Massachusetts was one of seven sentinel surveillance sites in the National Tuberculosis Genotyping and Surveillance Network. From 1996 through 2000, isolates from new patients with tuberculosis (TB) underwent genotyping. We describe the impact that genotyping had on public health practice in Massachusetts and some limitations of the technique. Through genotyping, we explored the dynamics of TB ...

Recent developments in sequencing methods have enabled whole genome sequencing of several species and the available sequence information has allowed the development of high throughput genotyping chips. However, these genotyping methods require high quality DNA. The possibility to genotype samples based on DNA from non-invasive sources would permit retrospective genotyping of previously collecte...

Genotyping experiments are widely used in clinical and basic research laboratories to identify associations between genetic variations and normal/abnormal phenotypes. Genotyping assay techniques vary from single genomic regions that are interrogated using PCR reactions to high throughput assays examining genome-wide sequence and structural variation. The resulting genotype data may include mill...

Several statistical methods have been proposed to estimate haplotype frequencies, either based on unrelated individuals or based on families. These estimates may yield insights on population genetics as well as associations between candidate regions and disease of interest. One limitation of the existing methods is that all these methods make the implicit assumption that there are no genotyping...

Genotyping errors are well-known to impact the power and type I error rate in single marker tests of association. Genotyping errors that happen according to the same process in cases and controls are known as non-differential genotyping errors, whereas genotyping errors that occur with different processes in the cases and controls are known as differential genotype errors. For single marker tes...