. Author manuscript; available in PMC: 2017 Sep 1.

Published in final edited form as: Hum Mutat. 2016 Jul 13;37(9):942–954. doi: 10.1002/humu.23027

Table 2.

Validated somatic insertions in SCC

Esophageal Squamous Cell Cancer Validated Insertions
Insertion number	Predicted breakpoint	Group	Sample	Patient Age	5’ end validated	Inversion	TSD sequence	Insertion size (w/o poly A)	Exact Genomic Breakpoint	Subclonal in NE	Likely clonal in SCC	Predicted Endo site	poly(A) length	Gene(s)	Stand of insertion (relative to hg19)
1	chr1:74225746	2	20T	79	Yes	No	300 bp (TATCTCCAGCTTACC	120 bp	chr1:74225531		Yes	AGAT/AA	80 bp		“-”
2	chr1:91054960	2	20T	79									50 bp		“+”
3	chr1:110159225	2	20T	79							Yes		100 bp		“+”
4	chr1:188390840	2	21T	71									60 bp		“+”
5	chr2:7391894	2	23T	76						Yes	Yes		40 bp		“-”
6	chr3:106586376	2	20T	79									100 bp	LINC00882	“-”
7	chr3:158778615	2	21T	71	Yes	Yes	15 bp (CAGAATATGCATTTT	1859 bp	chr3:158778722		Yes	TTCT/GA	150 bp		“-”
8	chr3:173244207	2	21T	71							Yes		75 bp	NLGN1	“+”
9	chr4:21015215	2	21T	71	yes	Yes	11 bp (TAAAGCTTCTTT)	1229 bp	chr4:21015270		Yes	CTTT/AT	75 bp	KCNIP4	“-”
10	chr4:21295696	2	20T	79	Yes	No	16 bp (AAAAACTGTTAATA	520 bp	chr4:21295716			TATG/AA	40 bp	KCNIP4	“+”
11	chr4:33062493	2	20T	79									100 bp		“-”
12	chr4:34773929	2	23T	76							Yes		45 bp		“-”
13	chr4:100470748	2	20T	79									50 bp	TRMT1	“-”
14	chr4:122022647	2	20T	79	Yes	No	5 bp (GTTTT)	1110 bp	chr4:122022858			AAAA/CA	50 bp		“-”
15	chr5:18343101	2	20T	79							Yes		100 bp		“-”
16	chr5:22972054	2	21T	71							Yes		50 bp		“+”
17	chr5:27118145	2	23T	76	Yes	No	376 bp (GTATATCTCCAAATT	121 bp	chr5:27117892		Yes	TATA/CA	150 bp		“-”
18	chr5:63570580	2	21T	71	Yes	No	389 bp deletion (TGACTCCTA	630 bp	chr5:63571024		Yes	Endo indep	50 bp	RNF180	“-”
19	chr5:146263689	2	21T	71	Yes	No	12 bp (AAACATTTACCA)	1039 bp	chr5:146263701	Yes	Yes	ATTT/AC	50 bp	PPP2R2B	“+”
20	chr6:54007315	2	20T	79	Yes	Yes	12 bp (TCTTTGATTTTT)	258 bp	chr6:54007426			AAAG/AC	80 bp	MLIP	“-”
21	chr6:65430273	2	20T	79						Yes	Yes		100 bp	EYS	“-”
22	chr6:93175977	2	20T	79							Yes				“+”
23	chr6:149512094	2	21T	71											“+”
24	chr6:167049997	2	21T	71									130 bp	RPS6KA2	“-”
25	chr7:78377347	2	20T	79	Yes	No	20 bp (AAAAAAAAAAAAA	773 bp	chr7:78377476		Yes	TTTT/TT	50 bp	MAGI2	“-”
26	chr7:84066697	2	22T	59	Yes	No	1 bp deletion	354 bp	chr7:84066755	Yes	Yes	Endo indep	55 bp		“-”
27	chr7:113098298	2	22T	59	Yes	No	None	1189 bp	chr7:113098416	Yes	Yes	GTTA/TA	100 bp		“-”
28	chr7:144876298	2	21T	71	Yes	No	11 bp (ACTGCTCTCTT)	361 bp	chr7: 144876634			GCAG/TG	50 bp		“-”
29	chr8:62731519	2	20T	79	Yes	No	5 bp (TTTTA)	568 bp	chr8:62731576			TAAA/AA	50 bp		“-”
30	chr8:63452731	2	23T	76						Yes	Yes		5 bp	NKAIN3	“-”
31	chr8:78650641	2	23T	76						Yes	Yes		70 bp		“+”
32	chr8:96814193	2	20T	79	Yes	No	2 bp (TC)	737 bp	chr8:96814250	Yes	Yes	CTTG/AA	50 bp	C8orf37-AS1, LOC100616530	“-”
33	chr8:105742587	2	21T	71									50 bp		“+”
34	chr8:130050500	2	23T	76						Yes	Yes		50 bp		“+”
35	chr8:137876889	2	21T	71									12		“-”
36	chr8:137876889	2	21T	71									25 bp		“+”
37	chr9:27521686	2	21T	71										MOB3B	“+”
38	chr9:30914267	2	21T	71	Yes	Yes	14 bp (AAGAAGGCATAGAA	1305 bp	chr9:82494253		Yes	GATC/AA	20 bp		“+”
39	chr9:82494252	2	21T	71	Yes	No	12 bp (AAAAAAAATCAA)	282 bp	chr9:30914249			ATCA/AG	100 bp	LINC01507	“+”
40	chr10:11187849	2	22T	59							Yes		100 bp	CELF2	“+”
41	chr10:55846139	2	23T	76	Yes	No	3 bp deletion	175 bp	chr10:55846282	Yes	Yes	Endo indep	40 bp	PCDH15	“-”
42	chr10:115267083	2	23T	76									55 bp		“+”
43	chr11:23140915	2	20T	79	Yes	No	14 bp (AAAAAACATAAACA	1043 bp	chr11:23140929			ACAT/AA	35 bp		“+”
44	chr11:43634948	2	23T	76											“+”
45	chr11:78577470	2	20T	79	Yes	Yes	109 bp deletion	346 bp	chr11:78577397		Yes	Endo indep	60 bp	TENM4	“+”
46	chr11:95617289	2	23T	76						Yes	Yes		70 bp	MTMR2	“-”
47	chr12:72582208	2	21T	71						Yes	Yes		130 bp		“+”
48	chr13:90364217	2	20T	79											“-”
49	chr14:21603456	2	20T	79							Yes		50 bp		“+”
50	chr14:95721343	2	20T	79									50 bp	CLMN	“+”
51	chr15:55401145	2	20T	79									50 bp		“-”
52	chr16:32621143	2	23T	76											“-”
53	chr18:7914950	2	21T	71									100 bp	PTPRM	“+”
54	chr19:31676750	2	23T	76									80 bp		“-”
55	chr20:12193544	2	21T	71									40 bp		“+”
56	chr20:31767412	2	20T	79									20 bp	BPIFA2	“+”
57	chr1:169592527	1	3T	51	Yes	No	3 bp (TAT)	290 bp	chr1:169592905		Yes			SELP	“-”
58	chr2:62784947	1	3T	51							Yes		50 bp		“-”
59	chr2:118147901	1	1T	76							Yes				“+”
60	chr2:192054832	1	1T	76							Yes	GATT/AA			“-”
61	chr3:108723582	1	8T	78							Yes		20 bp	MORC1	“+”
62	chr4:178589680	1	2T	67							Yes		74 bp	AK094945	“-”
63	chr5:8875319	1	3T	51							Yes			BC032891	“+”
64	chr5:6447510	1	8T	78							Yes				“-”
65	chr6:5599305	1	3T	51								CAGT/AT	83 bp	FARS2	“-”
66	chr7:69594334	1	8T	78	Yes	No	2 bp (TA)	365 bp	chr11:122340070		Yes			AUTS2	“+”
67	chr7:18316210	1	8T	78									10 bp	HDAC9	“-”
68	chr7:71682380	1	8T	78	Yes	No	6 bp (AGAAAA)	528 bp	chr7:71682386				30 bp	CALN1	“+”
69	chr9:8381705	1	1T	76									20 bp	PTPRD	“+”
70	chr9:81288257	1	8T	78									40 bp		“+”
71	chr11:122339699	1	3T	51							Yes		35 bp		“-”
72	chr14:81244336	1	3T	51							Yes	TTAT/AG		CEP128	“-”
73	chr16:20172684	1	3T	51							Yes		70 bp		“-”
74	chrX:144755675	1	3T	51							Yes		43 bp		“-”

In this table all of the validated somatic insertions’ information is listed, including: the group/ sample in which they were detected, the patient’s age, whether or not the 5’ end of the insertion was validated (including all of the related information such as the target-site duplication (TSD) and endonuclease cleavage site, etc.), if the insertion was amplified with a conventional PCR, whether or not the insertion was sub-clonal in normal esophagus, the gene into which the insertion occurred, and finally the strand, with respect to the hg19 reference assembly, into which the insertion occurred. All genomic positions listed in the table are from hg19.