Showing papers by "Andy G. Lynch published in 2009"
TL;DR: The proposed statistical algorithm, BayesPeak, uses a fully Bayesian hidden Markov model to detect enriched locations in the genome and is shown to provide high-confidence calls with low false positive rates.
Abstract: Background
High-throughput sequencing technology has become popular and widely used to study protein and DNA interactions. Chromatin immunoprecipitation, followed by sequencing of the resulting samples, produces large amounts of data that can be used to map genomic features such as transcription factor binding sites and histone modifications.
152 citations
TL;DR: A systematic comparison of data from four leading microarray technologies is described, indicating a generally high level of concordance between platforms, despite differences in the reproducibility, noise, and sensitivity.
Abstract: The accurate and high resolution mapping of DNA copy number aberrations has become an important tool by which to gain insight into the mechanisms of tumourigenesis. There are various commercially available platforms for such studies, but there remains no general consensus as to the optimal platform. There have been several previous platform comparison studies, but they have either described older technologies, used less-complex samples, or have not addressed the issue of the inherent biases in such comparisons. Here we describe a systematic comparison of data from four leading microarray technologies (the Affymetrix Genome-wide SNP 5.0 array, Agilent High-Density CGH Human 244A array, Illumina HumanCNV370-Duo DNA Analysis BeadChip, and the Nimblegen 385 K oligonucleotide array). We compare samples derived from primary breast tumours and their corresponding matched normals, well-established cancer cell lines, and HapMap individuals. By careful consideration and avoidance of potential sources of bias, we aim to provide a fair assessment of platform performance.
109 citations
TL;DR: The various common adaptations of the GoldenGate platform are reviewed, the analysis methods that are associated with each adaptation are reviewed and with the aid of a number of example data sets some of the improvements that can be made over the default analysis are illustrated.
Abstract: Illumina's GoldenGate technology is a two-channel microarray platform that allows for the simultaneous interrogation of about 1,500 locations in the genome. GoldenGate has proved a flexible platform not only in the choice of those 1,500 locations, but also in the choice of the property being measured at them. It retains the desirable properties of Illumina's BeadArrays in that the probes (in this case 'beads') are randomly arranged across the microarray, there are multiple instances of each probe and many samples can be processed simultaneously. As for other Illumina technologies, however, these properties are not exploited as they might be. Here we review the various common adaptations of the GoldenGate platform, review the analysis methods that are associated with each adaptation and then, with the aid of a number of example data sets we illustrate some of the improvements that can be made over the default analysis.
19 citations
TL;DR: The R&B classification provides a helpful guide to treatment in many cases of IBS, and results were significantly better in subgroups 1 and 2 than in those unclassified, even when allowance was made for a potential therapeutic placebo effect of 40%.
Abstract: Objective. The treatment of irritable bowel syndrome (IBS) remains unsatisfactory. There are no objective markers for diagnosis, and classification (currently based on symptoms) provides little insight into potential causes or optimal therapy. The aim of this study was to determine whether a Swedish classification of IBS based on cluster analysis of patients’ symptoms might provide a guide to successful treatment. Material and methods. Patients in a research clinic for IBS were classified according to criteria published by Ragnarsson & Bodemar (R&B) and also assessed independently by a clinician. Patients fulfilling the R&B criteria for subgroups 1 and 2 received specific treatments, either bulk laxatives or dietary treatment to reduce colonic fermentation, respectively. Patients who did not fit into these categories were given “best treatment” targeted at their predominant symptoms, but not limited in any way. Results before and after follow-up were assessed using a validated symptom-scoring scale. Resul...
9 citations