Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants

The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen), with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs). SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome.) To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost

Juvenile idiopathic scoliosis treated with posterior arthrodesis and segmental pedicle screw instrumentation before the age of 9 years: a 5-year follow-up

<p>Abstract</p> <p>Study design</p> <p>Retrospective study.</p> <p>Objective</p> <p>To evaluate the radiological results of fusion with segmental pedicle screw fixation in juvenile idiopathic scoliosis with a minimum 5-year follow-up.</p> <p>Summary of background data</p> <p>Progression of spinal deformity after posterior instrumentation and fusion in immature patients has been reported by several authors. Segmental pedicle screw fixation has been shown to be effective in controlling both coronal and sagittal plane deformities. However, there is no long term study of fusion with segmental pedicle screw fixation in these group of patients.</p> <p>Methods</p> <p>Seven patients with juvenile idiopathic scoliosis treated by segmental pedicle screw fixation and fusion were analyzed. The average age of the patients was 7.4 years (range 5–9 years) at the time of the operation. All the patients were followed up 5 years or more (range 5–8 years) and were all Risser V at the most recent follow up. Three dimensional reconstruction of the radiographs was obtained and 3DStudio Max software was used for combining, evaluating and modifying the technical data derived from both 2d and 3d scan data.</p> <p>Results</p> <p>The preoperative thoracic curve of 56 ± 15° was corrected to 24 ± 17° (57% correction) at the latest follow-up. The lumbar curve of 43 ± 14° was corrected to 23 ± 6° (46% correction) at the latest follow-up. The preoperative thoracic kyphosis of 37 ± 13° and the lumbar lordosis of 33 ± 13° were changed to 27 ± 13° and 42 ± 21°, respectively at the latest follow-up. None of the patients showed coronal decompensation at the latest follow-up. Four patients had no evidence of crankshaft phenomenon. In two patients slight increase in Cobb angle at the instrumented segments with a significant increase in AVR suggesting crankshaft phenomenon was seen. One patient had a curve increase in both instrumented and non instrumented segments due to incorrect strategy.</p> <p>Conclusion</p> <p>In juvenile idiopathic curves of Risser 0 patients with open triradiate cartilages, routine combined anterior fusion to prevent crankshaft may not be warranted by posterior segmental pedicle screw instrumentation.</p

Polyp measurement based on CT colonography and colonoscopy: variability and systematic differences

To assess the variability and systematic differences in polyp measurements on optical colonoscopy and CT colonography. Gastroenterologists measured 51 polyps by visual estimation, forceps comparison and linear probe. CT colonography observers randomly assessed polyp size two-dimensionally (abdominal and intermediate window) and three-dimensionally (manually and semi-automatically). Linear mixed models were used to assess the variability and systematic differences between CT colonography and optical colonoscopy techniques. The variability of forceps and linear probe measurements was comparable and both showed less variability than measurement by visual assessment. Measurements by linear probe were 0.7 mm smaller than measurements by visual assessment or by forceps. The variability of all CT colonography techniques was lower than for measurements by forceps or visual assessment and sometimes lower (only 2D intermediate window and manual 3D) compared with measurements by linear probe. All CT colonography measurements judged polyps to be larger than optical colonoscopy, with differences ranging from 0.7 to 2.3 mm. A linear probe does not reduce the measurement variability of endoscopists compared with the forceps. Measurement differences between observers on CT colonography were usually smaller than at optical colonoscopy. Polyps appeared larger when using various CT colonography techniques than when measured during optical colonoscop

Pediatric DXA: technique and interpretation

This article reviews dual X-ray absorptiometry (DXA) technique and interpretation with emphasis on the considerations unique to pediatrics. Specifically, the use of DXA in children requires the radiologist to be a “clinical pathologist” monitoring the technical aspects of the DXA acquisition, a “statistician” knowledgeable in the concepts of Z-scores and least significant changes, and a “bone specialist” providing the referring clinician a meaningful context for the numeric result generated by DXA. The patient factors that most significantly influence bone mineral density are discussed and are reviewed with respect to available normative databases. The effects the growing skeleton has on the DXA result are also presented. Most important, the need for the radiologist to be actively involved in the technical and interpretive aspects of DXA is stressed. Finally, the diagnosis of osteoporosis should not be made on DXA results alone but should take into account other patient factors

Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome

BACKGROUND: Cnidarians, including corals and anemones, offer unique insights into metazoan evolution because they harbor genetic similarities with vertebrates beyond that found in model invertebrates and retain genes known only from non-metazoans. Cataloging genes expressed in Acropora palmata, a foundation-species of reefs in the Caribbean and western Atlantic, will advance our understanding of the genetic basis of ecologically important traits in corals and comes at a time when sequencing efforts in other cnidarians allow for multi-species comparisons. RESULTS: A cDNA library from a sample enriched for symbiont free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the assembled sequences. Analysis of the assembled sequences indicated that 83-100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (~18,000-20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals. CONCLUSIONS: Currently available transcriptome data now make comparative studies of the mechanisms underlying coral's evolutionary success possible. Here we identified candidate genes that enable corals to maintain genomic integrity despite considerable exposure to genotoxic stress over long life spans, and showed conservation of important physiological pathways between corals and bilaterians

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

role of next generation sequencing technologies in personalized medicine

Following the completion of the Human Genome Project in 2003, research in oncology has progressively focused on the sequencing of cancer genomes, with the aim of better understanding the genetic basis of oncogenesis and identifying actionable alterations. The development of next-generation-sequencing (NGS) techniques, commercially available since 2006, allowed for a cost- and time-effective sequencing of tumor DNA, leading to a "genomic era" of cancer research and treatment. NGS provided a significant step forward in Personalized Medicine (PM) by enabling the detection of somatic driver mutations, resistance mechanisms, quantification of mutational burden, germline mutations, which settled the foundation of a new approach in cancer care. In this chapter, we discuss the history, available techniques, and applications of NGS in oncology, with a particular referral to the PM approach and the emerging role of the research field of pharmacogenomics