Validation of high throughput sequencing and microbial forensics applications

SnapShot: High-Throughput Sequencing Applications

Applications of High Throughput Nucleotide Sequencing

Background: Nonsense-mediated mRNA decay (NMD) affects the outcome of alternative splicing by degrading mRNA isoforms with premature termination codons. Splicing regulators constitute important NMD targets; however, the extent to which loss of NMD causes extensive deregulation of alternative splicing has not previously been assayed in a global, unbiased manner. Here, we combine mouse genetics a...

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications

SUMMARY VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic ge...

Microbial forensics: next-generation sequencing as catalyst

W hen Antonie van Leeuwenhoek experimented with his microscopes in the late 17 century, he observed, among many other small things, bacteria from the mouth cavity. van Leeuwenhoek’s detailed descriptions of bacteria, spermatozoa, and cells marked the beginning of microbiology; his successors Robert Koch and Louis Pasteur stoked further interest in the microbial world with their discoveries of t...

Applications of high-throughput DNA sequencing to benign hematology.

The development of novel technologies for high-throughput DNA sequencing is having a major impact on our ability to measure and define normal and pathologic variation in humans. This review discusses advances in DNA sequencing that have been applied to benign hematologic disorders, including those affecting the red blood cell, the neutrophil, and other white blood cell lineages. Relevant exampl...