Bioinformatics for Cancer Genomics

Kasaian, Katayoon; Li, Yvonne Y.; Jones, Steven J.M.

doi:10.1016/b978-0-12-396967-5.00009-8

Cited by 2 publications

(3 citation statements)

References 127 publications

(96 reference statements)

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“…Nucleotide positions were defined according to current mutation nomenclature guidelines, 30 ascribing the A of the first ATG translational initiation codon as nucleotide +1 (NM_203330.2). Due to the inability to reliably detect insertions and deletions (indels) using short‐read NGS techniques, 31 all 18 indel variants were removed before haplotype analysis (rs35899420, rs142232261, rs556364794, rs569759725, rs148567681, rs540281320, NG_008057.1:g.22953delA [novel], rs59130418, rs974178986, rs58642942, rs34595102, rs1404198012, rs1214882562, NG_008057.1:g.30750insG [novel], rs561316878, rs560607574, rs56892277, rs58634493).…”

Section: Methodsmentioning

confidence: 99%

“…Third, the inherent technical limitations of short-read Illumina sequencing in analyzing repetitive genomic regions prompted us to exclude indels from final analysis, as it had also been done in the RefSeqGene sequence (Table 3). 31,55 Frameshift and non-frameshift indels have been associated with multiple diseases including cancer. [56][57][58][59] None of the 18 indels that we observed were present in the CD59 coding sequence.…”

Section: Haplotypementioning

confidence: 99%

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CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities

Srivastava,

Yin,

Makuria

et al. 2024

Transfusion

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BackgroundCD59 deficiency due to rare germline variants in the CD59 gene causes disabilities, ischemic strokes, neuropathy, and hemolysis. CD59 deficiency due to common somatic variants in the PIG‐A gene in hematopoietic stem cells causes paroxysmal nocturnal hemoglobinuria. The ISBT database lists one nonsense and three missense germline variants that are associated with the CD59‐null phenotype. To analyze the genetic diversity of the CD59 gene, we determined long‐range CD59 haplotypes among individuals from different ethnicities.MethodsWe determined a 22.7 kb genomic fragment of the CD59 gene in 113 individuals using next‐generation sequencing (NGS), which covered the whole NM_203330.2 mRNA transcript of 7796 base pairs. Samples came from an FDA reference repository and our Ethiopia study cohorts. The raw genotype data were computationally phased into individual haplotype sequences.ResultsNucleotide sequencing of the CD59 gene of 226 chromosomes identified 216 positions with single nucleotide variants. Only three haplotypes were observed in homozygous form, which allowed us to assign them unambiguously as experimentally verified CD59 haplotypes. They were also the most frequent haplotypes among both cohorts. An additional 140 haplotypes were imputed computationally.DiscussionWe provided a large set of haplotypes and proposed three verified long‐range CD59 reference sequences, based on a population approach, using a generalizable rationale for our choice. Correct long‐range haplotypes are useful as template sequences for allele calling in high‐throughput NGS and precision medicine approaches, thus enhancing the reliability of clinical diagnostics. Long‐range haplotypes can also be used to evaluate the influence of genetic variation on the risk of transfusion reactions or diseases.

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Section: Methodsmentioning

confidence: 99%

Section: Haplotypementioning

confidence: 99%

CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities

Srivastava,

Yin,

Makuria

et al. 2024

Transfusion

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“…At present, there are no therapeutic regimens for the complete eradication of cancer. In recent years, bioinformatic tools have become essential for the analysis of genes associated with the incidence of cancer ( Kasaian et al, 2014 ). Owing to the complexity of the mechanisms underlying the occurrence of tumors, pan-cancer analysis is crucial for determining the principle of carcinogenesis.…”

Section: Introductionmentioning

confidence: 99%

Pan-cancer analysis of the prognostic and immunological roles of DEAD-box helicase 5 (DDX5) in human tumors

Liu

Zhang

et al. 2022

Front. Genet.

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Background: Recent studies have demonstrated the significance of the DEAD-box helicase 5 (DDX5) gene, which is involved in pathways concerning the modification of RNA structures. DDX5 functions as a coregulator of cellular transcription and splicing, and participates in the processing of small noncoding RNAs. The aberrant regulation of DDX5 expression possibly plays a significant role in the genesis of cancer. However, there are no comprehensive pan-cancer studies on DDX5. This study is the first to conduct a pan-cancer analysis of DDX5 for aiding the diagnosis and treatment of cancer.Methods: The gene expression, genetic alterations, protein phosphorylation, promoter methylation, immune infiltration, and enrichment analyses of DDX5 were performed using data retrieved from The Cancer Genome Atlas (TCGA), Genotype-tissue Expression (GTEx), Human Protein Atlas (HPA), Tumor Immunological Estimation Resource 2.0 (TIMER2.0), Gene Expression Profiling Interactive Analysis (GEPIA), DNA methylation interactive visualization database (DNMIVD), and Search Tool for the Retrieval of Interaction Genes/Proteins (STRING). Data analyses were performed with the R software and other webtools.Results: The expression of DDX5 mRNA decreased significantly in 17 cancer types, but increased significantly in eight cancer types. The enhanced expression of DDX5 mRNA in the tumor samples was related to decreased overall survival (OS), progression-free interval (PFI), and disease-specific survival (DSS) in three cancers, but increased OS, PFI, and DSS in other cancers. The DNA promoter methylation level was significantly reduced in eight cancer types, and there were exceptions in the methylation levels of the DDX5 promoter in four cancer types. The expression of DDX5 mRNA was highly correlated with the infiltration of CD8+ T cells, cancer-associated fibroblasts, and B cells in a wide variety of malignancies. The findings revealed a strong association between DDX5 and its co-expressed genes in numerous cancer types. Enrichment analysis suggested that DDX5 was associated with multiple cellular pathways, including RNA splicing, Notch signaling pathway, and viral carcinogenesis, which was consistent with the results of previous studies.Conclusion: The findings obtained herein provide further information on the oncogenic potential of DDX5 in diverse tumor types. We propose that DDX5 has important roles in tumor immunity and the diagnosis of cancer.

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Bioinformatics for Cancer Genomics

Cited by 2 publications

References 127 publications

CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities

CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities

Pan-cancer analysis of the prognostic and immunological roles of DEAD-box helicase 5 (DDX5) in human tumors

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