Typing methods based on whole genome sequencing data

Deriving group A Streptococcus typing information from short-read whole-genome sequencing data.

Typing of group A Streptococcus (GAS) is crucial for infection control and epidemiology. While whole-genome sequencing (WGS) is revolutionizing the way that bacterial organisms are typed, it is necessary to provide backward compatibility with currently used typing schemas to facilitate comparisons and understanding of epidemiological trends. Here, we sequenced the genomes of 191 GAS isolates re...

Data quality of Whole Genome Bisulfite Sequencing on Illumina platforms

Pan-PCR, a computational method for designing bacterium-typing assays based on whole-genome sequence data.

With increasing rates of antibiotic resistance, bacterial infections have become more difficult to treat, elevating the importance of surveillance and prevention. Effective surveillance relies on the availability of rapid, cost-effective, and informative typing methods to monitor bacterial isolates. PCR-based typing assays are fast and inexpensive, but their utility is limited by the lack of ta...

Whole genome sequencing based noninvasive prenatal test

NIFTY test by BGI detects trisomies 13, 18, and 21 as well as some sex chromosome aneuploidies and selected microdeletions [3]. Verinata Health, a subsidiary of Illumina offers the Verifi test for detection of trisomies 13, 18, 21, and the presence of monosomy X. The expanded version of this test also detects other aneuploidies and microdeletions [4]. Compared to other NIPT techniques such as t...

Whole-Genome Bisulfite Sequencing

Next-generation sequencing technology has enabled genome-wide analysis of 5mC nucleotides at single-nucleotide resolution. Previous methods for whole-genome bisulfite sequencing (WGBS) yielded reduced genomic representation due to required DNA shearing, ligation of methylated sequencing adapters, and bisulfite conversion of unmethylated cytidine residues prior to sequencing. One disadvantage of...