SCNVSim: somatic copy number variation and structure variation simulator

Background

Somatically acquired structure variations (SVs) and copy number variations (CNVs) can induce genetic changes that are directly related to tumor genesis. Somatic SV/CNV detection using next-generation sequencing (NGS) data still faces major challenges introduced by tumor sample characteristics, such as ploidy, heterogeneity, and purity. A simulated cancer genome with known SVs and CNVs can serve as a benchmark for evaluating the performance of existing somatic SV/CNV detection tools and developing new methods.

Results

SCNVSim is a tool for simulating somatic CNVs and structure variations SVs. Other than multiple types of SV and CNV events, the tool is capable of simulating important features related to tumor samples including aneuploidy, heterogeneity and purity.

Conclusions

SCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterozygosity (LOH), and event break points, which is essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies.     

Development changes of cuticular hydrocarbons in Chrysomya rufifacies larvae: potential for determining larval age

Age determination is the basis of determining the postmortem interval using necrophagous fly larvae. To explore the potential of using cuticular hydrocarbons for determining the ages of fly larvae, changes of cuticular hydrocarbons in developing larvae of Chrysomya rufifacies (Macquart) (Diptera: Calliphoridae) were investigated using gas chromatography with flame-ionization detection and gas chromatography-mass spectrometry. This study showed that the larvae produced cuticular hydrocarbons typical of insects. Most of the hydrocarbons identified were alkanes with the carbon chain length of 21-31, plus six kinds of alkenes. The hydrocarbon composition of the larvae correlated with age. The statistical results showed that simple peak ratios of n-C29 divided by another eight selected peaks increased significantly with age; their relationships with age could be modelled using exponential or power functions with R(2) close to or > 0.80. These results suggest that cuticular hydrocarbon composition is a useful indicator for determining the age of larval C. rufifacies, especially for post-feeding larvae, which are difficult to differentiate by morphology.     

A time–frequency approach to estimate critical time intervals in postural control

The critical time interval (CTI) is a parameter that has been used to distinguish open-loop from closed-loop control during upright stance. The aim of this study was to develop a new method to determine CTIs. The new approach, termed the intermittent critical time interval (ICTI) method, was motivated from evidence that upright standing is an intermittent rather than an asymptotic stability control process. For this ICTI method, center-of-pressure time series are first transformed to the time–frequency domain with a wavelet method. Subsequently, the CTI is assumed equal to the time span between two local maxima in the time–frequency domain within a distinct frequency band (i.e., 0.5–1.1 Hz). This new method may help facilitate better estimates of the transition time interval between open and closed-loop control during upright stance and can also be applied in future work such as in simulating postural control. In addition, this method can be used in future work to assess temporal changes in CTIs.