Informatics and data analysis - McMahon - MEWE 2013

Daniel Thewlis is developing PCR software to optimize and accelerate the polymerase chain reaction (PCR) DNA analysis market, which is currently a $6 billion industry. His software aims to reduce PCR processing time by 50% through features that streamline workflows, improve connectivity and automation, and ensure data security and integrity. The development plan includes launching a digital test tube platform, designing a software engine, building a beta model, and proceeding to commercialization in August 2016 after pilot and refinement phases.

The document provides an overview of handling 16S rRNA gene sequencing data, including typical workflows from sampling through bioinformatics analysis. It discusses sampling considerations, sequencing and sample preparation methods like PCR and Illumina sequencing. Key steps in bioinformatics analysis are clustering sequences into OTUs, assigning taxonomy by comparing to reference databases, and generating OTU tables to analyze microbial community composition across samples. Hands-on exercises are included for analyzing data in Excel and R.

El documento presenta información sobre 10 personas, incluyendo su nombre, ocupación, lugar de residencia y gustos. Más tarde, se añaden 3 personas más y se hacen preguntas sobre los detalles presentados para evaluar la memoria del lector.

High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses.

Molecular cloning can be sometimes tricky with significant challenges involved. Overcome the challenges with the essential knowledge and tips for successful cloning.

Pyrosequencing is a highly flexible technology that lets you rapidly analyze short- to medium-length sequences fast and quantitatively with high accuracy. The real-time, high-resolution sequence output makes the technology highly suitable for applications including complex mutation analysis, microbial identification and DNA methylation quantification. The main bottleneck in Pyrosequencing has been limited sequence length, which is critical for some applications. Our new technology, software, and chemistry overcome this bottleneck and give sequence reads that are typically twice as long as those from previous PyroMark systems. The new PyroMark Q24 Advanced system also reduces background noise, improving quantification even at sites distant from the sequencing start. The new system is ideal for applications requiring analysis of longer sequences, such as DNA methylation analysis in epigenetic research, frequency determination in mutation analysis, and various de novo sequencing applications. In this presentation, we will discuss the following applications and technology improvements: • DNA methylation analysis at single base resolution at CpG and CpN sites • Improved quantification of sequence variations at any sequence position • Easy and improved base calling functionality

This document discusses the use of 16S ribosomal RNA (rRNA) gene sequencing for bacterial identification and phylogenetic analysis. It explains that the 16S rRNA gene is highly conserved, making it useful for comparing distantly related organisms. The document outlines the process of 16S rRNA gene sequencing, including PCR amplification using conserved primer regions and sequencing of variable regions. It also discusses various methods that have been developed using 16S rRNA, such as TRFLP profiling and ribotyping, to study microbial communities.

Microbiome research is undergoing a crisis due to issues like the correlation-causation fallacy in studies and poor experimental design. The document discusses challenges with studying the microbiome, including biases and errors introduced from DNA extraction methods, sample storage conditions, and contamination from extraction kits. It emphasizes that every step in microbiome research, from sample collection to analysis, needs careful consideration to draw accurate conclusions.

High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.

Fusion genes are hybrid genes formed by the fusion of two separate genes. Translocation, interstitial deletion and chromosomal inversions are some of the genetic events that can lead to the formation of fusion genes. The occurrence of fusion genes and its implications in cancer have already been known, but the emergence of NGS technology – especially RNA sequencing – offers the potential to detect novel gene fusions. You can learn more about fusion genes and applying NGS to detect them at our upcoming webinar, presented by Raed Samara, Ph.D., QIAGEN’s Global Product Manager for NGS technologies. In this webinar, Dr. Raed Samara will cover: 1. Fusion genes: what they are and a historical perspective 2. Fusion gene detection: the current status 3. RNA sequencing vs. digital RNA sequencing 4. How to detect and accurately quantify novel fusion genes in your sample

With technological breakthroughs in single cell isolation, whole genome amplification (WGA) and NGS library preparation, experiments using single cells are now possible. However, challenges still exist. In particular, methods for the unbiased and complete amplification of a single genome and for the efficient conversion of that amplified DNA into a sequencer-compatible library face several technical limitations including incomplete amplification, the introduction of PCR errors, GC-bias and locus or allelic drop-out. The presentation covers the impact of these factors and how one can mitigate it.

1) The document discusses different whole genome amplification techniques for obtaining DNA from single cells, including PCR-based and PCR-free methods. 2) It provides comparisons of different whole genome amplification kits, finding that QIAGEN's REPLI-g Single Cell Kit has the highest genome coverage, lowest duplication rates, and best performance for detecting copy number variations and single nucleotide variations, making it optimal for single cell sequencing applications. 3) Case studies demonstrate that the REPLI-g Single Cell Kit provides more uniform coverage and significantly fewer sequencing errors compared to the MALBAC method.

Part 5 of the training sesson 'RNA-seq for differential expression analysis' considers the algorithm used for detecting differential expression between conditions. See http://www.bits.vib.be

In this slide deck, learn about the innovative technologies that form the basis of QIAGEN’s portfolio of QIAseq library prep solutions for metagenomics and microbiome sequencing. Whether your research starts from single microbial cells, 16s rRNA PCR amplicons, or gDNA for whole genome analysis, QIAseq technologies offer tips and tricks for capturing the genomic diversity of your samples in the most unbiased, streamlined way possible.

This talk, aimed at librarians, describes the data management issues surrounding paper and electronic lab notebooks. It offers several ways for librarians to support good practices and the transition from paper to electronic.