Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line

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Table 1 In silico analysis of restriction enzyme cutting statistics for the human reference genome (hg19)

Enzyme	Usable DNA fragments (%)			Average fragment size (kb)	Maximum fragment size (kb)	#Fragments >100 kb
	5–20 kb	6–15 kb	6–12 kb	Average fragment size (kb)	Maximum fragment size (kb)	#Fragments >100 kb
AflII	13.3	5.48	5.43	4.47	143.96	4
BamHI	99.22	92.95	92.9	7.92	153.92	21
*Kpn* I	99.95	99.88	99.51	9.98	171.76	65
NcoI	0.08	0.03	0.03	3.81	164.18	2
NheI	99.86	98.97	90.75	10.23	204.75	88
SpeI	99.28	96.71	94.55	7.27	311.48	101
BglII	2.33	0.81	0.8	3.71	109.69	1
EcoRI	2.21	0.79	0.79	3.67	86.14	0
MluI	0.34	0.01	0.01	135.32	2276.59	8295
NdeI	5.9	1.78	1.78	3.19	105.86	1
PvuII	0.03	0.02	0.02	2.66	173.76	6
XbaI	2.75	1.15	1.15	3.58	146.27	2
XhoI	17.02	6.37	2.21	23.78	430.88	3269

To select the restriction enzyme that cuts the human genome to maximize the fraction of fragments resulting in informative maps, the human genome was cut in silico with 13 commonly used restriction enzymes based on their canonical cutting sites. Usable restriction fragment sizes were defined as 5–20 kb, 6–15 kb, and 6–12 kb, since smaller DNA fragments do not allow accurate size estimates, and longer fragments can result in maps with too few fragments. KpnI was selected based on its high fraction of usable DNA fragments (highlighted in bold)

ISSN: 2047-217X