paneldecision	GeneName	sample	class	AAChange	dbsnp	Additional Somatic or Germline Lesions	#NHLBI Frequency	COSMIC	^PCGP Somatic Mutation	SIFT	Polyphen2	Mutation Assessor		PubMed References	Chr	WU_HG19_Pos	ReferenceAllele	MutantAllele	Flanking	Protein GI	mRNA accession	#Reads in Tumor		# Reads in Normal		#Read in Tumor		#Reads in Normal		#Read in Tumor		#Reads in Normal					
U	BMPR1A	SJBALL020570	missense	T280S						D	D	L	Silver		chr10	88677054	C	G	AGAAACAGAAATCTACCAAA[C/G]TGTGCTAATGCGCCATGAAA	41349437	NM_004329	23	40	6	25	.	.	.	.						none	no tumor contamination as it has EBF1 tumor only deletion	
U	CBL	SJBALL239	missense	R563C						D	D	L	Silver		chr11	119156022	C	T	CAGAATCCCGACCTCAAAGA[C/T]GCCCCTTGCCTTGTACACCA	52426745	NM_005188	32	49	11	19	.	.	.	.						none		
U	CBL	SJETV025	missense	R788Q	rs150811339		0.000615953			D	D	L	Silver		chr11	119169179	G	A	GCCGGCCGTGCTGGCCCGCC[G/A]AACTCTCTCAGATATCTCTA	52426745	NM_005188	16	42	17	35	.	.	.	.						none		
U	CBL	SJHGG033	missense	P566A						T	D	L	Silver		chr11	119156031	C	G	GACCTCAAAGACGCCCCTTG[C/G]CTTGTACACCAGGCGACTGT	52426745	NM_005188	17	36	12	20	.	.	.	.						none		
U	CBL	SJNBL001	missense	R617L						D	D	L	Silver		chr11	119156185	G	T	AGGAAGAGAATTAACCAACC[G/T]GCACTCACTTCCATTTTCAT	52426745	NM_005188	3	29	13	39	.	.	.	.						none		
U	CBL	SJPHALL020037	missense	G773W						D	D	L	Silver		chr11	119169133	G	T	AGTCAGAAAATGAGGATGAT[G/T]GGTATGATGTCCCAAAGCCA	52426745	NM_005188	11	22	11	18	.	.	.	.						none		
U	CDC73	SJCBF013	missense	V445I			0.000461326			T	D	M	Silver		chr1	193205402	G	A	GTAGGGACCGCGTTGTAGCC[G/A]TTTTTGTGCAGGGTCCTGCA	40018640	NM_024529	24	46	15	33	.	.	.	.						none		
U	CDH1	SJBALL021893	missense	T470I	rs370864592					D	D	M	Silver		chr16	68849506	C	T	GGTCTCTCTCACCACCTCCA[C/T]AGCCACCGTCACCGTGGATG	4757960	NM_004360	15	44	27	46	.	.	.	.						none		
U	CDH1	SJEPD031	missense	R224H	rs201511530					T	B	N	Silver		chr16	68842735	G	A	AGAGCCTCTGGATAGAGAAC[G/A]CATTGCCACATACACTGTAA	4757960	NM_004360	26	60	12	25	.	.	.	.						none		
U	CDH1	SJERG006	missense	T562A						T	B	M	Silver		chr16	68853301	A	G	ACGTGAAGAACAGCACGTAC[A/G]CAGCCCTAATCATAGCTACA	4757960	NM_004360	20	46	16	38	.	.	.	.						none	DJH: Note-> We may wish to consider revisiting this one to consider LB vs U. But U seems best classification given the amount of evidence and rarity of allele.	
U	CDH1	SJHYPER006	missense	A298T	rs142822590		0.000307787			T	D	M	Silver	PUBMED=15235021	chr16	68845646	G	A	ATGATGTGAACACCTACAAT[G/A]CCGCCATCGCTTACACCATC	4757960	NM_004360	18	35	16	26	18	53	21	38						none		
U	CDH1	SJHYPO013	missense	D433G	rs376097289					D	P	M	Silver		chr16	68847376	A	G	CACAAATCCAGTGAACAACG[A/G]TGGCATTTTGAAAACAGCAA	4757960	NM_004360	1	29	13	23	.	.	.	.						deletion of mutant copy		
U	CDH1	SJHYPO123	missense	D777N	rs372989292		0.000153894			T	D	M	Silver		chr16	68863590	G	A	GCCAGCTGCACAGGGGCCTG[G/A]ACGCTCGGCCTGAAGTGACT	4757960	NM_004360	30	36	15	26	.	.	.	.						deletion		
U	CDH1	SJMB036	missense	R774G						D	D	L	Silver		chr16	68863581	A	G	TTGACTTGAGCCAGCTGCAC[A/G]GGGGCCTGGACGCTCGGCCT	4757960	NM_004360	9	18	15	32	.	.	.	.						none		
U	CDH1	SJNBL001	missense	D805N	rs200894246		0.000615574			T	D	L	Silver	PUBMED=23197654	chr16	68863674	G	A	TTCCCCGCCCTGCCAATCCC[G/A]ATGAAATTGGAAATTTTATT	4757960	NM_004360	16	35	6	26	.	.	.	.						none		
U	CDH1	SJNBL138	missense	R732W						T	D	M	Silver	PUBMED=15235021	chr16	68862106	C	T	TGCTGCTCTTGCTGTTTCTT[C/T]GGAGGAGAGCGGTGGTCAAA	4757960	NM_004360	.	.	.	.	38	68	36	86						none		
LP	CDH1	SJPHALL018	missense	P373L						D	D	H	Silver		chr16	68846147	C	T	TGACACCAACGATAATCCTC[C/T]GATCTTCAATCCCACCACGG	4757960	NM_004360	30	58	18	31	.	.	.	.						none	DJH: See notes on slide presentation for this designation.	
U	CDK4	SJE2A006	missense	S52N						D	D	L	Silver	PUBMED=10398427	chr12	58145346	C	T	AAGCCACCTCACGAACTGTG[C/T]TGATGGGAAGGCCTCCTCCA	4502735	NM_000075	.	.	.	.	24	52	16	34						none		CDK9 p.E107Q
U	DICER1	SJACT060	missense	L460F						T	D	L	Silver		chr14	95584088	C	G	TGTTTGCCAGCTTCCTTTAT[C/G]AATCTAAGAAAATTATACAC	29294651	NM_177438	41	67	20	29	.	.	.	.						none		
U	DICER1	SJHYPER016	missense	E470D						T	D	N	Silver		chr14	95584058	C	G	TTGCTACTGATATAAGCCAG[C/G]TCTGGATCTTGTTTGCCAGC	29294651	NM_177438	24	67	10	25	12	49	11	30						none		
U	FH	SJEPD035	missense	A472D						D	D	H	Silver		chr1	241661246	G	T	CATTTTTGTGTGCTGTCTTA[G/T]CAATCTTTGCTGCCTTGTCA	19743875	NM_000143	25	60	17	36	.	.	.	.						none		
U	FH	SJETV190	missense	A194T						D	D	H	Silver		chr1	241672061	C	T	TGCAGCAGCAATGTGCATTG[C/T]TGTGGGAAAAGTATCATTTG	19743875	NM_000143	32	59	11	27	.	.	.	.						none		
U	FH	SJEWS001320	missense	R101Q	rs75086406					T	P	N	Silver	PUBMED=15663510	chr1	241676979	C	T	GGTTTACTTCAGCGGCCGCT[C/T]GCTTCAAGATGCCAAAAGCT	19743875	NM_000143	28	54	21	35	.	.	.	.						none		
U	FH	SJHGG057	missense	I120V	rs199641124					T	B	M	Silver		chr1	241676923	T	C	CTCATCTGCTGCCTTCATTA[T/C]TGCATTAGCAATCTTTGGAT	19743875	NM_000143	.	.	.	.	32	42	16	34						none		
U	FH	SJNBL135	missense	R74S	rs146739519		0.000153775			D	D	H	Silver		chr1	241680527	T	A	ATCTTAAAGTTCATCGTAGA[T/A]CTCACGGTCTGGGCGCCATA	19743875	NM_000143	.	.	.	.	53	114	57	96						none		
U	FH	SJOS001105	missense	P174R	rs199822819		0.00030755			D	D	M	Silver	PUBMED=NO ID	chr1	241675301	G	C	CATGATCGTTGGGATGCACA[G/C]GTATCTTGCTGCCAAGTTCA	19743875	NM_000143	28	49	14	32	.	.	.	.						none		
U	FH	SJPHALL020037	missense	E404D						D	D	M	Silver	PUBMED=16881969	chr1	241665767	C	A	ATTGGCTTGAAAACATTCAA[C/A]TCAAAATGTCCATTGCTGCC	19743875	NM_000143	18	45	15	31	32	47	34	65						none		
U	GATA2	SJINF002	missense	D23Y						D	D	L	Silver		chr3	128205808	C	A	CAGGCCCGGGTGGTGTGAGT[C/A]GGGGTGCTGCGCATTCAGCA	20070352	NM_032638	0	1	4	8	.	.	.	.						not well covered		
U	GATA2	SJINF010	missense	G273R						D	P	M	Silver		chr3	128204624	C	T	GGTGAAGCTGGAGGCCGGTC[C/T]CCCCAGGAAGCCTCCGGGGT	20070352	NM_032638	5	13	9	18	.	.	.	.						none		
U	MAP2K2	SJBALL087	missense	V202M						D	D	N	Silver		chr19	4101118	C	T	GATCTCCCCTCTAGAGTTCA[C/T]GAGGATGTTGGAGGGCTTCA	13489054	NM_030662	.	.	.	.	56	62	19	40						LOH		
U	MAP2K2	SJEPD001505	missense	L255P						D	D	M	Silver		chr19	4099354	A	G	CGGCCAGCTCCACCAGGGAC[A/G]GGCCCATGCTCCAGATGTCC	13489054	NM_030662	.	.	.	.	87	174	51	109						none		
U	MAP2K2	SJINF020031	missense	R313Q	rs151133017		0.00030755			T	D	N	Silver		chr19	4097323	C	T	CAAAGATGGCCATGGCAGGC[C/T]GGCTATCCATCCCGTGACCT	13489054	NM_030662	30	46	20	37	.	.	.	.						none	twins?	
U	MAP2K2	SJINF020032	missense	R313Q	rs151133017		0.00030755			T	D	N	Silver		chr19	4097323	C	T	CAAAGATGGCCATGGCAGGC[C/T]GGCTATCCATCCCGTGACCT	13489054	NM_030662	11	28	8	17	.	.	.	.						none	twins?	
U	MAP2K2	SJLGG029	missense	R164M						D	D	M	Silver		chr19	4102411	C	A	CCAGGATCTCCTCGGGAATC[C/A]TCTTGGCCTCTTTCAGCACC	13489054	NM_030662	22	48	6	17	.	.	.	.						none		
U	PALB2	SJAMLM7010475	missense	H394L						D	P	M	Silver		chr16	23646686	T	A	CTTCAGGCACTGTGCAAGAA[T/A]GTTTTTCTGCAGAAAGAGGA	27436910	NM_024675	.	.	.	.	38	78	60	97						none		
U	PALB2	SJBALL020516	missense	H549Q						T	P	M	Silver		chr16	23646220	G	T	AATTTTTCGTGCTGATATTT[G/T]TGTGAGGTGACTTCTTCCTT	27436910	NM_024675	32	51	28	47	.	.	.	.						none		
LB	PALB2	SJCBF016	missense	G1145S						T	D	L	Silver		chr16	23614908	C	T	GAGGAGGGCAGTACACTGAC[C/T]GAGAAGTAAGTCCCAAATGG	27436910	NM_024675	.	.	.	.	39	90	57	104						none		
U	PALB2	SJHYPO120	missense	E1083D	rs147045425		0.000153917	Yes		D	D	M	Silver		chr16	23619286	C	G	AACACAGGGCTTCGCAACGA[C/G]TCACTCTCTTTGGCACAGGG	27436910	NM_024675	2	28	19	34	.	.	.	.						deletion of mutant copy		
U	PALB2	SJNBL008	missense	E1083K						D	B	M	Silver		chr16	23619288	C	T	CACAGGGCTTCGCAACGACT[C/T]ACTCTCTTTGGCACAGGGAT	27436910	NM_024675	9	23	10	23	.	.	.	.						none		
U	PALB2	SJOS001108M1	missense	M1049T	rs138273800		0.000153917			D	P	M	Silver		chr16	23625380	A	G	GGTAAGAATCATCAATGTGC[A/G]TCTTTTTCAGGAGTTGACCA	27436910	NM_024675	17	23	20	46	.	.	.	.						none		
LP	PALB2	SJOS001118	frameshift	K550fs									Silver		chr16	23646219	T	-	TGCTGATATT(T>-)GTGTGAGGTG			3	32	17	44										deletion of mutant copy		
U	PALB2	SJRB020	missense	G439V						D	P	M	Silver		chr16	23646551	C	A	CCTTATTTTTATTTTTAAAC[C/A]CTTTTTTCTTGACATCCAAA	27436910	NM_024675	31	57	20	43	.	.	.	.						none		
U	PALB2	SJRHB001	missense	G1135E						D	D	M	Silver		chr16	23614937	C	T	AGTCCCAAATGGCAATTGTT[C/T]CAGAAGTCAAGATTGCTGCT	27436910	NM_024675	19	48	22	39	.	.	.	.						none		
U	PAX5	SJHYPER043	missense	G176R	rs142399779		0.000307645			T	D	L	Silver		chr9	37002723	C	G	GCTGATGGAGTACGACGAGC[C/G]GGCCGAATCCGTGCTCACCG	9951920	NM_016734	9	24	12	20	.	.	.	.	243	580	1354	2435	Valid	none		
U	PAX5	SJRHB048	missense	P321T						T	D	L	Silver		chr9	36882052	G	T	GTAGCTGCCCTGTCCAGCGG[G/T]GGGGACGTGTGGAGGGTACC	9951920	NM_016734	.	.	.	.	88	134	49	91	139	200	2064	3466	Valid	none		
LB	PHOX2B	SJHYPER011	missense	G289S						T	D	N	Silver		chr4	41747904	C	T	TAGGACGCTGGCGAAGGGAC[C/T]CCCAAGCGAATCCGGGATGG	12707580	NM_003924	3	3	1	1	.	.	.	.	208	438	707	1575	Valid	none		
U	PRKAR1A	SJEWS001304	missense	I149T						D	P	M	Silver		chr17	66520162	T	C	TTCTCTCTTTTGCAGTGATA[T/C]TTTTGATGCCATGTTTTCGG	47132583	NM_212472	20	50	15	30	.	.	.	.						none		
U	RAF1	SJCBF014	missense	Y574C	rs370242565		0.000153775			T	D	L	Silver		chr3	12626428	T	C	TTGCTTTGGGGCAGTTCTTA[T/C]ATAGCTTACTAAGATCTGGG	4506401	NM_002880	16	33	26	41	.	.	.	.						none		
U	RAF1	SJERG022	missense	N71S	rs184022679		0.000153775			T	B	M	Silver		chr3	12653557	T	C	AGCTCATTCCATTTCGCACA[T/C]TGACCTACAAACAAAGGACC	4506401	NM_002880	.	.	.	.	39	74	34	72						none		
U	RAF1	SJMB024	missense	N71S	rs184022679		0.000153775			T	B	M	Silver		chr3	12653557	T	C	AGCTCATTCCATTTCGCACA[T/C]TGACCTACAAACAAAGGACC	4506401	NM_002880	11	16	18	34	.	.	.	.						none		compound het
U	RAF1	SJMB024	missense	R40C						D	D	L	Silver		chr3	12660103	G	A	GCCATCATCTGATGCCCGGC[G/A]CTGATAGCCAAACTGCTGAA	4506401	NM_002880	9	25	22	29	.	.	.	.						none		compound het
U	RUNX1	SJAMLM7010475	missense	P359R						D	D	M	Silver		chr21	36164799	G	C	TGCCGATGCCCGAGGTGACC[G/C]GCGTCGGGGAGTAGGTGAAG	19923198	NM_001754	.	.	.	.	3	24	3	5	294	697	1153	2130	Valid	none		
U	RUNX1	SJBALL021372	missense	M25K	rs200431130		0.00093794			D	D	M	Silver		chr21	36259336	A	T	CCAGCGGCAACGCCTCGCTC[A/T]TCTTGCCTGGGCTCAGCGCG	49574546	NM_001001890	.	.	.	.	75	125	71	149	343	599	1272	2551	Valid	none		
U	RUNX1	SJBALL271	missense	E223G						T	D	M	Silver		chr21	36206844	T	C	GCTCCAGTTCACTGAGCCGC[T/C]CGGAAAAGGACAAGCTCCCG	19923198	NM_001754	102	109	8	20	.	.	.	.	43	48	592	1181	Valid	LOH		
U	RUNX1	SJHYPO040	missense	M25K	rs200431130		0.00093794			D	D	M	Silver		chr21	36259336	A	T	CCAGCGGCAACGCCTCGCTC[A/T]TCTTGCCTGGGCTCAGCGCG	49574546	NM_001001890	15	29	10	21	.	.	.	.	147	323	1034	2181	Valid	none		
LP	RUNX1	SJINF015	splice	R178_E4splice	N/A	none	NA						Gold		chr21	36206901	A	G	CTAGTTTCTGCCGATGTCCT[A/G]TTGTGGGGAGCAGGGAGGGG	49574546	NM_001001890	11	18	5	12	.	.	.	.	Sanger	Sanger	Sanger	Sanger	Valid	none		
P	RUNX1	SJLGG009	missense	N159D	N/A	none	NA			D	D	M	Silver		chr21	36252887	T	C	ACCGACAAACCTGAGGTCAT[T/C]AAATCTTGCAACCTGGTTCT	19923198	NM_001754	17	38	14	27	.	.	.	.	Sanger	Sanger	Sanger	Sanger	Valid	none		
LP	RUNX1	SJPHALL020044	missense	R204Q	N/A	none	NA	Yes		D	D	M	Silver	PUBMED=19357396	chr21	36231773	C	T	CCAAGTGGATGCACTTACTT[C/T]GAGGTTCTCGGGGCCCATCC	19923198	NM_001754	33	64	12	29	35	58	22	67	Sanger	Sanger	Sanger	Sanger	Valid	none		
LB	RUNX1	SJRHB037	missense	R233H	rs150042294		0.000461326			T	D	L	Silver		chr21	36206814	C	T	GGCTGACCCTCATGGCTGTG[C/T]GCCGCAGCTGCTCCAGTTCA	19923198	NM_001754	.	.	.	.	21	68	23	49	99	389	425	767		none		
LP	SDHA	SJMLL010	nonsense	R75*	N/A	none	NA			T			Silver	PUBMED=23750034	chr5	224547	C	T	GCGCTGGAGGGGCAGGCTTG[C/T]GAGCTGCATTTGGCCTTTCT	156416003	NM_004168	.	.	.	.	116	219	114	210	Sanger	Sanger	Sanger	Sanger	Valid	none		
U	SMAD4	SJHGG073	missense	P198R						D	D	L	Silver		chr18	48581289	C	G	GACAGAGACATACAGCACCC[C/G]AGCTCTGTTAGCCCCATCTG	4885457	NM_005359	.	.	.	.	21	44	18	56						none		
U	SMARCA4	SJBALL204	missense	T565M						D	D	M	Silver		chr19	11106989	C	T	CGAGTACGTGGCTAACCTCA[C/T]GGAGCTGGTGCGGCAGCACA	21071056	NM_003072	.	.	.	.	82	169	114	233						none		
U	SMARCA4	SJEWS001316	missense	I378V						D	B	M	Silver		chr19	11100006	A	G	CTCCCAGGCTGCAGGCTCGC[A/G]TCGCACACCGAATTCAGGAA	21071056	NM_003072	17	29	9	18	.	.	.	.						none		
U	SOS1	SJACT015	missense	Y215H						D	P	M	Silver		chr2	39281832	A	G	TAGATTTAGTTCCCTTATAT[A/G]TTGTCGAATTTCTGCCATAA	15529996	NM_005633	.	.	.	.	36	53	44	88						none		
U	SOS1	SJCBF107	missense	L791F						D	D	M	Silver		chr2	39239286	G	A	CCGGTATAGATCTGATTCAA[G/A]TAAAGTGAGTTGTCGAGCAA	15529996	NM_005633	.	.	.	.	60	129	48	102						none		
U	SOS1	SJERG011	missense	I82V						T	D	M	Silver		chr2	39285915	T	C	AGCTATTGCCCATTTATCAA[T/C]TGGATGAGGGAAACTTTTTT	15529996	NM_005633	31	61	20	41	.	.	.	.						none		
U	SOS1	SJMB009	missense	P1237A	rs371408734		0.00030755			T	D	L	Silver		chr2	39213258	G	C	GTCACTTTTTTTGCCCAAAG[G/C]GGGAGGTTGGAGATGTAGTG	15529996	NM_005633	14	36	18	28	.	.	.	.						none		
U	SOS1	SJOS001105	missense	I94V	rs144757941		0.000461396			D	B	M	Silver		chr2	39285879	T	C	TCTTCGCTTCCTCTTTTCAA[T/C]AGCTGATTGGGCATCAGCTA	15529996	NM_005633	22	60	12	22	.	.	.	.						none		
U	SUFU	SJACT067	missense	G294S	rs143807689		0.000461326			T	D	L	Silver		chr10	104357020	G	A	ACAGCCGGAGCATCTGCATC[G/A]GCACACAGCCCCGGCGACTC	19923479	NM_016169	14	27	15	24	.	.	.	.						none		
U	SUFU	SJHGG016	proteinIns	DEDinsS288									Silver		chr10	104357002	-	GACGAGGAC	TGACGAGGAC(--------->GACGAGGAC)AGCCGGAGCA			8	13	9	24										none		
U	SUFU	SJHGG069	missense	I57M						T	D	L	Silver		chr10	104264080	C	G	CCGCTCCAGGTTACCGCTAT[C/G]GTCAAGTACTGGTATGCTCT	19923479	NM_016169	12	22	6	23	.	.	.	.						none		
U	SUFU	SJHGG093	missense	P482L						T	D	N	Silver		chr10	104389902	C	T	TGACGTGGTGTTCGACAGTC[C/T]GCTACACTAGCCTGGGCTGG	19923479	NM_016169	.	.	.	.	18	33	12	30						none		
U	SUFU	SJNBL027	missense	Y397C						D	D	L	Silver		chr10	104377079	A	G	GCATGGACGGCACTTTACAT[A/G]TAAAAGTATCACAGGTGACA	19923479	NM_016169	13	24	19	30	.	.	.	.						none		
