| Literature DB >> 33447413 |
Rossana Berardi1, Gaia Goteri2, Silvia Pagliaretta1, Vittorio Paolucci1, Francesca Morgese1, Alessandro Conti3, Majed Refai4, Cecilia Pompili5, Claudia Duranti1, Giulia Marcantognini1, Agnese Savini1, Miriam Caramanti1, Silvia Rinaldi1, Mariangela Torniai1, Matteo Santoni1, Antonio Zizzi2, Paola Mazzanti1, Azzurra Onofri1, Giulia Ricci1, Marina Scarpelli2.
Abstract
BACKGROUND: We previously showed that selected single-nucleotide-polymorphisms (SNPs) of genes involved in angiogenesis influence the aggressiveness of thymic epithelial tumors (TETs). This study analyzes their role in TETs and in thymic benign lesions, in order to investigate potential correlation with risk and outcome.Entities:
Keywords: Thymic epithelial tumor (TETs); outcome; thymic cyst; thymic hyperplasia; thymic prognostic factor; thymolipoma
Year: 2020 PMID: 33447413 PMCID: PMC7797874 DOI: 10.21037/jtd-19-3720
Source DB: PubMed Journal: J Thorac Dis ISSN: 2072-1439 Impact factor: 2.895
Genotype and allele frequencies of evaluated genes polymorphisms in thymomas
| Gene | SNPs | Allele | Frequencies general population (%) | Frequencies study cohort (%) | n. sample | P | Yates | Odds ratio |
|---|---|---|---|---|---|---|---|---|
|
| rs2305948 | C | 92.00 | 90.20 | 51/51 | 0.6510 | 0.8364 | 1.25 |
| T | 8.00 | 9.80 | ||||||
|
| rs1870377 | T | 72.50 | 74.51 | 51/51 | 0.7450 | 0.8677 | 0.90 |
| A | 27.50 | 25.49 | ||||||
|
| rs2010963 | G | 68.82 | 60.78 | 51/51 | 0.2295 | 0.2914 | 1.42 |
| C | 31.18 | 39.22 | ||||||
|
| rs699947 | C | 52.20 | 60.78 | 51/51 | 0.2163 | 0.2734 | 0.70 |
| A | 47.80 | 39.22 | ||||||
|
| rs307821 | C | 90.59 | 87.25 | 51/51 | 0.4479 | 0.5921 | 1.41 |
| A | 9.41 | 12.75 | ||||||
|
| rs307826 | T | 89.80 | 85.29 | 51/51 | 0.3298 | 0.4458 | 1.52 |
| C | 10.20 | 14.71 | ||||||
|
| rs35597368 | T | 86.70 | 94.12 | 51/51 | 0.0720 | 0.1185 | 0.41 |
| C | 13.30 | 5.88 | ||||||
|
| rs2057482 | C | 90.30 | 76.47 | 51/51 | 0.0080 | 0.0137 | 2.86 |
| T | 9.70 | 23.53 | ||||||
|
| rs1951795 | C | 86.70 | 66.67 | 51/51 | 0.0007 | 0.0013 | 3.26 |
| A | 13.30 | 33.33 | ||||||
|
| rs2301113 | A | 82.70 | 67.00 | 50/50 | 0.0105 | 0.0166 | 2.35 |
| C | 17.30 | 33.33 | ||||||
|
| rs10873142 | T | 86.70 | 67.35 | 49/49 | 0.0013 | 0.0023 | 3.16 |
| C | 13.30 | 32.65 | ||||||
|
| rs11158358 | C | 88.24 | 73.53 | 51/51 | 0.0075 | 0.0126 | 2.70 |
| G | 11.76 | 26.47 | ||||||
|
| rs12434438 | A | 84.50 | 63.73 | 51/51 | 0.0007 | 0.0012 | 3.10 |
| G | 15.50 | 36.27 | ||||||
|
| rs11549465 | C | 92.50 | 83.33 | 51/51 | 0.0446 | 0.0729 | 2.47 |
| T | 7.50 | 16.67 | ||||||
|
| rs11549467 | G | 98.70 | 100.00 | 51/51 | 0.2480 | 0.7764 | 0.00 |
| A | 1.30 | 0.00 | ||||||
|
| rs11615 | A | 64.20 | 61.00 | 50/50 | 0.6400 | 0.7478 | 1.15 |
| G | 35.80 | 39.00 |
SNP, single-nucleotide-polymorphism.
Genotype and allele frequencies of evaluated genes polymorphisms in thymic carcinomas
| Gene | SNPs | Allele | Frequencies general population (%) | Frequencies study cohort (%) | n. sample | P | Yates | Odds ratio |
|---|---|---|---|---|---|---|---|---|
|
| rs2305948 | C | 92.00 | 91.67 | 6/6 | 0.9762 | 0.4743 | 1.05 |
| T | 8.00 | 8.33 | ||||||
|
| rs1870377 | T | 72.50 | 75.00 | 6/6 | 0.8893 | 0.7454 | 0.88 |
| A | 27.50 | 25.00 | ||||||
|
| rs2010963 | G | 68.82 | 70.00 | 5/5 | 0.9543 | 0.6686 | 0.95 |
| C | 31.18 | 30.00 | ||||||
|
| rs699947 | C | 52.20 | 75.00 | 6/6 | 0.2458 | 0.4614 | 0.36 |
| A | 47.80 | 25.00 | ||||||
|
| rs307821 | C | 90.59 | 100.00 | 4/4 | 0.3741 | 0.7704 | 0.00 |
| A | 9.41 | 0.00 | ||||||
|
| rs307826 | T | 89.80 | 83.33 | 6/6 | 0.6423 | 0.8933 | 1.76 |
| C | 10.20 | 16.67 | ||||||
|
| rs35597368 | T | 86.70 | 100.00 | 6/6 | 0.1910 | 0.6253 | 0.00 |
| C | 13.30 | 0.00 | ||||||
|
| rs2057482 | C | 90.30 | 91.67 | 6/6 | 0.9070 | 0.5513 | 0.85 |
| T | 9.70 | 8.33 | ||||||
|
| rs1951795 | C | 86.70 | 91.67 | 6/6 | 0.6953 | 0.7906 | 0.59 |
| A | 13.30 | 8.33 | ||||||
|
| rs2301113 | A | 82.70 | 91.67 | 6/6 | 0.5111 | 0.9630 | 0.43 |
| C | 17.30 | 8.33 | ||||||
|
| rs10873142 | T | 86.70 | 91.67 | 6/6 | 0.6953 | 0.7906 | 0.59 |
| C | 13.30 | 8.33 | ||||||
|
| rs11158358 | C | 88.24 | 91.67 | 6/6 | 0.7801 | 0.6893 | 0.68 |
| G | 11.76 | 8.33 | ||||||
|
| rs12434438 | A | 84.50 | 91.67 | 6/6 | 0.5879 | 0.9297 | 0.50 |
| G | 15.50 | 8.33 | ||||||
|
| rs11549465 | C | 92.50 | 100.00 | 6/6 | 0.3336 | 0.9144 | 0.00 |
| T | 7.50 | 0.00 | ||||||
|
| rs11549467 | G | 98.70 | 100.00 | 6/6 | 0.6919 | 0.0320 | 0.00 |
| A | 1.30 | 0.00 | ||||||
|
| rs11615 | A | 64.20 | 50.00 | 6/6 | 0.4822 | 0.7715 | 1.79 |
| G | 35.80 | 50.00 |
SNP, single-nucleotide-polymorphism.
Genotype and allele frequencies of evaluated genes polymorphisms in thymic benign lesions
| Gene | SNPs | Allele | Frequencies general population (%) | Frequencies study cohort (%) | n. sample | P | Yates | Odds ratio |
|---|---|---|---|---|---|---|---|---|
|
| rs2305948 | C | 92.00 | 97.14 | 35/35 | 0.1793 | 0.3321 | 0.34 |
| T | 8.00 | 2.86 | ||||||
|
| rs1870377 | T | 72.50 | 79.41 | 34/34 | 0.3456 | 0.4578 | 0.68 |
| A | 27.50 | 20.59 | ||||||
|
| rs2010963 | G | 68.82 | 55.71 | 35/35 | 0.1097 | 0.1541 | 1.75 |
| C | 31.18 | 44.29 | ||||||
|
| rs699947 | C | 52.20 | 72.86 | 35/35 | 0.0116 | 0.0188 | 0.41 |
| A | 47.80 | 27.14 | ||||||
|
| rs307821 | C | 90.59 | 91.43 | 35/35 | 0.8623 | 0.9029 | 0.90 |
| A | 9.41 | 8.57 | ||||||
|
| rs307826 | T | 89.80 | 82.86 | 35/35 | 0.2319 | 0.3423 | 1.82 |
| C | 10.20 | 17.14 | ||||||
| rs35597368 | T | 86.70 | 91.43 | 35/35 | 0.3701 | 0.5316 | 0.61 | |
| C | 13.30 | 8.57 | ||||||
| rs2057482 | C | 90.30 | 80.00 | 35/35 | 0.0866 | 0.1400 | 2.33 | |
| T | 9.70 | 20.00 | ||||||
| rs1951795 | C | 86.70 | 71.43 | 35/35 | 0.0264 | 0.0441 | 2.61 | |
| A | 13.30 | 28.57 | ||||||
| rs2301113 | A | 82.70 | 66.18 | 34/34 | 0.0272 | 0.0442 | 2.44 | |
| C | 17.30 | 28.57 | ||||||
| rs10873142 | T | 86.70 | 67.65 | 34/34 | 0.0081 | 0.0146 | 3.12 | |
| C | 13.30 | 32.35 | ||||||
| rs11158358 | C | 88.24 | 77.94 | 34/34 | 0.1091 | 0.1697 | 2.12 | |
| G | 11.76 | 22.06 | ||||||
| rs12434438 | A | 84.50 | 69.12 | 34/34 | 0.0336 | 0.0546 | 2.44 | |
| G | 15.50 | 30.88 | ||||||
| rs11549465 | C | 92.50 | 85.71 | 35/35 | 0.1976 | 0.3090 | 2.06 | |
| T | 7.50 | 14.29 | ||||||
| rs11549467 | G | 98.70 | 100.00 | 35/35 | 0.3385 | 0.9246 | 0.00 | |
| A | 1.30 | 0.00 | ||||||
|
| rs11615 | A | 64.20 | 52.86 | 35/35 | 0.1732 | 0.2338 | 1.60 |
| G | 35.80 | 47.14 |
SNP, single-nucleotide-polymorphism.
Patients characteristics
| Characteristics | Outcomes |
|---|---|
| Sex | |
| Male | 35 (38%) |
| Female | 57 (62%) |
| Type of disease | |
| Thymoma | 51 (55%) |
| Thymic carcinoma | 6 (7%) |
| Thymic hyperplasia | 19 (21%) |
| Thymic cist | 5 (5%) |
| Thymolipoma | 1 (1%) |
| Thymic remnant | 10 (11%) |
| Age at the diagnosis, years, median [range] | 52.5 [8–82] |
Chromosomal location, position in the gene, base exchange and MAF of polymorphism studied group
| Gene | ID SNP | Chr | Position CDS | AA change | Allele frequencies CEU (HapMap) | |
|---|---|---|---|---|---|---|
| Main allele | Minor allele | |||||
|
| rs2010963 | 6 | 5'UTR | – | G=0.6882 | C=0.3118 |
|
| rs699947 | 6 | UPSTREAM | – | C=0.522 | A=0.47 |
|
| rs2305948 | 4 | c.889 C>T | p.V297I | C=0.920 | T=0.080 |
|
| rs1870377 | 4 | c.1416A>T | p.Q472H | T=0.7529 | A=0.247 |
|
| rs307821 | 5 | c.3971 G>T | p.R1324L | G=0.9059 | T=0.0941 |
|
| rs307826 | 5 | c.1480 T>C | p.T494A | T=0.898 | C=0.102 |
| rs35597368 | 4 | c.1432T>C | p.S478P | T=0.867 | C=0.133 | |
| rs2057482 | 14 | 3'UTR | – | C=0.903 | T=0.097 | |
| rs1951795 | 14 | INTRONIC | – | C=0.867 | A=0.133 | |
| rs2301113 | 14 | INTRONIC | – | A=0.827 | C=0.173 | |
| rs10873142 | 14 | INTRONIC | – | T=0.867 | C=0.133 | |
| rs11158358 | 14 | INTRONIC | – | C=0.8824 | G=0.1176 | |
| rs12434438 | 14 | INTRONIC | – | A= 0.845 | G=0.155 | |
| rs11549465 | 14 | c.1744C>T | p.P582S | C=0.925 | T=0.075 | |
| rs11549467 | 14 | c.1762G>A | p.A588T | G=0.987 | A=0.013 | |
|
| rs11615 | 19 | c.354T>C | p.N118N | A=0.642 | G=0.358 |
MAF, minor allele frequency; SNP, single-nucleotide-polymorphism; CDS, CoDing Sequence; AA, amino acid; CEU, Northern Europeans from Utah.
Figure 1Linkage disequilibrium plot generated by Haploview software. LD is displayed as pairwise D’ values. Shading represents the magnitude and significance of pairwise LD, with a red-to-white gradient reflecting higher-to-lower LD values. Red diamond without a number corresponds to D’ values of 1.0.
Figure 2Single-nucleotide-polymorphisms (SNPs) distribution in the study groups. SNPs distribution in general population, thymic malignances and thymic benign lesions.