A novel tool for individual haplotype inference using mixed data

Background

In many studies, researchers may recruit samples consisting of independent trios and unrelated individuals. However, most of the currently available haplotype inference methods do not cope well with these kinds of mixed data sets.

Methods

We propose a general and simple methodology using a mixture of weighted multinomial (MIXMUL) approach that combines separate haplotype information from unrelated individuals and independent trios for haplotype inference to the individual level.

Results

The new MIXMUL procedure improves over existing methods in that it can accurately estimate haplotype frequencies from mixed data sets and output probable haplotype pairs in optimized reconstruction outcomes for all subjects that have contributed to estimation. Simulation results showed that this new MIXMUL procedure competes well with the EM-based method, i.e. FAMHAP, under a few assumed scenarios.

Conclusion

The results showed that MIXMUL can provide accurate estimates similar to those haplotype frequencies obtained from FAMHAP and output the probable haplotype pairs in the most optimal reconstruction outcome for all subjects that have contributed to estimation. If available data consist of combinations of unrelated individuals and independent trios, the MIXMUL procedure can be used to estimate the haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.     

A Randomized Controlled Trial: Efficacy and Safety of Azithromycin,Ofloxacin, Bismuth,and Omeprazole Compared With Amoxicillin,Clarithromycin, Bismuth,and Omeprazole as Second‐Line Therapy in Patients With Helicobacter pylori Infection

Background: Helicobacter pylori infection of the stomach is widespread among human populations and is considered to play a major role in the pathogenesis of various diseases such as peptic ulcer, adenocarcinoma, and mucosa associated lymphoid tissue (MALT) lymphoma of the stomach. To increase H. pylori eradication rate without increasing bacterial resistance, various regimens have been recommended. Commonly the association of at least two antibiotics with a proton‐pump inhibitor is used. The treatment regimens for second‐line therapy, suggested in studies from the western world may not be ideal in Iran. Aim: In this study, we evaluated the safety and efficacy of a new quadruple therapy regimen and compared it with the standard second‐line treatment for H. pylori eradication. Methods: We selected 220 H. pylori positive patients, with a clear indication of eradication therapy, who did not respond to a 2 weeks treatment with metronidazole, amoxicillin, omeprazole, and bismuth. They were randomized into two groups. Group A (n = 110) were treated with azithromycin, ofloxacin, bismuth, and omeprazole and group B (n = 110) with amoxicillin, clarithromycin, bismuth, and omeprazole for 2 weeks. Four weeks after the end of treatment, urea breath test was performed for all subjects to confirm eradication. Results: In intention‐to‐treat analysis, the rate of H. pylori eradication in groups A and B was 77.3% (85/110) and 64.5% (71/110) respectively (p = .027). In per‐protocol analysis, the rate of H. pylori eradication in groups A and B was 86.7 and 74.7%, respectively (p = .026). The incidence of poor compliance was lower, although not significantly so, in group A than group B (3.5 vs 4.3%). No major adverse events occurred in both groups. Conclusion: Two weeks of treatment with ofloxacin, azithromycin, omeprazole, and bismuth is an effective and safe regimen for H. pylori eradication as second‐line therapy.     

Ecological cues, gestation length, and birth timing in African buffalo (Syncerus caffer)

We examined annual variation in the timing of conception andparturition in the African buffalo (Syncerus caffer) and thesynchrony of birth timing with resource cues, using 8 yearsof monthly birth, rainfall, and vegetation data, measured asNormalized Difference Vegetation Index (NDVI). Monthly birthshad the strongest significant correlations with NDVI and rainfalllevels 12 and 13 months in the past, respectively. In addition,the synchrony of current year births corresponds most stronglyto the synchrony of the previous year's NDVI distribution. Becausethe gestation period of buffalo has been estimated to be around11 months, these findings suggest that improved protein levels,occurring approximately a month after the first green flushof the wet season, are either a trigger for conception or conceptionhas evolved to be synchronous with correlated environmentalcues that ensure females enter a period of peak body conditionaround the time of conception and/or parturition. With a gestationperiod of approximately 340 days, parturition occurs to takeadvantage of the period when forage has its highest proteincontent. A comparative analysis of gestation periods withinthe subfamily Bovinae indicates that African buffalo have aprotracted gestation for their body size, which we suggest isan adaptation to their seasonal environment. We also found thatinterannual variation in the birth distribution suggests a degreeof plasticity in the date of conception, and variation in thenumber of calves born each year suggest further synchrony ata timescale longer than a single year.