Mutation Analysis (MutSig v2.0)

Lung Adenocarcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by David Heiman (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C15Q4V5Z

- Overview

+ Introduction

- Summary

MAF used for this analysis:LUAD-TP.final_analysis_set.maf
Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt
Significantly mutated genes (q ≤ 0.1): 174
Mutations seen in COSMIC: 1121
Significantly mutated genes in COSMIC territory: 39
Significantly mutated genesets: 17
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 545 MAFs of type "Broad"
Total number of mutations in input MAFs: 255962
After removing 114 mutations outside chr1-24: 255848
After removing 8884 blacklisted mutations: 246964
After removing 16469 noncoding mutations: 230495
After collapsing adjacent/redundant mutations: 193597

Mutation Filtering

Number of mutations before filtering: 193597
After removing 9350 mutations outside gene set: 184247
After removing 428 mutations outside category set: 183819
After removing 15 "impossible" mutations in
gene-patient-category bins of zero coverage: 174026

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	3948
Frame_Shift_Ins	1681
In_Frame_Del	504
In_Frame_Ins	69
Missense_Mutation	118261
Nonsense_Mutation	9435
Nonstop_Mutation	192
Silent	41631
Splice_Site	7430
Translation_Start_Site	668
Total	183819

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->(A/T)	16940	861142629	2e-05	20	2.2	2.1
*Cp(A/C/T)->(A/T)	58245	7163719428	8.1e-06	8.1	0.9	2.7
flip	30450	15791237960	1.9e-06	1.9	0.21	5.3
A->(C/G)	13262	7766375903	1.7e-06	1.7	0.19	3.3
indel+null	22860	15791237960	1.4e-06	1.4	0.16	NaN
double_null	417	15791237960	2.6e-08	0.026	0.0029	NaN
Total	142174	15791237960	9e-06	9	1	3.5

+ Target Coverage for Each Individual

+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

+ Lego Plots

+ CoMut Plot

+ Significantly Mutated Genes

Column Descriptions:

N = number of sequenced bases in this gene across the individual set
n = number of (nonsilent) mutations in this gene across the individual set
npat = number of patients (individuals) with at least one nonsilent mutation
nsite = number of unique sites having a non-silent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type: *CpG->(A/T)
n2 = number of nonsilent mutations of type: *Cp(A/C/T)->(A/T)
n3 = number of nonsilent mutations of type: flip
n4 = number of nonsilent mutations of type: A->(C/G)
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
p_joint = p-value for clustering + conservation
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 174. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_classic	p_ns_s	p_clust	p_cons	p_joint	p	q
1	STK11	serine/threonine kinase 11	353629	87	80	69	2	1	16	6	5	59	0	2.33e-15	6.73e-08	1.2e-06	0.014	1.8e-06	0.000	0.000
2	TP53	tumor protein p53	667839	309	295	175	4	42	79	33	33	119	3	1.22e-15	<1.00e-15	0	0	0	<1.00e-15	<1.39e-12
3	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	373039	169	164	11	0	0	141	27	0	1	0	1.11e-15	4.91e-14	0	0	0	<1.00e-15	<1.39e-12
4	KEAP1	kelch-like ECH-associated protein 1	912683	96	95	85	2	24	28	13	9	22	0	<1.00e-15	6.90e-11	0.017	0	0	<1.00e-15	<1.39e-12
5	EGFR	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)	2137011	87	73	39	3	3	13	8	28	35	0	2.33e-15	0.000194	0	0.000027	0	<1.00e-15	<1.39e-12
6	ASTN2	astrotactin 2	1946454	63	57	62	20	9	25	14	3	10	2	1.000	0.219	4.4e-06	0.0045	0	<1.00e-15	<1.39e-12
7	BRAF	v-raf murine sarcoma viral oncogene homolog B1	1213204	44	41	21	1	2	18	14	1	8	1	6.55e-15	0.000560	0	0.0065	0	<1.00e-15	<1.39e-12
8	CDKN2A	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)	451726	23	22	19	2	3	7	4	2	7	0	1.05e-08	0.115	1.8e-06	0	0	<1.00e-15	<1.39e-12
9	NFE2L2	nuclear factor (erythroid-derived 2)-like 2	974172	17	17	17	0	0	5	5	4	3	0	0.000347	0.0351	0.000028	0.00049	0	<1.00e-15	<1.39e-12
10	POTEM	POTE ankyrin domain family, member M	312390	13	13	13	2	0	7	4	1	1	0	0.000311	0.452	0	0.72	0	<1.00e-15	<1.39e-12
11	U2AF1	U2 small nuclear RNA auxiliary factor 1	443093	13	13	3	1	0	12	1	0	0	0	0.000147	0.0861	0	0.000052	0	<1.00e-15	<1.39e-12
12	C6orf25	chromosome 6 open reading frame 25	431449	12	12	2	0	0	0	1	0	11	0	0.000818	0.845	0	0.93	0	<1.00e-15	<1.39e-12
13	ZNF595	zinc finger protein 595	1009299	7	7	5	6	0	5	0	0	2	0	0.991	0.979	1.4e-06	0.28	0	<1.00e-15	<1.39e-12
14	LPPR4		1138514	66	58	64	7	7	34	14	4	7	0	1.94e-14	0.00156	0.14	0.94	0.29	1.92e-13	2.47e-10
15	RBM10	RNA binding motif protein 10	1073502	37	35	35	2	1	5	0	0	31	0	7.86e-13	0.00407	0.4	0.0034	0.034	8.66e-13	1.04e-09
16	FSTL5	follistatin-like 5	1365825	53	45	52	3	3	25	11	6	8	0	3.25e-12	0.00111	0.11	0.74	0.17	1.58e-11	1.79e-08
17	OR4A5	olfactory receptor, family 4, subfamily A, member 5	505448	31	30	31	4	1	16	6	4	4	0	1.33e-11	0.0500	0.15	0.23	0.2	7.22e-11	7.68e-08
18	OR5D13	olfactory receptor, family 5, subfamily D, member 13	515537	35	32	35	4	1	17	10	6	1	0	6.97e-12	0.0210	0.57	0.2	0.54	1.03e-10	1.04e-07
19	RB1	retinoblastoma 1 (including osteosarcoma)	1393625	33	32	32	1	0	1	3	1	28	0	1.39e-10	0.0575	0.012	0.92	0.033	1.25e-10	1.14e-07
20	REG1B	regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)	283328	23	22	23	2	1	14	2	2	4	0	1.85e-11	0.0230	0.69	0.088	0.25	1.26e-10	1.14e-07
21	WDR49	WD repeat domain 49	1162480	40	38	40	3	2	16	13	3	6	0	9.17e-10	0.0272	0.029	0.19	0.038	8.83e-10	7.60e-07
22	LRRIQ3	leucine-rich repeats and IQ motif containing 3	979489	38	32	38	3	2	15	8	5	8	0	9.91e-10	0.0880	0.026	0.91	0.046	1.12e-09	9.24e-07
23	OR4C16	olfactory receptor, family 4, subfamily C, member 16	506644	35	32	34	6	1	15	12	3	4	0	1.58e-09	0.152	0.044	0.6	0.084	3.16e-09	2.48e-06
24	RGS7	regulator of G-protein signaling 7	827433	33	31	32	2	3	17	6	0	6	1	4.83e-10	0.0117	0.31	0.27	0.33	3.75e-09	2.83e-06
25	POTEG	POTE ankyrin domain family, member G	644380	37	36	34	6	3	19	7	2	5	1	8.23e-07	0.174	0.0005	0.98	0.0011	1.91e-08	1.38e-05
26	MUC7	mucin 7, secreted	622300	26	24	26	2	1	13	4	5	3	0	1.17e-08	0.0405	0.084	0.79	0.16	4.05e-08	2.82e-05
27	TAS2R1	taste receptor, type 2, member 1	490760	20	20	20	0	1	11	4	1	3	0	4.07e-09	0.00205	0.55	0.7	0.65	5.53e-08	3.70e-05
28	COL11A1	collagen, type XI, alpha 1	3066776	142	116	139	17	2	78	24	7	26	5	2.06e-08	0.0259	0.65	0.12	0.24	9.83e-08	6.34e-05
29	FERD3L	Fer3-like (Drosophila)	273884	21	21	19	3	0	13	3	2	3	0	8.73e-09	0.0456	0.5	0.43	0.6	1.05e-07	6.54e-05
30	KIAA0408	KIAA0408	1145889	20	19	8	1	0	4	2	1	13	0	0.000766	0.516	1.2e-06	0.37	9.6e-06	1.45e-07	8.74e-05
31	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	1306090	20	19	13	0	0	13	4	2	1	0	0.00295	0.0114	2e-07	0.0066	2.6e-06	1.51e-07	8.79e-05
32	TMTC1	transmembrane and tetratricopeptide repeat containing 1	1278236	59	51	56	9	9	28	9	3	10	0	4.65e-08	0.0104	0.15	0.22	0.2	1.78e-07	0.000100
33	OR5W2	olfactory receptor, family 5, subfamily W, member 2	505839	27	26	25	4	1	15	8	2	1	0	5.40e-08	0.0830	0.16	0.35	0.18	1.89e-07	0.000103
34	ZNF804A	zinc finger protein 804A	1984779	107	90	104	17	5	59	19	6	17	1	1.03e-08	0.0939	0.72	0.68	1	2.01e-07	0.000107
35	OR8K5	olfactory receptor, family 8, subfamily K, member 5	504960	21	21	20	2	0	12	5	2	2	0	6.94e-08	0.0472	0.83	0.044	0.16	2.17e-07	0.000112

+ COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 39. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	TP53	tumor protein p53	309	356	296	194020	42333	0	0
2	EGFR	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)	87	293	70	159685	25575	0	0
3	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	333	18	8	9810	8	1.8e-13	2e-10
4	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	169	52	168	28340	2255476	2.4e-13	2e-10
5	BRAF	v-raf murine sarcoma viral oncogene homolog B1	44	89	34	48505	129957	3.4e-13	2e-10
6	CDKN2A	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)	23	332	22	180940	425	3.9e-13	2e-10
7	MET	met proto-oncogene (hepatocyte growth factor receptor)	22	34	9	18530	73	4.1e-13	2e-10
8	STK11	serine/threonine kinase 11	87	130	56	70850	153	4.1e-13	2e-10
9	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	20	138	14	75210	4768	4.4e-13	2e-10
10	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	30	220	23	119900	7945	4.4e-13	2e-10

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

+ Geneset Analyses

Table 5. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 17. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_ns_s	p	q
1	TELPATHWAY	Telomerase is a ribonucleotide protein that adds telomeric repeats to the 3' ends of chromosomes.	AKT1, BCL2, EGFR, G22P1, HSPCA, IGF1R, KRAS2, MYC, POLR2A, PPP2CA, PRKCA, RB1, TEP1, TERF1, TERT, TNKS, TP53, XRCC5	15	AKT1(3), BCL2(5), EGFR(87), IGF1R(8), MYC(4), POLR2A(11), PPP2CA(1), PRKCA(10), RB1(33), TEP1(39), TERF1(4), TERT(7), TNKS(11), TP53(309), XRCC5(9)	22681635	541	351	357	50	62	137	64	70	205	3	<1.00e-15	<1.00e-15	<1.23e-13
2	RBPATHWAY	The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions.	ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH	12	ATM(53), CDC25A(4), CDC25B(1), CDC25C(8), CDK2(1), CDK4(3), CHEK1(7), MYT1(24), RB1(33), TP53(309), WEE1(4), YWHAH(1)	14151904	448	341	310	18	54	107	51	50	181	5	<1.00e-15	<1.00e-15	<1.23e-13
3	ARFPATHWAY	Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest.	ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1	16	ABL1(10), CDKN2A(23), E2F1(3), MDM2(5), MYC(4), PIK3CA(30), PIK3R1(4), POLR1A(13), POLR1B(11), POLR1D(2), RB1(33), TBX2(8), TP53(309), TWIST1(2)	16255854	457	322	307	32	58	124	63	43	166	3	<1.00e-15	<1.00e-15	<1.23e-13
4	TERTPATHWAY	hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers.	HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42	7	HDAC1(4), MAX(8), MYC(4), SP1(6), SP3(6), TP53(309), WT1(16)	5699587	353	306	218	17	48	96	38	36	132	3	<1.00e-15	<1.00e-15	<1.23e-13
5	RNAPATHWAY	dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation.	CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53	9	CHUK(7), DNAJC3(5), EIF2S2(3), NFKB1(6), NFKBIA(4), RELA(3), TP53(309)	7863806	337	303	203	18	43	87	37	38	129	3	<1.00e-15	<1.00e-15	<1.23e-13
6	ATMPATHWAY	The tumor-suppressing protein kinase ATM responds to radiation-induced DNA damage by blocking cell-cycle progression and activating DNA repair.	ABL1, ATM, BRCA1, CDKN1A, CHEK1, CHEK2, GADD45A, JUN, MAPK8, MDM2, MRE11A, NBS1, NFKB1, NFKBIA, RAD50, RAD51, RBBP8, RELA, TP53, TP73	19	ABL1(10), ATM(53), BRCA1(22), CDKN1A(2), CHEK1(7), CHEK2(10), GADD45A(2), JUN(3), MAPK8(2), MDM2(5), MRE11A(13), NFKB1(6), NFKBIA(4), RAD50(10), RAD51(2), RBBP8(6), RELA(3), TP53(309), TP73(7)	23963460	476	347	338	36	59	127	70	56	159	5	<1.00e-15	1.44e-15	1.44e-13
7	P53PATHWAY	p53 induces cell cycle arrest or apoptosis under conditions of DNA damage.	APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53	16	APAF1(10), ATM(53), BAX(3), BCL2(5), CCND1(3), CCNE1(7), CDK2(1), CDK4(3), CDKN1A(2), E2F1(3), GADD45A(2), MDM2(5), PCNA(1), RB1(33), TIMP3(4), TP53(309)	14566640	444	342	306	25	53	112	57	50	167	5	<1.00e-15	1.89e-15	1.44e-13
8	CHEMICALPATHWAY	DNA damage promotes Bid cleavage, which stimulates mitochondrial cytochrome c release and consequent caspase activation, resulting in apoptosis.	ADPRT, AKT1, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, CASP3, CASP6, CASP7, CASP9, CYCS, EIF2S1, PRKCA, PRKCB1, PTK2, PXN, STAT1, TLN1, TP53	20	AKT1(3), APAF1(10), ATM(53), BAD(1), BAX(3), BCL2(5), BCL2L1(3), BID(2), CASP3(5), CASP6(3), CASP7(3), CASP9(6), CYCS(2), PRKCA(10), PTK2(6), PXN(2), STAT1(7), TLN1(15), TP53(309)	22055995	448	350	311	45	54	128	57	52	152	5	2.33e-14	2.00e-15	1.44e-13
9	P53HYPOXIAPATHWAY	Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage.	ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53	19	ABCB1(45), AKT1(3), ATM(53), BAX(3), CDKN1A(2), CPB2(6), CSNK1A1(2), CSNK1D(7), FHL2(3), GADD45A(2), HIC1(1), HIF1A(2), IGFBP3(4), MAPK8(2), MDM2(5), NFKBIB(3), TP53(309)	16675533	452	346	315	29	53	132	58	51	153	5	<1.00e-15	2.11e-15	1.44e-13
10	ATRBRCAPATHWAY	BRCA1 and 2 block cell cycle progression in response to DNA damage and promote double-stranded break repair; mutations induce breast cancer susceptibility.	ATM, ATR, BRCA1, BRCA2, CHEK1, CHEK2, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, HUS1, MRE11A, NBS1, RAD1, RAD17, RAD50, RAD51, RAD9A, TP53, TREX1	21	ATM(53), ATR(26), BRCA1(22), BRCA2(34), CHEK1(7), CHEK2(10), FANCA(7), FANCC(2), FANCD2(5), FANCE(3), FANCF(6), FANCG(7), HUS1(4), MRE11A(13), RAD1(1), RAD17(6), RAD50(10), RAD51(2), RAD9A(2), TP53(309), TREX1(1)	35575939	530	355	393	37	58	146	87	68	166	5	<1.00e-15	2.78e-15	1.62e-13

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_ns_s	p	q
1	HSA00950_ALKALOID_BIOSYNTHESIS_I	Genes involved in alkaloid biosynthesis I	DDC, GOT1, GOT2, TAT, TYR	5	DDC(8), GOT1(3), GOT2(6), TAT(9), TYR(29)	3808360	55	53	55	9	8	22	11	6	8	0	0.033	0.65	1
2	HSA00401_NOVOBIOCIN_BIOSYNTHESIS	Genes involved in novobiocin biosynthesis	GOT1, GOT2, TAT	3	GOT1(3), GOT2(6), TAT(9)	2128311	18	18	18	2	5	7	3	2	1	0	0.076	0.66	1
3	IL18PATHWAY	Pro-inflammatory IL-18 is activated in macrophages by caspase-1 cleavage and, in conjunction with IL-12, stimulates Th1 cell differentiation.	CASP1, IFNG, IL12A, IL12B, IL18, IL2	6	CASP1(8), IFNG(7), IL12A(2), IL12B(3), IL2(7)	2403481	27	26	27	5	1	16	0	1	8	1	0.2	0.76	1
4	PLK3PATHWAY	Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis.	ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH	6	ATM(53), ATR(26), CDC25C(8), CHEK1(7), CHEK2(10), YWHAH(1)	12280972	105	90	103	9	9	26	18	19	31	2	0.00048	0.84	1
5	HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM	Genes involved in D-arginine and D-ornithine metabolism	DAO	1	DAO(7)	584333	7	7	7	3	2	1	0	2	2	0	0.74	0.93	1
6	PEPIPATHWAY	Proepithelin (PEPI) induces epithelial cells to secrete IL-8, which promotes elastase secretion by neutrophils.	ELA1, ELA2, ELA2A, ELA2B, ELA3B, GRN, IL8, SLPI	3	GRN(6), SLPI(1)	1382720	7	7	6	1	1	2	1	1	2	0	0.35	0.94	1
7	HSA00031_INOSITOL_METABOLISM	Genes involved in inositol metabolism	ALDH6A1, TPI1	2	ALDH6A1(2), TPI1(9)	1324024	11	10	11	3	1	3	5	0	2	0	0.59	0.96	1
8	HSA00785_LIPOIC_ACID_METABOLISM	Genes involved in lipoic acid metabolism	LIAS, LIPT1, LOC387787	2	LIAS(2), LIPT1(2)	1235104	4	4	4	0	0	1	0	1	2	0	0.5	0.97	1
9	ASBCELLPATHWAY	B cells require interaction with helper T cells to produce antigen-specific immunoglobulins as a key element of the human immune response.	CD28, CD4, CD80, HLA-DRA, HLA-DRB1, IL10, IL2, IL4, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6	8	CD28(5), CD4(8), CD80(3), HLA-DRA(3), HLA-DRB1(5), IL10(2), IL2(7), IL4(1)	3223968	34	29	30	7	1	14	1	4	14	0	0.39	0.98	1
10	SULFUR_METABOLISM		BPNT1, PAPSS1, PAPSS2, SULT1A2, SULT1A3, SULT1A3, SULT1A4, SULT1E1, SULT2A1, SUOX	7	BPNT1(7), PAPSS1(5), PAPSS2(10), SULT1A2(5), SULT1E1(11), SULT2A1(6), SUOX(5)	4954097	49	45	49	7	3	22	9	7	8	0	0.037	0.98	1

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