UPDG: Utilities package for data analysis of Pooled DNA GWAS

<p>Abstract</p> <p>Background</p> <p>Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS).</p> <p>Results</p> <p>UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.</p> <p>Conclusions</p> <p>UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.</p

Exploiting Sparsity in Automotive Radar Object Detection Networks

Having precise perception of the environment is crucial for ensuring the secure and reliable functioning of autonomous driving systems. Radar object detection networks are one fundamental part of such systems. CNN-based object detectors showed good performance in this context, but they require large compute resources. This paper investigates sparse convolutional object detection networks, which combine powerful grid-based detection with low compute resources. We investigate radar specific challenges and propose sparse kernel point pillars (SKPP) and dual voxel point convolutions (DVPC) as remedies for the grid rendering and sparse backbone architectures. We evaluate our SKPP-DPVCN architecture on nuScenes, which outperforms the baseline by 5.89% and the previous state of the art by 4.19% in Car AP4.0. Moreover, SKPP-DPVCN reduces the average scale error (ASE) by 21.41% over the baseline

Improving Indel Detection Specificity of the Ion Torrent PGM Benchtop Sequencer

10.1371/journal.pone.0045798PLoS ONE79

Technical Development and Clinical Evaluation of Intelligent Continence Management System at Nursing Home

International audienceUrinary incontinence and diaper use is common among elderly people with dementia staying at nursing homes. Delays in timely diaper change will cause personal, social and economic ramifications to those elderly as well as to the carers who provide nursing care. In order to alleviate these daily care issues, an intelligent continence management system leveraging on sensors, pervasive sensor network, ambient intelligence and reminders is designed and developed. Clinical trial is conducted with multiple elderly people with dementia at a nursing home to evaluate the applicability and usefulness of the developed system. The analysis of trial outcomes and usability studies proves that this will be a feasible and effective approach to tackle the problems faced in managing incontinence effectively at nursing home

Ablative efficiency of 532-nm laser vaporization compared to transurethral resection of the prostate: results from a prospective three-dimensional ultrasound volumetry study

Purpose: To assess and compare postoperative prostate volume changes following 532-nm laser vaporization (LV) and transurethral resection of the prostate (TURP). To investigate whether differences in volume reduction are associated with differences in clinical outcome. Methods: In this prospective, non-randomized study, 184 consecutive patients undergoing 120W LV (n=98) or TURP (n=86) were included. Transrectal three-dimensional ultrasound and planimetric volumetry of the prostate were performed preoperatively, after catheter removal, 6weeks, 6 and 12months. Additionally, clinical outcome parameters were recorded. Mann-Whitney U test and analysis of covariance were utilized for statistical analysis. Results: Postoperatively, a significant prostate volume reduction was detectable in both groups. However, the relative volume reduction was lower following LV (18.4 vs. 34.7%, p40ml. Re-operations were necessary in three patients following LV. Conclusions: The modest but significantly lower volume reduction following LV was associated with a lower PSA reduction, a lower Q max and more re-operations. Given the lack of long-term results after LV, our results are helpful for preoperative patient counseling. Patients with large prostates and no clear indication for the laser might not benefit from the procedure

Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at −70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy

Spectrum of Oncogenic Driver Mutations in Lung Adenocarcinomas from East Asian Never Smokers

PURPOSE:We previously showed that 90% (47 of 52; 95% CI, 0.79 to 0.96) of lung adenocarcinomas from East Asian never-smokers harbored well-known oncogenic mutations in just four genes: EGFR, HER2, ALK, and KRAS. Here, we sought to extend these findings to more samples and identify driver alterations in tumors negative for these mutations. EXPERIMENTAL DESIGN:We have collected and analyzed 202 resected lung adenocarcinomas from never smokers seen at Fudan University Shanghai Cancer Center. Since mutations were mutually exclusive in the first 52 examined, we determined the status of EGFR, KRAS, HER2, ALK, and BRAF in stepwise fashion as previously described. Samples negative for mutations in these 5 genes were subsequently examined for known ROS1 fusions by RT-PCR and direct sequencing. RESULTS:152 tumors (75.3%) harbored EGFR mutations, 12 (6%) had HER2 mutations, 10 (5%) had ALK fusions all involving EML4 as the 5' partner, 4 (2%) had KRAS mutations, and 2 (1%) harbored ROS1 fusions. No BRAF mutation were detected. CONCLUSION:The vast majority (176 of 202; 87.1%, 95% CI: 0.82 to 0.91) of lung adenocarcinomas from never smokers harbor mutant kinases sensitive to available TKIs. Interestingly, patients with EGFR mutant patients tend to be older than those without EGFR mutations (58.3 Vs 54.3, P = 0.016) and patient without any known oncogenic driver tend to be diagnosed at a younger age (52.3 Vs 57.9, P = 0.013). Collectively, these data indicate that the majority of never smokers with lung adenocarcinoma could benefit from treatment with a specific tyrosine kinase inhibitor