Table 1 Genes with high DLS scores in the TCGA dataset

From: Essential genes shape cancer genomes through linear limitation of homozygous deletions

GeneSymbol	Chr	Start	End	0.5 Mb			1 Mb			2 Mb
GeneSymbol	Chr	Start	End	r	90% CI	N	r	90% CI	N	r	90% CI	N
4q34.3 LINC00290
LOC90768^a	4	183,060,158	183,065,668				−0.976	[−0.988 to −0.921]	25
MIR1305^a	4	183,090,445	183,090,531				−0.971	[−0.988 to −0.911]	25
DCTD	4	183,811,243	183,838,630							−0.924	[−0.958 to −0.839]	25
FAM92A1P2^a	4	183,958,817	183,961,272							−0.906	[−0.956 to −0.81]	25
9p21.3 CDKN2A
FAM154A	9	18,927,890	19,033,256				0.932	[0.893 to 0.951]	40	0.991	[0.983 to 0.993]	86
RRAGA	9	19,049,371	19,051,021				0.944	[0.913 to 0.959]	41	0.992	[0.984 to 0.994]	93
HAUS6	9	19,053,134	19,102,940				0.962	[0.936 to 0.972]	41	0.993	[0.985 to 0.995]	102
SCARNA8^a	9	19,063,653	19,063,784				0.949	[0.919 to 0.962]	41
PLIN2	9	19,115,758	19,127,604				0.968	[0.945 to 0.977]	42	0.993	[0.984 to 0.995]	109
DENND4C	9	19,230,762	19,374,137	0.993	[0.971 to 0.995]	29	0.996	[0.985 to 0.997]	50	0.989	[0.975 to 0.995]	141
RPS6	9	19,376,253	19,380,235	0.997	[0.983 to 0.996]	32	0.996	[0.986 to 0.997]	50	0.988	[0.973 to 0.994]	141
ACO1	9	32,384,600	32,450,832							−0.919	[−0.944 to −0.716]	17
DDX58	9	32,455,299	32,526,322							−0.910	[−0.943 to −0.682]	17
10q23.31 PTEN
WAPAL	10	88,195,012	88,281,541							0.913	[0.893 to 0.923]	63
FAM22A	10	88,985,204	88,994,733	0.973	[0.944 to 0.984]	38	0.906	[0.883 to 0.922]	59
FAM22A-AS1^a	10	88,998,423	89,102,315	0.995	[0.984 to 0.995]	58	0.913	[0.884 to 0.931]	62
LOC439994	10	89,102,167	89103,331	0.994	[0.981 to 0.995]	56	0.913	[0.885 to 0.929]	62
FAM22D	10	89,117,476	89,130,452	0.965	[0.951 to 0.968]	56	0.911	[0.881 to 0.929]	63
HTR7	10	92,500,575	92,617,671							−0.933	[−0.959 to −0.867]	33
RPP30	10	92,631,708	92,668,312							−0.915	[−0.946 to −0.832]	28
ANKRD1	10	92,671,856	92,681,032							−0.908	[−0.941 to −0.819]	28
13q14.2 RB1
SUCLA2	13	48,516,790	48,575,462	0.962	[0.908 to 0.972]	25
NUDT15	13	48,611,702	48,621,282	0.975	[0.922 to 0.982]	26
MED4	13	48,649,863	48,669,277	0.971	[0.916 to 0.979]	26
MED4-AS1^a	13	48,651,272	48,654,129	0.975	[0.924 to 0.982]	26
17p12 MAP2K4
MYH13	17	10,204,182	10,276,322							0.977	[0.933 to 0.982]	20
MYH8	17	10,293,641	10,325,267							0.968	[0.924 to 0.977]	20
MYH4	17	10,346,607	10,372,876							0.960	[0.909 to 0.973]	20
MYH1	17	10,395,626	10,421,859							0.950	[0.894 to 0.969]	20
MYH2	17	10,424,464	10,452,940							0.943	[0.883 to 0.966]	20
MYH3	17	10,531,842	10,560,626							0.912	[0.838 to 0.946]	20
SCO1	17	10,583,648	10,600,885							0.901	[0.825 to 0.94]	20
ELAC2	17	12894928	12921381				−0.989	[−0.991 to −0.946]	19
17q11.2 NF1
GOSR1	17	28,804,425	28,853,832				0.901	[0.824 to 0.923]	18
SUZ12P1	17	29,036,625	29,097,068	0.951	[0.897 to 0.961]	18
CRLF3	17	29,109,701	29,151,778	0.974	[0.928 to 0.981]	18
ATAD5	17	29,159,022	29,222,295	0.964	[0.893 to 0.983]	17
TEFM	17	29,226,000	29,233,286	0.959	[0.899 to 0.982]	18
ADAP2	17	29,248,753	29,286,211	0.910	[0.823 to 0.953]	18
COPRS	17	30,178,883	30,186,326	−0.951	[−0.975 to −0.854]	15
LRRC37B	17	30,348,154	30,380,519				−0.925	[−0.946 to −0.852]	18
SH3GL1P1^a	17	30,367,354	30,369,851				−0.932	[−0.95 to −0.867]	18
RHOT1	17	30,469,472	30,552,746				−0.916	[−0.933 to −0.856]	18
ARGFXP2^a	17	30,477,386	30,478,590				−0.913	[−0.931 to −0.851]	18
18q21.2 SMAD4
CCDC11	18	47,753,562	47,792,865				0.914	[0.843 to 0.925]	15
MBD1	18	47,793,251	47,808,144				0.916	[0.841 to 0.928]	15
CXXC1	18	47,808,712	47,814,692				0.916	[0.841 to 0.928]	15
SKA1	18	47,901,391	47,920,538				0.920	[0.838 to 0.942]	15

Candidate deletion-limiting genes show a DLS > 0.8 (r) within a 0.5-, 1- and/or 2-Mb neighborhood based on at least 15 homozygous somatic deletion events within the neighborhood (N), as well as >5% frequency of hemizygous deletions. Positive and negative r-values indicate candidate genes at the p- and q-terminal, respectively. To estimate the robustness of DLS scores, we assigned 90% confidence intervals using 200-fold bootstrapping. The identified genes map to seven distinct genomic regions, characterized by a high frequency of somatic acquired deletions with well-known deletion targets
^aNon protein coding gene

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Table 1 Genes with high DLS scores in the TCGA dataset

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