Table 1

Concordant SNPs recovered from TCGA and AGS data, and associated genes

SNP

chr

gene

location

left_gene

right_gene

Genes correlated with SNP (R2)

AGS (P1)

TCGA (P2)

FDR


rs2736100+

5

TERT

5p15.33

SLC6A18

CLPTM1L

NA

5.30E-13

2.66E-04

7.38E-09


rs1412829*+

9

CDKN2A/B

9p21.3

LOC100130239

LOC729983

CDKN2A(1.0);

CDKN2B(1.0);

C9orf53(0.87)

3.40E-08

3.26E-03

1.27E-03


rs2157719

9

CDKN2A/B

9p21.3

LOC100130239

LOC729983

CDKN2A(0.97);

CDKN2B(0.97);

C9orf53(0.93);

RP11-145E5.4(0.97);

LOC100130239(0.97)

6.10E-08

8.00E-03

5.40E-03


rs1063192+

9

CDKN2A/B

9p21.3

CDKN2A

LOC100130239

CDKN2A(0.97);

CDKN2B(0.97);

C9orf53(0.93);

RP11-145E5.4(0.97);

LOC100130239(0.97)

9.20E-08

8.31E-03

7.95E-03


rs4977756+

9

CDKN2A/B

9p21.3

LOC100130239

LOC729983

CDKN2A(0.97);

CDKN2B(0.97);

C9orf53(0.93);

RP11-145E5.4(0.97);

LOC100130239(0.97)

4.20E-07

1.12E-02

3.90E-02


rs7530361

1

SLC35A3

1p21.2

LOC730081

HIAT1

SLC35A3(1.0);

CCDC76(0.95);

HIAT1(1.0);

LRRC39(0.95);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(1.0)

6.50E-07

2.19E-06

4.29E-05


rs501700

1

HIAT1

1p21.2

SLC35A3

SASS6

DBT(0.95);

RTCD1(0.89);

SLC35A3(1.0);

CCDC76(0.95);

HIAT1(1.0);

LRRC39(0.94);

SASS6(1.0);

BRI3P1(0.94);

LOC730081(1.0)

7.10E-07

5.99E-06

9.72E-05


rs1920116

3

LRRC31

3q26.2

LRRIQ4

KRT18P43

MYNN(0.89);

LRRC31(1);

ARPM1(0.85);

KRT18P43(1)

LRRC34(1)

1.40E-06

2.88E-03

2.81E-02


rs506044

1

SASS6

1p21.2

SASS6

LRRC39

DBT(1.0);

RTCD1(0.89);

SLC35A3(0.95);

CCDC76(1.0);

HIAT1(1.0);

LRRC39(1.0);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(0.94)

2.10E-06

2.45E-06

1.57E-04


rs640030

1

SASS6

1p21.2

HIAT1

CCDC76

DBT(1.0);

RTCD1(0.89);

SLC35A3(0.95);

CCDC76(1.0);

HIAT1(1.0);

LRRC39(1.0);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(0.94)

2.40E-06

2.57E-06

1.86E-04


rs687513

1

SASS6

1p21.2

SASS6

LRRC39

DBT(0.95);

RTCD1(0.90);

SLC35A3(0.94);

CCDC76(1.0);

HIAT1(1.0);

LRRC39(1.0);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(0.90)

2.90E-06

3.91E-06

3.03E-04


rs3779505

7

ITGB8

7p15.3

MACC1

LOC100130234

ITGB8(1.0)

3.00E-06

5.67E-04

1.35E-02


Concordant SNPs (FDR < 0.05) recovered from TCGA (n = 97) and AGS data (n = 692), and associated genes. The blue boldface indicates the genes that are known to be cancer-associated.

+ reported by Shete et, al.

* reported by Wrensch et, al. and validated on Mayo Clinic population

FDR: Bonferroni corrected False Discovery Rate = 3 × 105P12 (eq. 1)

Yang et al. BMC Medical Genomics 2011 4:63   doi:10.1186/1755-8794-4-63

Open Data