Pairwise comparative analysis of six haplotype assembly methods based on users' experience.

BACKGROUND: A haplotype is a set of DNA variants inherited together from one parent or chromosome. Haplotype information is useful for studying genetic variation and disease association. Haplotype assembly (HA) is a process of obtaining haplotypes using DNA sequencing data. Currently, there are many HA methods with their own strengths and weaknesses. This study focused on comparing six HA methods or algorithms: HapCUT2, MixSIH, PEATH, WhatsHap, SDhaP, and MAtCHap using two NA12878 datasets named hg19 and hg38. The 6 HA algorithms were run on chromosome 10 of these two datasets, each with 3 filtering levels based on sequencing depth (DP1, DP15, and DP30). Their outputs were then compared. RESULT: Run time (CPU time) was compared to assess the efficiency of 6 HA methods. HapCUT2 was the fastest HA for 6 datasets, with run time consistently under 2 min. In addition, WhatsHap was relatively fast, and its run time was 21 min or less for all 6 datasets. The other 4 HA algorithms' run time varied across different datasets and coverage levels. To assess their accuracy, pairwise comparisons were conducted for each pair of the six packages by generating their disagreement rates for both haplotype blocks and Single Nucleotide Variants (SNVs). The authors also compared them using switch distance (error), i.e., the number of positions where two chromosomes of a certain phase must be switched to match with the known haplotype. HapCUT2, PEATH, MixSIH, and MAtCHap generated output files with similar numbers of blocks and SNVs, and they had relatively similar performance. WhatsHap generated a much larger number of SNVs in the hg19 DP1 output, which caused it to have high disagreement percentages with other methods. However, for the hg38 data, WhatsHap had similar performance as the other 4 algorithms, except SDhaP. The comparison analysis showed that SDhaP had a much larger disagreement rate when it was compared with the other algorithms in all 6 datasets. CONCLUSION: The comparative analysis is important because each algorithm is different. The findings of this study provide a deeper understanding of the performance of currently available HA algorithms and useful input for other users.

Using survival prediction techniques to learn consumer-specific reservation price distributions.

A consumer's "reservation price" (RP) is the highest price that s/he is willing to pay for one unit of a specified product or service. It is an essential concept in many applications, including personalized pricing, auction and negotiation. While consumers will not volunteer their RPs, we may be able to predict these values, based on each consumer's specific information, using a model learned from earlier consumer transactions. Here, we view each such (non)transaction as a censored observation, which motivates us to use techniques from survival analysis/prediction, to produce models that can generate a consumer-specific RP distribution, based on features of each new consumer. To validate this framework of RP, we run experiments on realistic data, with four survival prediction methods. These models performed very well (under three different criteria) on the task of estimating consumer-specific RP distributions, which shows that our RP framework can be effective.

Simultaneous analysis of 2Cs, 25-NBOHs, 25-NBOMes and LSD in seized exhibits using liquid chromatography-tandem mass spectrometry: A targeted approach.

Blotter papers laced with lysergic acid diethylamide (LSD) have been abused traditionally for their hallucinogenic properties. In recent years, new psychedelic phenethylamines such as 2,5-dimethoxyphenethylamines (2C) and their N-benzylhydroxy (25-NBOH) and N-2-methoxybenzyl derivatives (25-NBOMe) have emerged in the illicit drugs market. Traditionally, gas chromatography-mass spectrometry (GC-MS) is regarded as the gold standard for illicit drugs analysis. However, with the emergence of new psychoactive substances (NPS) which are thermally labile (such as the 25-NBOH drugs which undergo thermal degradation to their respective 2C drugs), alternative non-thermal techniques have to be developed in order to prevent misidentification. In this study, a single, targeted, non-thermal analytical method using the liquid chromatography-tandem mass spectrometry (LC-MS/MS) to simultaneously identify these new phenethylamines and their derivatives was developed and validated. Twelve phenethylamines and their derivatives, as well as LSD were simultaneously analysed using the LC-MS/MS in a multiple reaction monitoring (MRM) detection mode. The method developed was validated and applied for the analysis of phenethylamines and their derivatives commonly found in seized exhibits such as blotter papers and Ecstasy tablets.