Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics.

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours.

The genotyping potential of the Mycoplasma synoviae vlhA gene.

Mycoplasma synoviae (MS) continues to cause significant losses to poultry producers, and studying the epizootiology of infection is an important component of MS control. The partial variable lipoprotein hemagglutinin A (vlhA) gene is the only genomic target identified so far for MS sequence typing. The vlhA gene codes for two variable cell surface proteins, lipoprotein and hemagglutinin, and the proposed mechanism for the variation is gene conversion between a single expressed gene and an array of pseudogenes.

Revised Mycoplasma synoviae vlhA PCRs.

Mycoplasma synoviae (MS) is an important pathogen of chickens and turkeys. In recent years sequence analysis of the partial MS variable lipoprotein and hemagglutinin A (vlhA) gene PCR product has been utilized routinely for MS strain genotyping. Several PCR assays have been proposed for the amplification of the conserved upstream region of the MS vlhA gene; however, in several clinical instances the published assays failed to generate vlhA PCR products from confirmed MS-positive cases.

Clonal dissemination of Escherichia coli O157:H7 subtypes among dairy farms in northeast Ohio.

To ascertain the extent to which indistinguishable strains of Escherichia coli O157:H7 are shared between farms, molecular characterization was performed on E. coli O157:H7 isolates recovered during a longitudinal study of 20 dairy farms in northeast Ohio. Of the 20 dairy farms sampled, 16 were located in a primary area and 4 were located in two other distant geographical areas.