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Identification of SNP markers for canine mammary gland tumours in females based on a genome-wide association study – preliminary results

Anna Mucha
Anna Mucha
, 
Błażej Nowak
Błażej Nowak
, 
Stanisław Dzimira
Stanisław Dzimira
, 
Bartłomiej Liszka
Bartłomiej Liszka
 e 
Magdalena Zatoń-Dobrowolska
Magdalena Zatoń-Dobrowolska
   | 20 set 2023
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Pubblicato online: 20 set 2023
Pagine: 427 - 436
Ricevuto: 21 gen 2023
Accettato: 28 giu 2023
DOI: https://doi.org/10.2478/jvetres-2023-0040
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© 2023 Anna Mucha et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Fig. 1.

Single nucleotide polymorphism (SNP) selection results geno 95% – SNPs for which the number of missing observations did not exceed 5%; MAF – minor allele frequency; MAF 5% – SNPs for which the frequency of the rarer allele was greater than 5%; HWE – Hardy–Weinberg equilibrium (SNP for which the genetic balance criterion was met)
Single nucleotide polymorphism (SNP) selection results geno 95% – SNPs for which the number of missing observations did not exceed 5%; MAF – minor allele frequency; MAF 5% – SNPs for which the frequency of the rarer allele was greater than 5%; HWE – Hardy–Weinberg equilibrium (SNP for which the genetic balance criterion was met)

The risk of mammary gland tumours associated with particular genotypes within single nucleotide polymorphisms (SNPs) for the dominant model

CHR SNP Genotype Genotype number (percentage) OR (95% CI) P-value
Control Case
1 BICF2P448058 A/A 34 (41.5%) 1 (2.5%) 24.79 1.57 × 10−6
G/A-G/G 48 (58.5) 35 (97.2%) (3.24; 189.80)
BICF2P501513 G/G 37 (45.1%) 2 (5.6%) 13.98 7.08 × 10−6
A/G-A/A 45 (54.9%) 34 (94.4%) (3.15; 62.08)
2 TIGRP2P33447_rs8841788 A/A 41 (50.0%) 3 (8.6%) 10.67 5.15 × 10−6
G/A-G/G 41 (50.0%) 32 (91.4%) (3.03; 37.61)
3 BICF2G630704243 A/A 19 (23.2%) 24 (66.7%) 0.15 7.02 × 10−6
G/A-G/G 63 (76.8%) 12 (33.3%) (0.06; 0.36)
8 BICF2S2308912 G/G 49 (59.8%) 35 (97.2%) 0.04 2.67 × 10−6
A/G-A/A 33 (40.2%) 1 (2.8%) (0.01; 0.33)
12 BICF2S23638049 G/G 55 (67.1%) 8 (22.9%) 6.87 7.92 × 10−6
A/G-A/A 27 (32.9%) 27 (77.1%) (2.76; 17.14)
13 TIGRP2P176993_rs9197628 G/G 65 (79.3%) 13 (36.1%) 6.76 6.52 × 10−6
A/G-A/A 17 (20.7%) 23 (63.9%) (2.85; 16.06)
TIGRP2P201649_rs8752112 G/G 38 (46.3%) 32 (88.9%) 0.11 4.35 × 10−6
A/G-A/A 44 (53.7%) 4 (11.1%) (0.03; 0.33)
15 BICF2S23334099 G/G 37 (45.1%) 32 (88.9%) 0.10 2.50 × 10−6
A/G-A/A 45 (54.9%) 4 (11.1%) (0.03; 0.32)
BICF2P352914 A/A 38 (46.3%) 32 (88.9%) 0.11 4.35 × 10−6
G/A-G/G 44 (53.7%) 4 (11.1%) (0.03; 0.33)
16 BICF2P1314057 G/G 60 (73.2%) 8 (23.5%) 8.86 6.14 × 10−7
A/G-A/A 22 (26.8%) 26 (76.5%) (3.49; 22.48)
23 BICF2P373712 A/A 21 (26.2%) 26 (72.2%) 0.14 2.77 × 10−6
G/A-G/G 59 (73.8%) 10 (27.8%) (0.06; 0.33)
28 BICF2G630269882 C/C 51 (62.2%) 6 (17.1%) 7.95 3.93 × 10−6
A/C-A/A 31 (37.8%) 29 (82.9%) (2.97; 21.31)
32 BICF2S23661944 G/G 50 (61.0%) 35 (97.2%) 0.04 4.52 × 10−6
A/G-A/A 32 (39.0%) 1 (2.8%) (0.01; 0.34)

Summary of single nucleotide polymorphisms (SNPs) statistically significantly associated with the occurrence of mammary gland tumours

SNP CHR Location (bp) Minor allele MAF (%) MAFcontrol (%) MAFcase (%) HWE P-value Candidate gene or locus/nearest gene or locus
BICF2P448058 1 65,212,166 G 46.19 37.20 66.67 0.85 LOC111096229 / TRMT11
BICF2P501513 1 65,293,673 A 42.37 32.93 63.89 1.00 - / LOC111096229, LOC111096230
BICF2P776685 1 65,819,801 A 46.61 56.71 23.61 0.46 - / LOC100684456, LOC102153070
BICF2S2334324 1 14,217,295 G 47.03 52.44 34.72 0.47 ZCCHC2 / -
BICF2P343250 1 67,922,585 A 27.97 32.32 18.06 0.25 LAMA2 / -
BICF2P825735 1 41,988,950 A 14.83 6.71 33.33 0.00 ARMT1
BICF2P345133 1 66,185,882 A 36.86 26.22 61.11 0.00 - / LOC111096246
TIGRP2P33447_rs8841788 2 82,135,437 G 39.32 32.93 54.29 0.70 ARHGEF19 / -
BICF2G630704243 3 27,421,551 G 41.53 51.22 19.44 0.34 HOMER1 / -
BICF2S23125394 3 36,857,983 A 49.57 57.93 30.00 0.06 - / MKRN3
BICF2G630704438 3 27,777,144 A 49.57 59.76 26.39 0.03 DMGDH / -
TIGRP2P107898_rs9044787 8 12664933 A 36.75 24.07 65.28 0.05 NPAS3 / -
BICF2S2308912 8 49,696,532 A 19.07 26.83 1.39 0.00 - / LOC111097115
BICF2P158200 8 34,943,508 A 17.37 11.59 30.56 0.34 CCDC175, JKAMP / -
BICF2P441276 8 56,964,583 A 39.57 37.80 43.94 0.02 LOC111097128 / FLRT2
BICF2S23760334 10 47,442,988 A 36.44 33.53 43.06 0.00 - /LOC100687001, PPM1B
BICF2P576198 11 61,345,663 G 47.88 56.71 27.78 0.01 - / LOC102156133, LOC612266, SMC2
BICF2S23118240 11 52,671,467 A 23.73 26.22 18.06 0.01 - / DNAJB5, C11H9orf131
BICF2S23638049 12 19,343,255 A 26.50 19.51 42.86 1.00 - / LOC119876904, LOC119874254
TIGRP2P176993_rs9197628 13 39,050,399 A 19.49 10.98 38.89 0.38 LIMCH1 / -
BICF2P797481 14 45,742,638 A 42.80 53.05 19.44 0.19 - / LOC106559680
BICF2P720053 14 45,744,668 G 42.37 52.44 19.44 0.19 - / LOC106559680
TIGRP2P201649_rs8752112 15 42,346,461 A 27.12 35.37 8.33 0.00 LOC119869373 / ASCL1
BICF2P352914 15 42,358,113 G 27.12 35.37 8.33 0.00 ASCL1 / -
BICF2S23334099 15 42,352,911 A 27.54 35.98 8.33 0.00 ASCL1 / -
BICF2P1314057 16 35,869,183 A 23.28 14.63 44.12 1.00 RBPMS / -
TIGRP2P268994_rs8894778 19 46,961,958 A 27.35 22.56 38.57 0.06 ARHGAP15 / -
BICF2P801296 22 7,706,835 A 49.15 56.10 32.86 0.10 ENOX1 / -
BICF2P373712 23 51,871,689 G 43.53 55.63 16.67 0.00 - / LOC111092021, VEPH1
BICF2S23648284 24 29,281,559 T 25.42 17.07 44.44 1.00 LOC119865549 / -
BICF2G630269882 28 20,841,387 A 29.91 21.95 48.57 1.00 - / LOC111092968
BICF2G630397948 30 35,183,072 A 42.37 31.71 66.67 0.00 THSD4 / -
BICF2S23661944 32 29,141,932 A 16.53 23.17 1.39 0.09 LOC106558120 / -
BICF2S23049081 34 30,205,708 G 49.58 39.02 73.61 0.07 - / LOC111093899
BICF2S23219997 35 20,654,940 A 22.03 14.63 38.89 0.01 - / LOC119867672
BICF2P28560 35 15,603,710 A 36.44 46.34 13.89 0.05 ATXN1 / -
BICF2G630136001 37 30,735,796 A 38.46 34.76 47.14 0.56 DLGAP2 / -
BICF2G630129768 37 24,240,716 G 38.98 35.98 45.83 0.44 - / LOC102156106, LOC111094390
BICF2G630127550 37 9,335,944 G 40.25 50.00 18.06 0.03 SPATS2L / -
BICF2S23347259 X 32,408,330 A 31.62 25.61 45.71 0.20 LANCL3 / -

The risk of mammary gland tumours associated with particular genotypes within single nucleotide polymorphisms (SNPs) for the codominant model

CHR SNP Genotype Genotype number (percentage) OR 95% CI P-value
Control Case
1 BICF2P448058 A/A 34 (41.5%) 1 (2.8%) 1.00
G/A 35 (42.7%) 22 (61.1%) 2.73 (2.73; 167.5) 6.1 × 10−6
G/G 13 (15.9%) 13 (36.1%) 4.03 (4.03; 286.7)
BICF2P501513 G/G 37 (45.1%) 2 (5.6%) 1.00
A/G 36 (43.9%) 22 (61.1%) 11.31 (2.48; 51.61) 7.1 × 10−6
A/A 9 (11.0%) 12 (33.3%) 24.67 (4.67; 130.35)
BICF2P776685 G/G 16 (19.5%) 20 (55.6%) 1.00
A/G 39 (47.6%) 15 (41.7%) 0.13 (0.13; 0.75) 8.9 × 10−6
A/A 27 (32.9%) 1 (2.8%) 0.00 (0.00; 0.24)
8 TIGRP2P107898_rs9044787 G/G 46 (56.8%) 6 (16.7%) 1.00
A/G 31 (38.3%) 13 (36.1%) 3.22 (1.10; 9.37) 5.7 × 10−8
A/A 4 (4.9%) 17 (47.2%) 32.58 (8.18; 129.78)
14 BICF2P797481 G/G 19 (23.2%) 23 (63.9%) 1.00
A/G 39 (47.6%) 12 (33.3%) 0.25 (0.10; 0.62) 8.8 × 10−6
A/A 24 (29.3%) 1 (2.8%) 0.03 (0.00; 0.28)
16 BICF2P1314057 G/G 60 (73.2%) 8 (23.5%) 1.00
A/G 20 (24.4%) 22 (64.7%) 8.25 (3.18; 21.43) 3.2 × 10−6
A/A 2 (2.4%) 4 (11.8%) 15.00 (2.36; 95.47)
19 TIGRP2P268994_rs8894778 G/G 56 (68.3%) 10 (28.6%) 1.00
A/G 15 (18.3%) 23 (65.7%) 8.59 (3.37; 21.89) 4.8 × 10−6
A/A 11 (13.4%) 2 (5.7%) 1.02 (0.20; 5.30)
23 BICF2P373712 A/A 21 (26.2%) 26 (72.2%) 1.00
G/A 29 (36.2%) 8 (22.2%) 0.22 (0.08; 0.59) 2.9 × 10−6
G/G 30 (37.5%) 2 (5.6%) 0.05 (0.01; 0.25)
37 BICF2G630136001 G/G 42 (51.2%) 4 (11.4%) 1.00
A/G 23 (28.0%) 29 (82.9%) 13.24 (4.14; 42.34) 1.5 × 10−7
A/A 17 (20.7%) 2 (5.7%) 1.24 (0.21; 7.39)

Single nucleotide polymorphisms statistically significantly associated with the occurrence of mammary gland tumours

Chromosomes Codominant Dominant Recessive Overdominant Log-additive
1

BICF2P448058

BICF2P501513

BICF2P776685

BICF2P448058

BICF2P501513

 BICF2S2334324 BICF2P343250

BICF2P825735

BICF2P501513

BICF2P776685

BICF2P345133
2 -

TIGRP2P33447_rs8

841788

 - - -
3 - BICF2G630704243 BICF2S23125394 -

BICF2G630704243

BICF2G630704438
8

TIGRP2P107898_rs

9044787

 BICF2S2308912

TIGRP2P107898_rs

9044787

 BICF2P158200

TIGRP2P107898_rs

9044787*
10 - - - BICF2S23760334 -
11 - - BICF2P576198 BICF2S23118240 -
12 - BICF2S23638049 - - -
13 -

TIGRP2P176993_rs

9197628

 - -

TIGRP2P176993_rs

9197628
14 BICF2P797481 - - -

BICF2P797481

BICF2P720053
15 -

TIGRP2P201649_rs

8752112

BICF2S23334099

BICF2P352914

 - - -
16 BICF2P1314057 BICF2P1314057 - - BICF2P1314057
19

TIGRP2P268994_rs

8894778

 - -

TIGRP2P268994_rs

8894778

 -
22 - - BICF2P801296 - -
23 BICF2P373712 BICF2P373712 - - BICF2P373712
24 - - - - BICF2S23648284
28 - BICF2G630269882 - - -
30 - - - - BICF2G630397948
32 - BICF2S23661944 - - -
34 - - BICF2S23049081 - BICF2S23049081
35 - - BICF2S23219997 - BICF2P28560
37 BICF2G630136001 - -

BICF2G630129768

BICF2G630136001*

 BICF2G630127550
X - - - BICF2S23347259 -

The risk of mammary gland tumours associated with particular genotypes within single nucleotide polymorphisms (SNPs) for the overdominant model

CHR SNP Genotype Genotype number (percentage) OR (95% CI) P-value
Control Case
1 BICF2P343250 G/G-A/A 43 (52.4%) 33 (91.7%) 0.10 9.99 × 10−6
A/G 39 (47.6%) 3 (8.3%) (0.03; 0.35)
8 BICF2P158200 G/G-A/A 71 (86.6%) 16 (44.4%) 8.07 3.03 × 10−6
A/G 11 (13.4%) 20 (55.6%) (3.23; 20.13)
BICF2P441276 G/G-A/A 62 (75.6%) 10 (30.3%) 7.13 6.16 × 10−6
A/G 20 (24.4%) 23 (69.7%) (2.91; 17.49)
10 BICF2S23760334 G/G-A/A 65 (79.3%) 13 (36.1%) 6.76 6.52 × 10−6
A/G 17 (20.7%) 23 (63.9%) (2.85; 16.06)
11 BICF2S23118240 G/G-A/A 51 (62.2%) 35 (97.2%) 0.05 7.59 × 10−6
A/G 31 (37.8%) 1 (2.8%) (0.01; 0.36)
19 TIGRP2P268994_rs8894778 G/G-A/A 67 (81.7%) 12 (34.3%) 8.56 7.49 × 10−7
A/G 15 (18.3%) 23 (65.7%) (3.50; 20.95)
37 BICF2G630129768 A/A-G/G 57 (69.5%) 9 (25.0%) 6.84 5.72 × 10−6
G/A 25 (30.5%) 27 (75.0%) (2.81; 16.64)
BICF2G630136001 G/G-A/A 59 (72.0%) 6 (17.1%) 12.4 2.14 × 10−8
A/G 23 (28.0%) 29 (82.9%) (4.55; 33.78)
X BICF2S23347259 G/G-A/A 62 (75.6%) 11 (31.4%) 6.76 6.79 × 10−6
A/G 20 (24.4%) 24 (68.6%) (2.82; 16.20)

The risk of mammary gland tumours associated with particular genotypes within single nucleotide polymorphisms (SNPs) for the recessive model

CHR SNP Genotype Genotype number (percentage) OR (95% CI) P-value
Control Case
1 BICF2S2334324 A/A-G/A 54 (65.9%) 36 (100%) 0 9.24 × 10−6
G/G 28 (34.1%) 0 (0%) 0
3 BICF2S23125394 C/C-A/C 49 (59.8%) 34 (97.1%) 0.04 3.70 × 10−6
A/A 33 (40.2%) 1 (2.9%) (0.01; 0.33)
8 TIGRP2P107898_rs9044787 G/G-A/G 77 (95.1%) 19 (52.8%) 17.22 9.55 × 10−8
A/A 4 (4.9%) 17 (47.2%) (5.19; 57.15)
11 BICF2P576198 A/A-G/A 49 (59.8%) 35 (97.2%) 0.04 2.67 × 10−6
G/G 33 (40.2%) 1 (2.8%) (0.01; 0.33)
22 BICF2P801296 G/G-A/G 50 (61.0%) 34 (97.1%) 0.05 6.19 × 10−6
A/A 32 (39.0%) 1 (2.9%) (0.01; 0.35)
34 BICF2S23049081 A/A-G/A 69 (84.1%) 15 (41.7%) 7.43 4.35 × 10−6
G/G 13 (15.9%) 21 (58.3%) (3.05; 18.08)
35 BICF2S23219997 G/G-A/G 81 (98.8%) 26 (72.2%) 31.15 8.60 ×10−6
A/A 1 (1.2%) (27.8%) (3.81; 255.00)

The risk of mammary gland tumours associated with particular genotypes within single nucleotide polymorphisms (SNPs) for the log-additive model

CHR SNP Genotype OR 95% CI P-value
1 BICF2P825735 0, 1, 2 4.66 (2.17; 9.99) 9.95 × 10−6
BICF2P501513 0, 1, 2 4.21 (2.11; 8.37) 5.17 × 10−6
BICF2P776685 0, 1, 2 0.23 (0.12; 0.46) 2.40 × 10−6
BICF2P345133 0, 1, 2 3.25 (1.87; 5.67) 8.34 × 10−6
3 BICF2G630704243 0, 1, 2 0.23 (0.11; 0.47) 4.23 × 10−6
BICF2G630704438 0, 1, 2 0.28 (0.15; 0.52) 8.86 × 10−6
8 TIGRP2P107898_rs9044787 0, 1, 2 5.46 (2.76; 10.81) 1.60 × 10−8
13 TIGRP2P176993_rs9197628 0, 1, 2 5.39 (2.50; 11.61) 2.19 × 10−6
14 BICF2P797481 0, 1, 2 0.22 (0.11; 0.45) 1.62 × 10−6
BICF2P720053 0, 1, 2 0.23 (0.12; 0.46) 2.89 × 10−6
16 BICF2P1314057 0, 1, 2 5.87 (2.65; 13.03) 1.16 × 10−6
23 BICF2P373712 0, 1, 2 0.23 (0.12; 0.45) 4.49 × 10−7
24 BICF2S23648284 0, 1, 2 4.78 (2.27; 10.08) 6.34 × 10−6
30 BICF2G630397948 0, 1, 2 3.39 (1.91; 6.03) 6.58 × 10−6
34 BICF2S23049081 0, 1, 2 3.92 (2.07; 7.41) 2.84 × 10−6
35 BICF2P28560 0, 1, 2 0.22 (0.10; 0.46) 2.81 × 10−6
37 BICF2G630127550 0, 1, 2 0.26 (0.13; 0.51) 9.59 × 10−6
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