAR. Three intervention scenarios were examined: (i) strengthening basic TB services (including private sector engagement), (ii) accelerating TB case-finding and notification, and (iii) deployment of a prognostic biomarker test by 2025, to guide mass preventive therapy of latent TB infection. Each scenario was built on the preceding ones, in successive combination. Results: Comprehensive improvements in basic TB services by 2020, in combination with accelerated case-finding to increase TB detection by at least two-fold by 2020, could lead to a reduction in TB incidence rates in SEAR by 67.3 per cent [95% credible intervals (CrI) 65.3-69.8] and TB deaths by 80.9 per cent (95% CrI 77.9-84.7) in 2035, relative to 2015. These interventions alone would require an additional investment of at least US$ 25 billion. However, their combined effect is insufficient to reach the end TB targets of 80 per cent by 2030 and 90 per cent by 2035. Model projections show how additionally, deployment of a biomarker test by 2025 could end TB in the region by 2035. Targeting specific risk groups, such as slum dwellers, could mitigate the coverage needed in the general population, to end TB in the Region. Interpretation & conclusions: While the scale-up of currently available strategies may play an important role in averting TB cases and deaths in the Region, there will ultimately be a need for novel, mass preventive measures, to meet the end TB goals. Achieving these impacts will require a substantial escalation in funding for TB control in the Region.

Floating-Harbor syndrome (FHS) is a rare condition characterized by short stature, delayed osseous maturation, expressive-language deficits, and a distinctive facial appearance. Occurrence is generally sporadic, although parent-to-child transmission has been reported on occasion. Employing whole-exome sequencing, we identified heterozygous truncating mutations in SRCAP in five unrelated individuals with sporadic FHS. Sanger sequencing identified mutations in SRCAP in eight more affected persons. Mutations were de novo in all six instances in which parental DNA was available. SRCAP is an SNF2-related chromatin-remodeling factor that serves as a coactivator for CREB-binding protein (CREBBP, better known as CBP, the major cause of Rubinstein-Taybi syndrome [RTS]). Five SRCAP mutations, two of which are recurrent, were identified; all are tightly clustered within a small (111 codon) region of the final exon. These mutations are predicted to abolish three C-terminal AT-hook DNA-binding motifs while leaving the CBP-binding and ATPase domains intact. Our findings show that SRCAP mutations are the major cause of FHS and offer an explanation for the clinical overlap between FHS and RTS. © 2012 The American Society of Human Genetics.

Brachydactyly mental retardation syndrome (BDMR) is associated with a deletion involving chromosome 2q37. BDMR presents with a range of features, including intellectual disabilities, developmental delays, behavioral abnormalities, sleep disturbance, craniofacial and skeletal abnormalities (including brachydactyly type E), and autism spectrum disorder. To date, only large deletions of 2q37 have been reported, making delineation of a critical region and subsequent identification of candidate genes difficult. We present clinical and molecular analysis of six individuals with overlapping deletions involving 2q37.3 that refine the critical region, reducing the candidate genes from >20 to a single gene, histone deacetylase 4 (HDAC4). Driven by the distinct hand and foot anomalies and similar cognitive features, we identified other cases with clinical findings consistent with BDMR but without a 2q37 deletion, and sequencing of HDAC4 identified de novo mutations, including one intragenic deletion probably disrupting normal splicing and one intragenic insertion that results in a frameshift and premature stop codon. HDAC4 is a histone deacetylase that regulates genes important in bone, muscle, neurological, and cardiac development. Reportedly, Hdac4−/− mice have severe bone malformations resulting from premature ossification of developing bones. Data presented here show that deletion or mutation of HDAC4 results in reduced expression of RAI1, which causes Smith-Magenis syndrome when haploinsufficient, providing a link to the overlapping findings in these disorders. Considering the known molecular function of HDAC4 and the mouse knockout phenotype, taken together with deletion or mutation of HDAC4 in multiple subjects with BDMR, we conclude that haploinsufficiency of HDAC4 results in brachydactyly mental retardation syndrome.

The Hutterian Bretheren is an isolated population living on the North American prairies, the current community exceeding 40,000 in number. Their unique genetic history has contributed to a founder effect, which is reflected in the Mendelian disorders present in this population today. Genetic studies in the Hutterite population have led to the identification of a number of genes over the last several years and highlights the power of this population for gene identification. However, for the more than 30 autosomal recessive conditions currently recognized in this population, the gene or Hutterite specific mutation remains to be identified for over half and novel autosomal recessive syndromes continue to be recognized. This review summarizes what is currently understood about the molecular etiology of the Mendelian disorders and highlights the cardinal features of those disorders that are unique to or over-represented in this population.

We describe a four-generation Chinese family that included five members who had an isolated bilateral lop ear anomaly. The presentation suggested a dominant mode of inheritance. The absence of male-to-male transmission does not exclude an X-linked dominant mode of inheritance. Since the phenotypic anomaly of the male proband was no more severe than the affected female members, an autosomal dominant mode of inheritance is most likely.

Meckel syndrome (MKS) is a rare lethal autosomal recessive disorder characterized by the presence of occipital encephalocele, cystic kidneys, fibrotic changes of the liver and polydactyly. Joubert syndrome (JS)-related disorders (JSRDs) or cerebello-oculo-renal syndromes (CORS) are a group of recessively inherited conditions characterized by a molar tooth sign (MTS) on cranial MRI, a set of core clinical features (developmental delay/mental retardation, hypotonia, ataxia, episodic breathing abnormalities, abnormal eye movements) and variable involvement of other systems including renal, ocular, central nervous system, craniofacial, hepatic, and skeletal. A significant clinical overlap between MKS and JSRD/CORS has been recognized in the literature. We describe a group of 10 Hutterite patients, of which 7 had been previously diagnosed with MKS, with a JSRD. Clinical features include variable early mortality, cognitive handicap, a characteristic dysmorphic facial appearance, hypotonia, ataxia, abnormal breathing pattern, nystagmus, and MTS on MRI. Additional features include occipital encephalocele, posterior fossa fluid collections resembling Dandy-Walker malformation, hydrocephalus, coloboma, and renal disease. This JSRD is a recognizable dysmorphic syndrome characterized by hypertelorism, deep-set eyes, down-slanting palpebral fissures, ptosis, arched eyebrows with medial sparseness, square nasal tip, short philtrum with tented upper lip, open mouth with down-turned corners, and posteriorly rotated low-set ears. Renal disease is present in 70% of patients and is characterized by cystic kidneys, abnormalities in renal function and hypertension. Homozygous deletions of NPHP1 and the known loci for JS/JSRD and MKS were excluded by identity-by-descent mapping studies suggesting that this condition in the Hutterites represents yet another locus for a JSRD.

Male siblings developed acute hemorrhagic leukoencephalitis (AHL) at age five months and eight months, respectively. This rare condition has not been reported in individuals less than two years of age or with a recurrence in the family. The diagnosis was based on neuropathologic features after ruling out potentially mimicking conditions. Genetic counseling of early onset AHL should include the possibility of recurrence in siblings.

Schimke immuno-osseous dysplasia (SIOD, MIM 242900) is an autosomal-recessive pleiotropic disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction and T-cell immunodeficiency. Using genome-wide linkage mapping and a positional candidate approach, we determined that mutations in SMARCAL1 (SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1), are responsible for SIOD. Through analysis of data from persons with SIOD in 26 unrelated families, we observed that affected individuals from 13 of 23 families with severe disease had two alleles with nonsense, frameshift or splicing mutations, whereas affected individuals from 3 of 3 families with milder disease had a missense mutation on each allele. These observations indicate that some missense mutations allow retention of partial SMARCAL1 function and thus cause milder disease.

To the Editor: Van der Woude Syndrome [VWS] is a Mendelian disorder with an autosomal dominant inheritance pattern. It is a common cause of syndromic orofacial clefting, accounting for 2% of cleft lip and palate (CL/P) cases [Schutte et al., 1996]. Lower lip pits, usually bilateral, are the most common congenital malformation in VWS [Cervenka et al., 1967]. It is one of the few syndromes where it is common to find a mixture of cleft lip (CL) and cleft palate (CP) phenotypes in the same family. We present a case of confirmed monozygotic (MZ) female twins both affected with VWS due to an IRF6 mutation, but with markedly different phenotypes. To our knowledge, a case such as this has not previously been reported, and contributes further evidence for modifying factors in the expression of this condition. A G1P0 woman, pregnant with monochorionic, diamniotic female twins, presented to the Prenatal Genetics Clinic due to the finding of bilateral cleft lip and palate in Twin A on the 20-week antenatal ultrasound. Twin B appeared to be unaffected, and the ultrasound for both was otherwise normal. Family history was positive for bilateral lower lip pits in the father, as well as numerous members of the paternal family with cleft lip and palate, cleft palate, cleft lip and/or lip pits (Fig. 1). The twins' father was subsequently examined and found to have bilateral paramedian lower lip pits, but no orofacial clefting. Given this information, a probable diagnosis of VWS was made for Twin A. The family was counseled that Twin B might also have features of this condition, since the likelihood of monozygosity was high, given the monochorionicity. Figure 1 A five generation pedigree showing multiple affected individuals in multiple generations. The * indicates individuals who were examined in our clinic. The mother had pre-existing hypertension and took labetolol for the first two months of pregnancy, after which her blood pressure normalized and the medication was discontinued until after delivery. She did not smoke or drink alcohol during the pregnancy. The pregnancy was monitored closely, and the twins grew well until the 36th week, when an ultrasound showed oligohydramnios and poor interval growth. For these reasons, the twins were delivered by caesarean at 36 and 3/7 weeks. At delivery, Twin A weighed 1820g (3rd centile), and Twin B 1955g (5th centile). Both twins experienced transient tachypnea of the newborn, for which Twin A required oxygen. Both were otherwise well and were discharged home at 3 days of age. Features of VWS were observed in both twins. Twin A was found to have bilateral cleft lip and cleft palate, as well as bilateral lower lip pits. Twin B showed no evidence of cleft lip or palate, but did show bilateral lower lip pits (Fig 2a,b). Neither twin was found to have other anomalies and both were otherwise healthy and developing normally. Based on their features and the family history, both twins were diagnosed with VWS. Figure 2 a. Twin A at 14 days showing bilateral paramedian lower lip pits and bilateral cleft lip. Templates for sequencing of all exons of IRF6 were generated by polymerase chain reaction (PCR) in an Applied Biosystem Gene Amp PCR System 9700 (Applied Biosystem, Foster City, CA). Sequencing was then performed at Functional Biosciences, Inc, Madison, WI following in-house protocols. A missense mutation in exon 4 of the IRF6 gene (p.Y97C:c.290A>G) was found in both the twins and their father. Although this mutation has not been previously reported in VWS [de Lima et al., 2009] it is predicted to be damaging by Polyphen. The tyrosine at this position is completely conserved in mammals, frogs and chickens, Zygosity was established in the molecular diagnostic laboratory of the Alberta Children’s Hospital in Calgary, using a total of 15 microsatellite markers from both the AmpFlSTR Profiler Plus kit (Applied Biosystems) and additional microsatellite markers developed in house, as per the laboratory protocol. The zygosity testing showed that alleles were shared at all 15 loci, giving a > 0.9999 probability of monozygosity. There have been several reported cases of VWS in MZ twins, summarized in Table I. Ours is not the first reported case of discordant presentation in twins with VWS; however, it appears to be the first reported case of markedly discordant MZ twins where both are shown to have inherited the same missense mutation. The twins reported by Kondo et al. [2002] were fully discordant for the syndrome due to a new mutation in one of the twins. The cases of MZ twins with discordant presentations of VWS included Cervenka et al. [1967], where zygosity was determined by physical examination and blood group, and Tokat et al. [2005], where no details regarding how zygosity was determined are provided. In the Cervenka et al. case, both twins had lip pits and one had a cleft lip. The case reported by Tokat et al. was of twins who both had lip pits, one had a cleft lip and the other a cleft palate. Phenotype concordance in MZ twins has been reported by Hersh and Verdi [1992] and Vignale et al. [1998]. TABLE I Cases of Likely Monozygotic Twins with Van der Woude Syndrome in the Literature Intrafamilial variability is a recognized characteristic of VWS [Rizos and Spyropoulos, 2004]. Although concordant features are observed in some MZ twin pairs, the possibility of discordant phenotypes in MZ twins has been suggested by some reports. To our knowledge, we are reporting the first set of MZ twins, confirmed by zygosity testing, who both have VWS due to an IRF6 gene mutation and who have strikingly different phenotypes of this condition. They provide evidence that MZ twins with VWS may have discordant phenotypes and that this is likely due to modifying factors. Potential causes for discordant presentations of single gene disorders include genetic/epigenetic factors, those relating to the intrauterine environment, and stochastic effects. There has been little research into the causes of variable expressivity in VWS. Several studies have assessed potential genetic causes for intrafamilial variability. Moghe et al. [2010] looked at the relationship between an increase of heterochromatin on chromosome 9q and different phenotypes in VWS, and found there to be no connection. Sertie et al. [1999] suggested a locus predisposing to cleft palate in VWS at 17p11.2-17p11.1 in their linkage analysis study. Subsequently, another linkage study by Wong et al. [2001] excluded 17p11.2-17p11.1 as a modifying locus in their study of five Finnish families. In summary, we present confirmed MZ twins with markedly variable expression of VWS. Both twins showed a missense mutation in IRF6. Lip pits were present in both twins; however, CL/P was present in only one twin. This demonstrates the complexity of the expression of the VWS phenotype, and reinforces the need for further studies of modifier genes, epigenetics and environmental factors.

Elucidating the function of highly conserved regulatory sequences is a significant challenge in genomics today. Certain intragenic highly conserved elements have been associated with regulating levels of core components of the spliceosome and alternative splicing of downstream genes. Here we identify mutations in one such element, a regulatory alternative exon of SNRPB as the cause of cerebro–costo–mandibular syndrome. This exon contains a premature termination codon that triggers nonsense-mediated mRNA decay when included in the transcript. These mutations cause increased inclusion of the alternative exon and decreased overall expression of SNRPB. We provide evidence for the functional importance of this conserved intragenic element in the regulation of alternative splicing and development, and suggest that the evolution of such a regulatory mechanism has contributed to the complexity of mammalian development., Cerebro–costo–mandibular syndrome, CCMS, is a severe human multiple malformation disorder. Here, the authors report that mutations in SNRPB disrupt the normal regulation of alternative splicing at this gene, and in so doing, may be responsible for the development of CCMS.

Background The genetics of congenital heart disease (CHD) remain incompletely understood. Exome sequencing has been successfully used to identify disease-causing mutations in familial disorders in which candidate gene analyses and linkage mapping have failed. Methods We studied a large family characterized by autosomal dominant isolated secundum atrial septal defect (ASD) (MIM No. 612794). Candidate gene resequencing and linkage analysis were uninformative. Results Whole-exome sequencing of 2 affected family members identified 44 rare shared variants, including a nonsynonymous mutation (c.532A>T, p.M178L, NM_005159.4) in alpha-cardiac actin ( ACTC1 ). This mutation was absent from 1834 internal controls as well as from the 1000 Genomes and the Exome Sequencing Project (ESP) databases, but predictions regarding its effect on protein function were divergent. However, p.M178L was the only rare mutation segregating with disease in our family. Conclusions Our results provide further evidence supporting a causative role for ACTC1 mutations in ASD. Massively parallel sequencing of the exome allows for the detection of novel rare variants causing CHD without the limitations of a candidate gene approach. When mutation prediction algorithms are not helpful, studies of familial disease can help distinguish rare pathologic mutations from benign variants. Consideration of the family history can lead to genetic insights into CHD.

Treacher Collins syndrome (TCS), the best known form of mandibulofacial dysostosis (MFD) comprises a recognizable pattern of anomalies. In 1985, Lowry et al. reported on two Hutterite sisters born to apparently unaffected parents with TCS, raising the possibility of an autosomal recessive (AR) variant of TCS, subsequently given a unique Mendelian Inheritance of Man (MIM) number (248390). Recently, biallelic mutations in POLR1C were found in TCS patients, confirming AR TCS as a distinct entity. The Hutterites, an endogamous Anabaptist group, like other genetically isolated populations, provide a powerful resource for mapping AR disorders. We elected to study the molecular basis of TCS in the Hutterite population including the original kindred described in 1985, and another unrelated Hutterite patient. Prior to starting this study, a TCOF1 mutation had apparently been excluded in the original family at two outside institutions. We hypothesized that an AR variant of TCS was present in the three Hutterite patients, but homozygosity mapping did not show convincing evidence of shared regions between the affected individuals. TCOF1 analysis was undertaken and mutations were found in the three affected patients and an unaffected parent. These data show that the initial Hutterite family reported with AR TCS in fact has classic TCS due to a TCOF1 mutation, despite recent data confirming the existence of AR TCS in other populations. These results have significant counseling implications for the affected families in the Hutterite population and in the population at large. © 2013 Wiley Periodicals, Inc.

We describe a Chinese family among whom five members in three generations had a flat umbilicus with vertical and male to male transmission indicative of autosomal dominant inheritance. Except the proband, who also had Tetralogy of Fallot, other affected members had a flat umbilicus as an isolated anomaly. Autosomal dominant transmission of isolated flat umbilicus has not been reported previously.

Management of grazing lands for the accumulation of soil carbon stocks (CS) has been proposed as an effective way to reduce net greenhouse gas emissions from agriculture. However, there are conflicting reports on the effects of grazing management on soil carbon. Most comparisons have involved some combination of no grazing, rotational grazing and set stocking. In the present study we compared two adjacent commercial grazing systems, distinguished on the basis of inputs and livestock productivity, located on New England basaltic landscapes experiencing a cool temperate climate. The high-intensity (H) system sustains an average stocking rate of 18 dry sheep equivalents (dse) ha–1, with a turnoff rate of 9dseha–1year–1, with high levels of investment in assets, management and fertiliser. The low-intensity (L) system, with less intensive management and half the fertiliser of the H system, sustains a stocking rate of 9dseha–1, with a turnoff rate of 3dseha–1year–1, which is slightly higher than the regional average. Pasture biomass production was inferred (back-calculated) from stocking rates and animal feed requirements using published data. From the H and L systems, seven paired landscapes from valley floor to upper hillslopes and plateaux were selected. The seventh included a forest reserve. One hundred and eighty-six undisturbed soil cores (0–0.5m depth) were assessed for bulk density, total C and N, particulate C and a range of plant nutrients. There were few differences in CS, soil pH and nutrient levels between H and L grazing systems. Average CS (0–0.3m) in pasture soils was 103Mgha–1, but was higher in the forest soil at 190Mgha–1. Regression of CS versus soil mass was a satisfactory method of dealing with the bias introduced by the higher soil bulk density in perennial pasture systems compared with the forest. The similarity of CS in H and L pasture soils was despite inferred net primary production being 1.9–3.6MgCha–1year–1 greater in H than L systems, implying higher rates of C turnover in the former. The global warming potential of the inferred annual emissions of CH4 and N2O in the H and L systems was equivalent to approximately 19% and 13% of the cycling atmospheric–plant CO2 carbon respectively.

Background Arteriosclerosis and emphysema develop in individuals with Schimke immuno-osseous dysplasia (SIOD), a multisystem disorder caused by biallelic mutations in SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1). However, the mechanism by which the vascular and pulmonary disease arises in SIOD remains unknown. Methods We reviewed the records of 65 patients with SMARCAL1 mutations. Molecular and immunohistochemical analyses were conducted on autopsy tissue from 4 SIOD patients. Results Thirty-two of 63 patients had signs of arteriosclerosis and 3 of 51 had signs of emphysema. The arteriosclerosis was characterized by intimal and medial hyperplasia, smooth muscle cell hyperplasia and fragmented and disorganized elastin fibers, and the pulmonary disease was characterized by panlobular enlargement of air spaces. Consistent with a cell autonomous disorder, SMARCAL1 was expressed in arterial and lung tissue, and both the aorta and lung of SIOD patients had reduced expression of elastin and alterations in the expression of regulators of elastin gene expression. Conclusions This first comprehensive study of the vascular and pulmonary complications of SIOD shows that these commonly cause morbidity and mortality and might arise from impaired elastogenesis. Additionally, the effect of SMARCAL1 deficiency on elastin expression provides a model for understanding other features of SIOD.

A Shared Founder Mutation Underlies Restrictive Dermopathy in Old Colony (Dutch-German) Mennonite and Hutterite Patients in North America Catrina Loucks, Jillian S. Parboosingh, Jessica X. Chong, Carole Ober, Victoria M. Siu, Robert A. Hegele, C. Anthony Rupar, D. Ross McLeod, Alfredo Pinto, Albert E. Chudley, and A. Micheil Innes* Department of Medical Genetics, Alberta Children’s Hospital and Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada Department of Human Genetics, The University of Chicago, Chicago, Illinois Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois Department of Paediatrics and Biochemistry, University of Western Ontario, London, Ontario, Canada Departments of Biochemistry and Medicine, Robarts Research Institute and Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada Department of Pathology and Lab Medicine, University of Calgary, Calgary, Alberta, Canada Program in Genetic and Metabolism, Children’s Hospital, Department of Pediatrics and Child Health and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada

Joubert syndrome related disorders (JSRDs) have broad but variable phenotypic overlap with other ciliopathies. The molecular etiology of this overlap is unclear but probably arises from disrupting common functional module components within primary cilia. To identify additional module elements associated with JSRDs, we performed homozygosity mapping followed by next-generation sequencing (NGS) and uncovered mutations in TMEM237 (previously known as ALS2CR4). We show that loss of the mammalian TMEM237, which localizes to the ciliary transition zone (TZ), results in defective ciliogenesis and deregulation of Wnt signaling. Furthermore, disruption of Danio rerio (zebrafish) tmem237 expression produces gastrulation defects consistent with ciliary dysfunction, and Caenorhabditis elegans jbts-14 genetically interacts with nphp-4, encoding another TZ protein, to control basal body-TZ anchoring to the membrane and ciliogenesis. Both mammalian and C. elegans TMEM237/JBTS-14 require RPGRIP1L/MKS5 for proper TZ localization, and we demonstrate additional functional interactions between C. elegans JBTS-14 and MKS-2/TMEM216, MKSR-1/B9D1, and MKSR-2/B9D2. Collectively, our findings integrate TMEM237/JBTS-14 in a complex interaction network of TZ-associated proteins and reveal a growing contribution of a TZ functional module to the spectrum of ciliopathy phenotypes.

This paper draws on published reports, data from the Global Fund to Fight AIDS, Tuberculosis, and Malaria and the Asian Development Bank, and analysis by the Commission on AIDS in Asia to estimate financial resources required to achieve universal access for HIV in low-income and middle-income countries of Asia. It explores optimal use of available resources to mount effective response to AIDS in Asia against an uncertain economic climate. Although there is global commitment to tackle the HIV pandemic, available financing falls short of minimum requirements to achieve universal access to prevention and treatment. To support essential HIV priorities in Asia, the Commission on AIDS in Asia estimated annual resource needs to be US$ 3.1 billion. Yet, in 2007, according to one study, estimated total public spending on AIDS in 14 major Asian countries was only US$ 0.9 billion. Hence, scarce resources need to be carefully applied to address the concentrated HIV epidemics in Asia and achieve universal coverage by prioritizing investment in high-impact interventions to maximally avert new infections and deaths, intensifying multisectoral efforts through catalytic financing that mainstreams HIV interventions into existing services, particularly for low-impact prevention programs, and ensuring countries with growing economies mobilize increased amounts of domestic funding to match international financing.

The Hutterites are a genetically isolated Anabaptist group living on the North American prairies; their population numbers over 40,000, the majority of whom are descendants of 89 founders. An autosomal recessive developmental disorder was identified in four patients from two consanguineous Hutterite families. To our knowledge the clinical presentation is unique and undescribed. The patients have distinctive facial features, congenital malformations of the heart and genitourinary system, head circumference at the 2nd centile and developmental delay. The facial features include tall forehead with high anterior hairline, deep-set eyes with short, upslanted palpebral fissures, long nose with low-hanging columella, and thick vermilion of the upper and lower lip. Karyotype and baseline metabolic studies were normal. An identity-by-descent mapping approach was used to localize the gene for this disorder. The patients were genotyped using Affymetrix GeneChip Human Mapping 10 K (Xba 2.0) and 50 K (Xba 240) Arrays which identified a single 5.5 Mb homozygous region at chromosome 16p13.3. To confirm and refine the boundaries of this region, microsatellite markers were used to genotype the patients, their parents, and the available unaffected siblings. The disease locus was refined to a region of 5.1 Mb containing 173 known or predicted genes. No other recessive disorders with similar clinical features are currently mapped to this region. The coding regions of over fifteen genes, prioritized by microarray expression analysis and information available in public databases, have been sequenced, but no potential pathogenic mutations have been identified. The identification of the gene for this syndrome will provide new insights into development and learning.

Asymmetry can be either directional or fluctuating. Detection of abnormal amounts of asymmetry has important implications for clinical diagnosis, but measurement of subtle levels is very difficult. We describe a method and normative values for asymmetry quantification using hand radiographs.

As countries in Asia strive to meet their universal access targets, harm-reduction programmes are yet to be scaled up to reach effective levels of coverage. Resource tracking and estimation of resource needs and gaps is critical to inform the financing decisions of major donors of harm-reduction programmes in the region. This study aimed at estimating the financial resource needs and gaps for scaling-up harm reduction in the region, building on previous research conducted by the Independent Commission on AIDS in Asia. The overall resource need for achieving universal access in the target population in 2009 was US $0.5 billion, with NSP and OST accounting for nearly 70% of the overall regional resource need. A significant resource gap, approximately 90%, of the resource need in 2009, was identified for harm reduction in the region, representing less than 2% of the overall global resource need to address AIDS. Additional resources will be required to support the introduction and scaling-up of integrated, comprehensive harm-reduction programmes that provide a full range of services to reduce HIV transmission among people who inject drugs.

The occurrence of melanonychia is usually sporadic. We describe a Chinese family with three affected members in two generations, suggesting a dominant mode of inheritance. The familial occurrence of melanonychia striata has not been reported previously.

Germline mutations in the STK11 gene have been identified in 10-70% of patients with Peutz-Jeghers syndrome (PJS), an autosomal-dominant hamartomatous polyposis syndrome. A second locus was assumed in a large proportion of PJS patients. To date, STK11 alterations comprise mainly point mutations; only a small number of large deletions have been reported. We performed a mutation analysis for the STK11 gene in 71 patients. Of these, 56 met the clinical criteria for PJS and 12 were presumed to have PJS because of mucocutaneous pigmentation only or bowel problems due to isolated PJS polyps. No clinical information was available for the remaining three patients. By direct sequencing of the coding region of the STK11 gene, we identified point mutations in 37 of 71 patients (52%). We examined the remaining 34 patients by means of the multiplex ligation-dependent probe amplification (MLPA) method, and detected deletions in 17 patients. In four patients the deletion extended over all 10 exons, and in eight patients only the promoter region and exon 1 were deleted. The remaining deletions encompassed exons 2-10 (in two patients), exons 2-3, exons 4-5, or exon 8. When only patients who met the clinical criteria for PJS are considered, the overall mutation detection rate increases to 94% (64% point mutations and 30% large deletions). No mutation was identified in any of the 12 presumed cases. In conclusion, we found that approximately one-third of the patients who met the clinical PJS criteria exhibited large genomic deletions that were readily detectable by MLPA. Screening for point mutations and large deletions by direct sequencing or MLPA, respectively, increased the mutation detection rate in the STK11 gene up to 94%. There may be still other mutations in the STK11 gene that are not detectable by the methods applied here. Therefore, it is questionable whether a second PJS locus exists at all.

An autosomal recessive syndrome of nonprogressive cerebellar ataxia and mental retardation is associated with inferior cerebellar hypoplasia and mild cerebral gyral simplification in the Hutterite population. An identity-by-descent mapping approach using eight patients from three interrelated Hutterite families localized the gene for this syndrome to chromosome region 9p24. Haplotype analysis identified familial and ancestral recombination events and refined the minimal region to a 2-Mb interval between markers D9S129 and D9S1871. A 199-kb homozygous deletion encompassing the entire very low density lipoprotein receptor (VLDLR) gene was present in all affected individuals. VLDLR is part of the reelin signaling pathway, which guides neuroblast migration in the cerebral cortex and cerebellum. To our knowledge, this syndrome represents the first human lipoprotein receptor malformation syndrome and the second human disease associated with a reelin pathway defect.

Individuals with a germ-line mutation in one of the DNA mismatch repair (MMR) genes are at significant risk for colorectal cancer and other tumors. Three families have previously been reported with individuals homozygous for mutations in the MMR gene MLH1 that are predicted to compromise MMR. These individuals develop hematological malignancies and/or neurofibromatosis type 1 at an early age. Here, in an individual, we demonstrate that a homozygous novel mutation in the MMR gene MSH2 is associated with leukemia and multiple café-au-lait spots, a feature of neurofibromatosis type 1. Because the hematological malignancies observed in the individuals homozygous for the loss of MMR are reflective of the lymphomas seen in mice lacking MMR, the mice may provide a useful model for human neoplasia.

Indonesia’s depreciation vastly exceeded that of all other countries hit by the Asian crisis. It also experienced far higher inflation. This paper argues that there is a close medium- to long-term relationship between money growth and inflation in Indonesia, and that this has not been greatly disturbed by the crisis. It argues that Indonesia’s disappointing performance in relation to maintaining the value of the rupiah can be explained by the central bank’s failure to sterilise the monetary impact on base money of its last resort lending to the banks. The fundamental lesson is that Bank Indonesia would be well advised to adopt slow and steady growth of base money as the nominal anchor for monetary policy, now that the pre-crisis policy of slow and steady depreciation of the rupiah has been abandoned.

The impact of cropping on the hydrology and fertility of Vertosols in the northern Darling Basin (average annual rainfall >550 mm) has received much attention, together with the constraints placed on crop growth by naturally occurring subsoil salt stocks. These factors have not been quantified in the drier (450–550 mm), marginal cropping areas to the west. With widespread adoption of zero tillage technology and the potential for large increases in the capture and storage of rainfall in good seasons, mobilisation of salt could be exacerbated should crop water use be constrained by salt toxicity and/or nutrient deficiency. We investigated the size of salt stocks, historic deep drainage, and nutrient depletion under continuous cropping in the Grey and Brown Vertosols of the Walgett and Coonamble districts of north-western NSW. Soils collected from seven paired sites (cropped v. control native vegetation) showed chloride concentrations >500 mg/kg within 0–1.2 m, high exchangeable sodium percentage (~30%) at depth and deficiency in phosphorus, manganese and zinc. Soil total nitrogen decreased from an average stock of 4.9 t/ha at a rate of 0.008 t/ha.year under cropping within 0–0.1 m and soil carbon stocks decreased from 39 t/ha by 0.20 t/ha.year within 0–0.5 m.. Despite low rainfall, high evaporation and the large water-holding capacity of the cracking clays, there were significant downward shifts in chloride concentrations under cropping. Estimates of deep drainage under continuous cropping using chloride mass balance, chloride-front displacement and crop water-balance modelling with the Agricultural Production Systems Simulator (APSIM) generally agreed (range 0.1–2% of average annual rainfall). Simulations suggested that deep drainage may be increased 5–10-fold under zero-tillage winter cropping due to enhanced capture of rainfall by zero tillage compared with traditional practices. The associated flushing of salt from the root-zone together with correction of nutrient deficiency would enhance crop water use and productivity. Current methods indicate little storage in the subsoil for future deep drainage and that hydraulic conductivity is very low. Hence, the long-term effects of any increase in drainage rates, due to changes in cropping practices and/or climate, on the potential for salinisation of groundwater or transient water logging of the surface, are equivocal.

We describe clinical, pathological and radiological findings in 15 cases of sporadic and familial lower spine agenesis with additional anomalies of the axial skeleton and internal organs and speculate about the cause and pathogenesis of this malformation complex. We show that all of these findings are defects of blastogenesis, originate in the primary developmental field and/or the progenitor fields, thus representing polytopic field defects. This concept appears applicable in our cases and makes such terms such as "caudal regression syndrome" or "axial mesodermal dysplasia spectrum" redundant.

Background We recently described a novel autosomal recessive neurodevelopmental disorder with intellectual disability in four patients from two related Hutterite families. Identity-by-descent mapping localized the gene to a 5.1 Mb region at chromosome 16p13.3 containing more than 170 known or predicted genes. The objective of this study was to identify the causative gene for this rare disorder. Methods and results Candidate gene sequencing followed by exome sequencing identified a homozygous missense mutation p.Gly46Arg, in THOC6. No other potentially causative coding variants were present within the critical region on chromosome 16. THOC6 is a member of the THO/TREX complex which is involved in coordinating mRNA processing with mRNA export from the nucleus. In situ hybridization showed that thoc6 is highly expressed in the midbrain and eyes. Cellular localization studies demonstrated that wild-type THOC6 is present within the nucleus as is the case for other THO complex proteins. However, mutant THOC6 was predominantly localized to the cytoplasm, suggesting that the mutant protein is unable to carry out its normal function. siRNA knockdown of THOC6 revealed increased apoptosis in cultured cells. Conclusion Our findings associate a missense mutation in THOC6 with intellectual disability, suggesting the THO/TREX complex plays an important role in neurodevelopment.

Background Jacobsen syndrome is a rare contiguous gene disorder that results from a terminal deletion of the long arm of chromosome 11. It is typically characterized by intellectual disability, a variety of physical anomalies and a distinctive facial appearance. The 11q deletion has traditionally been identified by routine chromosome analysis. Array-based comparative genomic hybridization (array-CGH) has offered new opportunities to identify and refine chromosomal abnormalities in regions known to be associated with clinical syndromes. Results Using the 1 Mb BAC array (Spectral Genomics), we screened 70 chromosomally normal children with idiopathic intellectual disability (ID) and congenital abnormalities, and identified five cases with submicroscopic abnormalities believed to contribute to their phenotypes. Here, we provide detailed molecular cytogenetic descriptions and clinical presentation of two unrelated subjects with de novo submicroscopic deletions within chromosome bands 11q24-25. In subject 1 the chromosome rearrangement consisted of a 6.18 Mb deletion (from 128.25–134.43 Mb) and an adjacent 5.04 Mb duplication (from 123.15–128.19 Mb), while in subject 2, a 4.74 Mb interstitial deletion was found (from 124.29–129.03 Mb). Higher resolution array analysis (385 K Nimblegen) was used to refine all breakpoints. Deletions of the 11q24-25 region are known to be associated with Jacobsen syndrome (JBS: OMIM 147791). However, neither of the subjects had the typical features of JBS (trigonocephaly, platelet disorder, heart abnormalities). Both subjects had ID, dysmorphic features and additional phenotypic abnormalities: subject 1 had a kidney abnormality, bilateral preauricular pits, pectus excavatum, mild to moderate conductive hearing loss and behavioral concerns; subject 2 had macrocephaly, an abnormal MRI with delayed myelination, fifth finger shortening and squaring of all fingertips, and sensorineural hearing loss. Conclusion Two individuals with ID who did not have the typical clinical features of Jacobsen syndrome were found to have deletions within the JBS region at 11q24-25. Their rearrangements facilitate the refinement of the JBS critical region and suggest that a) deletion of at least 3 of the 4 platelet function critical genes (ETS-1, FLI-1 and NFRKB and JAM3) is necessary for thrombocytopenia; b) one of the critical regions for heart abnormalities (conotruncal heart defects) may lie within 129.03 – 130.6 Mb; c) deletions of KCNJ1 and ADAMTS15 may contribute to the renal anomalies in Jacobsen Syndrome; d) the critical region for MRI abnormalities involves a region from 124.6 – 129.03 Mb. Our results reiterate the benefits of array-CGH for description of new phenotype/genotype associations and refinement of previously established ones.