A comparative analysis of current phasing and imputation software.

Whole-genome data has become significantly more accessible over the last two decades. This can largely be attributed to both reduced sequencing costs and imputation models which make it possible to obtain nearly whole-genome data from less expensive genotyping methods, such as microarray chips. Although there are many different approaches to imputation, the Hidden Markov Model (HMM) remains the most widely used. In this study, we compared the latest versions of the most popular HMM-based tools for phasing and imputation: Beagle5.4, Eagle2.4.1, Shapeit4, Impute5 and Minimac4. We benchmarked them on four input datasets with three levels of chip density. We assessed each imputation software on the basis of accuracy, speed and memory usage, and showed how the choice of imputation accuracy metric can result in different interpretations. The highest average concordance rate was achieved by Beagle5.4, followed by Impute5 and Minimac4, using a reference-based approach during phasing and the highest density chip. IQS and R2 metrics revealed that Impute5 and Minimac4 obtained better results for low frequency markers, while Beagle5.4 remained more accurate for common markers (MAF>5%). Computational load as measured by run time was lower for Beagle5.4 than Minimac4 and Impute5, while Minimac4 utilized the least memory of the imputation tools we compared. ShapeIT4, used the least memory of the phasing tools examined with genotype chip data, while Eagle2.4.1 used the least memory phasing WGS data. Finally, we determined the combination of phasing software, imputation software, and reference panel, best suited for different situations and analysis needs and created an automated pipeline that provides a way for users to create customized chips designed to optimize their imputation results.

Spermatogenic Cycle and Steroidogenic Control of Spermatogenesis in Mytilus galloprovincialis Collected in the Bay of Naples.

The aim of the present article was to study the spermatogenic cycle of Mytilus galloprovincialis collected in the Bay of Naples during a whole year and to acquire new insights into the mechanism of control. Knowledge of the Mytilus cycle in this geographic area is of particular interest as, to the best of our knowledge, the male gonad cycle has been hitherto unexplored. Testis organization was evaluated together with the localization of the enzymes 3ß-HSD, 17ß-HSD, and P450-aromatase, which are strictly connected to the synthesis of two key hormones involved in the testis activity: testosterone and 17ß-estradiol. It was demonstrated that: (1) the spermatogenic cycle starts in late Summer-early Fall and continues until early Winter, when the first spawning occurs; after rapid gonad restoration, several spawning events take place until June, when the testis becomes non-active again; (2) in the testis, true Leydig and Sertoli cells are present; (3) during the reproductive period, Sertoli, Leydig, germ, and adipogranular cells (ADGs) are positive to 3ß-HSD and 17ß-HSD, while only germ cells are positive to P450 aromatase; by contrast, during the resting period, only ADGs are positive to 3ß-HSD and 17ß-HSD, and P450-aromatase is no longer recognizable. The presence of a hermaphrodite sample is also described. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:1881-1894, 2017. © 2017 Wiley Periodicals, Inc.