A Scalable CMOS Molecular Electronics Chip for Single-Molecule Biosensing

This work reports the first CMOS molecular electronics chip. It is configured as a biosensor, where the primary sensing element is a single molecule "molecular wire" consisting of a ∼100 GΩ, 25 nm long alpha-helical peptide integrated into a current monitoring circuit. The engineered peptide contains a central conjugation site for attachment of various probe molecules, such as DNA, proteins, enzymes, or antibodies, which program the biosensor to detect interactions with a specific target molecule. The current through the molecular wire under a dc applied voltage is monitored with millisecond temporal resolution. The detected signals are millisecond-scale, picoampere current pulses generated by each transient probe-target molecular interaction. Implemented in a 0.18 μm CMOS technology, 16k sensors are arrayed with a 20 μm pitch and read out at a 1 kHz frame rate. The resulting biosensor chip provides direct, real-time observation of the single-molecule interaction kinetics, unlike classical biosensors that measure ensemble averages of such events. This molecular electronics chip provides a platform for putting molecular biosensing "on-chip" to bring the power of semiconductor chips to diverse applications in biological research, diagnostics, sequencing, proteomics, drug discovery, and environmental monitoring.

INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex

Oral-facial-digital (OFD) syndromes are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. Mutations within 12 cilia-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline variants in INTS13, a subunit of the Integrator complex. This multiprotein complex associates with RNA Polymerase II and cleaves nascent RNA to modulate gene expression. We determined that INTS13 utilizes its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline variants p.S652L and p.K668Nfs*9. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos leads to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions between components of the Integrator complex.

Genetic Characteristics of Polycythemia Vera and Essential Thrombocythemia in Korean Patients

BACKGROUND

Despite recent advances in the investigation of myeloproliferative neoplasms (MPN), the impact of genetic heterogeneity on its molecular pathogenesis has not been fully elucidated. Thus, in this study, we aim to characterize the genetic complexity in Korean patients with polycythemia vera (PV) and essential thrombocythemia (ET).

METHODS

We conducted association studies using 84 single-nucleotide polymorphisms (SNPs) in 229 patients (96 with PV and 133 with ET) and 170 controls. Further, whole-genome sequencing was performed in six patients (two with JAK2 V617F and four with wild-type JAK2), and putative somatic mutations were validated in a further 69 ET patients. Clinical and laboratory characteristics were also analyzed.

RESULTS

Several germline SNPs and the 46 haplotype were significantly associated with PV and ET. Three somatic mutations in MPDZ, IQCH, and CALR genes were selected and validated. The frequency of the CALR mutation was 58.0% (40/69) in ET patients, who did not carry JAK2/MPL mutations. Moreover, compared with JAK2 V617F-positive patients, those with CALR mutations showed lower hemoglobin and hematocrit levels (P = 0.004 and P = 0.002, respectively), higher platelet counts (P =0.008), and a lower frequency of cytoreductive therapy (P = 0.014).

CONCLUSION

This study was the first comprehensive investigation of the genetic characteristics of Korean patients with PV and ET. We found that somatic mutations and the 46 haplotype contribute to PV and ET pathogenesis in Korean patients.

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

Background

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.

Results

A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization.

Conclusions

The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.

Progress in ion torrent semiconductor chip based sequencing

In order for next-generation sequencing to become widely used as a diagnostic in the healthcare industry, sequencing instrumentation will need to be mass produced with a high degree of quality and economy. One way to achieve this is to recast DNA sequencing in a format that fully leverages the manufacturing base created for computer chips, complementary metal-oxide semiconductor chip fabrication, which is the current pinnacle of large scale, high quality, low-cost manufacturing of high technology. To achieve this, ideally the entire sensory apparatus of the sequencer would be embodied in a standard semiconductor chip, manufactured in the same fab facilities used for logic and memory chips. Recently, such a sequencing chip, and the associated sequencing platform, has been developed and commercialized by Ion Torrent, a division of Life Technologies, Inc. Here we provide an overview of this semiconductor chip based sequencing technology, and summarize the progress made since its commercial introduction. We described in detail the progress in chip scaling, sequencing throughput, read length, and accuracy. We also summarize the enhancements in the associated platform, including sample preparation, data processing, and engagement of the broader development community through open source and crowdsourcing initiatives.

Familial cortical myoclonus with a mutation in NOL3

OBJECTIVE

Myoclonus is characterized by sudden, brief involuntary movements, and its presence is debilitating. We identified a family suffering from adult onset, cortical myoclonus without associated seizures. We performed clinical, electrophysiological, and genetic studies to define this phenotype.

METHODS

A large, 4-generation family with a history of myoclonus underwent careful questioning, examination, and electrophysiological testing. Thirty-five family members donated blood samples for genetic analysis, which included single nucleotide polymorphism mapping, microsatellite linkage, targeted massively parallel sequencing, and Sanger sequencing. In silico and in vitro experiments were performed to investigate functional significance of the mutation.

RESULTS

We identified 11 members of a Canadian Mennonite family suffering from adult onset, slowly progressive, disabling, multifocal myoclonus. Somatosensory evoked potentials indicated a cortical origin of the myoclonus. There were no associated seizures. Some severely affected individuals developed signs of progressive cerebellar ataxia of variable severity late in the course of their illness. The phenotype was inherited in an autosomal dominant fashion. We demonstrated linkage to chromosome 16q21-22.1. We then sequenced all coding sequence in the critical region, identifying only a single cosegregating, novel, nonsynonymous mutation, which resides in the gene NOL3. Furthermore, this mutation was found to alter post-translational modification of NOL3 protein in vitro.

INTERPRETATION

We propose that familial cortical myoclonus is a novel movement disorder that may be caused by mutation in NOL3. Further investigation of the role of NOL3 in neuronal physiology may shed light on neuronal membrane hyperexcitability and pathophysiology of myoclonus and related disorders.

CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium

Tubulin glutamylation is a post-translational modification that occurs predominantly in the ciliary axoneme and has been suggested to be important for ciliary function. However, its relationship to disorders of the primary cilium, termed ciliopathies, has not been explored. Here we mapped a new locus for Joubert syndrome (JBTS), which we have designated as JBTS15, and identified causative mutations in CEP41, which encodes a 41-kDa centrosomal protein. We show that CEP41 is localized to the basal body and primary cilia, and regulates ciliary entry of TTLL6, an evolutionarily conserved polyglutamylase enzyme. Depletion of CEP41 causes ciliopathy-related phenotypes in zebrafish and mice and results in glutamylation defects in the ciliary axoneme. Our data identify CEP41 mutations as a cause of JBTS and implicate tubulin post-translational modification in the pathogenesis of human ciliary dysfunction.

Abstract LB-245: Loss of function of the TGFβRI receptor leads to the spontaneously regressing squamous carcinoma condition, multiple self-healing squamous epithelioma (Ferguson-Smith disease)

A re-examination has been carried out of the region on chromosome 9 containing the locus responsible for Ferguson-Smith disease, or multiple self-healing squamous epithelioma (MSSE/FSD); this is a rare autosomal dominant inherited condition first identified in the west of Scotland, that presents with multiple squamous cell skin carcinomas which grow, invade locally and then spontaneously regress.

Approach: A 4Mb locus on chromosome 9 was earlier identified by genetic mapping in a cluster of families. In this study a wider region encompassing 24Mb around this earlier identified locus was examined using high-throughput sequencing with exon capture, followed by Sanger sequencing.

Result: This effort identified mutations in the TGFBR1 gene in 18 out of 22 families diagnosed as affected by MSSE/FSD. These include 11 different mutations. The tumours occur in sun-exposed areas of the skin, and loss-of-heterozygosity in tumours is frequently seen. The sequence variants disturb the function of the TGFβRI receptor such that although heterozygous carriers are asymptomatic during development, loss of the second (wild-type) allele ablates the receptor function and leads to local cancer susceptibility.

Conclusions: The nature of the mutations sets the mechanism apart from that involved in Marfan syndrome-related disorders, in which developmental defects in vasculature are also caused by mutations in this gene. The involvement of TGFβ receptors in this condition is intriguing as TGFβ pathway effects are known to be biphasic and opposing at different stages of cancer development.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-245. doi:10.1158/1538-7445.AM2011-LB-245

Island-Size Distributions for Submonolayer Epitaxy: Rate Equations and Beyond

The scanning tunnelling microscope has revolutionized the quantitative analysis of epitaxial phenomena. This, in turn, has spawned a huge theoretical effort aimed at analyzing various aspects of the morphology of growing surfaces. One of the most important general approaches to have emerged from this effort is based on the application of scaling concepts to epitaxial island-size distributions in the regime of submonolayer coverage prior to coalescence. We first discuss the analytical basis for scaling solutions to rate equations. In the limit of irreversible aggregation, a solution is obtained in terms of the capture numbers which agrees with previous work. For reversible aggregation, we identify a new quantity that may be regarded as a continuous analogue of a critical island size. We then examine the influence of spatial correlations by introducing a method for modeling epitaxial phenomena in terms of the motion of island boundaries, which is implemented numerically using the level set method. This island dynamics model is continuous in the lateral directions, but retains atomic scale discreteness in the growth direction. Several choices for the island boundary velocity are discussed and computations of the island dynamics model using the level set method are presented.

SeqWare Query Engine: storing and searching sequence data in the cloud

Background

Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands.

Results

In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net).

Conclusions

The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets.

Loss of CHSY1, a secreted FRINGE enzyme, causes syndromic brachydactyly in humans via increased NOTCH signaling

We delineated a syndromic recessive preaxial brachydactyly with partial duplication of proximal phalanges to 16.8 Mb over 4 chromosomes. High-throughput sequencing of all 177 candidate genes detected a truncating frameshift mutation in the gene CHSY1 encoding a chondroitin synthase with a Fringe domain. CHSY1 was secreted from patients' fibroblasts and was required for synthesis of chondroitin sulfate moieties. Noticeably, its absence triggered massive production of JAG1 and subsequent NOTCH activation, which could only be reversed with a wild-type but not a Fringe catalytically dead CHSY1 construct. In vitro, depletion of CHSY1 by RNAi knockdown resulted in enhanced osteogenesis in fetal osteoblasts and remarkable upregulation of JAG2 in glioblastoma cells. In vivo, chsy1 knockdown in zebrafish embryos partially phenocopied the human disorder; it increased NOTCH output and impaired skeletal, pectoral-fin, and retinal development. We conclude that CHSY1 is a secreted FRINGE enzyme required for adjustment of NOTCH signaling throughout human and fish embryogenesis and particularly during limb patterning.

High-density SNP association study of the 17q21 chromosomal region linked to autism identifies CACNA1G as a novel candidate gene

Chromosome 17q11-q21 is a region of the genome likely to harbor susceptibility to autism (MIM(209850)) based on earlier evidence of linkage to the disorder. This linkage is specific to multiplex pedigrees containing only male probands (MO) within the Autism Genetic Resource Exchange (AGRE). Earlier, Stone et al.(1) completed a high-density single nucleotide polymorphism association study of 13.7 Mb within this interval, but common variant association was not sufficient to account for the linkage signal. Here, we extend this single nucleotide polymorphism-based association study to complete the coverage of the two-LOD support interval around the chromosome 17q linkage peak by testing the majority of common alleles in 284 MO trios. Markers within an interval containing the gene, CACNA1G, were found to be associated with Autism Spectrum Disorder at a locally significant level (P=1.9 × 10(-5)). While establishing CACNA1G as a novel candidate gene for autism, these alleles do not contribute a sufficient genetic effect to explain the observed linkage, indicating that there is substantial genetic heterogeneity despite the clear linkage signal. The region thus likely harbors a combination of multiple common and rare alleles contributing to the genetic risk. These data, along with earlier studies of chromosomes 5 and 7q3, suggest few if any major common risk alleles account for Autism Spectrum Disorder risk under major linkage peaks in the AGRE sample. This provides important evidence for strategies to identify Autism Spectrum Disorder genes, suggesting that they should focus on identifying rare variants and common variants of small effect.

Local alignment of generalized k-base encoded DNA sequence

BACKGROUND

DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base individually. The encoded DNA sequence may contain technical errors, and therefore encoded sequencing errors must be incorporated when comparing an encoded DNA sequence to a reference DNA sequence.

RESULTS

Although two-base encoding is currently used in practice, many other encoding schemes are possible, whereby two ore more bases are encoded at a time. A generalized k-base encoding scheme is presented, whereby feasible higher order encodings are better able to differentiate errors in the encoded sequence from true DNA sequence variants. A generalized version of the previous two-base encoding DNA sequence comparison algorithm is used to compare a k-base encoded sequence to a DNA reference sequence. Finally, simulations are performed to evaluate the power, the false positive and false negative SNP discovery rates, and the performance time of k-base encoding compared to previous methods as well as to the standard DNA sequence comparison algorithm.

CONCLUSIONS

The novel generalized k-base encoding scheme and resulting local alignment algorithm permits the development of higher fidelity ligation-based next generation sequencing technology. This bioinformatic solution affords greater robustness to errors, as well as lower false SNP discovery rates, only at the cost of computational time.

U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line

U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30× genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library. A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides. All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants. The aligned sequence reads and mate-pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100 bp), 191,743 small (<21 bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs). Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list. Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy: 93.83% of all SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy. Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions, and translocations. In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions, and 35 by interchromosomal translocations to reveal a highly mutated cell line genome. Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP. These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers. The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date.

Glioblastoma has a particularly dismal prognosis with median survival time of less than fifteen months. Here, we describe the broad genome sequencing of U87MG, a commonly used and thus well-studied glioblastoma cell line. One of the major features of the U87MG genome is the large number of chromosomal abnormalities, which can be typical of cancer cell lines and primary cancers. The systematic, thorough, and accurate mutational analysis of the U87MG genome comprehensively identifies different classes of genetic mutations including single-nucleotide variations (SNVs), insertions/deletions (indels), and translocations. We found 2,384,470 SNVs, 191,743 small indels, and 1,314 large structural variations. Known gene models were used to predict the effect of these mutations on protein-coding sequence. Mutational analysis revealed 512 genes homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions, and up to 35 by interchromosomal translocations. The major mutational mechanisms in this brain cancer cell line are small indels and large structural variations. The genomic landscape of U87MG is revealed to be much more complex than previously thought based on lower resolution techniques. This mutational analysis serves as a resource for past and future studies on U87MG, informing them with a thorough description of its mutational state.

Lethal skeletal dysplasia in mice and humans lacking the golgin GMAP-210

BACKGROUND

Establishing the genetic basis of phenotypes such as skeletal dysplasia in model organisms can provide insights into biologic processes and their role in human disease.

METHODS

We screened mutagenized mice and observed a neonatal lethal skeletal dysplasia with an autosomal recessive pattern of inheritance. Through genetic mapping and positional cloning, we identified the causative mutation.

RESULTS

Affected mice had a nonsense mutation in the thyroid hormone receptor interactor 11 gene (Trip11), which encodes the Golgi microtubule-associated protein 210 (GMAP-210); the affected mice lacked this protein. Golgi architecture was disturbed in multiple tissues, including cartilage. Skeletal development was severely impaired, with chondrocytes showing swelling and stress in the endoplasmic reticulum, abnormal cellular differentiation, and increased cell death. Golgi-mediated glycosylation events were altered in fibroblasts and chondrocytes lacking GMAP-210, and these chondrocytes had intracellular accumulation of perlecan, an extracellular matrix protein, but not of type II collagen or aggrecan, two other extracellular matrix proteins. The similarities between the skeletal and cellular phenotypes in these mice and those in patients with achondrogenesis type 1A, a neonatal lethal form of skeletal dysplasia in humans, suggested that achondrogenesis type 1A may be caused by GMAP-210 deficiency. Sequence analysis revealed loss-of-function mutations in the 10 unrelated patients with achondrogenesis type 1A whom we studied.

CONCLUSIONS

GMAP-210 is required for the efficient glycosylation and cellular transport of multiple proteins. The identification of a mutation affecting GMAP-210 in mice, and then in humans, as the cause of a lethal skeletal dysplasia underscores the value of screening for abnormal phenotypes in model organisms and identifying the causative mutations.

Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing

Background

The emergence of next-generation sequencing technology presents tremendous opportunities to accelerate the discovery of rare variants or mutations that underlie human genetic disorders. Although the complete sequencing of the affected individuals' genomes would be the most powerful approach to finding such variants, the cost of such efforts make it impractical for routine use in disease gene research. In cases where candidate genes or loci can be defined by linkage, association, or phenotypic studies, the practical sequencing target can be made much smaller than the whole genome, and it becomes critical to have capture methods that can be used to purify the desired portion of the genome for shotgun short-read sequencing without biasing allelic representation or coverage. One major approach is array-based capture which relies on the ability to create a custom in-situ synthesized oligonucleotide microarray for use as a collection of hybridization capture probes. This approach is being used by our group and others routinely and we are continuing to improve its performance.

Results

Here, we provide a complete protocol optimized for large aggregate sequence intervals and demonstrate its utility with the capture of all predicted amino acid coding sequence from 3,038 human genes using 241,700 60-mer oligonucleotides. Further, we demonstrate two techniques by which the efficiency of the capture can be increased: by introducing a step to block cross hybridization mediated by common adapter sequences used in sequencing library construction, and by repeating the hybridization capture step. These improvements can boost the targeting efficiency to the point where over 85% of the mapped sequence reads fall within 100 bases of the targeted regions.

Conclusions

The complete protocol introduced in this paper enables researchers to perform practical capture experiments, and includes two novel methods for increasing the targeting efficiency. Coupled with the new massively parallel sequencing technologies, this provides a powerful approach to identifying disease-causing genetic variants that can be localized within the genome by traditional methods.

BFAST: an alignment tool for large scale genome resequencing

BACKGROUND

The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.

METHODOLOGY

We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.

CONCLUSIONS

We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net).

Mutations in PYCR1 cause cutis laxa with progeroid features

Autosomal recessive cutis laxa (ARCL) describes a group of syndromal disorders that are often associated with a progeroid appearance, lax and wrinkled skin, osteopenia and mental retardation. Homozygosity mapping in several kindreds with ARCL identified a candidate region on chromosome 17q25. By high-throughput sequencing of the entire candidate region, we detected disease-causing mutations in the gene PYCR1. We found that the gene product, an enzyme involved in proline metabolism, localizes to mitochondria. Altered mitochondrial morphology, membrane potential and increased apoptosis rate upon oxidative stress were evident in fibroblasts from affected individuals. Knockdown of the orthologous genes in Xenopus and zebrafish led to epidermal hypoplasia and blistering that was accompanied by a massive increase of apoptosis. Our findings link mutations in PYCR1 to altered mitochondrial function and progeroid changes in connective tissues.

Local alignment of two-base encoded DNA sequence

Background

DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity.

Results

We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions.

Conclusion

The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data.

Effect of early versus deferred antiretroviral therapy for HIV on survival

BACKGROUND

The optimal time for the initiation of antiretroviral therapy for asymptomatic patients with human immunodeficiency virus (HIV) infection is uncertain.

METHODS

We conducted two parallel analyses involving a total of 17,517 asymptomatic patients with HIV infection in the United States and Canada who received medical care during the period from 1996 through 2005. None of the patients had undergone previous antiretroviral therapy. In each group, we stratified the patients according to the CD4+ count (351 to 500 cells per cubic millimeter or >500 cells per cubic millimeter) at the initiation of antiretroviral therapy. In each group, we compared the relative risk of death for patients who initiated therapy when the CD4+ count was above each of the two thresholds of interest (early-therapy group) with that of patients who deferred therapy until the CD4+ count fell below these thresholds (deferred-therapy group).

RESULTS

In the first analysis, which involved 8362 patients, 2084 (25%) initiated therapy at a CD4+ count of 351 to 500 cells per cubic millimeter, and 6278 (75%) deferred therapy. After adjustment for calendar year, cohort of patients, and demographic and clinical characteristics, among patients in the deferred-therapy group there was an increase in the risk of death of 69%, as compared with that in the early-therapy group (relative risk in the deferred-therapy group, 1.69; 95% confidence interval [CI], 1.26 to 2.26; P<0.001). In the second analysis involving 9155 patients, 2220 (24%) initiated therapy at a CD4+ count of more than 500 cells per cubic millimeter and 6935 (76%) deferred therapy. Among patients in the deferred-therapy group, there was an increase in the risk of death of 94% (relative risk, 1.94; 95% CI, 1.37 to 2.79; P<0.001).

CONCLUSIONS

The early initiation of antiretroviral therapy before the CD4+ count fell below two prespecified thresholds significantly improved survival, as compared with deferred therapy.

Ciliary abnormalities due to defects in the retrograde transport protein DYNC2H1 in short-rib polydactyly syndrome

The short-rib polydactyly (SRP) syndromes are a heterogeneous group of perinatal lethal skeletal disorders with polydactyly and multisystem organ abnormalities. Homozygosity by descent mapping in a consanguineous SRP family identified a genomic region that contained DYNC2H1, a cytoplasmic dynein involved in retrograde transport in the cilium. Affected individuals in the family were homozygous for an exon 12 missense mutation that predicted the amino acid substitution R587C. Compound heterozygosity for one missense and one null mutation was identified in two additional nonconsanguineous SRP families. Cultured chondrocytes from affected individuals showed morphologically abnormal, shortened cilia. In addition, the chondrocytes showed abnormal cytoskeletal microtubule architecture, implicating an altered microtubule network as part of the disease process. These findings establish SRP as a cilia disorder and demonstrate that DYNC2H1 is essential for skeletogenesis and growth.

A recessive skeletal dysplasia, SEMD aggrecan type, results from a missense mutation affecting the C-type lectin domain of aggrecan

Analysis of a nuclear family with three affected offspring identified an autosomal-recessive form of spondyloepimetaphyseal dysplasia characterized by severe short stature and a unique constellation of radiographic findings. Homozygosity for a haplotype that was identical by descent between two of the affected individuals identified a locus for the disease gene within a 17.4 Mb interval on chromosome 15, a region containing 296 genes. These genes were assessed and ranked by cartilage selectivity with whole-genome microarray data, revealing only two genes, encoding aggrecan and chondroitin sulfate proteoglycan 4, that were selectively expressed in cartilage. Sequence analysis of aggrecan complementary DNA from an affected individual revealed homozygosity for a missense mutation (c.6799G --> A) that predicts a p.D2267N amino acid substitution in the C-type lectin domain within the G3 domain of aggrecan. The D2267 residue is predicted to coordinate binding of a calcium ion, which influences the conformational binding loops of the C-type lectin domain that mediate interactions with tenascins and other extracellular-matrix proteins. Expression of the normal and mutant G3 domains in mammalian cells showed that the mutation created a functional N-glycosylation site but did not adversely affect protein trafficking and secretion. Surface-plasmon-resonance studies showed that the mutation influenced the binding and kinetics of the interactions between the aggrecan G3 domain and tenascin-C. These findings identify an autosomal-recessive skeletal dysplasia and a significant role for the aggrecan C-type lectin domain in regulating endochondral ossification and, thereby, height.

Molecular dynamics of extreme mass segregation in a rapidly collapsing bubble

A molecular dynamic simulation of a mixture of light and heavy gases in a rapidly imploding sphere exhibits virtually complete segregation. The lighter gas collects at the focus of the sphere and reaches a temperature that is several orders of magnitude higher than when its concentration is 100%. Implosion parameters are chosen via a theoretical fit to an observed sonoluminescing bubble with an extreme expansion ratio (25:1) of maximum to ambient radii.

Paclitaxel-eluting versus bare-metal stents in acute ST elevation myocardial infarction (STEMI)

INTRODUCTION

Data comparing efficacy and safety of drug eluting stents (DES), particularly paclitaxel stent with bare metal stents (BMS) in the setting of acute ST elevation myocardial infarction (STEMI) is limited and inconclusive. The aim of our study is to compare the efficacy and safety of paclitaxel stent with bare metal stent in acute STEMI.

METHODS

A retrospective cohort study was performed on patients from our single community hospital who participated in the C-PORT trial from January 2003 to May 2005. One hundred forty-three patients treated exclusively with either BMS or paclitaxel DES were included (79 with paclitaxel DES and 64 with BMS) and were followed at 1, 3, and 6 months. The primary outcome was occurrence of major adverse cardiac events defined as cardiac death, STEMI or NSTEMI or the need for target vessel revascularization. Variables were compared using appropriate statistics and event free survival curves were estimated.

RESULTS

Baseline clinical characteristics in BMS and paclitaxel DES groups were well matched. No statistical difference between BMS and DES groups in the rate of cardiac death (6% vs. 9%, P = 0.56), STEMI or NSEMI (1.6% vs. 1.3% respectively, P = 0.88) and composite end point (13% vs. 10%, P = 0.65) was observed while a significant reduction in target vessel revascularization was seen in DES group (6% vs. 0% respectively, P = 0.02) was noticed.

CONCLUSION

In our patient group with acute STEMI, the use of paclitaxel DES did not show significant decrease in cumulative end points, cardiac mortality and recurrent STEMI or NSTEMI compared with BMS over a 6-month follow-up period. However, a significant reduction in revascularization of target vessel was seen.

The Asthma Control and Communication Instrument: a clinical tool developed for ethnically diverse populations

BACKGROUND

Lower levels of quality asthma care among racially diverse populations might be due to inaccurate disease status assessments. The Asthma Control and Communication Instrument (ACCI) is a new tool that captures patient report of disease status during routine care.

OBJECTIVE

We sought to test the ACCI's psychometric properties in a racially diverse population.

METHODS

We performed a cross-sectional study. Subjects were recruited from specialist and generalist urban outpatient clinics. The ACCI and measures of asthma control, quality of life, lung function, and specialist rating of asthma status were collected. Four ACCI domains were separately validated: Acute Care, Bother, Control, and Direction. Principal component analysis, internal consistency, concurrent, discriminative, known-groups validity, and accuracy were evaluated.

RESULTS

Two hundred seventy asthmatic patients (77% female subjects, 55% black) participated. ACCI Control domain internal consistency was 0.80. ACCI Bother, Control, and Direction domains showed strong concurrent validity with asthma control and quality-of-life measures (all P < .001). ACCI Acute Care and Direction domains showed strong concurrent validity with individual validation items (all P < .001). The ACCI Control domain discriminated clinically important levels of disease status measured by asthma control, quality of life (both P < .001), and percent predicted peak expiratory flow rate (P = .005) and was associated with specialist rating of disease status (P < .001), confirming known-groups validity. The accuracy of the ACCI Control domain in classifying patients with uncontrolled asthma was very good (area under the curve, 0.851; 95% CI, 0.742-0.95870). Results were similar for both black and white subjects.

CONCLUSION

The ACCI is a promising clinical tool that measures asthma disease status during routine health care and is valid for use in both black and white populations.

Patient factors used by pediatricians to assign asthma treatment

OBJECTIVE

Although asthma is often inappropriately treated in children, little is known about what information pediatricians use to adjust asthma therapy. The purpose of this work was to assess the importance of various dimensions of patient asthma status as the basis of pediatrician treatment decisions.

PATIENTS AND METHODS

We conducted a cross-sectional, random-sample survey, between November 2005 and May 2006, of 500 members of the American Academy of Pediatrics using standardized case vignettes. Vignettes varied in regard to (1) acute health care use (hospitalized 6 months ago), (2) bother (parent bothered by the child's asthma status), (3) control (frequency of symptoms and albuterol use), (4) direction (qualitative change in symptoms), and (5) wheezing during physical examination. Our primary outcome was the proportion of pediatricians who would adjust treatment in the presence or absence of these 5 factors.

RESULTS

Physicians used multiple dimensions of asthma status other than symptoms to determine treatment. Pediatricians were significantly more likely to increase treatment for a recently hospitalized patient (45% vs 18%), a bothered parent (67% vs 18%), poorly controlled symptoms (4-5 times per week; 100% vs 18%), or if there was wheezing on examination (45% vs 18%) compared with patients who only had well-controlled symptoms. Pediatricians were significantly less likely to decrease treatment for a child with well-controlled symptoms and recent hospitalization (28%), parents who reported being bothered (43%), or a child whose symptoms had worsened since the last doctor visit (10%) compared with children with well-controlled symptoms alone.

CONCLUSIONS

Pediatricians treat asthma on the basis of multiple dimensions of asthma status, including hospitalization, bother, symptom frequency, direction, and wheezing but use these factors differently to increase and decrease treatment. Tools that systematically assess multiple dimensions of asthma may be useful to help further improve pediatric asthma care.

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.

Patient factors that physicians use to assign asthma treatment

BACKGROUND

Asthma guidelines recommend severity assessment to assign treatment, often quantified as current control. It is unknown how strongly control assessment affects clinician treatment decisions, nor if control is sufficient.

METHODS

To determine patient factors used by physicians to assign treatment, we surveyed pulmonary specialists (PSs) and family physicians (FPs) using vignettes. We tested whether recent acute care (hospitalization 6 months ago), bother (patient bothered by asthma), control (symptom or reliever medication frequency), and direction (change since last visit) influence treatment decisions. Factors used for stepping up and stepping down were assessed.

RESULTS

A total of 461 physicians participated (236 PSs and 225 FPs). As expected, physicians indicated a greater likelihood of stepping up treatment for persistent (4-5 times per week) than for intermittent (1 time per 2 weeks) symptoms (PSs 97% vs 24%, P < .001; FPs 97% vs 33%, P < .001). All else being equal, physicians were more likely to step up treatment of a patient with intermittent symptoms if the patient reported recent acute care (PSs 49% vs 24%; FPs 72% vs 33%), was bothered (PSs 81% vs 24%; FPs 80% vs 33%), or was worse since the last visit (PSs 68% vs 24%; FPs 66% vs 33%) (all P < .001). These factors were also predictive of stepping down from high-intensity therapy and remained significant in multivariate analyses (all P < .05).

CONCLUSIONS

Asthma control greatly influences physician decisions about asthma treatments. However, recent acute care, bother, and direction of illness also influence decisions, particularly those that involve increasing the amount of medication prescribed. Further work is needed to determine if use of these additional indicators leads to better asthma outcomes.

Are physician estimates of asthma severity less accurate in black than in white patients?

BACKGROUND

Racial differences in asthma care are not fully explained by socioeconomic status, care access, and insurance status. Appropriate care requires accurate physician estimates of severity. It is unknown if accuracy of physician estimates differs between black and white patients, and how this relates to asthma care disparities.

OBJECTIVE

We hypothesized that: 1) physician underestimation of asthma severity is more frequent among black patients; 2) among black patients, physician underestimation of severity is associated with poorer quality asthma care.

DESIGN, SETTING AND PATIENTS

We conducted a cross-sectional survey among adult patients with asthma cared for in 15 managed care organizations in the United States. We collected physicians' estimates of their patients' asthma severity. Physicians' estimates of patients' asthma as being less severe than patient-reported symptoms were classified as underestimates of severity.

MEASUREMENTS

Frequency of underestimation, asthma care, and communication.

RESULTS

Three thousand four hundred and ninety-four patients participated (13% were black). Blacks were significantly more likely than white patients to have their asthma severity underestimated (OR = 1.39, 95% CI 1.08-1.79). Among black patients, underestimation was associated with less use of daily inhaled corticosteroids (13% vs 20%, p < .05), less physician instruction on management of asthma flare-ups (33% vs 41%, p < .0001), and lower ratings of asthma care (p = .01) and physician communication (p = .04).

CONCLUSIONS

Biased estimates of asthma severity may contribute to racially disparate asthma care. Interventions to improve physicians' assessments of asthma severity and patient-physician communication may minimize racial disparities in asthma care.

High density SNP association study of a major autism linkage region on chromosome 17

A region on chromosome 17 has recently been highlighted as linked to autism (MIM[209850]) in multiple studies and evidence has accumulated suggesting that male-only families (those families that have produced only affected males) provide the major contribution to linkage at this locus. In an attempt to comprehensively test for association of common variants to autism within the region on chromosome 17 defined in Stone et al. (Stone, J.L., Merriman, B., Cantor, R.M., Yonan, A.L., Gilliam, T.C., Geschwind, D.H. and Nelson, S.F. (2004) Evidence for sex-specific risk alleles in autism spectrum disorder. Am. J. Hum. Genet., 75, 1117-1123), a dense panel of single nucleotide polymorphisms (SNPs) was selected across the linkage peak and analyzed in a trio-based study design. SNPs were genotyped in 219 independent trios at an average intermarker distance of 6.1 kb across the 13.7 Mb interval. This provided ~80% coverage of common HapMap variation present in Caucasians, testing exonic, intronic, promoter and intergenic regions, as knowledge of important functional regions within the genome is currently limited. In this comprehensive association study of a linkage region in autism, no single SNP or haplotype association was sufficient to account for the initial linkage signal. Nominally significant single SNP and/or haplotype-based association results were detected in 15 genes, of which, MYO1D, ACCN1 and LASP1 stand out as genes with autism risk alleles requiring further study, with potential GRRs in the range of 1.34-2.29.

Repetitive sequence environment distinguishes housekeeping genes

Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes by their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element-1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, was used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.

Mortality in patients hospitalized for asthma exacerbations in the United States

RATIONALE

Hospitalizations for asthma exacerbations are common in the United States, but there are no national estimates of outcomes in this population. It is also not known if race disparities in asthma deaths exist among hospitalized patients.

OBJECTIVES

To estimate outcomes of patients hospitalized for asthma in the United States and to determine if the risk of death in this population is higher among black patients compared with white patients.

METHODS

We used the Nationwide Inpatient Sample for 2000. Admissions for asthma exacerbations among patients > 5 yr of age were included. Mortality was the primary outcome; secondary outcomes were length of stay and total hospital charges.

MEASUREMENTS AND MAIN RESULTS

In-hospital asthma mortality was 0.5% (99% confidence interval [CI], 0.4-0.6), with mean hospital stay of 2.7 d (99% CI, 2.6-2.8 d) and 9,078 dollars (99% CI, 8,300-9,855 dollars) in hospital charges. Deaths in this population accounted for about one-third of all asthma deaths reported in the United States. Black patients hospitalized for asthma exacerbations were less likely to die when compared with white patients (0.3 vs. 0.6%; p < 0.001). However, in multivariable analyses, there were no significant race differences in hospital deaths.

CONCLUSIONS

Mortality among patients hospitalized for asthma exacerbations accounts for one-third of all deaths from asthma. The higher overall risk of death from asthma in black patients compared with white patients in the United States is not explained by race differences in hospital deaths and therefore is attributable to factors preceding hospitalization.

Appendiceal cancer and peritoneal carcinomatosis: a report of 29 cases

Peritoneal surface malignancies of appendiceal origin arise from a perforated neoplasm with gradual expansion of the tumor within the abdomen. We report our experience with 29 patients. Between February 2000 and November 2004, 29 patients were classified into one of three groups based on the features of their peritoneal dissemination. Group 1 included those with extracellular mucin with little cellular atypia (disseminated peritoneal adenomucinosis/low-grade mucinous adenocarcinomas). Group 2 included those with peritoneal mucinous carcinomatosis/high-grade mucinous adenocarcinomas, and Group 3 included those with nonmucinous carcinomatosis. There were 17 patients in Group 1, 9 in Group 2, and 3 in Group 3. The majority had cytoreductive surgery and intraperitoneal chemotherapy. There were no operative deaths. Mean follow-up was 21 months. Median survival for Groups 1 and 2 has not been reached. Group 3 patients were more likely to die than Group 1 patients, with a hazard ratio of 48.0 (P = 0.001), and Group 2 patients with a hazard ratio of 7.8 (P = 0.029). Median survival for Group 3 was 5 months. These data add to the growing evidence that supports cytoreductive surgery and intraperitoneal chemotherapy in a selected group of patients. Those with mucinous peritoneal dissemination are more likely to benefit from this approach. It appears that in patients with nonmucinous carcinomatosis, the biology of the tumor predicts their outcome.

Appendiceal Cancer and Peritoneal Carcinomatosis: A Report of 29 Cases

Peritoneal surface malignancies of appendiceal origin arise from a perforated neoplasm with gradual expansion of the tumor within the abdomen. We report our experience with 29 patients. Between February 2000 and November 2004, 29 patients were classified into one of three groups based on the features of their peritoneal dissemination. Group 1 included those with extracellular mucin with little cellular atypia (disseminated peritoneal adenomucinosis/low-grade mucinous adenocarcinomas). Group 2 included those with peritoneal mucinous carcinomatosis/high-grade mucinous adenocarcinomas, and Group 3 included those with nonmucinous carcinomatosis. There were 17 patients in Group 1, 9 in Group 2, and 3 in Group 3. The majority had cytoreductive surgery and intraperitoneal chemotherapy. There were no operative deaths. Mean follow-up was 21 months. Median survival for Groups 1 and 2 has not been reached. Group 3 patients were more likely to die than Group 1 patients, with a hazard ratio of 48.0 ( P = 0.001), and Group 2 patients with a hazard ratio of 7.8 ( P = 0.029). Median survival for Group 3 was 5 months. These data add to the growing evidence that supports cytoreductive surgery and intraperitoneal chemotherapy in a selected group of patients. Those with mucinous peritoneal dissemination are more likely to benefit from this approach. It appears that in patients with nonmucinous carcinomatosis, the biology of the tumor predicts their outcome.

Comparison of open and closed techniques of delivery of hyperthermic chemotherapy following cytoreductive surgery in patients with peritoneal carcinomatosis

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Background: Intraperitoneal hyperthermic chemotherapy (IPHC) combined with Cytoreductive surgery (CRS) is an effective approach in the management of peritoneal carcinomatosis. A controversy exists concerning the use of an open or closed technique of delivery of the hyperthermic chemotherapy. A retrospective study of a prospective data base was performed to compare these two techniques with respect to overall survival, disease-free survival, length of hospital stay (LOS), and incidence of complications. Methods: From 1998 to 2005, 64 patients underwent CRS and IPHC. Nineteen patients underwent open technique and forty-five underwent closed technique. The pathological diagnoses included appendiceal carcinoma (35), pseudomyxoma peritonei (10), ovarian carcinoma (7), colon carcinoma (6), mesothelioma (5), and sarcoma (1). Cox Proportional-Hazards Regression analysis was performed. Results: Overall 5- year survival and disease free survival was 46% and 22%, respectively. No significant difference in overall survival (p=0.58), disease-free survival (p=0.37), or incidence of complications (p=0.66) was found between the groups. Open technique patients had a significantly shorter LOS than closed with a mean of 8.7 vs. 11.4 days [p=0.01] and a median of 8 vs.11 days [p=0.002] (Kruskal-Wallis Rank Sum Test). Conclusions: The improved survival seen in patients undergoing CRS and IPHC is not dependent on the choice of technique of delivery of the hyperthermic chemotherapy

No significant financial relationships to disclose.

Long term survival following cytoreductive surgery and intraperitoneal hyperthermic chemotherapy for disseminated appendiceal tumors

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Background: Appendiceal tumors represent 2.8% of gastrointestinal tumors and less than 0.5% of gastrointestinal malignancies, but frequently involve intraperitoneal spread. Controversial treatment of disseminated tumor has consisted of extensive debulking surgery, peritonectomy, and intraperitoneal chemotherapy. We evaluated the disease free and overall survival, morbidity and mortality of patients with disseminated appendiceal tumors treated by cytoreductive surgery (CRS) and intraperitoneal hyperthermic chemotherapy (IPHC). Methods: A retrospective review of a prospective database was performed between 1999 and 2005. Thirty-one patients underwent CRS followed by IPHC using mitomycin 40 mg infused over 90 minutes at 40–42°C. Patients were given a Peritoneal Carcinomatosis Index (PCI) score pre and post operatively. Postoperatively, patients were assigned cytoreductive scores, indicating completeness of resection: CC-0 = no residual disease, CC-1 ≤ 0.25 cm, CC-2 = 0.25–2.5 cm, CC-3 ≥ 2.5 cm. Cox proportional-hazards models were used to test the influence of different variables on survival. The models were adjusted for age, grade of differentiation, histology and cytoreductive score. Results: There were 14 females and 17 males with a mean age 50 years (range 33–80). Two-thirds of all patients had a preoperative PCI score of >20. The overall survival at 1 year was 96% (95% CI, 74% to 99%) and at 3 years was 69% (95% CI, 38% to 86%). Disease free survival at 3 years was 30% ( 95% CI, 8% to 56%). There was no mortality from the procedure. Overall morbidity, including Grades 1–5 as described by the CTCAE guidelines, was 48%. A multivariate analysis was performed for grade of differentiation and was not found to be statistically significant. However, log rank test for equality of survivor functions in patients with CC scores of 0 or 1 experience recurrence of disease at a slower rate than patients with scores of 2 or 3 (p < 0.001). Conclusions: Although further study is necessary, Cytoreductive surgery followed by IPHC, where a low PCI score and a CC score of ≤1 is achieved, can lead to increased survival for selected patients having advanced appendiceal cancer with peritoneal dissemination.

No significant financial relationships to disclose.

Segmental uniparental isodisomy on 5q32-qter in a patient with childhood-onset schizophrenia

Schizophrenia is a severe mental disorder affecting approximately 1% of the world's population. Although the aetiology of schizophrenia is complex and multifactorial, with estimated heritabilities as high as 80%, genetic factors are the most compelling. Childhood-onset schizophrenia (COS), defined as onset of schizophrenia before the age of 13 years, is a rare and malignant form of the illness that may have more salient genetic influence. The first known case of paternal segmental uniparental isodisomy (iUPD) on 5q32-qter in a patient with COS is described, which adds to the previously known high rates of chromosomal abnormalities reported in this sample. iUPD is a rare genetic condition in which the offspring receives two chromosomal homologues from one parent. Segmental UPD is defined as UPD on a portion of a chromosome with biparental inheritance seen in the rest of the homologous pair. Complications owing to this abnormality may arise from malfunctioning imprinted genes or homozygosity of recessive disease-causing mutations. This aberration became apparent during whole-genomic screening of a COS cohort and is of particular interest because 5q has been implicated in schizophrenia by several genomewide linkage studies and positive gene associations. This report, therefore, presents more evidence that schizophrenia susceptibility gene, or genes, may be found on distal 5q.

Scanning systems and protocols used during imaging for acute pulmonary embolism: how much do our clinical colleagues know?

RATIONALE AND OBJECTIVES

The imaging systems and protocols used during ventilation-perfusion lung (V-P) scintigraphy and computed tomographic (CT) pulmonary angiography (CTPA) can affect diagnostic performance. We investigated the level of awareness of these factors among US clinicians who refer patients for imaging for suspected acute pulmonary embolism.

MATERIALS AND METHODS

Between September 2004 and February 2005, we conducted a mail survey of 855 physicians selected at random from three professional organizations. We asked participants how important the availability of state-of-the-art equipment was in their imaging decisions, whether V-P scintigraphy was performed with planar or single-photon emission CT (SPECT) equipment in their communities, to identify the most advanced type of CT scanner used for CTPA, and whether CT venography (CTV) was performed routinely after CTPA.

RESULTS

We received completed surveys from 240 (29.8%) physicians practicing in 44 states. One hundred sixty-six respondents (70.9%) indicated that state-of-the-art equipment was an extremely or very important factor when they made imaging decisions. However, 191 clinicians (80.3%) did not know whether SPECT equipment was used for V-P scintigraphy, and 119 (50.6%) did not know the type of CT scanner used for CTPA in their communities. Of respondents, 39.2% reported access to multidetector row CT technology for CTPA, whereas 10.2% referred patients to facilities using single-detector CT. Only 9.3% of respondents indicated that CTV was performed routinely after CTPA.

CONCLUSION

Although state-of-the-art equipment is important to them, clinicians practicing in the United States have limited knowledge of the equipment being used during CTPA and V-P scintigraphy scanning in their communities. Radiologists should intensify efforts to familiarize their clinical colleagues with the equipment they use.

CT pulmonary angiography is the first-line imaging test for acute pulmonary embolism: a survey of US clinicians

RATIONALE AND OBJECTIVES

Our aim is to document current imaging practices for diagnosing acute pulmonary embolism (PE) among physicians practicing in the United States and explore factors associated with these practices.

MATERIALS AND METHODS

Between September 2004 and February 2005, we surveyed by mail 855 physicians selected at random from membership lists of three professional organizations. Physicians reported their imaging practices and experiences in managing patients with suspected acute PE during the preceding 12 months.

RESULTS

Completed questionnaires were received from 240 of 806 eligible participants (29.8%) practicing in 44 states: 86.7% of respondents believed that computed tomographic pulmonary angiography (CTPA) was the most useful imaging procedure for patients with acute PE compared with 8.3% for ventilation-perfusion (V-P) scintigraphy and 2.5% for conventional pulminary angiography (PA). After chest radiography, CTPA was the first imaging test requested 71.4% of the time compared with V-P scintigraphy (19.7%) and lower-limb venous ultrasound (5.8%). Participants received indeterminate or inconclusive results 46.4% of the time for V-P scintigraphy, 10.6% of the time for CTPA, and 2.2% of the time for PA. CTPA was available around the clock to 88.3% of participants compared with 53.8% for V-P scintigraphy and 42.5% for PA. A total of 68.6% of respondents received CTPA results in 2 hours or less (vs 37.5% for V-P scintigraphy and 22.9% for PA). CTPA also provided an alternative diagnosis to PE or showed other significant abnormalities 28.5% of the time, and these findings frequently altered management.

CONCLUSION

US clinicians unequivocally prefer CTPA in patients with suspected acute PE. Reasons for this preference include availability and timely reporting, a lower rate of inconclusive results, and the additional diagnostic capabilities that CTPA can provide.