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WholeGenome LLC wholegenome sequencing
Wholegenome Sequencing, supplied by WholeGenome LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/dna+methylation+array+platform/wholegenome+sequencing/pm36893482-478-27-22
Average 90 stars, based on 1 article reviews
wholegenome sequencing - by Bioz Stars, 2026-10
90/100 stars

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Related Articles

RNA Sequencing:

Article Title: T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.
Article Snippet: .. Keywords: T-DNA, T-DNA insertion site, Unannotated T-DNA, RNA-seq, Wholegenome sequencing (WGS), ChIP-seq, Bioinformatic tool Background Agrobacterium tumefaciens is a phytopathogenic soil bacterium that infects wounded plant tissues and causes crown gall disease by delivering transfer DNA (T-DNA) into host plant cells through a bacterial type IV secretion system [1, 2]. ..

Sequencing:

Article Title: T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.
Article Snippet: .. Keywords: T-DNA, T-DNA insertion site, Unannotated T-DNA, RNA-seq, Wholegenome sequencing (WGS), ChIP-seq, Bioinformatic tool Background Agrobacterium tumefaciens is a phytopathogenic soil bacterium that infects wounded plant tissues and causes crown gall disease by delivering transfer DNA (T-DNA) into host plant cells through a bacterial type IV secretion system [1, 2]. ..

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Article Title: Recomb-Mix: fast and accurate local ancestry inference.
Article Snippet: .. The input data were individuals in WholeGenome Sequencing (WGS) form from various populations in the study of the 1000 Genomes Project (TGP) (Auton et al. 2015, Clarke et al. 2017) and the Human Genome Diversity Project (HGDP) (Bergstr€om et al. 2020). ..

Article Title: Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma
Article Snippet: .. We expanded our investigation of genomic instability in STS with an additional cohort of 21 cases of angiosarcoma, a malignancy that affects blood and lymphatic vessels, that were profiled using wholegenome sequencing. ..

Article Title: AI-Accelerated Identification of Novel Antimicrobial Peptides for Inhibiting Fusarium graminearum .
Article Snippet: Fusarium head blight caused by Fusarium graminearum threatens global wheat production, causing substantial yield reduction and mycotoxin accumulation.. This study harnessed machine learning to accelerate the discovery of antifungal peptides targeting this phytopathogen.. By developing a de novo antimicrobial peptide database and extracting six critical physicochemical features, we established four predictive models with XGBoost demonstrating superior performance (R2 = 0.77, RMSE = 1.8).

Article Title: Are Babesia vogeli genotypes associated with Rhipicephalus sanguineus and Rhipicephalus linnaei distribution?
Article Snippet: .. Wholegenome sequencing of both genotypes of B. vogeli and closely related piroplasmids is greatly needed to shed light on the diversity of these parasites and their relationships with different tick species belonging to the R. sanguineus group worldwide [46]. ..

Article Title: Genome-wide association studies and candidate genes networks affecting reproductive traits using Iranian Holstein sequence data.
Article Snippet: .. Daetwyler HD, Capitan A, Pausch H, Stothard P, Van Binsbergen R, Brøndum RF, Liao X, Djari A, Rodriguez SC, Grohs C, Esquerré D. Wholegenome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. ..

Article Title: GPC3: a novel mutated gene in pleuropulmonary blastoma.
Article Snippet: .. Keywords Pleuropulmonary blastoma, GPC3 mutation, Prognostic biomarker, Wholegenome sequencing, Immunohistochemistry, Pediatric sarcoma Registry estimate PPB incidence at approximately 1 in 250,000 individuals, with 93% of cases occurring in children under six years of age. ..

Chromatin Immunoprecipitation:

Article Title: T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.
Article Snippet: .. Keywords: T-DNA, T-DNA insertion site, Unannotated T-DNA, RNA-seq, Wholegenome sequencing (WGS), ChIP-seq, Bioinformatic tool Background Agrobacterium tumefaciens is a phytopathogenic soil bacterium that infects wounded plant tissues and causes crown gall disease by delivering transfer DNA (T-DNA) into host plant cells through a bacterial type IV secretion system [1, 2]. ..

Marker:

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Expressing:

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Staining:

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Imaging:

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Whole Complete genome sequencing:

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Mutagenesis:

Article Title: Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer
Article Snippet: .. Marker expression analysis demonstrated similar staining patterns for Ki67, p53, and Muc2 (Figure 1C), with proportions of Ki67-positive cells further correlating with PDTO growth rates as determined by time-lapse imaging (Figure 1D).25 Wholegenome sequencing (WGS) of PDTOs at a median passage of 7 (range 1–22) and matched tumor and germline DNA from 21 patients demonstrated similar total mutation loads and point mutation types, including for two hypermutated cases with dMMR deficiency (WCB046) andDNApolymerase epsilon (POLE)mutation (WCB268) (Figure 2A). ..

Article Title: GPC3: a novel mutated gene in pleuropulmonary blastoma.
Article Snippet: .. Keywords Pleuropulmonary blastoma, GPC3 mutation, Prognostic biomarker, Wholegenome sequencing, Immunohistochemistry, Pediatric sarcoma Registry estimate PPB incidence at approximately 1 in 250,000 individuals, with 93% of cases occurring in children under six years of age. ..

Biomarker Discovery:

Article Title: GPC3: a novel mutated gene in pleuropulmonary blastoma.
Article Snippet: .. Keywords Pleuropulmonary blastoma, GPC3 mutation, Prognostic biomarker, Wholegenome sequencing, Immunohistochemistry, Pediatric sarcoma Registry estimate PPB incidence at approximately 1 in 250,000 individuals, with 93% of cases occurring in children under six years of age. ..

Immunohistochemistry:

Article Title: GPC3: a novel mutated gene in pleuropulmonary blastoma.
Article Snippet: .. Keywords Pleuropulmonary blastoma, GPC3 mutation, Prognostic biomarker, Wholegenome sequencing, Immunohistochemistry, Pediatric sarcoma Registry estimate PPB incidence at approximately 1 in 250,000 individuals, with 93% of cases occurring in children under six years of age. ..



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The upper lines show original <t>DNA</t> sequence and the lower lines bisulfite modified DNA sequence assuming that all of cytosines (C) followed by guanine (G) are methylated. The candidate CpGs for <t>methylation</t> are in bold and gray. DNA sequences flanking the MSP and qMSP primer sites amplifying methylated (M) and unmethylated (U) products are underlined. The site corresponding to the Probe # CG26741280 of the Illumina DNA methylation array is underlined and bolded in original DNA sequence. There are two SP1 binding sites in 5-HTT promoter region which are marked with yellow color (GGGCGG and CCGCCC).
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The upper lines show original DNA sequence and the lower lines bisulfite modified DNA sequence assuming that all of cytosines (C) followed by guanine (G) are methylated. The candidate CpGs for methylation are in bold and gray. DNA sequences flanking the MSP and qMSP primer sites amplifying methylated (M) and unmethylated (U) products are underlined. The site corresponding to the Probe # CG26741280 of the Illumina DNA methylation array is underlined and bolded in original DNA sequence. There are two SP1 binding sites in 5-HTT promoter region which are marked with yellow color (GGGCGG and CCGCCC).

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: The upper lines show original DNA sequence and the lower lines bisulfite modified DNA sequence assuming that all of cytosines (C) followed by guanine (G) are methylated. The candidate CpGs for methylation are in bold and gray. DNA sequences flanking the MSP and qMSP primer sites amplifying methylated (M) and unmethylated (U) products are underlined. The site corresponding to the Probe # CG26741280 of the Illumina DNA methylation array is underlined and bolded in original DNA sequence. There are two SP1 binding sites in 5-HTT promoter region which are marked with yellow color (GGGCGG and CCGCCC).

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: Sequencing, Modification, Methylation, DNA Methylation Assay, Binding Assay

A. Bisulfite sequencing of 5-HTT promoter region in representative samples for identification overall methylation pattern and partially methylated sites (indicated by arrows) for subsequent MSP and qMSP analysis. The original DNA sequence (top line) and bisulfite modified DNA sequence (bottom line) are placed at the top of sequence traces. The red segment of the bottom line shows a representative differentially methylated site. B. MSP analysis of a representative control (1), SCZ (2) and BD (3) using post-mortem brain samples. Placental DNA (P) was used as a negative control for methylation. C. MSP analysis of saliva DNA of a representative control subject (1) and a SCZ patient (2) using F1R1 qMSP primers. The β-Actin promoter amplified with primers designed from a CpG free region was used for the normalization of unmethylated (U) and methylated (M) products during qMSP analysis. L indicates a 100bp DNA ladder. D. Serial dilution of standard samples to optimize conditions for qMSP analysis in the test trials.

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: A. Bisulfite sequencing of 5-HTT promoter region in representative samples for identification overall methylation pattern and partially methylated sites (indicated by arrows) for subsequent MSP and qMSP analysis. The original DNA sequence (top line) and bisulfite modified DNA sequence (bottom line) are placed at the top of sequence traces. The red segment of the bottom line shows a representative differentially methylated site. B. MSP analysis of a representative control (1), SCZ (2) and BD (3) using post-mortem brain samples. Placental DNA (P) was used as a negative control for methylation. C. MSP analysis of saliva DNA of a representative control subject (1) and a SCZ patient (2) using F1R1 qMSP primers. The β-Actin promoter amplified with primers designed from a CpG free region was used for the normalization of unmethylated (U) and methylated (M) products during qMSP analysis. L indicates a 100bp DNA ladder. D. Serial dilution of standard samples to optimize conditions for qMSP analysis in the test trials.

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: Methylation Sequencing, Methylation, Sequencing, Modification, Control, Negative Control, Amplification, Serial Dilution

A. There was higher promoter DNA methylation in SCZ patients compared to the controls and first degree relatives of SCZ patients (SCZ FM) at site A. Notably, SCZ patients and drug naïve SCZ patients (DN SCZ) exhibit higher degree of DNA methylation. Drug use in SCZ patients (DU SCZ) reduced 5-HTT promoter DNA hypermethylation. B. Similar to site A, the 5-HTT promoter DNA methylation in SCZ was higher than controls at site B, particularly in drug naïve patients.

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: A. There was higher promoter DNA methylation in SCZ patients compared to the controls and first degree relatives of SCZ patients (SCZ FM) at site A. Notably, SCZ patients and drug naïve SCZ patients (DN SCZ) exhibit higher degree of DNA methylation. Drug use in SCZ patients (DU SCZ) reduced 5-HTT promoter DNA hypermethylation. B. Similar to site A, the 5-HTT promoter DNA methylation in SCZ was higher than controls at site B, particularly in drug naïve patients.

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: DNA Methylation Assay

A: The Y axis indicates promoter DNA methylation of 5-HTT (site B) normalized with the PCR product of β-Actin promoter in SCZ and BD versus controls. B: The Y axis indicates relative expression of 5-HTT normalized with β-Actin expression. As shown, in SCZ the expression of 5-HTT is significantly less than controls as well as BD patients.

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: A: The Y axis indicates promoter DNA methylation of 5-HTT (site B) normalized with the PCR product of β-Actin promoter in SCZ and BD versus controls. B: The Y axis indicates relative expression of 5-HTT normalized with β-Actin expression. As shown, in SCZ the expression of 5-HTT is significantly less than controls as well as BD patients.

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: DNA Methylation Assay, Expressing