Whole Exome-Wide Association Identifies Rare Variants in APC Associated with High-Risk Colorectal Cancer in the Middle East
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patient Selection
2.2. DNA Extraction
2.3. Whole Exome Sequencing
2.4. Statistical Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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N = 146 | |
---|---|
Age (years) | |
Median (IQR), years | 41.0 (34.0–48.9) |
<50 | 119 (81.5) |
≥50 | 27 (18.5) |
Gender | |
Female | 64 (43.8) |
Male | 82 (56.2) |
Family history of cancer | |
Positive | 53 (36.3) |
Negative | 93 (63.7) |
Family history of colon cancer | |
Positive | 28 (19.2) |
Negative | 118 (80.8) |
Body mass index (kg/m2) | |
<30 | 92 (63.0) |
≥30 | 40 (27.4) |
Unknown | 14 (9.6) |
History of diabetes mellitus | |
Present | 19 (13.0) |
Absent | 97 (66.4) |
Unknown | 30 (20.5) |
Histologic subtype | |
Adenocarcinoma | 127 (87.0) |
Mucinous | 19 (13.0) |
Tumor location | |
Left colon | 113 (77.4) |
Right colon | 26 (17.8) |
Transverse colon | 7 (4.8) |
Histologic grade | |
Well differentiated | 8 (5.5) |
Moderately differentiated | 113 (77.4) |
Poorly differentiated | 14 (9.6) |
Unknown | 11 (7.5) |
pT | |
T1 | 4 (2.8) |
T2 | 17 (11.7) |
T3 | 90 (61.6) |
T4 | 24 (16.4) |
Unknown | 11 (7.5) |
pN | |
N0 | 56 (38.4) |
N1/N2 | 79 (54.1) |
Nx | 11 (7.5) |
pM | |
M0 | 111 (76.0) |
M1 | 28 (19.2) |
Mx | 7 (4.8) |
TNM Stage | |
I | 17 (11.7) |
II | 38 (26.0) |
III | 55 (37.7) |
IV | 28 (19.2) |
Unknown | 8 (5.4) |
S No | Gene | Chr | Position | Ref | Alt | Variant Type | No. of Cases | % | No. of Controls | % | p-Value | Odds Ratio |
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | APC | chr5 | 112,154,963 | C | T | Missense | 3 | 2.1 | 0 | 0.0 | 8.36 × 10−8 | 68.1 |
2 | APC | chr5 | 112,128,191 | C | T | Missense | 1 | 0.7 | 0 | 0.0 | 0.002 | 28.8 |
3 | APC | chr5 | 112,155,042 | G | C | Missense | 1 | 0.7 | 0 | 0.0 | 0.002 | 28.8 |
4 | APC | chr5 | 112,174,112 | G | T | Missense | 1 | 0.7 | 0 | 0.0 | 0.002 | 28.8 |
5 | APC | chr5 | 112,175,077 | T | - | Frameshift Deletion | 0 | 0.7 | 1 | 0.0 | 0.746 | −3.1 |
6 | RIMS1 | chr6 | 72,974,704 | T | G | Missense | 4 | 2.7 | 0 | 0.0 | 6.01 × 10−10 | 88.1 |
7 | RIMS1 | chr6 | 72,975,696 | - | TC | Frameshift Insertion | 1 | 0.7 | 0 | 0.0 | 0.002 | 28.8 |
8 | RIMS1 | chr6 | 72,945,397 | T | C | Missense | 0 | 0.0 | 1 | 0.1 | 0.746 | 3.2 |
9 | RIMS1 | chr6 | 72,984,083 | C | T | Missense | 0 | 0.0 | 1 | 0.1 | 0.746 | 3.2 |
10 | ST6GALNAC2 | chr17 | 74,566,661 | T | - | Frameshift Deletion | 2 | 1.4 | 1 | 0.1 | 0.001 | 19.4 |
11 | ST6GALNAC2 | chr17 | 74,568,782 | G | - | Frameshift Deletion | 1 | 0.7 | 1 | 0.1 | 0.050 | 9.6 |
S No | Gene | No. of Cases | % Cases | No. of Controls | % Controls | p-Value | Odds Ratio |
---|---|---|---|---|---|---|---|
1 | APC * | 6 | 4.1 | 1 | 0.1 | 5.08 × 10−12 | 59.7 |
2 | CD36 | 6 | 4.1 | 25 | 1.8 | 0.058 | 2.3 |
3 | RIMS1 * | 5 | 3.4 | 2 | 0.1 | 2.03 × 10−8 | 24.7 |
4 | ACOT4 | 3 | 2.1 | 4 | 0.3 | 0.003 | 7.3 |
5 | ST6GALNAC2 # | 3 | 2.1 | 2 | 0.1 | 1.12 × 10−4 | 14.6 |
6 | FSIP2 | 3 | 2.1 | 7 | 0.5 | 0.026 | 4.2 |
7 | PNPLA7 | 3 | 2.1 | 9 | 0.6 | 0.065 | 3.2 |
8 | TTN | 2 | 1.4 | 32 | 2.3 | 0.470 | 0.6 |
9 | TTLL10 | 2 | 1.4 | 5 | 0.4 | 0.084 | 3.9 |
10 | ITGA10 | 2 | 1.4 | 52 | 3.7 | 0.140 | 0.4 |
S No | Gene | No. of Cases | % Cases | No. of Controls | % Controls | p-Value | Odds Ratio |
---|---|---|---|---|---|---|---|
1 | TNXB | 10 | 6.8 | 1 | 0.1 | 0.00 × 10−0 | 102.5 |
2 | GPR112 | 7 | 4.8 | 0 | 0.0 | 0.00 × 10−0 | 150.1 |
3 | COL11A2 | 5 | 3.4 | 0 | 0.0 | 4.42 × 10−12 | 108.5 |
4 | ANKRD33B | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
5 | TBKBP1 | 5 | 3.4 | 2 | 0.1 | 2.03 × 10−8 | 24.7 |
6 | OR5K4 | 5 | 3.4 | 2 | 0.1 | 2.03 × 10−8 | 24.7 |
7 | MTAP | 5 | 3.4 | 2 | 0.1 | 2.03 × 10−8 | 24.7 |
8 | SHANK1 | 10 | 6.8 | 13 | 0.9 | 2.02 × 10−8 | 7.8 |
9 | SPRED1 | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
10 | MPP2 | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
11 | KANSL1 | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
12 | PIAS4 | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
13 | TNNI3 | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
14 | BTNL2 | 4 | 2.7 | 1 | 0.1 | 6.91 × 10−8 | 39.3 |
15 | CAPZA1 | 4 | 2.7 | 2 | 0.1 | 1.64 × 10−6 | 19.6 |
16 | OSTC | 4 | 2.7 | 2 | 0.1 | 1.64 × 10−6 | 19.6 |
17 | SOX4 | 4 | 2.7 | 2 | 0.1 | 1.64 × 10−6 | 19.6 |
S No | Gene | No. of Cases | % Cases | No. of Controls | % Controls | p-Value | Odds Ratio |
---|---|---|---|---|---|---|---|
1 | TNXB | 16 | 11.0 | 1 | 0.1 | 0.00 × 10−0 | 171.6 |
2 | TAP2 | 8 | 5.5 | 0 | 0.0 | 0.00 × 10−0 | 171.3 |
3 | GPSM3 | 7 | 4.8 | 0 | 0.0 | 0.00 × 10−0 | 150.1 |
4 | ADGRG4 | 7 | 4.8 | 0 | 0.0 | 0.00 × 10−0 | 150.1 |
5 | TMEM229A | 8 | 5.5 | 4 | 0.3 | 1.11 × 10−11 | 20.2 |
6 | ANKRD33B | 6 | 4.1 | 1 | 0.1 | 5.08 × 10−12 | 59.7 |
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Siraj, A.K.; Bu, R.; Azam, S.; Qadri, Z.; Iqbal, K.; Parvathareddy, S.K.; Al-Dayel, F.; Al-Kuraya, K.S. Whole Exome-Wide Association Identifies Rare Variants in APC Associated with High-Risk Colorectal Cancer in the Middle East. Cancers 2024, 16, 3720. https://doi.org/10.3390/cancers16213720
Siraj AK, Bu R, Azam S, Qadri Z, Iqbal K, Parvathareddy SK, Al-Dayel F, Al-Kuraya KS. Whole Exome-Wide Association Identifies Rare Variants in APC Associated with High-Risk Colorectal Cancer in the Middle East. Cancers. 2024; 16(21):3720. https://doi.org/10.3390/cancers16213720
Chicago/Turabian StyleSiraj, Abdul Khalid, Rong Bu, Saud Azam, Zeeshan Qadri, Kaleem Iqbal, Sandeep Kumar Parvathareddy, Fouad Al-Dayel, and Khawla S. Al-Kuraya. 2024. "Whole Exome-Wide Association Identifies Rare Variants in APC Associated with High-Risk Colorectal Cancer in the Middle East" Cancers 16, no. 21: 3720. https://doi.org/10.3390/cancers16213720