Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer
Abstract
:1. Introduction
2. Experimental Section
2.1. Samples
2.2. Genomic Array Analysis
2.3. Statistical, Pathway and Annotation Analysis
3. Results and Discussion
3.1. Resolution
3.2. CNV Detection
CNV Count | CNV Size (Kb) | ||||||
---|---|---|---|---|---|---|---|
Participants | Total CNVs per group | Median CNVs per sample | Mean CNVs per sample | Total CNV affected genome per group | Mean total CNV affected genome per sample | Mean size of a CNV | |
Patients | 125 | 439 | 2 | 3.51 | 35,508.53 | 284.07 | 70.08 |
Controls | 40 | 104 | 2 | 2.60 | 11,820.75 | 295.52 | 106.57 |
p | − | − | − | 0.2980 | − | 0.9121 | 0.0165 * |
3.3. MMR Gene Interrogation
Gene | Chr. | Start (bp) | End (bp) | Size (Kb) | Search start (bp) | Search end (bp) |
---|---|---|---|---|---|---|
EXO1 | 1 | 240,078,157 | 240,119,671 | 42 | 240,028,157 | 240,169,671 |
RPA2 | 1 | 28,090,635 | 28,113,823 | 23 | 28,040,635 | 28,163,823 |
MSH2 | 2 | 47,783,766 | 47,563,864 | 80 | 47,733,766 | 47,613,864 |
MSH6 | 2 | 47,863,724 | 47,887,596 | 24 | 47,813,724 | 47,937,596 |
PMS1 | 2 | 190,357,055 | 190,450,600 | 94 | 190,307,055 | 190,500,600 |
MLH1 | 3 | 37,009,982 | 37,067,341 | 57 | 36,959,982 | 37,117,341 |
RFC4 | 3 | 187,990,375 | 188,007,178 | 17 | 187,940,375 | 188,057,178 |
RFC1 | 4 | 38,965,470 | 39,044,390 | 79 | 38,915,470 | 39,094,390 |
MSH3 | 5 | 79,986,049 | 80,208,390 | 222 | 79,936,049 | 80,258,390 |
PMS2 | 7 | 5,979,395 | 6,015,263 | 36 | 5,929,395 | 6,065,263 |
POLD2 | 7 | 44,120,810 | 44,129,672 | 9 | 44,070,810 | 44,179,672 |
RFC2 | 7 | 73,283,767 | 73,306,674 | 23 | 73,233,767 | 73,356,674 |
RPA3 | 7 | 7,643,099 | 7,724,763 | 82 | 7,593,099 | 7,774,763 |
POLD3 | 11 | 73,981,276 | 74,031,413 | 50 | 73,931,276 | 74,081,413 |
POLD4 | 11 | 66,875,594 | 66,877,593 | 2 | 66,825,594 | 66,927,593 |
RFC5 | 12 | 116,938,890 | 116,954,422 | 16 | 116,888,890 | 117,004,422 |
RFC3 | 13 | 33,290,205 | 33,438,695 | 148 | 33,240,205 | 33,488,695 |
MLH3 | 14 | 74,550,219 | 74,587,988 | 38 | 74,500,219 | 74,637,988 |
RPA1 | 17 | 1,680,022 | 1,749,598 | 70 | 1,630,022 | 1,799,598 |
LIG1 | 19 | 53,310,514 | 53,365,372 | 55 | 53,260,514 | 53,415,372 |
POLD1 | 19 | 55,579,404 | 55,613,083 | 34 | 55,529,404 | 55,663,083 |
PCNA | 20 | 5,043,598 | 5,055,268 | 12 | 4,993,598 | 5,105,268 |
3.4. Occurrence and Distribution of CNVs in Patients and Controls
Type | 2 CNV events | 3 CNV events | 4 CNV events | |||
---|---|---|---|---|---|---|
Gains | ADARB2 | DEFB125 | ITGA1 | PSG8 | GK5 | LOC642597 |
APC | DEFB126 | KIAA1680 | RBCK1 | IGSF11 | ||
ARHGAP19 | DEFB127 | LATS2 | RNF125 | LCP1 | ||
B2M | DEFB128 | MLL | RNF138 | XRN1 | ||
BBOX1 | DEFB129 | MSI2 | SOX12 | NAMPT | ||
C10orf139 | DEFB132 | NRSN2 | TBC1D20 | |||
C14orf23 | EPHA7 | NXPH1 | TFG | |||
C20orf96 | FAM134B | ODZ4 | TRIB3 | |||
C3orf33 | FOXG1 | PELO | TRIM69 | |||
CNTN5 | GPR128 | PHC3 | WDR37 | |||
CNTNAP2 | GPR160 | PRKCI | ZCCHC3 | |||
CSNK2A1 | GYPE | PSG10 | ZMYND11 | |||
Losses | CNTN4 | CTNNA3 | ||||
DCDC1 | ||||||
PPP2R3C | ||||||
Both | NRG3 |
Chr. | Start (bp) | End (bp) | Size (Kb) | Conf | Probes |
---|---|---|---|---|---|
2 CNV gains | |||||
3 | 189,058,439 | 189,098,718 | 40.28 | 0.93 | 31 |
3 | 189,069,317 | 189,088,009 | 18.69 | 0.94 | 26 |
4 | 44,664,798 | 44,699,744 | 34.95 | 0.92 | 41 |
4 | 44,664,798 | 44,699,744 | 34.95 | 0.90 | 41 |
8 | 120,414,388 | 120,438,172 | 23.78 | 0.91 | 27 |
8 | 120,419,721 | 120,451,773 | 32.05 | 0.91 | 30 |
11 | 29,547,229 | 29,593,722 | 46.49 | 0.90 | 39 |
11 | 29,547,756 | 29,593,722 | 45.97 | 0.91 | 37 |
16 | 25,330,672 | 25,438,375 | 107.70 | 0.92 | 46 |
16 | 25,330,672 | 25,438,375 | 107.70 | 0.92 | 46 |
3 CNV gains | |||||
3 | 19,014,033 | 19,041,376 | 27.34 | 0.90 | 31 |
3 | 19,016,875 | 19,041,376 | 24.50 | 0.91 | 28 |
3 | 19,016,875 | 19,041,376 | 24.50 | 0.91 | 28 |
5 | 59,744,695 | 59,807,906 | 63.21 | 0.92 | 52 |
5 | 59,744,695 | 59,811,770 | 67.08 | 0.93 | 54 |
5 | 59,749,693 | 59,807,906 | 58.21 | 0.92 | 51 |
9 | 103,982,826 | 104,016,588 | 33.76 | 0.91 | 27 |
9 | 103,982,826 | 104,017,715 | 34.89 | 0.90 | 28 |
9 | 103,991,205 | 104,017,715 | 26.51 | 0.91 | 26 |
11 | 15,765,333 | 15,791,331 | 26.00 | 0.90 | 30 |
11 | 15,770,233 | 15,796,302 | 26.07 | 0.92 | 30 |
11 | 15,776,946 | 15,795,665 | 18.72 | 0.91 | 24 |
12 | 16,469,855 | 16,503,960 | 34.11 | 0.91 | 33 |
12 | 16,469,855 | 16,503,960 | 34.11 | 0.91 | 33 |
12 | 16,476,470 | 16,506,851 | 30.38 | 0.92 | 33 |
4 CNV gains | |||||
16 | 63,364,955 | 63,389,659 | 24.70 | 0.91 | 33 |
16 | 63,369,029 | 63,389,029 | 20.00 | 0.92 | 30 |
16 | 63,369,960 | 63,388,189 | 18.23 | 0.90 | 28 |
16 | 63,371,038 | 63,397,352 | 26.31 | 0.92 | 38 |
5 CNV gains | |||||
5 | 116,651,923 | 116,698,621 | 46.70 | 0.91 | 36 |
5 | 116,655,439 | 116,692,153 | 36.71 | 0.92 | 27 |
5 | 116,656,039 | 116,695,730 | 39.69 | 0.91 | 29 |
5 | 116,660,694 | 116,697,347 | 36.65 | 0.93 | 28 |
5 | 116,660,694 | 116,693,035 | 32.34 | 0.91 | 24 |
2 CNV losses | |||||
1 | 82,801,000 | 82,821,932 | 20.93 | 0.93 | 31 |
1 | 82,801,000 | 82,821,932 | 20.93 | 0.94 | 31 |
2 | 22,087,558 | 22,261,901 | 174.34 | 0.91 | 110 |
2 | 22,087,558 | 22,261,901 | 174.34 | 0.93 | 110 |
2 | 215,167,158 | 215,204,595 | 37.44 | 0.93 | 49 |
2 | 215,167,158 | 215,204,595 | 37.44 | 0.91 | 49 |
3 | 6,562,398 | 6,603,706 | 41.31 | 0.94 | 42 |
3 | 6,562,398 | 6,603,706 | 41.31 | 0.93 | 42 |
3 | 166,523,809 | 166,565,186 | 41.38 | 0.95 | 39 |
3 | 166,525,250 | 166,565,186 | 39.94 | 0.93 | 38 |
5 | 61,460,851 | 61,504,678 | 43.83 | 0.95 | 31 |
5 | 61,460,851 | 61,504,678 | 43.83 | 0.93 | 31 |
7 | 92,319,307 | 92,343,906 | 24.60 | 0.94 | 26 |
7 | 92,319,307 | 92,343,906 | 24.60 | 0.94 | 26 |
9 | 104,331,902 | 104,396,632 | 64.73 | 0.96 | 35 |
9 | 104,331,902 | 104,396,632 | 64.73 | 0.96 | 35 |
5 CNV losses | |||||
3 | 177,370,126 | 177,396,832 | 26.71 | 0.93 | 26 |
3 | 177,370,126 | 177,396,832 | 26.71 | 0.94 | 26 |
3 | 177,370,126 | 177,396,832 | 26.71 | 0.96 | 26 |
3 | 177,370,126 | 177,399,625 | 29.50 | 0.93 | 27 |
3 | 177,370,126 | 177,396,832 | 26.71 | 0.93 | 26 |
2 CNV gain and loss | |||||
7 * | 110,748,452 | 111,047,157 | 298.71 | 0.93 | 291 |
7 ** | 111,007,466 | 111,052,498 | 45.03 | 0.94 | 25 |
3 ** | 21,228,980 | 21,313,310 | 84.33 | 0.90 | 88 |
3 * | 21,273,619 | 21,339,035 | 65.42 | 0.92 | 62 |
3.5. Pathway Analysis
KEGG Pathway | Genes in Pathway | Observed | Expected | p |
---|---|---|---|---|
Carbohydrate digestion and absorption | 44 | 5 | 0.32 | 0.0012 |
Starch and sucrose metabolism | 54 | 5 | 0.4 | 0.0017 |
Metabolic pathways | 1,130 | 21 | 8.31 | 0.0023 |
Salivary secretion | 89 | 5 | 0.65 | 0.0058 |
Tight junction | 132 | 6 | 0.97 | 0.0058 |
Neurotrophin signaling pathway | 127 | 6 | 0.93 | 0.0058 |
Propanoate metabolism | 32 | 3 | 0.24 | 0.017 |
Valine, leucine and isoleucine degradation | 44 | 3 | 0.32 | 0.0251 |
Prostate cancer | 89 | 4 | 0.65 | 0.0251 |
Ribosome biogenesis in eukaryotes | 80 | 4 | 0.59 | 0.0251 |
ErbB signaling pathway | 87 | 4 | 0.64 | 0.0251 |
mRNA surveillance pathway | 83 | 4 | 0.61 | 0.0251 |
Terpenoid backbone biosynthesis | 15 | 2 | 0.11 | 0.0285 |
Malaria | 51 | 3 | 0.37 | 0.0293 |
Endometrial cancer | 52 | 3 | 0.38 | 0.0293 |
Glycerolipid metabolism | 50 | 3 | 0.37 | 0.0293 |
Olfactory transduction | 388 | 8 | 2.85 | 0.0346 |
beta-Alanine metabolism | 22 | 2 | 0.16 | 0.0439 |
3.6. MicroRNA Annotation
Category | # sub-categories | # of Sig. Categories | Significant Findings |
---|---|---|---|
Family | 22 | 1 | miR-17 |
Cluster | 33 | 0 | − |
Function | 39 | 8 | Onco-miRs, Apoptosis, Cell cycle related |
HMDD | 162 | 20 | Cancer (80%), Cardiovascular (4%), Infection (4%) and Psychological disorders (10%) |
Tissue | 5 | 1 | Placenta |
3.7. CNV Burden
3.8. CNV Bias
4. Conclusions
Acknowledgements
Conflicts of Interest
References
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Masson, A.L.; Talseth-Palmer, B.A.; Evans, T.-J.; Grice, D.M.; Duesing, K.; Hannan, G.N.; Scott, R.J. Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer. Genes 2013, 4, 536-555. https://doi.org/10.3390/genes4040536
Masson AL, Talseth-Palmer BA, Evans T-J, Grice DM, Duesing K, Hannan GN, Scott RJ. Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer. Genes. 2013; 4(4):536-555. https://doi.org/10.3390/genes4040536
Chicago/Turabian StyleMasson, Amy L., Bente A. Talseth-Palmer, Tiffany-Jane Evans, Desma M. Grice, Konsta Duesing, Garry N. Hannan, and Rodney J. Scott. 2013. "Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer" Genes 4, no. 4: 536-555. https://doi.org/10.3390/genes4040536
APA StyleMasson, A. L., Talseth-Palmer, B. A., Evans, T. -J., Grice, D. M., Duesing, K., Hannan, G. N., & Scott, R. J. (2013). Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer. Genes, 4(4), 536-555. https://doi.org/10.3390/genes4040536