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. Author manuscript; available in PMC: 2012 Jul 19.
Published in final edited form as: Nature. 2012 Jan 11;481(7381):329–334. doi: 10.1038/nature10733

Table 1.

Summary of Somatic Mutations and Structural Alterations in Retinoblastoma

1Sample 2Tier 1 3Non-Silent
Tier 1		 Genes 5Tier 2 6Tier 3 7Tier 4 Total Mutation
Rate		 7Structural
Variations
SJRB001
D-G		 7 4 RB1,
CCNC,TMEM195,
RHBG 		16 117 85 225 1.03×10−7 4
2SJRB001
X-D		 0 0 n.a. 8 68 9 85 5.87×10−8 4
SJRB002
D-G		 1 0 n.a. 1 25 29 56 2.17×10−8 0
SJRB003
D-G		 7 4 RB1, HNMT,
LHX8, STOML2 		5 67 50 129 5.79×10−8 24
SJRB004
D-G		 8 5 RB1, CD300LG,
SDK1, TXK,
DMWD 		13 100 137 258 8.63×10−8 12
1

D refers to diagnostic tumor, G refers to germline (blood DNA) and X refers to xenograft sample.

2

Tier 1 mutations are found in genes and include exons, 5’ and 3’ UTRs and splice sites. Introns are not included.

3

Non-silent Tier 1 mutations change amino acids in genes.

4

All of the somatic mutations in SJRB001 D-G were identified in SJRB001X. This row highlights the new mutations acquired in the xenograft compared to the primary tumor.

5

Tier 2 mutations are found in regions of the genome that are conserved between humans and mice.

6

Tier 3 mutations are found in regions of the genome that are not evolutionarily conserved.

7

Tier 4 mutations are in repetitive regions of the genome.

7

Structural variations include focal amplifications and deletions, LOH, interchromosomal and intrachromosomal translocations.

Background mutation rate was calculated based on the ratio of Tier 3 mutations to the number of Tier 3 bases covered at least 10x in tumor and germline for each pair.