Quantitative and Qualitative Analyses of the SNRPN Gene Using Real-Time PCR with Melting Curve Analysis

Hung, Chi‐Ren; Lin, Shu-Yung; Lin, Shuan Pei; Chen, Chih Ping Chen; Chen, Lang Yao; Lee, Chien‐Nan; Su, Yi Ning

doi:10.1016/j.jmoldx.2011.06.005

Cited by 8 publications

(4 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further analysis of allele discrimination using SNP primers showed that the marker (C-12) effectively distinguished GG allele. Melting curve analysis by qPCR is a powerful and reliable technique for variant scanning and genotyping (Wittwer 2009;Hung et al 2011). Our previous study on date palm(Wang et a l. 2020) utilized qPCR melting curve analysis to determine sex alleles (X and Y).…”

Section: Discussionmentioning

confidence: 99%

GWAS determined genetic loci associated with callus induction in oil palm tissue culture

Htwe,

Shi,

Zhang

et al. 2024

Plant Cell Rep

View full text Add to dashboard Cite

E cient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male in orescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two-and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed and correlation analysis revealed a positive association of C1 with both C2 (R=0.81) and C3 (R=0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only signi cant SNPs in C1 (including samples with and without callus) were identi ed to develop markers for screeningindividuals with high potential of callus induction. Among 21 signi cant SNPs (P ≤ 0.05) in C1, LD block analysis revealed 6 SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identi ed from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our ndings facilitated markerassisted selection for speci c palms with high potential of callus induction using immature male in orescence as explant, aiding ortet palm selection in oil palm tissue culture. Key messageSix loci potentially linked to callus induction was identi ed by GWAS and a SNP marker that can select the individuals with high potential of callus induction was developed.

show abstract

Section: Discussionmentioning

confidence: 99%

GWAS determined genetic loci associated with callus induction in oil palm tissue culture

Htwe,

Shi,

Zhang

et al. 2024

Plant Cell Rep

View full text Add to dashboard Cite

show abstract

“…Small nuclear ribonucleoprotein polypeptide N(SNRPN), has not been studied in depth in tumors. Currently its has become one of the bio-diagnostic markers for Prader-Willi syndrome and Angerman syndrome [45] . The potential biological function of SNRPN in tumors, or in gastric cancer, remains to be investigated and explored.…”

Section: Discussionmentioning

confidence: 99%

Identification of TNF-related gene subtypes, development of a prognostic model and exploration of the tumor immune landscape in gastric cancer

Gao

et al. 2023

Preprint

View full text Add to dashboard Cite

Background Gastric cancer (GC) is a common cancer in the world, with a high prevalence in East Asia. Tumor necrosis factor (TNF) is considered a high correlation to the development of tumor. This study aim to establish a prognostic model based on TNF-related genes (TNFRG), and to analyze the role of TNFRG in immune function. Method RNA sequencing data and information on clinical features of GC samples were extracted from TCGA-STAD and GEO (GSE84437) databases. Molecular and gene subtypes were identified and derived out using unsupervised clustering analysis. Prognostic models were determined and constructed later by univariate and multivariat cox regression, and LASSO regression. Reliability of prognostic models was verified using ROC curves and Kaplan-Meier analysis. The nomogram was used to quantify the probability of survival. Immune-related functions were analyzed using CIBERSORT and ssGSEA. Finally, RT-qPCR determined the expression of risk genes in GC. Result We confirmed two molecular subtypes and three gene subtypes by two clustering analyses. Both molecular cluster A and gene cluster C had higher levels of immune cell infiltration and better prognosis than others. A prognostic model comprised of four risk genes was constructed, which had different responses to TME, immune checkpoints, immune scores, immune cell infiltration and chemotherapy drug sensitivity, respectively. Conclussion This study enhances our understanding of TNFRG in GC, and provides a theoretical basis for predicting tumor prognosis and clinical treatments.

show abstract

“…Melting curve analysis by qPCR is a powerful and reliable technique for variant scanning and genotyping (Wittwer 2009;Hung et al 2011). Our previous study on date palm (Wang et al 2020) utilized qPCR melting curve analysis to determine sex alleles (X and Y).…”

Section: Analysis Of Snp Primers For Allele Discriminationmentioning

confidence: 99%

Insights into callus induction by GWAS and development of SNP marker for donor plants selection in oil palm tissue culture

Htwe,

Shi,

Zhang

et al. 2024

Preprint

View full text Add to dashboard Cite

Efficient callus induction is vital for successful tissue culture of oil palm, yet identifying genomic loci and markers for early identification of specific individuals with high potential of callus induction is still unclear. In this study, callus induction rate at 1-, 2-, and 3-months after inoculation (C1, C2 and C3) of 198 oil palm individuals were investigated as phenotypes, and totally 11,475,258 high quality single nucleotide polymorphisms (SNPs) were generated by resequencing as genotypes. Genome-wide association study (GWAS) was performed accordingly using these phenotypes and genotypes. Correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50). Therefore, only SNPs in C1 were identified to develop markers for screening individuals capable of callus induction at early stage. A total of 21 significant SNPs were observed in C1, in which six of them on chromosome 12 (Chr12) potentially linked to callus induction were further revealed by the linkage disequilibrium (LD) block analysis. Totally 13 SNP markers from these six loci were tested accordingly and only the marker C-12 at locus Chr12_12704856 effectively distinguishing the GG allele, which showed the highest probability (69%) of callus induction. Moreover, the method for rapid SNP variant detection without electrophoresis was established via qPCR analysis. Notably, individuals S30 and S46, carrying the GG allele, consistently showed high callus induction rates (> 50%) from C1 to C3. Our findings facilitated marker-assisted selection for specific individuals with high potential of callus induction, thereby providing valuable assistance for donor plants selection in oil palm tissue culture.

show abstract

Quantitative and Qualitative Analyses of the SNRPN Gene Using Real-Time PCR with Melting Curve Analysis

Cited by 8 publications

References 23 publications

GWAS determined genetic loci associated with callus induction in oil palm tissue culture

GWAS determined genetic loci associated with callus induction in oil palm tissue culture

Identification of TNF-related gene subtypes, development of a prognostic model and exploration of the tumor immune landscape in gastric cancer

Insights into callus induction by GWAS and development of SNP marker for donor plants selection in oil palm tissue culture

Contact Info

Product

Resources

About