Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis
Abstract
:Simple Summary
Abstract
1. Introduction
2. Methods
2.1. Animals
2.2. Pedigree Construction
2.3. Genotyping and Imputation
2.4. Genome-Wide Association Study (GWAS)
2.5. Haplotype Analysis
2.6. Relationship Networks (NetView)
2.7. Restricted Maximum Likelihood (REML) Analysis
3. Results
3.1. Pedigree Investigations
3.2. GWAS with Quantitative Phenotype
3.3. GWAS with Binary Phenotype
3.4. Phenotypic Variance Explained by Genetic Variance (Heritability)
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Location (Chr:BP) | p-Value | q-Value | A1 | A2 | A1 Freq | b | SE | Gene | Frequency of A1A1 (No. of Dogs) | Frequency of A1A2 (No. of Dogs) | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Lym. | Carr. | Cont. | Lym. | Carr. | Cont. | |||||||||
18:38704682 | 1.32 × 10−5 | 0.022 | A | G | 0.32 | 0.36 | 0.08 | - | 0.26 (8) | 0.19 (5) | 0.08 (9) | 0.55 (17) | 0.33 (9) | 0.37 (44) |
18:38233567 | 2.80 × 10−5 | 0.022 | A | G | 0.12 | 0.55 | 0.13 | - | 0.06 (2) | 0 (0) | 0 (0) | 0.42 (13) | 0.41 (11) | 0.13 (15) |
18:38719709 | 4.12 × 10−5 | 0.022 | G | A | 0.32 | 0.34 | 0.08 | - | 0.23 (7) | 0.22 (6) | 0.08 (9) | 0.55 (17) | 0.37 (10) | 0.34 (41) |
18:38502268 | 4.15 × 10−5 | 0.022 | A | G | 0.14 | 0.50 | 0.12 | ZDHHC5 | 0.1 (3) | 0 (0) | 0 (0) | 0.39 (12) | 0.41 (11) | 0.16 (19) |
18:38507461 | 4.15 × 10−5 | 0.022 | A | G | 0.14 | 0.50 | 0.12 | ZDHHC5 | 0.1 (3) | 0 (0) | 0 (0) | 0.39 (12) | 0.41 (11) | 0.16 (19) |
18:38510335 | 4.15 × 10−5 | 0.022 | A | G | 0.14 | 0.50 | 0.12 | ZDHHC5 | 0.1 (3) | 0 (0) | 0 (0) | 0.39 (12) | 0.41 (11) | 0.16 (19) |
18:37737740 | 5.70 × 10−5 | 0.022 | C | A | 0.14 | 0.49 | 0.12 | - | 0.06 (2) | 0 (0) | 0 (0) | 0.45 (14) | 0.41 (11) | 0.16 (19) |
18:39140112 | 5.97 × 10−5 | 0.022 | G | A | 0.25 | 0.38 | 0.09 | LOC100688997 | 0.16 (5) | 0.07 (2) | 0.03 (4) | 0.58 (18) | 0.33 (9) | 0.34 (41) |
18:41229735 | 6.06 × 10−5 | 0.022 | A | G | 0.44 | 0.33 | 0.08 | LOC100684610 (OR4C5) | 0.45 (14) | 0.22 (6) | 0.13 (15) | 0.42 (13) | 0.56 (15) | 0.49 (58) |
18:38350947 | 8.02 × 10−5 | 0.023 | A | G | 0.12 | 0.51 | 0.13 | - | 0.06 (2) | 0 (0) | 0 (0) | 0.42 (13) | 0.41 (11) | 0.13 (16) |
18:38456518 | 8.02 × 10−5 | 0.023 | A | G | 0.12 | 0.51 | 0.13 | CTNND1 | 0.06 (2) | 0 (0) | 0 (0) | 0.42 (13) | 0.41 (11) | 0.13 (16) |
18:40281122 | 9.65 × 10−5 | 0.026 | A | G | 0.42 | 0.31 | 0.08 | - | 0.42 (13) | 0.19 (5) | 0.13 (16) | 0.42 (13) | 0.56 (15) | 0.45 (53) |
18:40286669 | 1.22 × 10−4 | 0.030 | G | A | 0.43 | 0.31 | 0.08 | - | 0.42 (13) | 0.19 (5) | 0.13 (16) | 0.42 (13) | 0.56 (15) | 0.47 (56) |
18:38326192 | 1.54 × 10−4 | 0.030 | A | G | 0.14 | 0.46 | 0.12 | OR10C10 | 0.06 (2) | 0 (0) | 0 (0) | 0.42 (13) | 0.41 (11) | 0.17 (20) |
18:41436427 | 1.63 × 10−4 | 0.030 | C | A | 0.50 | −0.31 | 0.08 | - | 0.1 (3) | 0.07 (2) | 0.35 (42) | 0.42 (13) | 0.67 (18) | 0.45 (53) |
18:41854962 | 1.64 × 10−4 | 0.030 | C | G | 0.15 | 0.42 | 0.11 | - | 0.1 (3) | 0.04 (1) | 0.01 (1) | 0.32 (10) | 0.44 (12) | 0.17 (20) |
18:37862012 | 1.69 × 10−4 | 0.030 | A | T | 0.18 | 0.40 | 0.11 | - | 0.19 (6) | 0.04 (1) | 0 (0) | 0.32 (10) | 0.41 (11) | 0.24 (28) |
18:37867871 | 1.69 × 10−4 | 0.030 | A | G | 0.18 | 0.40 | 0.11 | OR5B21 | 0.19 (6) | 0.04 (1) | 0 (0) | 0.32 (10) | 0.41 (11) | 0.24 (28) |
18:40667579 | 2.48 × 10−4 | 0.042 | C | A | 0.47 | 0.30 | 0.08 | - | 0.45 (14) | 0.22 (6) | 0.15 (18) | 0.45 (14) | 0.56 (15) | 0.5 (60) |
18:40653765 | 2.87 × 10−4 | 0.046 | A | C | 0.47 | 0.30 | 0.08 | - | 0.45 (14) | 0.22 (6) | 0.15 (18) | 0.45 (14) | 0.56 (15) | 0.53 (63) |
18:39177075 | 3.56 × 10−4 | 0.053 | A | G | 0.32 | 0.32 | 0.09 | - | 0.23 (7) | 0.15 (4) | 0.08 (9) | 0.55 (17) | 0.44 (12) | 0.38 (45) |
18:40418483 | 3.64 × 10−4 | 0.053 | A | G | 0.47 | 0.29 | 0.08 | - | 0.42 (13) | 0.22 (6) | 0.16 (19) | 0.48 (15) | 0.52 (14) | 0.52 (62) |
18:55380537 | 3.89 × 10−4 | 0.054 | A | T | 0.44 | −0.30 | 0.08 | TMEM109 | 0 (0) | 0 (0) | 0.29 (35) | 0.48 (15) | 0.59 (16) | 0.47 (56) |
18:37249960 | 4.14 × 10−4 | 0.055 | A | G | 0.14 | 0.40 | 0.11 | LOC483451 | 0.1 (3) | 0 (0) | 0.01 (1) | 0.39 (12) | 0.37 (10) | 0.16 (19) |
18:39727438 | 5.07 × 10−4 | 0.065 | G | A | 0.31 | 0.29 | 0.08 | - | 0.29 (9) | 0.11 (3) | 0.08 (9) | 0.45 (14) | 0.48 (13) | 0.35 (42) |
18:38838399 | 6.64 × 10−4 | 0.082 | G | A | 0.48 | 0.26 | 0.08 | - | 0.45 (14) | 0.33 (9) | 0.21 (25) | 0.45 (14) | 0.37 (10) | 0.43 (51) |
18:38807806 | 7.17 × 10−4 | 0.085 | A | G | 0.15 | 0.41 | 0.12 | SSRP1 | 0.06 (2) | 0 (0) | 0 (0) | 0.45 (14) | 0.37 (10) | 0.2 (24) |
18:40076496 | 8.15 × 10−4 | 0.093 | G | A | 0.21 | 0.34 | 0.10 | - | 0.13 (4) | 0.04 (1) | 0.02 (2) | 0.48 (15) | 0.41 (11) | 0.29 (34) |
Location (Chr:BP) | p-Value | q-Value | A1 | A2 | A1 Freq | b | SE | Gene | Frequency of A1A1 (No. of Dogs) | Frequency of A1A2 (No. of Dogs) | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Lym. | Carr. | Cont. | Lym. | Carr. | Cont. | |||||||||
27:8892980 | 3.55 × 10−5 | 0.038 | C | G | 0.22 | 0.36 | 0.09 | ANO6 | 0.16 (5) | 0.04 (1) | 0.04 (5) | 0.55 (17) | 0.37 (10) | 0.25 (30) |
27:3594560 | 4.29 × 10−5 | 0.038 | G | A | 0.15 | 0.42 | 0.10 | BIN2 | 0.13 (4) | 0.07 (2) | 0 (0) | 0.45 (14) | 0.26 (7) | 0.18 (21) |
27:5364442 | 4.35 × 10−5 | 0.038 | A | G | 0.18 | 0.39 | 0.10 | LOC111092735 | 0.16 (5) | 0.07 (2) | 0.01 (1) | 0.42 (13) | 0.33 (9) | 0.22 (26) |
27:5112245 | 5.50 × 10−5 | 0.038 | A | G | 0.24 | 0.34 | 0.09 | SPATS2 | 0.29 (9) | 0.11 (3) | 0.02 (2) | 0.39 (12) | 0.52 (14) | 0.27 (32) |
27:3234647 | 6.07 × 10−5 | 0.038 | G | A | 0.18 | 0.39 | 0.10 | SCN8A | 0.13 (4) | 0.07 (2) | 0.03 (3) | 0.48 (15) | 0.26 (7) | 0.19 (23) |
27:8331252 | 1.13 × 10−4 | 0.053 | G | A | 0.12 | 0.44 | 0.11 | - | 0.06 (2) | 0.04 (1) | 0 (0) | 0.45 (14) | 0.26 (7) | 0.13 (15) |
27:3197949 | 1.26 × 10−4 | 0.053 | G | A | 0.18 | 0.37 | 0.10 | SCN8A | 0.13 (4) | 0.07 (2) | 0.03 (3) | 0.48 (15) | 0.26 (7) | 0.21 (25) |
27:5467028 | 1.33 × 10−4 | 0.053 | G | A | 0.36 | 0.30 | 0.08 | - | 0.32 (10) | 0.11 (3) | 0.09 (11) | 0.52 (16) | 0.48 (13) | 0.41 (49) |
27:8646723 | 1.87 × 10−4 | 0.066 | G | A | 0.13 | 0.41 | 0.11 | - | 0.06 (2) | 0.04 (1) | 0 (0) | 0.45 (14) | 0.26 (7) | 0.17 (20) |
27:8883501 | 2.21 × 10−4 | 0.070 | A | G | 0.15 | 0.37 | 0.10 | ANO6 | 0.13 (4) | 0.04 (1) | 0.01 (1) | 0.42 (13) | 0.26 (7) | 0.17 (20) |
27:8767784 | 2.67 × 10−4 | 0.077 | T | A | 0.14 | 0.40 | 0.11 | LOC111092890 | 0.06 (2) | 0.04 (1) | 0 (0) | 0.45 (14) | 0.26 (7) | 0.18 (21) |
27:3501246 | 3.35 × 10−4 | 0.082 | C | A | 0.37 | −0.30 | 0.08 | - | 0.03 (1) | 0.11 (3) | 0.2 (24) | 0.29 (9) | 0.33 (9) | 0.47 (56) |
27:3054141 | 3.62 × 10−4 | 0.082 | A | G | 0.23 | 0.32 | 0.09 | - | 0.13 (4) | 0.07 (2) | 0.04 (5) | 0.55 (17) | 0.48 (13) | 0.25 (30) |
27:8842830 | 4.22 × 10−4 | 0.082 | A | C | 0.13 | 0.38 | 0.11 | LOC111092890 | 0.06 (2) | 0.04 (1) | 0.01 (1) | 0.45 (14) | 0.26 (7) | 0.14 (17) |
27:8884575 | 4.22 × 10−4 | 0.082 | A | G | 0.13 | 0.38 | 0.11 | ANO6 | 0.06 (2) | 0.04 (1) | 0.01 (1) | 0.45 (14) | 0.26 (7) | 0.14 (17) |
27:1953293 | 4.40 × 10−4 | 0.082 | G | A | 0.23 | 0.33 | 0.09 | LOC111092799 | 0.13 (4) | 0.07 (2) | 0.03 (3) | 0.52 (16) | 0.48 (13) | 0.3 (36) |
27:3154712 | 4.58 × 10−4 | 0.082 | A | G | 0.34 | 0.29 | 0.08 | FIGNL2 | 0.26 (8) | 0.15 (4) | 0.08 (10) | 0.55 (17) | 0.41 (11) | 0.4 (48) |
27:5603116 | 4.67 × 10−4 | 0.082 | A | G | 0.39 | 0.28 | 0.08 | WNT10B | 0.42 (13) | 0.26 (7) | 0.05 (6) | 0.35 (11) | 0.48 (13) | 0.52 (62) |
27:5478927 | 5.41 × 10−4 | 0.083 | A | G | 0.31 | 0.29 | 0.08 | LMBR1L | 0.23 (7) | 0.22 (6) | 0.03 (4) | 0.52 (16) | 0.33 (9) | 0.43 (51) |
27:7188905 | 5.43 × 10−4 | 0.083 | A | G | 0.28 | 0.30 | 0.09 | - | 0.23 (7) | 0.11 (3) | 0.04 (5) | 0.48 (15) | 0.44 (12) | 0.34 (41) |
27:3104073 | 5.47 × 10−4 | 0.083 | A | G | 0.23 | 0.31 | 0.09 | ANKRD33 | 0.13 (4) | 0.07 (2) | 0.03 (4) | 0.52 (16) | 0.48 (13) | 0.26 (31) |
27:5806033 | 6.73 × 10−4 | 0.089 | A | G | 0.22 | 0.32 | 0.10 | CCNT1 | 0.13 (4) | 0.22 (6) | 0.01 (1) | 0.55 (17) | 0.33 (9) | 0.25 (30) |
27:5817551 | 6.73 × 10−4 | 0.089 | G | A | 0.22 | 0.32 | 0.10 | - | 0.13 (4) | 0.22 (6) | 0.01 (1) | 0.55 (17) | 0.33 (9) | 0.25 (30) |
27:5512765 | 6.89 × 10−4 | 0.089 | A | G | 0.36 | 0.28 | 0.08 | RHEBL1 | 0.29 (9) | 0.11 (3) | 0.08 (9) | 0.52 (16) | 0.48 (13) | 0.47 (56) |
27:6657558 | 7.32 × 10−4 | 0.089 | G | A | 0.23 | 0.31 | 0.09 | - | 0.19 (6) | 0.07 (2) | 0.03 (3) | 0.45 (14) | 0.37 (10) | 0.31 (37) |
27:6660738 | 7.32 × 10−4 | 0.089 | A | G | 0.23 | 0.31 | 0.09 | - | 0.19 (6) | 0.07 (2) | 0.03 (3) | 0.45 (14) | 0.37 (10) | 0.31 (37) |
27:1488082 | 7.65 × 10−4 | 0.090 | G | A | 0.35 | 0.27 | 0.08 | LOC486504 | 0.29 (9) | 0.11 (3) | 0.12 (14) | 0.45 (14) | 0.44 (12) | 0.39 (46) |
27:5822515 | 8.18 × 10−4 | 0.093 | G | A | 0.22 | 0.31 | 0.09 | - | 0.13 (4) | 0.22 (6) | 0.01 (1) | 0.55 (17) | 0.37 (10) | 0.25 (30) |
27:1719544 | 9.13 × 10−4 | 0.100 | A | G | 0.34 | 0.27 | 0.08 | TARBP2 | 0.26 (8) | 0.07 (2) | 0.17 (20) | 0.45 (14) | 0.41 (11) | 0.31 (37) |
No. of SNPs | Start SNP | End SNP | Haplotype | p-Value | Genes in Region | Frequency of Homozygosity (No. of Dogs) | ||
---|---|---|---|---|---|---|---|---|
Lym. | Carr. | Cont. | ||||||
12 | 18:38038090 | 18:38129762 | AACAAAACAACG | 7.75 × 10−8 | LOC106559970, OR08G08, LOC483477, COR5BC3, LOC483479, LOC610022, LOC483480 | 0.06 (2) | 0 (0) | 0 (0) |
2 | 18:39123584 | 18:39140112 | AG | 1.65 × 10−7 | LOC100688997 | 0.1 (3) | 0.07 (2) | 0.02 (2) |
2 | 18:37724157 | 18:37737740 | CC | 5.77 × 10−7 | LOC100686230 | 0.06 (2) | 0 (0) | 0 (0) |
5 | 18:38383741 | 18:38426687 | GGGAG | 6.09 × 10−7 | CTNND1 | 0.06 (2) | 0 (0) | 0 (0) |
3 | 18:38456518 | 18:38478390 | AAC | 6.09 × 10−7 | CTNND1, BTBD18 | 0.06 (2) | 0 (0) | 0 (0) |
5 | 18:38498673 | 18:38511357 | AAAAT | 2.31 × 10−6 | ZDHHC5 | 0.1 (3) | 0 (0) | 0 (0) |
2 | 18:55380537 | 18:55385901 | TG | 3.36 × 10−6 | TMEM109 | 0.52 (16) | 0.41 (11) | 0.24 (28) |
2 | 18:37862012 | 18:37867871 | AA | 6.12 × 10−6 | OR5B21 | 0.19 (6) | 0.04 (1) | 0 (0) |
2 | 18:37862012 | 18:37867871 | TG | 6.12 × 10−6 | OR5B21 | 0.48 (15) | 0.56 (15) | 0.76 (91) |
2 | 18:38317284 | 18:38326192 | AA | 1.07 × 10−5 | OR10C10 | 0.06 (2) | 0 (0) | 0 (0) |
14 | 18:13130318 | 18:13325298 | AGAAAAAAGAAGAG | 1.27 × 10−5 | COG5 | 0 (0) | 0 (0) | 0 (0) |
3 | 18:41713196 | 18:41740841 | GGG | 4.05 × 10−5 | LOC106559997 | 0.06 (2) | 0.07 (2) | 0.33 (39) |
3 | 18:38805092 | 18:38807806 | AGA | 4.45 × 10−5 | SSRP1 | 0.06 (2) | 0 (0) | 0 (0) |
2 | 18:41422687 | 18:41436427 | AC | 6.03 × 10−5 | - | 0.1 (3) | 0.07 (2) | 0.35 (42) |
3 | 18:39168396 | 18:39195972 | AAA | 6.86 × 10−5 | LOC483503, OR04E05 | 0.1 (3) | 0.04 (1) | 0.01 (1) |
5 | 18:39846804 | 18:39860197 | AGGAA | 8.23 × 10−5 | LOC483541, LOC100685982 | 0.16 (5) | 0.04 (1) | 0.01 (1) |
2 | 18:40663070 | 18:40667579 | GC | 8.38 × 10−5 | - | 0.45 (14) | 0.22 (6) | 0.15 (18) |
3 | 18:38719709 | 18:38732149 | GAA | 8.47 × 10−5 | SLC43A3 | 0.23 (7) | 0.22 (6) | 0.08 (9) |
No. of SNPs | Start SNP | End SNP | Haplotype | p-Value | Genes in Region | Frequency of Homozygosity (No. of Dogs) | ||
---|---|---|---|---|---|---|---|---|
Lym. | Carr. | Cont. | ||||||
9 | 27:5104085 | 27:5241391 | AAAAGCGAA | 9.37 × 10−9 | SPATS2 | 0.29 (9) | 0.07 (2) | 0.02 (2) |
6 | 27:4662318 | 27:4728424 | GAAGGA | 1.27 × 10−8 | ASIC1, RACGAP1, LOC111092823 | 0.13 (4) | 0.07 (2) | 0 (0) |
5 | 27:5304179 | 27:5340118 | GAAAC | 2.04 × 10−8 | PRPH, LOC100856405 | 0.16 (5) | 0.07 (2) | 0.01 (1) |
4 | 27:5919807 | 27:5983459 | AGAA | 8.05 × 10−8 | cOR8S6P, LOC102156933, LOC100855426, COR8S14, LOC111092874 | 0.1 (3) | 0.07 (2) | 0 (0) |
4 | 27:8010819 | 27:8043205 | AGAA | 1.11 × 10−7 | LOC102154451, LOC102155835 | 0.06 (2) | 0.04 (1) | 0 (0) |
5 | 27:3590788 | 27:3615721 | AGAGA | 1.33 × 10−7 | BIN2, SMAGP | 0.13 (4) | 0.07 (2) | 0 (0) |
5 | 27:5762992 | 27:5817551 | GAGAG | 1.74 × 10−7 | LOC111092830, CCNT1 | 0.13 (4) | 0.22 (6) | 0.01 (1) |
9 | 27:8396219 | 27:8548130 | AGCGCGGGG | 2.27 × 10−7 | SCAF11, ARID2 | 0.06 (2) | 0.04 (1) | 0 (0) |
2 | 27:8314156 | 27:8331252 | AG | 2.57 × 10−7 | LOC111092841 | 0.06 (2) | 0.04 (1) | 0 (0) |
13 | 27:3197949 | 27:3347721 | GTCGAGGAG GGGC | 3.97 × 10−7 | SCN8A | 0.13 (4) | 0.07 (2) | 0 (0) |
4 | 27:5919807 | 27:5983459 | AAAA | 2.70 × 10−6 | cOR8S6P, LOC102156933, LOC100855426, COR8S14, LOC111092874 | 0.16 (5) | 0.11 (3) | 0.45 (53) |
3 | 27:5261130 | 27:5265185 | GGA | 4.07 × 10−6 | DNAJC22 | 0.29 (9) | 0.19 (5) | 0.08 (9) |
4 | 27:8583844 | 27:8646723 | CAAG | 5.07 × 10−6 | LOC102155300 | 0.06 (2) | 0.04 (1) | 0 (0) |
3 | 27:8842830 | 27:8861426 | AAA | 8.77 × 10−6 | LOC111092890 | 0.06 (2) | 0.04 (1) | 0.01 (1) |
6 | 27:8883501 | 27:8885135 | AGAAAA | 8.77 × 10−6 | ANO6 | 0.06 (2) | 0.04 (1) | 0.01 (1) |
2 | 27:8767784 | 27:8775933 | TG | 1.81 × 10−5 | LOC111092890 | 0.06 (2) | 0.04 (1) | 0 (0) |
3 | 27:5281537 | 27:5282177 | CAG | 2.24 × 10−5 | C1QL4 | 0.23 (7) | 0.22 (6) | 0.05 (6) |
6 | 27:21881521 | 27:21942273 | AAAGGG | 2.33 × 10−5 | LOC111092834 | 0.03 (1) | 0.04 (1) | 0.02 (2) |
3 | 27:5861077 | 27:5870632 | GGA | 2.99 × 10−5 | LYZF2 | 0.35 (11) | 0.3 (8) | 0.12 (14) |
4 | 27:1460779 | 27:1471371 | AAGG | 3.26 × 10−5 | LOC486504 | 0.32 (10) | 0.22 (6) | 0.06 (7) |
3 | 27:1250330 | 27:1251390 | AGA | 3.96 × 10−5 | LOC607625 | 0.1 (3) | 0.07 (2) | 0.01 (1) |
5 | 27:4735827 | 27:4744789 | AAGCA | 3.96 × 10−5 | AQP5, AQP2 | 0.35 (11) | 0.22 (6) | 0.09 (11) |
3 | 27:5261130 | 27:5265185 | AGA | 4.21 × 10−5 | DNAJC22 | 0.03 (1) | 0 (0) | 0.13 (15) |
3 | 27:3102259 | 27:3104073 | GAA | 4.74 × 10−5 | ANKRD33 | 0.13 (4) | 0.07 (2) | 0.03 (4) |
5 | 27:11605144 | 27:11653990 | CGAGA | 5.17 × 10−5 | LOC106557903 | 0.1 (3) | 0.3 (8) | 0.05 (6) |
2 | 27:2965369 | 27:2966261 | GC | 5.84 × 10−5 | - | 0.87 (27) | 0.74 (20) | 0.53 (63) |
5 | 27:21532742 | 27:21616626 | GCAGC | 7.16 × 10−5 | RASSF8, LOC106557908 | 0.03 (1) | 0.04 (1) | 0.02 (2) |
19 | 27:4373882 | 27:4565172 | AAAGAGGAGGAGAGAAAAG | 8.25 × 10−5 | LARP4, FAM186A, LIMA1 | 0.13 (4) | 0.07 (2) | 0.03 (4) |
4 | 27:6639027 | 27:6661792 | CGAA | 9.24 × 10−5 | PFKM | 0.19 (6) | 0.07 (2) | 0.03 (3) |
Location (Chr:BP) | p-Value | q-Value | A1 | A2 | A1 Freq | b | SE | Gene | Frequency of A1A1 (No. of Dogs) | Frequency of A1A2 (No. of Dogs) | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Lym. | Cont. | Lym. | Cont. | |||||||||
13:17399337 | 5.78 × 10−5 | 0.087 | A | C | 0.02 | 0.63 | 0.16 | EXT1 | 0 (0) | 0 (0) | 0.19 (6) | 0.01 (1) |
13:18910196 | 3.42 × 10−5 | 0.077 | A | G | 0.02 | 0.69 | 0.17 | DEPTOR | 0 (0) | 0 (0) | 0.16 (5) | 0.01 (1) |
13:18913685 | 3.42 × 10−5 | 0.077 | A | G | 0.02 | 0.69 | 0.17 | DEPTOR | 0 (0) | 0 (0) | 0.16 (5) | 0.01 (1) |
13:20734477 | 7.72 × 10−5 | 0.087 | A | G | 0.03 | 0.53 | 0.13 | LOC111098540 | 0 (0) | 0 (0) | 0.23 (7) | 0.03 (3) |
14:3945297 | 5.97 × 10−5 | 0.084 | A | G | 0.07 | 0.36 | 0.09 | EXOC4 | 0.1 (3) | 0 (0) | 0.19 (6) | 0.08 (10) |
14:4095927 | 5.97 × 10−5 | 0.084 | A | G | 0.07 | 0.36 | 0.09 | - | 0.1 (3) | 0 (0) | 0.19 (6) | 0.08 (10) |
14:54260890 | 8.46 × 10−5 | 0.084 | A | G | 0.02 | 0.72 | 0.18 | - | 0 (0) | 0 (0) | 0.13 (4) | 0.01 (1) |
18:37737740 | 3.07 × 10−4 | 0.066 | C | A | 0.12 | 0.25 | 0.07 | - | 0.06 (2) | 0 (0) | 0.45 (14) | 0.16 (19) |
18:37862012 | 4.81 × 10−4 | 0.074 | A | T | 0.17 | 0.21 | 0.06 | - | 0.19 (6) | 0 (0) | 0.32 (10) | 0.24 (28) |
18:37867871 | 4.81 × 10−4 | 0.074 | A | G | 0.17 | 0.21 | 0.06 | OR5B21 | 0.19 (6) | 0 (0) | 0.32 (10) | 0.24 (28) |
18:38233567 | 1.74 × 10−4 | 0.053 | A | G | 0.11 | 0.29 | 0.08 | - | 0.06 (2) | 0 (0) | 0.42 (13) | 0.13 (15) |
18:38350947 | 3.76 × 10−4 | 0.066 | A | G | 0.11 | 0.27 | 0.08 | - | 0.06 (2) | 0 (0) | 0.42 (13) | 0.13 (16) |
18:38456518 | 3.76 × 10−4 | 0.066 | A | G | 0.11 | 0.27 | 0.08 | CTNND1 | 0.06 (2) | 0 (0) | 0.42 (13) | 0.13 (16) |
18:38502268 | 2.16 × 10−4 | 0.053 | A | G | 0.12 | 0.26 | 0.07 | ZDHHC5 | 0.1 (3) | 0 (0) | 0.39 (12) | 0.16 (19) |
18:38507461 | 2.16 × 10−4 | 0.053 | A | G | 0.12 | 0.26 | 0.07 | ZDHHC5 | 0.1 (3) | 0 (0) | 0.39 (12) | 0.16 (19) |
18:38510335 | 2.16 × 10−4 | 0.053 | A | G | 0.12 | 0.26 | 0.07 | ZDHHC5 | 0.1 (3) | 0 (0) | 0.39 (12) | 0.16 (19) |
18:38704682 | 4.49 × 10−5 | 0.053 | A | G | 0.32 | 0.20 | 0.05 | - | 0.26 (8) | 0.08 (9) | 0.55 (17) | 0.37 (44) |
18:38719709 | 1.45 × 10−4 | 0.053 | G | A | 0.30 | 0.18 | 0.05 | - | 0.23 (7) | 0.08 (9) | 0.55 (17) | 0.34 (41) |
18:39140112 | 8.21 × 10−5 | 0.053 | G | A | 0.26 | 0.22 | 0.06 | LOC100688997 | 0.16 (5) | 0.03 (4) | 0.58 (18) | 0.34 (41) |
18:39727438 | 3.38 × 10−4 | 0.066 | G | A | 0.31 | 0.17 | 0.05 | - | 0.29 (9) | 0.08 (9) | 0.45 (14) | 0.35 (42) |
18:40281122 | 8.35 × 10−5 | 0.053 | A | G | 0.41 | 0.18 | 0.05 | - | 0.42 (13) | 0.13 (16) | 0.42 (13) | 0.45 (53) |
18:40286669 | 9.66 × 10−5 | 0.053 | G | A | 0.42 | 0.18 | 0.05 | - | 0.42 (13) | 0.13 (16) | 0.42 (13) | 0.47 (56) |
18:40418483 | 2.44 × 10−4 | 0.056 | A | G | 0.47 | 0.17 | 0.05 | - | 0.42 (13) | 0.16 (19) | 0.48 (15) | 0.52 (62) |
18:40653765 | 2.05 × 10−4 | 0.053 | A | C | 0.47 | 0.18 | 0.05 | - | 0.45 (14) | 0.15 (18) | 0.45 (14) | 0.53 (63) |
18:40667579 | 1.95 × 10−4 | 0.053 | C | A | 0.46 | 0.17 | 0.05 | - | 0.45 (14) | 0.15 (18) | 0.45 (14) | 0.5 (60) |
18:41229735 | 6.77 × 10−5 | 0.053 | A | G | 0.43 | 0.19 | 0.05 | LOC100684610 | 0.45 (14) | 0.13 (15) | 0.42 (13) | 0.49 (58) |
18:41436427 | 1.54 × 10−4 | 0.053 | C | A | 0.52 | −0.17 | 0.05 | - | 0.1 (3) | 0.35 (42) | 0.42 (13) | 0.45 (53) |
18:41713196 | 4.34 × 10−4 | 0.073 | A | G | 0.15 | 0.24 | 0.07 | - | 0.06 (2) | 0.03 (3) | 0.45 (14) | 0.18 (21) |
18:41726488 | 1.92 × 10−4 | 0.053 | A | G | 0.15 | 0.26 | 0.07 | - | 0.06 (2) | 0.02 (2) | 0.45 (14) | 0.18 (22) |
18:41854962 | 1.82 × 10−4 | 0.053 | C | G | 0.13 | 0.24 | 0.06 | - | 0.1 (3) | 0.01 (1) | 0.32 (10) | 0.17 (20) |
18:42270324 | 3.78 × 10−4 | 0.066 | A | G | 0.07 | 0.33 | 0.09 | - | 0 (0) | 0.01 (1) | 0.35 (11) | 0.08 (9) |
27:3054141 | 8.03 × 10−4 | 0.096 | A | G | 0.22 | 0.18 | 0.05 | - | 0.13 (4) | 0.04 (5) | 0.55 (17) | 0.25 (30) |
27:3154712 | 2.20 × 10−4 | 0.041 | A | G | 0.34 | 0.18 | 0.05 | FIGNL2 | 0.26 (8) | 0.08 (10) | 0.55 (17) | 0.4 (48) |
27:3197949 | 7.78 × 10−5 | 0.027 | G | A | 0.18 | 0.23 | 0.06 | SCN8A | 0.13 (4) | 0.03 (3) | 0.48 (15) | 0.21 (25) |
27:3234647 | 4.84 × 10−5 | 0.027 | G | A | 0.17 | 0.24 | 0.06 | SCN8A | 0.13 (4) | 0.03 (3) | 0.48 (15) | 0.19 (23) |
27:3501246 | 1.13 × 10−4 | 0.027 | C | A | 0.38 | −0.18 | 0.05 | - | 0.03 (1) | 0.2 (24) | 0.29 (9) | 0.47 (56) |
27:3594560 | 2.29 × 10−5 | 0.027 | G | A | 0.14 | 0.27 | 0.06 | BIN2 | 0.13 (4) | 0 (0) | 0.45 (14) | 0.18 (21) |
27:4561667 | 7.57 × 10−4 | 0.095 | A | C | 0.23 | 0.18 | 0.05 | LIMA1 | 0.13 (4) | 0.05 (6) | 0.58 (18) | 0.25 (30) |
27:5112245 | 6.08 × 10−5 | 0.027 | A | G | 0.22 | 0.20 | 0.05 | SPATS2 | 0.29 (9) | 0.02 (2) | 0.39 (12) | 0.27 (32) |
27:5364442 | 4.76 × 10−5 | 0.027 | A | G | 0.17 | 0.24 | 0.06 | LOC111092735 | 0.16 (5) | 0.01 (1) | 0.42 (13) | 0.22 (26) |
27:5467028 | 1.07 × 10−4 | 0.027 | G | A | 0.36 | 0.18 | 0.05 | - | 0.32 (10) | 0.09 (11) | 0.52 (16) | 0.41 (49) |
27:5478927 | 2.36 × 10−4 | 0.042 | A | G | 0.30 | 0.19 | 0.05 | LMBR1L | 0.23 (7) | 0.03 (4) | 0.52 (16) | 0.43 (51) |
27:5512765 | 5.03 × 10−4 | 0.072 | A | G | 0.36 | 0.17 | 0.05 | RHEBL1 | 0.29 (9) | 0.08 (9) | 0.52 (16) | 0.47 (56) |
27:5603116 | 4.20 × 10−4 | 0.063 | A | G | 0.37 | 0.17 | 0.05 | WNT10B | 0.42 (13) | 0.05 (6) | 0.35 (11) | 0.52 (62) |
27:5806033 | 1.17 × 10−4 | 0.027 | A | G | 0.19 | 0.24 | 0.06 | CCNT1 | 0.13 (4) | 0.01 (1) | 0.55 (17) | 0.25 (30) |
27:5817551 | 1.17 × 10−4 | 0.027 | G | A | 0.19 | 0.24 | 0.06 | - | 0.13 (4) | 0.01 (1) | 0.55 (17) | 0.25 (30) |
27:5822515 | 1.17 × 10−4 | 0.027 | G | A | 0.19 | 0.24 | 0.06 | - | 0.13 (4) | 0.01 (1) | 0.55 (17) | 0.25 (30) |
27:7188905 | 5.73 × 10−4 | 0.078 | A | G | 0.27 | 0.18 | 0.05 | - | 0.23 (7) | 0.04 (5) | 0.48 (15) | 0.34 (41) |
27:8331252 | 3.49 × 10−5 | 0.027 | G | A | 0.11 | 0.30 | 0.07 | - | 0.06 (2) | 0 (0) | 0.45 (14) | 0.13 (15) |
27:8646723 | 8.78 × 10−5 | 0.027 | G | A | 0.13 | 0.28 | 0.07 | - | 0.06 (2) | 0 (0) | 0.45 (14) | 0.17 (20) |
27:8767784 | 1.51 × 10−4 | 0.030 | T | A | 0.13 | 0.26 | 0.07 | LOC111092890 | 0.06 (2) | 0 (0) | 0.45 (14) | 0.18 (21) |
27:8842830 | 2.80 × 10−4 | 0.044 | A | C | 0.12 | 0.24 | 0.07 | LOC111092890 | 0.06 (2) | 0.01 (1) | 0.45 (14) | 0.14 (17) |
27:8883501 | 1.39 × 10−4 | 0.030 | A | G | 0.14 | 0.24 | 0.06 | ANO6 | 0.13 (4) | 0.01 (1) | 0.42 (13) | 0.17 (20) |
27:8884575 | 2.80 × 10−4 | 0.044 | A | G | 0.12 | 0.24 | 0.07 | ANO6 | 0.06 (2) | 0.01 (1) | 0.45 (14) | 0.14 (17) |
27:8892980 | 6.60 × 10−5 | 0.027 | C | G | 0.22 | 0.21 | 0.05 | ANO6 | 0.16 (5) | 0.04 (5) | 0.55 (17) | 0.25 (30) |
27:11672173 | 6.00 × 10−4 | 0.078 | A | C | 0.16 | 0.23 | 0.07 | LOC106557903 | 0.03 (1) | 0 (0) | 0.55 (17) | 0.24 (28) |
No. of SNPs | Start SNP | End SNP | Haplotype | Odds Ratio | p-Value | Genes in Region | Frequency of Homozygosity (No. of Dogs) | |
---|---|---|---|---|---|---|---|---|
Lym. | Cont. | |||||||
14 | 18:38233567 | 18:38383741 | AAGAGGGAAAAAGG | 5.61 | 7.66 × 10−5 | LOC483485, LOC610080, LOC106559985, OR10C10, LOC610127, COR5BA2 | 0.06 (2) | 0 (0) |
3 | 18:38502268 | 18:38510335 | AAA | 4.91 | 7.86 × 10−5 | ZDHHC5 | 0.1 (3) | 0 (0) |
3 | 18:38502268 | 18:38510335 | GGG | 0.204 | 7.86 × 10−5 | ZDHHC5 | 0.52 (16) | 0.84 (100) |
2 | 18:37862012 | 18:37867871 | AA | 3.98 | 9.97 × 10−5 | OR5B21 | 0.19 (6) | 0 (0) |
2 | 18:37862012 | 18:37867871 | TG | 0.251 | 9.97 × 10−5 | OR5B21 | 0.48 (15) | 0.76 (91) |
No. of SNPs | Start SNP | End SNP | Haplotype | Odds Ratio | p-Value | Genes in Region | Frequency of Homozygosity (No. of Dogs) | |
---|---|---|---|---|---|---|---|---|
Lym. | Cont. | |||||||
8 | 27:5112245 | 27:5241391 | AAAGCGAA | 4.94 | 2.82 × 10−6 | SPATS2 | 0.29 (9) | 0.02 (2) |
2 | 27:3590788 | 27:3594560 | AG | 6.26 | 5.33 × 10−6 | BIN2 | 0.13 (4) | 0 (0) |
12 | 27:3211312 | 27:3347721 | TCGAGGAGGGGC | 5.95 | 7.53 × 10−6 | SCN8A | 0.13 (4) | 0 (0) |
2 | 27:5806033 | 27:5817551 | AG | 5.31 | 1.51 × 10−5 | CCNT1 | 0.13 (4) | 0.01 (1) |
2 | 27:5806033 | 27:5817551 | GA | 0.188 | 1.51 × 10−5 | CCNT1 | 0.32 (10) | 0.74 (88) |
4 | 27:8752431 | 27:8792430 | GTGG | 5.24 | 6.12 × 10−5 | LOC111092890 | 0.06 (2) | 0 (0) |
2 | 27:5592820 | 27:5603116 | CA | 3.65 | 6.83 × 10−5 | WNT10B | 0.42 (13) | 0.05 (6) |
Chromosome | Prevalence | V(G)/Vp ± SE (%) | V(G)/Vp_L ± SE (%) | p-Value |
---|---|---|---|---|
All autosomes | 0.025 | 100 ± 20.52 | 106.09 ± 21.77 | 1.43 × 10−6 |
0.05 | 129.37 ± 26.55 | |||
0.1 | 160.4 ± 32.92 | |||
Chr 18 | 0.025 | 31.27 ± 12.77 | 33.17 ± 13.54 | 1.21 × 10−3 |
0.05 | 40.45 ± 16.52 | |||
0.1 | 50.16 ± 20.48 | |||
Chr 18 37 to 56 Mb region | 0.025 | 40.91 ± 12.1 | 43.4 ± 12.83 | 7.10 × 10−6 |
0.05 | 52.93 ± 15.65 | |||
0.1 | 65.63 ± 19.4 | |||
Chr 27 | 0.025 | 40.71 ± 11.26 | 43.19 ± 11.94 | 1.34 × 10−6 |
0.05 | 52.67 ± 14.56 | |||
0.1 | 65.3 ± 18.06 | |||
Chr 27 1 to 9 Mb region | 0.025 | 26.12 ± 9.6 | 27.71 ± 10.18 | 2.50 × 10−7 |
0.05 | 33.79 ± 12.42 | |||
0.1 | 41.9 ± 15.4 |
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Soh, P.X.Y.; Khatkar, M.S.; Williamson, P. Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis. Vet. Sci. 2023, 10, 581. https://doi.org/10.3390/vetsci10090581
Soh PXY, Khatkar MS, Williamson P. Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis. Veterinary Sciences. 2023; 10(9):581. https://doi.org/10.3390/vetsci10090581
Chicago/Turabian StyleSoh, Pamela Xing Yi, Mehar Singh Khatkar, and Peter Williamson. 2023. "Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis" Veterinary Sciences 10, no. 9: 581. https://doi.org/10.3390/vetsci10090581