Table 3.

The genome-wide Mutation Frequency (MF).

Genome-Wide MF	Melanoma Study1	Melanoma Study2	Prostate Cancer	SCLC	CLL	Colorectal Cancer	Watson	HuRef
Constant Early	0.068	0.197	0.0119	0.047	0.00187	0.0300	6.63	9.84
Constant Late	0.176	0.352	0.0172	0.139	0.00571	0.0746	8.27	12.1
Core	0.064	0.194	0.0119	0.045	0.00185	0.0295	6.56	9.72
	0.173	0.343	0.0167	0.124	0.00616	0.0752	8.05	11.8
Periphery	0.104	0.226	0.0121	0.065	0.00208	0.0351	7.25	10.9
	0.177	0.356	0.0173	0.143	0.00555	0.0744	8.34	12.3
Low CpGI	0.079	0.216	0.0112	0.054	0.00228	0.0352	7.03	10.1
	0.178	0.362	0.0172	0.145	0.00596	0.0772	8.23	12.0
High CpGI	0.068	0.204	0.0120	0.047	0.00183	0.0296	6.59	9.80
	0.164	0.318	0.0169	0.105	0.00429	0.0603	8.45	12.1
Low RR	0.067	0.216	0.0122	0.047	0.00171	0.0303	5.91	8.65
	0.184	0.358	0.0173	0.149	0.00630	0.0775	7.86	11.5
High RR	0.069	0.195	0.0117	0.048	0.00199	0.0298	7.17	10.7
	0.161	0.323	0.0165	0.123	0.00489	0.0685	8.92	13.0
Low GC	0.063	0.208	0.0112	0.051	0.00167	0.0313	5.77	8.20
Percent	0.178	0.360	0.0175	0.147	0.00601	0.0778	8.16	11.9
High GC	0.069	0.196	0.0120	0.047	0.00189	0.0299	6.71	10.0
Percent	0.165	0.316	0.0154	0.114	0.00428	0.0592	8.78	12.8
Gene Poor	0.073	0.204	0.0115	0.051	0.00220	0.0328	7.27	9.74
	0.179	0.357	0.0172	0.142	0.00593	0.0766	8.37	11.1
Gene Rich	0.068	0.196	0.0120	0.047	0.00182	0.0296	6.52	10.4
	0.154	0.322	0.0168	0.111	0.00427	0.0617	7.59	12.3
GPos	0.066	0.201	0.0117	0.049	0.00201	0.0308	6.52	9.64
	0.177	0.354	0.0171	0.143	0.00596	0.0757	8.25	12.2
GNeg	0.070	0.195	0.0120	0.046	0.00181	0.0296	6.28	9.94
	0.164	0.337	0.0163	0.126	0.00504	0.0676	8.21	12.0

The MF (x10⁻⁴) is shown for five cancer types (1 sample of melanoma of study 1²⁵, 25 samples of melanoma of study 2²⁶, 7 samples of prostate cancer²⁷, 1 sample of small cell lung cancer²⁸, 4 samples of chronic lymphocytic leukemia²⁹, 9 samples of colorectal cancer³⁰) and two completely sequenced personal genomes (Watson³¹ and HuRef genomes³²) for ‘constant early’ (purple) and ‘constant late’ replicating regions (orange); and after stratifying by six different genomic features (nuclear lamina-associated domains¹¹, CpG islands, recombination rate, GC percentage, gene density, and chromatin status). CpG island data generated by Wu et al⁵³ were obtained from the UCSC genome browser. GC percentage was calculated for each 1Mb window using gc5base⁵⁴. Chromatin status was derived from Giemsa-staining-based g-banding patterns⁵⁰. We also used RefSeq genes in the control analyses. The recombination rate based on either the deCODE⁵⁵, Marshfield⁵⁶, or Genethon genetic maps⁵⁷ was downloaded from UCSC genome browser. RR –recombination rate. CpGI – CpG island. GPos – Giemsa positive. Gneg – Giemsa negative.