Assessing the performance of methods for cell clustering from single-cell DNA sequencing data.

BACKGROUND: Many cancer genomes have been known to contain more than one subclone inside one tumor, the phenomenon of which is called intra-tumor heterogeneity (ITH). Characterizing ITH is essential in designing treatment plans, prognosis as well as the study of cancer progression. Single-cell DNA sequencing (scDNAseq) has been proven effective in deciphering ITH. Cells corresponding to each subclone are supposed to carry a unique set of mutations such as single nucleotide variations (SNV). While there have been many studies on the cancer evolutionary tree reconstruction, not many have been proposed that simply characterize the subclonality without tree reconstruction. While tree reconstruction is important in the study of cancer evolutionary history, typically they are computationally expensive in terms of running time and memory consumption due to the huge search space of the tree structure. On the other hand, subclonality characterization of single cells can be converted into a cell clustering problem, the dimension of which is much smaller, and the turnaround time is much shorter. Despite the existence of a few state-of-the-art cell clustering computational tools for scDNAseq, there lacks a comprehensive and objective comparison under different settings. RESULTS: In this paper, we evaluated six state-of-the-art cell clustering tools-SCG, BnpC, SCClone, RobustClone, SCITE and SBMClone-on simulated data sets given a variety of parameter settings and a real data set. We designed a simulator specifically for cell clustering, and compared these methods' performances in terms of their clustering accuracy, specificity and sensitivity and running time. For SBMClone, we specifically designed an ultra-low coverage large data set to evaluate its performance in the face of an extremely high missing rate. CONCLUSION: From the benchmark study, we conclude that BnpC and SCG's clustering accuracy are the highest and comparable to each other. However, BnpC is more advantageous in terms of running time when cell number is high (> 1500). It also has a higher clustering accuracy than SCG when cluster number is high (> 16). SCClone's accuracy in estimating the number of clusters is the highest. RobustClone and SCITE's clustering accuracy are the lowest for all experiments. SCITE tends to over-estimate the cluster number and has a low specificity, whereas RobustClone tends to under-estimate the cluster number and has a much lower sensitivity than other methods. SBMClone produced reasonably good clustering (V-measure > 0.9) when coverage is > = 0.03 and thus is highly recommended for ultra-low coverage large scDNAseq data sets.

Spatio-temporal assessment of water quality of a tropical decaying river in India for drinking purposes and human health risk characterization.

River water pollution and water-related health problems are common issues across the world. The present study aims to examine the Jalangi River's water quality to assess its suitability for drinking purposes and associated human health risks. The 34 water samples were collected from the source to the mouth of Jalangi River in 2022 to depict the spatial dynamics while another 119 water samples (2012-2022) were collected from a secondary source to portray the seasonal dynamics. Results indicate better water quality in the lower reach of the river in the monsoon and post-monsoon seasons. Principal component analysis reveals that K+, NO3-, and total alkalinity (TA) play a dominant role in controlling the water quality of the study region, while, CaCO3, Ca2+, and EC in the pre-monsoon, EC, TDS, Na+, and TA in the monsoon, and EC, TDS and TA in the post-monsoon controlled the water quality. The results of ANOVA reveal that BOD, Ca2+, and CaCO3 concentrations in water have significant spatial dynamics, whereas pH, BOD, DO, Cl-, SO42-, Na+, Mg2+, Ca2+, CaCO3, TDS, TA, and EC have seasonal dynamics (p < 0.05). The water quality index depicts that the Jalangi River's water quality ranged from 6.23 to 140.83, i.e., excellent to unsuitable for drinking purposes. Human health risk analysis shows that 32.35% of water samples have non-carcinogenic health risks for all three groups of people, i.e., adults, children, and infants while only 5.88% of water samples have carcinogenic health risks for adults and children. The gradual decay of the Jalangi River coupled with the disposal of urban and agricultural effluents induces river pollution that calls for substantial attention from the various stakeholders to restore the water quality.