TABLE 1.

The 17 HK2 loci that are not in the human reference genome^j

Cytoband	Coordinatea	Other name(s)	Flanking region	Frequency
				TCGA (n = 26)	WGS500 (n = 332)	Lee et al. (n = 44b)
1p21.1	106015874–106015881		—c	0.04	0.003	0
1p13.2d	111802591–111802598	DE5, ERVK1	L1	0.62	0.593	0.35
1q41	223578303–223578310	ERVK2	L1	0	0.006	0.02
4q22.3	9603239–9603245	ERVK6	ERV	0.96	0.958	0.86
5q12.3	64388439–64388446	ERVK9	L1	0.15	0.075	0.12
5q14.1	80442265–80442272	DE6, NE1, ERVK10	RASGRF2 intron	0	0.093	0.14
6p21.32	32648035–32648041e		L1	0.46	0.443	0
6q26	161270898–16127090	DE2, ERVK12	—c	0.96	0.834	0.70
9q34.11	132205208f	DE7, ERVK16	MaLR	1.00	0.961	0.33
11q12.2	60449889f	DE4, ERVK18	L1g	0	0.003	0.02
12q12h	44313656–44313662	ERVK20	L1 in TMEM117 intron	0.31	0.241	0.14
12q24.31	124066476–124066483	ERVK21	Alug	0.35	0.238	0.14
13q31.3	90743182–90743189	NE2, ERVK22	AT richg,i	0.15	0.190	0.12
15q22.2	63374593–63374600	ERVK24	Alu	0.81	0.889	0.79
19p12	21841536–21841542	K113, DE1, ERVK26	—c	0.08	0.087	0.08
19q12d	29855781–29855787	DE3, ERVK28	—g	0.54	0.678	0.56
20p12.1h	12402386–12402392	ERVK30	—c	0	0.015	0.05

^aThe 5- or 6-nt difference between coordinates is the length of the target site duplication (hg19).

^bFrom 41 germ line genomes from cancer patients plus 3 healthy individuals from the HapMap project (21).

^cSingle-copy nontranscribed DNA region.

^dAlso found by Kahyo et al. (35).

^eLocus present in some publicly available HLA haplotype sequences.

^fWe found evidence for only one side of the integration.

^gWithin long noncoding RNA.

^hAs validated by PCR by Lee et al. (21), one integration and one preintegration site for both loci.

ⁱThe locus is also 12 nt from an Alu.

^jThe distribution of loci among individuals and zygosity in the 26 TCGA patients are given in Table S1 in the supplemental material. Cytobands are taken from http://www.tallphil.co.uk/bioinformatics/cytobands.