Publications & Literature

Possible differentiation of cerebral glioblastoma into pleomorphic xanthoastrocytoma: an unusual case in an infant, Case report

J Neurosurg: Pediatrics, Volume 9, May 2012. Michael M. H. Yang, M. Biotech., Ash Singhal, M.D, Christopher Dunham, M.D., F.R.C.P.C, et al.

Abstract: The authors describe an infant girl who, at 10 months of age, presented with a large right parietooccipital tumor causing increased intracranial pressure, mass effect, and midline shift. The tumor was completely resected, and the entirety of the histology was consistent with glioblastoma. She was subsequently placed on adjuvant high-dose chemotherapy consisting of carboplatin, vincristine, and temozolomide, according to Head Start III, Regimen C. Three months after the complete resection, tumor recurrence was noted on MR imaging, during the third cycle of chemotherapy, and biopsy revealed malignant astrocytoma. Given the recurrence and the patient's intolerance to chemotherapy, a palliative course was pursued. Unexpectedly, the patient was alive and had made significant developmental improvements 18 months into palliation. Subsequently, however, signs of increased intracranial pressure developed and imaging demonstrated a very large new tumor growth at the site of prior resection. The recurrence was again fully resected, but microscopy surprisingly revealed pleomorphic xanthoastrocytoma throughout. The clinicopathological and genetic features of this girl's unusual neoplasm are detailed and potential pathogenic hypotheses are explored in this report... read more

 

 

Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank

J. Bacteriol. 2012, 194(10):2759. DOI: 10.1128/JB.00377-12, Gilda Rose S. Amaral, Bruno Sergio de O. Silva, Fabiano L. Thompson, et al.

Abstract: Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number of coding sequences (CDS) is 6,359, as determined according to the Rapid Annotation using Subsystem Technology (RAST) server. The number of ribosomal genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A contains genes related to virulence and fitness, including a complete proteorhodopsin cluster, complete type II and III secretion systems, incomplete type I, IV, and VI secretion systems, a hemolysin, and CTXΦ... read more

 

 

Rapid Detection of the ACMG/ACOG-Recommended 23 CFTR Disease-Causing Mutations Using Ion Torrent Semiconductor Sequencing.

J Biomol Tech. 2012 Apr;23(1):24-30, Elliott AM, Radecki J, Moghis B, Li X, Kammesheidt A. et al.

Abstract: Cystic fibrosis (CF) is one of the most frequently diagnosed autosomal-recessive diseases in the Caucasian population. For general-population CF carrier screening, the American College of Medical Genetics (ACMG)/American College of Obstetricians and Gynecologists (ACOG) have recommended a core panel of 23 mutations that will identify 49-98% of carriers, depending on ethnic background. Using a genotyping technology that can rapidly identify disease-causing mutations is important for high-throughput general-population carrier screening, confirming clinical diagnosis, determining treatment options, and prenatal diagnosis. Here, we describe a proof-of-concept study to determine whether the Ion Torrent Personal Genome Machine (PGM) sequencer platform can reliably identify all ACMG/ACOG 23 CF transmembrane conductance regulator (CFTR) mutations. A WT CF specimen along with mutant DNA specimens representing all 23 CFTR mutations were sequenced bidirectionally on the Ion Torrent 314 chip to determine the accuracy of the PGM for CFTR variant detection. We were able to reliably identify all of the targeted mutations except for 2184delA, which lies in a difficult, 7-mer homopolymer tract. Based on our study, we believe PGM sequencing may be a suitable technology for identifying CFTR mutations in the future. However, as a result of the elevated rate of base-calling errors within homopolymer stretches, mutations within such regions currently need to be evaluated carefully using an alternative method... read more

 

 

Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

J Clin Microbiol. 2012 Mar 29, Vogel U, Szczepanowski R, Claus H, Jünemann S, Prior K, Harmsen D.

Abstract: Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers and adolescents worldwide. DNA sequence based typing has become the standard for molecular epidemiology of the organism including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens. However, PCR of multiple targets and consecutive Sanger sequencing provides logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next generation sequencers (NGS) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine™ (PGM™) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM™ technology generated sequence information for almost all target genes addressed. The results were 100% concordant with conventional typing results with no further editing necessary. In addition, the amount of typing information, i.e. nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In a near future, affordable and fast benchtop-NGS machines like the PGM™ might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workload and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability and antibiotic resistance gene monitoring... read more

 

 

Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR

PLoS pathogens, 2011, doi:10.1371/journal.ppat.1002359, Benjamin P. Howden, Timothy P. Stinear, et al.

Abstract: Antimicrobial resistance in Staphylococcus aureus is a major public health threat, compounded by emergence of strains with resistance to vancomycin and daptomycin, both last line antimicrobials. Here we have performed high throughput DNA sequencing and comparative genomics for five clinical pairs of vancomycin-susceptible (VSSA) and vancomycin intermediate ST239 S. aureus (VISA); each pair isolated before and after vancomycin treatment failure. These comparisons revealed a frequent pattern of mutation among the VISA strains within the essential walKR two-component regulatory locus involved in control of cell wall metabolism. We then conducted bi-directional allelic exchange experiments in our clinical VSSA and VISA strains and showed that single nucleotide substitutions within either walK or walR lead to co-resistance to vancomycin and daptomycin, and caused the typical cell wall thickening observed in resistant clinical isolates. Ion Torrent genome sequencing confirmed no additional regulatory mutations had been introduced into either the walR or walK VISA mutants during the allelic exchange process. However, two potential compensatory mutations were detected within putative transport genes for the walK mutant... read more

 

 

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

27 July 2011: The New England Journal of Medicine, Drs. Rohde, Qin, Cui, D. Li, and Loman; and Drs. Pallen, J. Wang, Aepfelbacher, and R. Yang.

Abstract: An outbreak caused by Shiga-toxin–producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.... read more

 

 

An integrated semiconductor device enabling non-optical genome sequencing

Nature 475, Pages: 348-352, 21 July 2011, published online 20 July 2011, Jonathan M. Rothberg, Wolfgang Hinz, Todd M. Rearick, et al.

Abstract: The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome....read more

 

 

Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing An integrated semiconductor device enabling non-optical genome sequencing technology

PLoS One. 30 Jun 2011, Alexander Mellmann, Dag Harmsen, Craig A. Cummings, et al.

Abstract: An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past. To prospectively elucidate the unique characteristics of this strain in the early stages of this outbreak, we applied whole genome sequencing on the Life Technologies Ion Torrent PGM™ sequencer and Optical Mapping to characterize one outbreak isolate (LB226692) and a historic O104:H4 HUS isolate from 2001 (01-09591)...read more

 

 

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).

Proc Natl Acad Sci (PNAS). 27 Jun 2011. [Epub ahead of print], Miller W, Schuster SC, et al. Pennsylvania State University, Center for Comparative Genomics and Bioinformatics

Abstract: The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes...read more

 

 

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