ABSTRACT
MicroRNA (miRNA) serves as a pivotal regulator of numerous cellular processes, and the identification of miRNA-disease associations (MDAs) is crucial for comprehending complex diseases. Recently, graph neural networks (GNN) have made significant advancements in MDA prediction. However, these methods tend to learn one type of node representation from a single heterogeneous network, ignoring the importance of multiple network topologies and node attributes. Here, we propose SMDAP (Sequence hierarchical modeling-based Mirna-Disease Association Prediction framework), a novel GNN-based framework that incorporates multiple network topologies and various node attributes including miRNA seed and full-length sequences to predict potential MDAs. Specifically, SMDAP consists of two types of MDA representation: following a heterogeneous pattern, we construct a transfer learning-like synchronous mutual learning network to learn the first MDA representation in conjunction with the miRNA seed sequence. Meanwhile, following a homogeneous pattern, we design a subgraph-inspired asynchronous multi-scale embedding network to obtain the second MDA representation based on the miRNA full-length sequence. Subsequently, an adaptive fusion approach is designed to combine the two branches such that we can score the MDAs by the downstream classifier and infer novel MDAs. Comprehensive experiments demonstrate that SMDAP integrates the advantages of multiple network topologies and node attributes into two branch representations. Moreover, the area under the receiver operating characteristic curve is 0.9622 on DB1, which is a 5.06% increase from the baselines. The area under the precision-recall curve is 0.9777, which is a 7.33% increase from the baselines. In addition, case studies on three human cancers validated the predictive performance of SMDAP. Overall, SMDAP represents a powerful tool for MDA prediction.
Subject(s)
MicroRNAs , Neural Networks, Computer , MicroRNAs/genetics , Humans , Algorithms , Computational Biology/methodsABSTRACT
Recent studies have shed light on the potential of circular RNA (circRNA) as a biomarker for disease diagnosis and as a nucleic acid vaccine. The exploration of these functionalities requires correct circRNA full-length sequences; however, existing assembly tools can only correctly assemble some circRNAs, and their performance can be further improved. Here, we introduce a novel feature known as the junction contig (JC), which is an extension of the back-splice junction (BSJ). Leveraging the strengths of both BSJ and JC, we present a novel method called JCcirc (https://github.com/cbbzhang/JCcirc). It enables efficient reconstruction of all types of circRNA full-length sequences and their alternative isoforms using splice graphs and fragment coverage. Our findings demonstrate the superiority of JCcirc over existing methods on human simulation datasets, and its average F1 score surpasses CircAST by 0.40 and outperforms both CIRI-full and circRNAfull by 0.13. For circRNAs below 400 bp, 400-800 bp, 800 bp-1200 bp and above 1200 bp, the correct assembly rates are 0.13, 0.09, 0.04 and 0.03 higher, respectively, than those achieved by existing methods. Moreover, JCcirc also outperforms existing assembly tools on other five model species datasets and real sequencing datasets. These results show that JCcirc is a robust tool for accurately assembling circRNA full-length sequences, laying the foundation for the functional analysis of circRNAs.
Subject(s)
RNA, Circular , RNA , Humans , RNA, Circular/genetics , Sequence Analysis, RNA/methods , Protein Isoforms/genetics , RNA/geneticsABSTRACT
One nucleotide substitution in codon 116 of HLA-B*40:06:01:12 results in a novel allele, HLA-B*40:537.
Subject(s)
East Asian People , HLA-B Antigens , Humans , Alleles , High-Throughput Nucleotide Sequencing , Histocompatibility Testing , HLA-B Antigens/genetics , Sequence Analysis, DNAABSTRACT
One nucleotide change (G > C) in intron 1 of HLA-C*12:02:02:01 results in novel HLA allele HLA-C*12:02:02:22.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , Introns , India , High-Throughput Nucleotide SequencingABSTRACT
Circular RNAs (circRNAs) are RNA molecules formed by joining a downstream 3 splice donor site and an upstream 5 splice acceptor site. Several recent studies have identified circRNAs as potential biomarker for different diseases. A number of methods are available for the identification of circRNAs. The circRNA identification methods cannot provide full-length sequences. Reconstruction of the full-length sequences is crucial for the downstream analyses of circRNA research including differential expression analysis, circRNA-miRNA interaction analysis and other functional studies of the circRNAs. However, a limited number of methods are available in the literature for the reconstruction of full-length circRNA sequences. We developed a new method, circRNA-full, for full-length circRNA sequence reconstruction utilizing chimeric alignment information from the STAR aligner. To evaluate our method, we used full-length circRNA sequences produced by isocirc and ciri-long using long-reads RNA-seq data. Our method achieved better reconstruction rate, precision, sensitivity and F1 score than the existing full-length circRNA sequence reconstruction tool ciri-full for both human and mouse data.
Subject(s)
RNA Splice Sites , RNA, Circular , Animals , Mice , RNA/genetics , RNA/metabolism , RNA, Circular/genetics , RNA-SeqABSTRACT
Next generation sequencing based HLA typing has led to the identification of a novel allele HLA-B*44:256. The novel allele HLA-B*44:256 differs from B*44:02:01:01 by eight nucleotides in exon 3.
Subject(s)
HLA-B Antigens , High-Throughput Nucleotide Sequencing , Alleles , Exons/genetics , HLA-B Antigens/genetics , Humans , IndiaABSTRACT
BACKGROUND: As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored. RESULTS: We develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data and randomly select one 149 bp read as a model. Specific reverse transcription primers are designed to amplify its both ends, followed by next generation sequencing. Then we design a statistical model based on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1556 bp, with insertion mutations in microsatellite structure. CONCLUSION: We believe this method would be a useful strategy to extract the sequences information from the unmapped RNA-seq data. Further, it is an alternative way to get the full length sequence of unknown cDNA.
Subject(s)
High-Throughput Nucleotide Sequencing , DNA, Complementary , RNA-Seq , Sequence Analysis, RNA , Exome SequencingABSTRACT
The mitochondrial genome of the Disckless-fingered Odorous Frog, Odorrana grahami (Anura: Ranidae), was sequenced using high-throughput sequencing technology. The genome length was 17864 bp, including 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 1 control region (D-loop). The AT content of the mitochondrial genome was 55.9%. The composition of mitochondrial genome of O. grahami is similar to that of other species of the genus Odorrana. Phylogenetic analysis of the mitochondrial genomes of six congeners shows that O. grahami is sister to O. margaretae, but the analysis using 16S rRNA gene of additional congeners do not resolve their relationships.
ABSTRACT
C*08:190 differs from C*08:01:01:01 by one nucleotide change at nucleotide 503 in exon 3 from A to G.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Alleles , Cloning, Molecular , HLA-C Antigens/genetics , Humans , Sequence Analysis, DNAABSTRACT
In this study, zoonotic Anisakis simplex was isolated and identified from the outermost layer of the stomach of diseased Anoplopoma fimbria at an industrial farm in Liaoning, North China (122.1842 E, 39.2616 N). With the completion of A. simplex mitochondrial genome sequencing, the full-length mitochondrial genome of A. simplex was assembled and analyzed. All results indicate that the complete mitochondrial genome of A. simplex was 13,899 bp. There were 20 tRNAs and 12 protein-coding genes (PCGs), and two rRNA all located at the heavy (H) strand. Besides, the phylogenetic tree of 19 A. simplex isolated from different host species was constructed. The results showed that A. simplex isolated from A. fimbria was clustered with Oncorhynchus nerka isolate in a clade. To sum up, our research results would further provide essential data for systematics and evolution study of A. simplex.
ABSTRACT
Confirmed the full-length sequence of HLA-C*03:40:01 by cloning and sequencing in a Chinese donor.
Subject(s)
Alleles , HLA-C Antigens/genetics , Base Sequence , Exons/genetics , Humans , Introns/geneticsABSTRACT
Confirmed the full-length sequence of HLA-C*03:02:01 by cloning and sequencing in a Chinese donor.
Subject(s)
Alleles , HLA-C Antigens/genetics , Base Sequence , Humans , Introns/geneticsABSTRACT
Confirmed the full-length sequence of HLA-C*15:13:01:01 by cloning and sequencing in a Chinese donor.
Subject(s)
HLA-C Antigens/genetics , Base Sequence , Exons/genetics , Humans , Sequence Analysis, DNAABSTRACT
The fulllength sequence of HLAB*59:01:01:01.
Subject(s)
HLA-B Antigens/genetics , Sequence Analysis, DNA , Alleles , Asian People/genetics , Base Sequence , Cloning, Molecular , HumansABSTRACT
Confirmed the full-length sequence of HLA-B*44:03:02 by cloning and sequencing in a Chinese donor.
Subject(s)
Cloning, Molecular , HLA-B44 Antigen/genetics , Sequence Analysis, DNA , HumansABSTRACT
Full-length sequences of HLA-B*48:03:01 and B*48:04:01, confirmed by cloning and sequencing in Chinese donors.
Subject(s)
Cloning, Molecular , HLA-B Antigens/genetics , Sequence Analysis, DNA , Asian People , HumansABSTRACT
Full-length sequences of HLA-B*40:01:01, B*40:03 and B*40:40, confirmed by cloning and sequencing in Chinese donors.
Subject(s)
Alleles , Exons , HLA-B40 Antigen/genetics , Polymorphism, Genetic , Tissue Donors , Asian People , Base Sequence , Cloning, Molecular , Codon/chemistry , Gene Expression , HLA-B40 Antigen/immunology , Hematopoietic Stem Cell Transplantation , Histocompatibility Testing , Humans , Introns , Polymerase Chain Reaction , Sequence Alignment , Sequence Analysis, DNAABSTRACT
Full-length sequences of HLA -B*27:04:01, B*27:07:01 and B*27:25, confirmed by cloning and sequencing in Chinese donors.
Subject(s)
Alleles , Exons , HLA-B27 Antigen/genetics , Polymorphism, Single Nucleotide , Asian People , Base Sequence , Cloning, Molecular , Codon/chemistry , Gene Expression , Genotype , HLA-B27 Antigen/immunology , Hematopoietic Stem Cell Transplantation , Histocompatibility Testing , Humans , Polymerase Chain Reaction , Sequence Alignment , Sequence Analysis, DNA , Tissue DonorsABSTRACT
Full-length sequence of HLA-B*55:02:01:01, confirmed by cloning and sequencing in a Chinese donor.
Subject(s)
Alleles , Exons , HLA-B Antigens/genetics , Polymorphism, Single Nucleotide , Tissue Donors , Asian People , Base Sequence , Cloning, Molecular , Codon/chemistry , Gene Expression , Genotype , HLA-B Antigens/immunology , Hematopoietic Stem Cell Transplantation , Histocompatibility Testing , Humans , Polymerase Chain Reaction , Sequence Alignment , Sequence Analysis, DNAABSTRACT
Full-length sequences of HLA-B*07:05:01:01, B*14:01:01 and B*18:02, confirmed by cloning and sequencing in Chinese donors.