Publications by authors named "Barry Merriman"

54 Publications

Emergency Department and Inpatient Health Care Services Utilization by the Elderly Population: Hurricane Sandy in The State of New Jersey.

Disaster Med Public Health Prep 2018 12 22;12(6):730-738. Epub 2018 Mar 22.

Health Division,Logistic Management Institute,Tysons,Virginia.

Objective: In this investigation, we reported the increase in emergency department and inpatient admission cases during the month of November 2012 post Hurricane Sandy as compared with baseline (November 2010, 2011, and 2013) for elderly patients aged 65 and up.

Methods: Medical claims data for patients aged 65 and over treated at emergency department and inpatient health care facilities in New Jersey were analyzed to examine the surge in frequencies of diagnoses treated immediately following Hurricane Sandy. The differences were quantified using gap analysis for 2 years before and 1 year after the event.

Results: There was an average increase of 1700 cases for the month of November 2012 relative to baseline for the top 15 most frequently diagnosed emergency department medical conditions. On a daily basis, a volume increase by an average 57 cases could be expected, including significant numbers of limb fractures and other trauma cases for these most frequently encountered medical conditions.

Conclusions: Understanding the surge level in medical services needed in emergency departments and inpatient facilities during a natural disaster aftermath is critical for effective emergency preparation and response for the elderly population. (Disaster Med Public Health Preparedness. 2018;12:730-738).
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http://dx.doi.org/10.1017/dmp.2018.1DOI Listing
December 2018

Genetic Characteristics of Polycythemia Vera and Essential Thrombocythemia in Korean Patients.

J Clin Lab Anal 2016 Nov 2;30(6):1061-1070. Epub 2016 May 2.

Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.

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.
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http://dx.doi.org/10.1002/jcla.21981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6807207PMC
November 2016

Multiple self-healing palmoplantar carcinoma: a familial predisposition to skin cancer with primary palmoplantar and conjunctival lesions.

J Invest Dermatol 2015 Jan 22;135(1):304-308. Epub 2014 Jul 22.

Laboratory of Human Embryology and Genetics, Institute of Medical Biology, A*STAR, Singapore, Singapore; Department of Paediatrics, National University of Singapore, Singapore, Singapore. Electronic address:

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http://dx.doi.org/10.1038/jid.2014.311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269804PMC
January 2015

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

Genome Biol 2014 Mar 25;15(3):R53. Epub 2014 Mar 25.

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.
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http://dx.doi.org/10.1186/gb-2014-15-3-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073084PMC
March 2014

Simple computation of reaction-diffusion processes on point clouds.

Proc Natl Acad Sci U S A 2013 Jun 20;110(23):9209-14. Epub 2013 May 20.

Mathematical Institute, University of Oxford, Oxford OX1 3LB, United Kingdom.

The study of reaction-diffusion processes is much more complicated on general curved surfaces than on standard Cartesian coordinate spaces. Here we show how to formulate and solve systems of reaction-diffusion equations on surfaces in an extremely simple way, using only the standard Cartesian form of differential operators, and a discrete unorganized point set to represent the surface. Our method decouples surface geometry from the underlying differential operators. As a consequence, it becomes possible to formulate and solve rather general reaction-diffusion equations on general surfaces without having to consider the complexities of differential geometry or sophisticated numerical analysis. To illustrate the generality of the method, computations for surface diffusion, pattern formation, excitable media, and bulk-surface coupling are provided for a variety of complex point cloud surfaces.
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http://dx.doi.org/10.1073/pnas.1221408110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677480PMC
June 2013

Progress in ion torrent semiconductor chip based sequencing.

Electrophoresis 2012 Dec;33(23):3397-417

Ion Torrent, A Division of Life Technologies, Inc., Guilford, CT 06437, USA.

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.
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http://dx.doi.org/10.1002/elps.201200424DOI Listing
December 2012

Bioinformatics. Introduction.

Yale J Biol Med 2012 Sep;85(3):305-8

CEO of Ion Torrent, a division of Life Technologies, Inc.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447194PMC
September 2012

Familial cortical myoclonus with a mutation in NOL3.

Ann Neurol 2012 Aug;72(2):175-83

Department of Neurology, School of Medicine, University of California at San Francisco, San Francisco, CA 94158, USA.

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.
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http://dx.doi.org/10.1002/ana.23666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431191PMC
August 2012

Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1.

Nat Genet 2012 May 13;44(6):709-13. Epub 2012 May 13.

Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.

Using homozygosity mapping and locus resequencing, we found that alterations in the homeodomain of the IRX5 transcription factor cause a recessive congenital disorder affecting face, brain, blood, heart, bone and gonad development. We found through in vivo modeling in Xenopus laevis embryos that Irx5 modulates the migration of progenitor cell populations in branchial arches and gonads by repressing Sdf1. We further found that transcriptional control by Irx5 is modulated by direct protein-protein interaction with two GATA zinc-finger proteins, GATA3 and TRPS1; disruptions of these proteins also cause craniofacial dysmorphisms. Our findings suggest that IRX proteins integrate combinatorial transcriptional inputs to regulate key signaling molecules involved in the ontogeny of multiple organs during embryogenesis and homeostasis.
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http://dx.doi.org/10.1038/ng.2259DOI Listing
May 2012

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

Nat Genet 2012 Jan 15;44(2):193-9. Epub 2012 Jan 15.

Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA.

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.
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http://dx.doi.org/10.1038/ng.1078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267856PMC
January 2012

Multiple self-healing squamous epithelioma is caused by a disease-specific spectrum of mutations in TGFBR1.

Nat Genet 2011 Feb 27;43(4):365-9. Epub 2011 Feb 27.

Human Genetics Unit, University of Dundee College of Medicine, Dentistry and Nursing, Dundee, UK.

Multiple self-healing squamous epithelioma (MSSE), also known as Ferguson-Smith disease (FSD), is an autosomal-dominant skin cancer condition characterized by multiple squamous-carcinoma-like locally invasive skin tumors that grow rapidly for a few weeks before spontaneously regressing, leaving scars. High-throughput genomic sequencing of a conservative estimate (24.2 Mb) of the disease locus on chromosome 9 using exon array capture identified independent mutations in TGFBR1 in three unrelated families. Subsequent dideoxy sequencing of TGFBR1 identified 11 distinct monoallelic mutations in 18 affected families, firmly establishing TGFBR1 as the causative gene. The nature of the sequence variants, which include mutations in the extracellular ligand-binding domain and a series of truncating mutations in the kinase domain, indicates a clear genotype-phenotype correlation between loss-of-function TGFBR1 mutations and MSSE. This distinguishes MSSE from the Marfan syndrome-related disorders in which missense mutations in TGFBR1 lead to developmental defects with vascular involvement but no reported predisposition to cancer.
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http://dx.doi.org/10.1038/ng.780DOI Listing
February 2011

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

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S2. Epub 2010 Dec 21.

UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.

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.
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http://dx.doi.org/10.1186/1471-2105-11-S12-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040528PMC
December 2010

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

Am J Hum Genet 2010 Dec;87(6):768-78

Institute of Medical Biology, A(∗)STAR, Singapore.

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.
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http://dx.doi.org/10.1016/j.ajhg.2010.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997365PMC
December 2010

Local alignment of generalized k-base encoded DNA sequence.

BMC Bioinformatics 2010 Jun 24;11:347. Epub 2010 Jun 24.

Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA.

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.
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http://dx.doi.org/10.1186/1471-2105-11-347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911458PMC
June 2010

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

PLoS Genet 2010 Jan 29;6(1):e1000832. Epub 2010 Jan 29.

Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America.

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 30x 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.
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http://dx.doi.org/10.1371/journal.pgen.1000832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813426PMC
January 2010

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

N Engl J Med 2010 Jan;362(3):206-16

Orthopedic Research Laboratories, Department of Orthopedic Surgery, Children's Hospital, Boston, MA 02115, USA.

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.
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http://dx.doi.org/10.1056/NEJMoa0900158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108191PMC
January 2010

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

BMC Genomics 2009 Dec 31;10:646. Epub 2009 Dec 31.

Department of Human Genetics, University of California, Los Angeles, California, USA.

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.
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http://dx.doi.org/10.1186/1471-2164-10-646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808330PMC
December 2009

BFAST: an alignment tool for large scale genome resequencing.

PLoS One 2009 Nov 11;4(11):e7767. Epub 2009 Nov 11.

Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.

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).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007767PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770639PMC
November 2009

Complete cytoreduction offers longterm survival in patients with peritoneal carcinomatosis from appendiceal tumors of unfavorable histology.

J Am Coll Surg 2009 Sep 9;209(3):308-12. Epub 2009 Jul 9.

Division of Surgery, Section of Surgical Oncology, Institute of Cancer Care, Mercy Medical Center, 227 St. Paul Pl., Baltimore, MD 21202, USA.

Background: Cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy (HIPEC) is a rapidly evolving treatment for metastatic appendiceal neoplasms. The aim of this study was to show the effect of complete cytoreduction (CC) on survival in patients undergoing CRS and HIPEC for high-grade appendiceal neoplasm.

Study Design: A retrospective study of a prospective database of 56 patients (from 1999 to 2007) with appendiceal neoplasms treated with CRS and HIPEC was carried out. Histology of the disease, CC score, and peritoneal cancer index (PCI) score were assessed independently and collectively for each group of patients. Survival analysis was performed using the Cox proportional hazard model.

Results: Three-year overall survival was 60%. The median peritoneal cancer index score was 25 or higher. Survival analysis by tumor histology was 80% for patients with low-grade tumors and 52% for patients with high-grade tumors (p = 0.024). Survival by completeness of cytoreduction was 78% for patients with a low CC score (0 to 1) and 28% in patients with a high CC score (2 to 3; p = 0.01). There was no statistically significant difference in survival between the low-grade and high-grade tumors when a complete cytoreduction was performed in both groups of patients: 80% versus 68% (p = 0.69).

Conclusions: CRS and HIPEC is an effective treatment for patients with disseminated appendiceal tumors. High-grade tumors also benefit from this approach and should not be excluded from CRS and HIPEC. Every effort should be made to achieve a complete cytoreduction regardless of the tumor histology.
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http://dx.doi.org/10.1016/j.jamcollsurg.2009.04.019DOI Listing
September 2009

Mutations in PYCR1 cause cutis laxa with progeroid features.

Nat Genet 2009 Sep 2;41(9):1016-21. Epub 2009 Aug 2.

Institute of Medical Biology, A*STAR, Singapore, Singapore.

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.
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http://dx.doi.org/10.1038/ng.413DOI Listing
September 2009

Local alignment of two-base encoded DNA sequence.

BMC Bioinformatics 2009 Jun 9;10:175. Epub 2009 Jun 9.

Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA.

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.
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http://dx.doi.org/10.1186/1471-2105-10-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709925PMC
June 2009

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

Am J Hum Genet 2009 Apr;84(4):542-9

Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.

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.
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http://dx.doi.org/10.1016/j.ajhg.2009.03.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667993PMC
April 2009

Effect of early versus deferred antiretroviral therapy for HIV on survival.

N Engl J Med 2009 Apr 1;360(18):1815-26. Epub 2009 Apr 1.

University of Washington, Harborview Medical Center, 325 Ninth Ave., Box 359931, Seattle, WA 98104, USA.

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.
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http://dx.doi.org/10.1056/NEJMoa0807252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854555PMC
April 2009

Molecular dynamics of extreme mass segregation in a rapidly collapsing bubble.

Phys Rev Lett 2008 Dec 5;101(23):234301. Epub 2008 Dec 5.

Department of Physics and Astronomy, University of California at Los Angeles, Los Angeles, California 90095, USA.

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.
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http://dx.doi.org/10.1103/PhysRevLett.101.234301DOI Listing
December 2008

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

Am J Hum Genet 2009 Jan 24;84(1):72-9. Epub 2008 Dec 24.

Medical Genetics Institute, Steven Spielberg Building, Cedars-Sinai Medical Center, 8723 Alden Drive, Los Angeles, CA 90048, USA.

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.
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http://dx.doi.org/10.1016/j.ajhg.2008.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668039PMC
January 2009

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

Crit Pathw Cardiol 2008 Dec;7(4):232-8

Department of Internal Medicine, St Agnes Hospital, Baltimore, MD, USA.

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.
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http://dx.doi.org/10.1097/HPC.0b013e3181805e0bDOI Listing
December 2008

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

J Allergy Clin Immunol 2008 Nov 11;122(5):936-943.e6. Epub 2008 Oct 11.

Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

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.
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http://dx.doi.org/10.1016/j.jaci.2008.08.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516631PMC
November 2008

Patient factors used by pediatricians to assign asthma treatment.

Pediatrics 2008 Jul;122(1):e195-201

Department of Pediatrics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21287-0005, USA.

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.
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http://dx.doi.org/10.1542/peds.2007-2271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725186PMC
July 2008

Gain-of-function mutations in TRPV4 cause autosomal dominant brachyolmia.

Nat Genet 2008 Aug 29;40(8):999-1003. Epub 2008 Jun 29.

Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA.

The brachyolmias constitute a clinically and genetically heterogeneous group of skeletal dysplasias characterized by a short trunk, scoliosis and mild short stature. Here, we identify a locus for an autosomal dominant form of brachyolmia on chromosome 12q24.1-12q24.2. Among the genes in the genetic interval, we selected TRPV4, which encodes a calcium permeable cation channel of the transient receptor potential (TRP) vanilloid family, as a candidate gene because of its cartilage-selective gene expression pattern. In two families with the phenotype, we identified point mutations in TRPV4 that encoded R616Q and V620I substitutions, respectively. Patch clamp studies of transfected HEK cells showed that both mutations resulted in a dramatic gain of function characterized by increased constitutive activity and elevated channel activation by either mechano-stimulation or agonist stimulation by arachidonic acid or the TRPV4-specific agonist 4alpha-phorbol 12,13-didecanoate (4alphaPDD). This study thus defines a previously unknown mechanism, activation of a calcium-permeable TRP ion channel, in skeletal dysplasia pathogenesis.
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http://dx.doi.org/10.1038/ng.166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525077PMC
August 2008