scholarly journals Genetic classification of ovarian carcinoma based on microsatellite analysis: Relationship to clinicopathological features and patient survival

2008 ◽  
Author(s):  
Zhang Huan ◽  
Kentaro Nakayama ◽  
Naomi Nakayama ◽  
Masako Ishibashi ◽  
Shamima Yeasmin ◽  
...  
Keyword(s):  
Ovarian Carcinoma ◽  
Patient Survival ◽  
Microsatellite Analysis ◽  
Clinicopathological Features ◽  
Genetic Classification

scholarly journals Reclassification of Kidney Clear Cell Carcinoma Based on Immune Cell Gene-Related DNA CpG Pairs

Biomedicines ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 215
Author(s):  
Qizhan Luo ◽  
Thomas-Alexander Vögeli
Keyword(s):  
Cell Carcinoma ◽  
Immune Cell ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Pairwise Comparison ◽  
Clinicopathological Features ◽  
Immune Checkpoints ◽  
Potential Mechanism ◽  
Tissue Samples

Background: A new method was developed based on the relative ranking of gene expression level, overcoming the flaw of the batch effect, and having reliable results in various studies. In the current study, we defined the two methylation sites as a pair. The methylation level in a specific sample was subject to pairwise comparison to calculate a score for each CpGs-pair. The score was defined as a CpGs-pair score. If the first immune-related CpG value was higher than the second one in a specific CpGs-pair, the output score of this immune-related CpGs-pair was 1; otherwise, the output score was 0. This study aimed to construct a new classification of Kidney Clear Cell Carcinoma (KIRC) based on DNA CpGs (methylation sites) pairs. Methods: In this study, the biomarkers of 28 kinds of immune infiltration cells and corresponding methylation sites were acquired. The methylation data were compared between KIRC and normal tissue samples, and differentially methylated sites (DMSs) were obtained. Then, DNA CpGs-pairs were obtained according to the pairs of DMSs. In total, 441 DNA CpGs-pairs were utilized to construct a classification using unsupervised clustering analysis. We also analyzed the potential mechanism and therapy of different subtypes, and validated them in a testing set. Results: The classification of KIRC contained three subgroups. The clinicopathological features were different across three subgroups. The distribution of immune cells, immune checkpoints and immune-related mechanisms were significantly different across the three clusters. The mutation and copy number variation (CNV) were also different. The clinicopathological features and potential mechanism in the testing dataset were consistent with those in the training set. Conclusions: Our findings provide a new accurate and stable classification for developing personalized treatments for the new specific subtypes.

Prognostic impact of β-2-microglobulin expression in colorectal cancers stratified by mismatch repair status

2012 ◽  
Vol 65 (11) ◽  
pp. 996-1002 ◽  
Author(s):  
Viktor Hendrik Koelzer ◽  
Kristi Baker ◽  
Daniela Kassahn ◽  
Daniel Baumhoer ◽  
Inti Zlobec
Keyword(s):  
Protein Expression ◽  
Mismatch Repair ◽  
Immune Cell ◽  
Prognostic Significance ◽  
Clinicopathological Features ◽  
Prognostic Impact ◽  
Mismatch Repair Status ◽  
First Time ◽  
Intra Class Correlation Coefficient

Backgroundβ-2-microglobulin (B2M) is essential for antigen presentation, yet may also possess proto-oncogenic properties.AimTo determine the prognostic impact of B2M in patients with mismatch repair (MMR) proficient and deficient colorectal cancer (CRC) and to investigate whether this effect on outcome is dependent on the local immune response. MethodsB2M protein expression and tumour-infiltrating immune cells (CD3, CD16, CD163, CD20, CD4, CD45RO, CD56, CD68, CD8, FoxP3, GranzymeB, iNOS, mast cell tryptase, MUM1, PD1, TIA-1) were evaluated in a well characterised tissue microarray of 408 CRCs. The predictive value for clinicopathological features and the prognostic significance of B2M expression were analysed, stratified by MMR status and the immunohistological characteristics of immune cell infiltrates. ResultsInterobserver agreement for B2M staining was high (intra-class correlation coefficient=0.91). Complete B2M loss was more frequent in MMR-deficient (19.4%) compared to MMR-proficient (7.1%) tumours (p<0.001). In MMR-deficient cases, B2M loss predicted rare local recurrence (p=0.034), infrequent nodal-positivity (p=0.035), absence of distant metastasis (p=0.048; sensitivity=100%) and a trend towards favourable survival (p=0.124) independent of immune infiltrates. No associations between B2M and clinicopathological features were observed in MMR-proficient cases.ConclusionsOur data show for the first time that absence of B2M protein expression identifies MMR-deficient cancers with a favourable clinical course and absence of metastatic disease. Validation of B2M protein expression for sub-classification of MMR-deficient CRC is recommended for future clinical trials.

Abstract 2276: Genetic classification of colorectal cancer

2021 ◽  
Author(s):  
Yoshikage Inoue ◽  
Nobuyuki Kakiuchi ◽  
Kenichi Yoshida ◽  
Yasuhito Nanya ◽  
Yusuke Shiozawa ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Genetic Classification

scholarly journals In-vitro Antioxidant Capacities and Genetic Classification of Indonesian Selected Pigmented Rice

2021 ◽  
pp. 107
Author(s):  
Keyword(s):  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Radical Scavenging ◽  
Free Radical Scavenging ◽  
Genetic Classification ◽  
Pigmented Rice ◽  
The Relationship ◽  
Simple Sequence

Rice is a world-famous cereal food divided into pigmented and non-pigmented rice. Pigmented rice is popular as healthier food than non-pigmented rice due to its potency as an antioxidant. Nevertheless, the potential of pigmented rice has not been widely studied. Indonesian selected pigmented rice protein’s antioxidant potential and the non-protein compound were in-vitro studied. The antioxidant potencies were evaluated by extracting fresh seeds of nine pigmented rice (Aek Sibundong, Beureum Taleus, Gogo Niti-2, Lamongan-1, Merah SP, Merah Wangi, Mota, Ketan Hitam-2, and Super Manggis) and non-pigmented rice (IR-64) as control. Various free radical scavenging methods to determine the antioxidant activity (ABTS•+, DPPH•, OH• and O2-) were conducted. Meanwhile, the genetic classification was performed by a simple sequence repeat (SSR) marker to determine the relationship between varieties. The results showed that protein of Ketan Hitam-2 had the highest ABTS•+ radical scavenging (98.06%), followed by Beureum Taleus (42.54%). Ketan Hitam-2 protein also showed the highest OH• and O2- activities (43.49% and 6.02%, respectively). The highest DPPH• potency of the non-protein compounds also shown by Ketan Hitam-2 (32.23%) with the activity of OH• and O2- (20.63% and 14.56%, respectively). These results showed that Ketan Hitam-2 has the highest potency as an antioxidant, which could be recommended as a nutraceuticals compound.

scholarly journals RAPID GENETIC CLASSIFICATION OF GLIOMAS USING RAMAN SPECTROSCOPY

2018 ◽  
Vol 20 (suppl_5) ◽  
pp. v346-v346
Author(s):  
Laurent James Livermore ◽  
Martin Isabelle ◽  
Ian Bell ◽  
Puneet Plaha ◽  
Claire Vallance ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Genetic Classification ◽  
Classification Of Gliomas
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