Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer

Table 2

(a) Top 30 genes containing both germline and somatic mutations among genes significantly associated with TNBC

Genes	Chromosome position	Genetic variant	GWAS value	Expression value	Mutation events
CREBBP	16p13.3	rs12920416			7
ARID1B	6q25.3	rs140842923			6
BRCA1	17q21.31	rs1799950			5
ERBB4	2q34	rs13393577			5
FHOD3	18q12	rs9956546			5
TNRC6B	22q13.1	rs12483853			5
ARHGAP24	4q21.23	rs71599425			4
ARHGAP5	14q12	rs140783387			4
CNTNAP2	7q35	rs10487920			4
DMD	Xp21.1	rs1293906			4
EFR3B	2p23.3	rs1971136			4
KIAA0907	1q22	rs11406084			4
MSH3	5q11-q12	rs6151904			4
MYO10	5p15.1-p14.3	rs2562343			4
MYT1	20q13.33	rs6062356			4
RELN	7q22	rs17157903			4
SPAG17	1p12	rs1962373			4
TRIM46	1q22	rs4971059			4
ZFPM2	8q23.1	rs12546444			4
ADCY9	16p13.3	rs11076805			3
AKAP9	7q21.2	rs10644111			3
ASH1L	1q22	rs10796944			3
ASXL2	2p23.3	rs144079028			3
ATM	11q22-q23	rs1801516			3
ATXN1	6p22.3	rs3819405			3
BAHCC1	17q25.3	rs8074440			3
CASZ1	1p36.22	rs199867187			3
CHST9	18q11.2	rs1436904			3
CNTNAP1	17q21.2	rs72826962			3
DNAH11	7p15.3	rs7971			3

(b) Top 30 genes containing germline and somatic mutations significantly associated with non-TNBC

Genes	Chromosome position	Genetic variant	GWAS value	Expression value	Mutation events
DMD	Xp21.1	rs1293906			41
NOTCH2	1p12	rs372562666			27
RELN	7q22	rs17157903			22
ATM	11q22-q23	rs1801516			21
RB1	13q14.2	rs2854344			20
ERBB2	6p21.3	rs1801201			19
ASH1L	1q22	rs10796944			18
MADD	11p11.2	rs11039183			18
ITPR1	3p26.1	rs6787391			17
FAM208B	10p15.1	rs55910451			16
ABCA8	17q24.2	rs36059695			15
ASXL2	2p23.3	rs144079028			15
CNTNAP2	7q35	rs10487920			15
GRIN3A	9q31.1	rs10512287			15
PIK3R1	5q13.1	rs184886			15
TNRC6B	22q13.1	rs12483853			15
CASZ1	1p36.22	rs199867187			14
FRMD4A	10p13	rs10906522			14
KCNH7	2q24.3	rs148760487			14
TACC2	10q26.13	rs2253762			14
ABCC4	13q32.1	rs1926657			13
ADCY9	16p13.3	rs11076805			13
CCDC88C	14q32.11	rs941764			13
FGFR2	10q26.13	rs35054928			13
SPTBN2	11q13.2	rs55908905			13
ATR	3q23	rs1802904			12
BRCA1	17q21.31	rs1799950			12
BRCA2	13q13.1	rs11571833			12
CASP8	2q33.1	rs3769821			12
CDH12	5p14.3	rs66783663			12

(c) Top 30 genes with both germline and somatic mutations distinguishing TNBC from non-TNBC

Gene name	Chromosome position	SNP_ID	GWAS value	Expression value	GWAS event	TNBC mutation event	Non-TNBC mutation event
AGPAT9	4q21.23	rs1963045			1	2
FKBPL	6p21.32	rs169494			1	2
IGSF21	1p36.13	rs2992756			1	2
BABAM1	19p13.11	rs8170			1	1
MCM8	20p12.3	rs16991615			1	1
MYC	8q24.21	rs11780156			1	1
NFIX	19p13.13	rs78269692			1	1
FRMD4A	10p13	rs10906522			1		14
KCNH7	2q24.2	rs148760487			1		14
ABCC4	13q32.1	rs1926657			1		13
CCDC88C	14q32.11	rs941764			1		13
CDH12	5p14.3	rs66783663			1		12
MAGI3	1p13.2	rs1230666			1		12
TNS1	2q35	rs6436017			1		11
BLM	15q26.1	rs8037430			2		10
DNM3	1q24.3	rs1894633			1		10
L3MBTL3	6q23.1	rs6569648			1		10
BRIP1	17q23.2	Deletion			2		9
FOXP1	3p13	rs6805189			1		9
ABCF1	6p21.33	rs3132610			1		8
ADCY3	2p23.3	rs6725517			1		8
COL1A1	17q21.33	rs2075555			1		8
CUX1	7q22.1	rs71559437			1		8
EWSR1	22q12.2	rs132390			1		8
EXOC3	5p15.33	rs190811224			1		8
IGF1R	15q26.3	rs1546713			2		8