Design and implementation of a generalized laboratory data model

Background

Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable.

Results

We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions.

Conclusion

The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.

Multisite pooling study using ligase chain reaction in screening for genital Chlamydia trachomatis infections

BACKGROUND

Ligase chain reaction (LCR), a nucleic acid amplification assay, is a highly specific and sensitive test for detecting Chlamydia trachomatis in cervical and urethral swabs as well as first-void urine specimens.

GOAL

To examine the suitability of using the LCR test to detect C trachomatis in pooled cervical specimens.

STUDY DESIGN

The performance of LCR in pooled specimens was compared with individual specimen testing at six laboratories using 3,170 cervical swab specimens randomly selected from specimens received for routine testing in the participating laboratories. These samples then were combined consecutively into 634 pools of 5 specimens and 317 pools of 10 specimens. A reduced sample to cutoff ratio of 0.2 or more was used for the pooled specimens.

RESULTS

Of the 188 positive specimens (98.9%), 186 were identified when single specimens were analyzed. When pools of 5 or 10 specimens were evaluated, 99.5% and 98.9% of the positive swabs, respectively, were identified correctly. Two positive specimens were detected only through pooling.

CONCLUSIONS

Pooling samples for detection of C trachomatis by LCR is sensitive and specific. Depending on the prevalence of infection (positivity), LCR testing may result in cost savings, as compared with individual testing of specimens.

New selective medium for the isolation of Neisseria gonorrhoeae

GC-Lect, a new selective medium for the isolation of Neisseria gonorrhoeae which contains five antimicrobial agents, was evaluated with stock cultures and with 500 clinical specimens. With stock cultures, vancomycin-resistant Staphylococcus epidermidis that grew on modified Thayer-Martin medium (MTM) was inhibited on the new medium. Also, vancomycin-susceptible strains of N. gonorrhoeae were much less inhibited on the new medium than on Martin-Lewis agar or MTM. With oropharyngeal cultures of healthy volunteers, Capnocytophaga species were frequently isolated on MTM from two of three manufacturers but were completely inhibited on GC-Lect. In the clinical study, visible growth of N. gonorrhoeae occurred within 24 h in 72% of the positive cultures on GC-Lect, compared with only 52% on the reference medium. A total of 50 positive cultures were obtained with GC-Lect, compared with 49 obtained with MTM. The selectivity of GC-Lect was superior, with only 19 cultures producing growth of normal flora, compared with 78 cultures on MTM after 24 h of incubation. The selectivity was especially improved on GC-Lect with regard to yeasts (2 versus 30 cultures) and gram-positive cocci (5 versus 31 cultures).