4 research outputs found
The design of a prescriptive approach for Port Master Planning
No full textTechnology, Policy and Managemen
The sequence and analysis of duplication-rich human chromosome 16
No full textHuman chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.Joel Martin, Cliff Han, Laurie A. Gordon, Astrid Terry, Shyam Prabhakar, Xinwei She, Gary Xie, Uffe Hellsten, Yee Man Chan, Michael Altherr, Olivier Couronne, Andrea Aerts, Eva Bajorek, Stacey Black, Heather Blumer, Elbert Branscomb, Nancy C. Brown, William J. Bruno, Judith M. Buckingham, David F. Callen, Connie S. Campbell, Mary L. Campbell, Evelyn W. Campbell, Chenier Caoile, Jean F. Challacombe, Leslie A. Chasteen, Olga Chertkov, Han C. Chi, Mari Christensen, Lynn M. Clark, Judith D. Cohn, Mirian Denys, John C. Detter, Mark Dickson, Mira Dimitrijevic-Bussod, Julio Escobar, Joseph J. Fawcett, Dave Flowers, Dea Fotopulos, Tijana Glavina, Maria Gomez, Eidelyn Gonzales, David Goodstein, Lynne A. Goodwin, Deborah L. Grady, Igor Grigoriev, Matthew Groza, Nancy Hammon, Trevor Hawkins, Lauren Haydu, Carl E. Hildebrand, Wayne Huang, Sanjay Israni, Jamie Jett, Phillip B. Jewett, Kristen Kadner, Heather Kimball, Arthur Kobayashi, Marie-Claude Krawczyk, Tina Leyba, Jonathan L. Longmire, Frederick Lopez, Yunian Lou, Steve Lowry, Thom Ludeman, Chitra F. Manohar, Graham A. Mark, Kimberly L. McMurray, Linda J. Meincke, Jenna Morgan, Robert K. Moyzis, Mark O. Mundt, A. Christine Munk, Richard D. Nandkeshwar, Sam Pitluck, Martin Pollard Paul Predki, Beverly Parson-Quintana, Lucia Ramirez, Sam Rash, James Retterer, Darryl O. Ricke, Donna L. Robinson, Alex Rodriguez, Asaf Salamov, Elizabeth H. Saunders, Duncan Scott, Timothy Shough, Raymond L. Stallings, Malinda Stalvey, Robert D. Sutherland, Roxanne Tapia, Judith G. Tesmer, Nina Thayer, Linda S. Thompson, Hope Tice, David C. Torney, Mary Tran-Gyamfi, Ming Tsai, Levy E. Ulanovsky, Anna Ustaszewska, Nu Vo, P. Scott White, Albert L. Williams, Patricia L. Wills, Jung-Rung Wu, Kevin Wu, Joan Yang, Pieter DeJong, David Bruce, Norman A. Doggett, Larry Deaven, Jeremy Schmutz, Jane Grimwood, Paul Richardson, Daniel S. Rokhsar, Evan E. Eichler, Paul Gilna, Susan M. Lucas, Richard M. Myers, Edward M. Rubin and Len A. Pennacchi
Identification of cancer associated molecular changes in histologically benign vulval disease found in association with vulval squamous cell carcinoma using Fourier transform infrared spectroscopy
No full textThis is the author accepted manuscript. The final version is available from Royal Society of Chemistry via the DOI in this record.This study evaluates the capability of Fourier transform infrared spectroscopy (FTIR-S) in the differentiation of molecular changes in vulval intraepithelial neoplasia (VIN) and lichen sclerosus (LS) found in association with vulval squamous cell carcinoma (SCC), compared with VIN and LS found in isolation. 48 sections of vulval epithelium with features of VIN (n = 24) or LS (n = 24) underwent FTIR-S micro-spectroscopic mapping. Spectra from each section were correlated with the pathological diagnoses and the presence of concurrent SCC. Spectral variance was explored using principal component analysis and a multivariate linear discriminant classification model was developed and validated with leave one sample out cross validation. The discriminant model was able to correctly identify FTIR-S spectra taken from samples of VIN and LS found in association with SCC from those found in isolation with a sensitivity of 82% and specificity of 93% for LS and sensitivity of 75% and specificity of 94% for VIN. The discriminant model was adjusted to maximise sensitivity whilst conceding specificity on a per patient basis and could differentiate LS associated with SCC with a sensitivity of 100% and specificity of 84% and VIN associated with SCC sensitivity of 100% and specificity 58%. In distinguishing VIN and LS found in association with SCC from that found in isolation FTIR-S offers a potential technique for the assessment of molecular changes in the vulva that predispose to the development of SCC. Further study is needed to assess the ability of FTIR-S to risk stratify patients with VIN or LS.We acknowledge the British Society for the Study of Vulval Disease and the Gloucestershire Hospitals NHS Foundation Trust Research and Innovation Forum for financial support. We thank Jo Motte and the team at the Gloucestershire Hospitals NHS Foundation Trust histopathology department for the preparation of the tissue sections. The study was supported by the NIHR Exeter Clinical Research Facility. The interpretations of data in the paper are those of the authors and not of NIHR or the Department of Health
Raman spectroscopy and multivariate analysis for the non invasive diagnosis of clinically inconclusive vulval lichen sclerosus.
No full textPublished onlineJournal ArticleThis is the author accepted manuscript. The final version is available from Royal Society of Chemistry via the DOI in this record.Vulval lichen sclerosus (LS) is a common inflammatory condition associated with an increased risk of developing vulval carcinoma. Diagnosis is usually clinical although biopsy is necessary if the diagnosis is uncertain or if there is a failure to respond to adequate initial treatment. Raman spectroscopy has the potential to be applied in vivo for near real time objective non-invasive optical diagnosis, avoiding the need for invasive tissue biopsies. The aim of this study was to evaluate the diagnostic performance of Raman spectroscopy for differentiating LS from other vulval conditions in fresh vulval biopsies. Biopsies were analysed from 27 women with suspected LS in whom the attending gynaecologist could not establish the diagnosis on clinical presentation alone. Spectral variance was explored using principal component analysis and in conjunction with the histological diagnoses was used to develop and test a multivariate linear discriminant classification model. This model was validated with leave one sample out cross validation and the diagnostic performance of the technique assessed in comparison with the pathology gold standard. After cross validation the technique was able to correctly differentiate LS from other inflammatory vulval conditions with a sensitivity of 91% and specificity of 80%. This study demonstrates Raman spectroscopy has potential as a technique for in vivo non-invasive diagnosis of vulval skin conditions. Applied in the clinical setting this technique may reduce the need for invasive tissue biopsy. Further in vivo study is needed to assess the ability of Raman spectroscopy to diagnose other vulval conditions before clinical application.We acknowledge the British Society for the Study of Vulval Disease and the Gloucestershire Hospitals NHS Foundation Trust Research and Innovation Forum for financial support. We thank Jo Motte and the team at the Gloucestershire Hospitals NHS Foundation Trust histopathology department for the preparation of the tissue sections. The study was supported by the NIHR Exeter Clinical Research Facility. The interpretations of data in the paper are those of the authors and not of NIHR or the Department of Health
