Distortion-free PCA on sample space for highly variable gene detection from single-cell RNA-seq data

Single-cell RNA-seq (scRNA-seq) allows the analysis of gene expression in each cell, which enables the detection of highly variable genes (HVG) that contribute to cell-to-cell variation within a homogeneous cell population. HVG detection is necessary for clustering analysis to improve the clustering result. scRNA-seq includes some genes that are expressed with a certain probability in all cells which make the cells indistinguishable. These genes are referred to as background noise. To remove the background noise and select the informative genes for clustering analysis, in this paper, we propose an effective HVG detection method based on principal component analysis (PCA). The proposed method utilizes PCA to evaluate the genes (features) on the sample space. The distortion-free principal components are selected to calculate the distance from the origin to gene as the weight of each gene. The genes that have the greatest distances to the origin are selected for clustering analysis. Experimental results on both synthetic and gene expression datasets show that the proposed method not only removes the background noise to select the informative genes for clustering analysis, but also outperforms the existing HVG detection methods.

SIEVE: identifying robust single cell variable genes for single-cell RNA sequencing data

Single-cell RNA-seq data analysis generally requires quality control,normalization,highly variable genes screening,dimensionality reduction and clustering.Among these processes,downstream analysis including dimensionality reduction and clustering are sensitive to the selection of highly variable genes.Though increasing number of tools for selecting the highly variable genes have been developed,an evaluation of theirperformances and a general strategy are lack.Here,wecompare the performance of nine commonly usedmethods for screening variable genes by using single-cell RNA-seq data from hematopoietic stem/progenitor cells and mature blood cells,and find that SCHS outperforms other methods regarding to reproducibility and accuracy.However,this method prefers the selection of highly expressed genes.We further propose a new strategy SIEVE(SIngle-cEll Variable gEnes)bymultiple rounds of randomsampling,therefore minimizing the stochastic noise and identifying a robust set of variable genes.Moreover,SIEVE recovers lowly expressed genes as variable genes and substantially improves the accuracy of single cell classification,especially for the methods with lower reproducibility.The SIEVE software is freely available at https://github.com/YinanZhang522/SIEVE.

CLONING AND SEQUENCING OF IMMUNOGLOBULINVARIABLE－REGION GENE OF A MONOCLONALANTIBODY SPECIFIC FOR HUMANHEPATOCARCINOMA

A murine monoclonal antibody HAb27 specific for human hepatocarcinoma has been developed for radioimmunolocalization in animal models. The isotype of this antibody was IgGl, k. In the present study, we used a set of oligonucleotide primers to amplify the cDNA of mouse immunoglobulin heavy and light chain variable region genes by the polymerase chain reaction. Sequence analysis of the heavy variable region indicated that the VH region was highly homologous to the plasmacytoma cell line MOPC21 gene, and closely related to germline genes of the VHⅢ family. The JH region was encoded by the JH3 gene. For the light chain, the VK segment of the antibody showed the highest homology to the germline VKOXl gene,and the JK region was JK5.

Associations between IL-1RN variable number of tandem repeat, IL-1β (-511) and IL-1β (+3954) gene polymorphisms and urolithiasis in Uighur children of China

Objective:Interleukin-1(IL-1)is a pro-inflammatory cytokine which may be related to urolithiasis.Genetic polymorphisms of the interleukin-1beta(IL-1β)have been proposed as markers for urolithiasis in some areas.Due to the high incidence of urolithiasis in Uighur children(Xinjiang,China)and existence of ethnic difference,our aim is to explore the potential of IL-1 gene polymorphisms and urolithiasis among these children.Methods:Genomic DNA extracted from peripheral blood of 115 patients and 98 controls were used for genotype polymorphisms analyses.IL-1 receptor antagonist(IL-1RN)gene variable number of tandem repeat(VNTR)gene polymorphisms were analyzed by PCR method.PCR-based restriction analysis was done for the IL-1β(-511)and IL-1β(+3954)gene polymorphisms by endonucleases Ava I and Taq I,respectively.The genotype distribution,allele frequencies,carriage rate,and haplotype frequencies were statistically analyzed.Results:No significant differences were observed in genotypic frequencies between pediatric urolithiasis patients and control group for IL-1RN gene(χ^(2)=1.906,p=0.605),IL-1β(-511)gene(χ^(2)=0.105,p=0.949),or IL-1β(+3954)gene(χ^(2)=3.635,p=0.169).There were yet no significant differences of the allele frequencies of IL-1RN VNTR gene(p=0.779),IL-1β(-511)gene(p=0.941),and IL-1β(+3954)gene(p=0.418)in the case and control groups,as well as the carriage rate and haplotype of them(all p>0.05).Conclusions:The associations between IL-1RN VNTR,IL-1β(-511)and IL-1β(+3954)genes polymorphisms and urolithiasis were not significant in Uighur children.The results need to be confirmed in studies with larger population sample size,as well as in other ethnic groups.

Cloning, sequencing and analyzing of the heavy chain V region genes of human polyreactive antibodies

The heavy chain variable region genes of 5 human polyreactive mAbs generated in our laboratory have been cloned and sequenced using polymerase chain reaction (PCR) technique. We found that 2 and 3 mAbs utilized genes of the VHIV and VHIII families, respectively. The former 2 VH segments were in germline configuration. A common VH segment, with the best similarity of 90.1 % to the published VHIII germline genes, was utilized by 2 different rearranged genes encoding the V regions of other 3 mAbs. This strongly suggests that the common VH segment is a unmutated copy of an unidentified germline VHIII gene. All these polyreactive mAbs displayed a large NDN region (VH-D-JH junction). The entire H chain V regions of these polyreactive mAbs are unusually basic. The analysis of the charge properties of these mAbs as well as those of other poly- and mono- reactive mAbs from literatures prompts us to propose that the charged amino acids with a particular distribution along the H chain V region,especially the binding sites (CDRs), may be an important structural feature involved in antibody polyreactivity.