Genomic Benefits and Potential Harms of COVID-19 Vaccines Indicated from High-Performance Genomic Biomarkers

Zhang, Zhengjun

doi:10.21203/rs.3.rs-1918598/v1

Cited by 3 publications

(3 citation statements)

References 6 publications

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“…In this section, we use additional twelve datasets to cross-validate the genes identified in Section 3. These datasets include GSE152641 37 , GSE155454 38 , GSE163151 39 , GSE166190 40 , GSE166253 41 , GSE166530 42 , GSE177477 43 , GSE179448 44 , GSE184401 45 , GSE189039 46;47 , GSE190680 48 , and GSE201530 47;49 .…”

Section: Genomic Differences Between Np/op Swaps Pcr Samples and Whol...mentioning

confidence: 99%

“…The platform was GPL24676 Illumina NovaSeq 6000 (Homo sapiens). The following Table 20 is adapted from our work on vaccine study 49 .…”

Section: Genomic Differences Between Np/op Swaps Pcr Samples and Whol...mentioning

confidence: 99%

“…The platform was GPL24676 Illumina NovaSeq 6000 (Homo sapiens). The following Table 20 is adapted from our work on vaccine study 49 . It is significant to note that the genes identified from blood samples in our earlier work 17 again work for various SARS-CoV-2 variants, including Omicron.…”

Section: Genomic Differences Between Np/op Swaps Pcr Samples and Whol...mentioning

confidence: 99%

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Genomic Biomarker Heterogeneities Between SARS-CoV-2 and COVID-19

Zhang¹

2022

Preprint

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Genes functionally associated with SARS-CoV-2 and genes functionally related to COVID-19 disease can be different, whose distinction will become the first essential step for successfully fighting against the COVID-19 pandemic. Unfortunately, this first step has not been completed in all biological and medical research. Using a newly developed max-competing logistic classifier, two genes, ATP6V1B2 and IFI27, stand out to be critical in transcriptional response to SARS-CoV-2 with differential expressions derived from NP/OP swab PCR. This finding is evidenced by combining these two genes with one another gene in predicting disease status to achieve better-indicating power than existing classifiers with the same number of genes. In addition, combining these two genes with three other genes to form a five-gene classifier outperforms existing classifiers with ten or more genes. With their exceptional predicting power, these two genes can be critical in fighting against the COVID-19 pandemic as a new focus and direction. Comparing the functional effects of these genes with a five-gene classifier with 100% accuracy identified and tested from blood samples in the literature, genes and their transcriptional response and functional effects to SARS-CoV-2 and genes and their functional signature patterns to COVID-19 antibody are significantly different, which can be interpreted as the former is the point of a phenomenon, and the latter is the essence of the disease. Such significant findings can help explore the causal and pathological clue between SARS-CoV-2 and COVID-19 disease and fight against the disease with more targeted vaccines, antiviral drugs, and therapies.

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Section: Genomic Differences Between Np/op Swaps Pcr Samples and Whol...mentioning

confidence: 99%

“…The platform was GPL24676 Illumina NovaSeq 6000 (Homo sapiens). The following Table 20 is adapted from our work on vaccine study 49 .…”

Section: Genomic Differences Between Np/op Swaps Pcr Samples and Whol...mentioning

confidence: 99%

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Genomic Biomarker Heterogeneities Between SARS-CoV-2 and COVID-19

Zhang¹

2022

Preprint

Self Cite

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The Initial COVID-19 Reliable Interactive DNA Methylation Markers and Biological Implications

Zhang

2024

Biology

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Earlier research has established the existence of reliable interactive genomic biomarkers. However, reliable DNA methylation biomarkers, not to mention interactivity, have yet to be identified at the epigenetic level. This study, drawing from 865,859 methylation sites, discovered two miniature sets of Infinium MethylationEPIC sites, each having eight CpG sites (genes) to interact with each other and disease subtypes. They led to the nearly perfect (96.87–100% accuracy) prediction of COVID-19 patients from patients with other diseases or healthy controls. These CpG sites can jointly explain some post-COVID-19-related conditions. These CpG sites and the optimally performing genomic biomarkers reported in the literature become potential druggable targets. Among these CpG sites, cg16785077 (gene MX1), cg25932713 (gene PARP9), and cg22930808 (gene PARP9) at DNA methylation levels indicate that the initial SARS-CoV-2 virus may be better treated as a transcribed viral DNA into RNA virus, i.e., not as an RNA virus that has concerned scientists in the field. Such a discovery can significantly change the scientific thinking and knowledge of viruses.

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Genomic Biomarker Heterogeneities between SARS-CoV-2 and COVID-19

Zhang

2022

Vaccines

View full text Add to dashboard Cite

Genes functionally associated with SARS-CoV-2 infection and genes functionally related to the COVID-19 disease can be different, whose distinction will become the first essential step for successfully fighting against the COVID-19 pandemic. Unfortunately, this first step has not been completed in all biological and medical research. Using a newly developed max-competing logistic classifier, two genes, ATP6V1B2 and IFI27, stand out to be critical in the transcriptional response to SARS-CoV-2 infection with differential expressions derived from NP/OP swab PCR. This finding is evidenced by combining these two genes with another gene in predicting disease status to achieve better-indicating accuracy than existing classifiers with the same number of genes. In addition, combining these two genes with three other genes to form a five-gene classifier outperforms existing classifiers with ten or more genes. These two genes can be critical in fighting against the COVID-19 pandemic as a new focus and direction with their exceptional predicting accuracy. Comparing the functional effects of these genes with a five-gene classifier with 100% accuracy identified and tested from blood samples in our earlier work, the genes and their transcriptional response and functional effects on SARS-CoV-2 infection, and the genes and their functional signature patterns on COVID-19 antibodies, are significantly different. We will use a total of fourteen cohort studies (including breakthrough infections and omicron variants) with 1481 samples to justify our results. Such significant findings can help explore the causal and pathological links between SARS-CoV-2 infection and the COVID-19 disease, and fight against the disease with more targeted genes, vaccines, antiviral drugs, and therapies.

show abstract

Genomic Benefits and Potential Harms of COVID-19 Vaccines Indicated from High-Performance Genomic Biomarkers

Cited by 3 publications

References 6 publications

Genomic Biomarker Heterogeneities Between SARS-CoV-2 and COVID-19

Genomic Biomarker Heterogeneities Between SARS-CoV-2 and COVID-19

The Initial COVID-19 Reliable Interactive DNA Methylation Markers and Biological Implications

Genomic Biomarker Heterogeneities between SARS-CoV-2 and COVID-19

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