TABLE S1. Publication Sources of Mtdna Tumor Mutation Data. References Are Listed Below

TABLE S1. Publication sources of mtDNA tumor mutation data. References are listed below the table and numbered independently of the main article.

No. Samples Total No. Tumor reported with Sequence Ref Samples Sample names Type somatic method queried mutation

1 Renal 7 15 DHPLC 1-7

6, 7, 8, 9, 11, 14, 15, 16, 18, 19, Automated 23, 25, 26, 28, 29, 35, 36, 37, 39, 2 Lung 33 55 --ABI 3700 46, 47, 48, 49, 52, 53, 54, 56, 57, 58, 59, 60, 61, 62

Automated Ov8, Ov28, Ov30, Ov32, Ov34, 3 Ovarian 6 10 --ABI 310 Ov38

TTGE, Esophage E02, E05, E09, E10, E12, E14, 4 11 20 automated al E15, E16, E17, E18, E19 ABI 377

TTGE, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 5 Oral 14 18 Automated Oral Ca5, Oral Ca14, Oral Ca18, --ABI 377 Oral Ca19

Automated 105T, 123 A, 123 B, 123 C, 192 6 Renal 7 9 -LiCor T, 195 T, 94B 4200

7 Thyroid 6 14 dHPLC 1, 2, 4, 6, 9, 11

Automated 8 Renal 5 8 -LiCor 1177, 1282, 1604, 1608, 1627 4200

BRCA1, BRCA3, BRCA4, Microarray BRCA5, BRCA6, BRCA8, -MitoAll BRCA9, BRCA10, BRCA12, 9 Breast 17 20 Resequenci BRCA13, BRCA14, BRCA15, ng BRCA16, BRCA17, BRCA18, BRCA19, BRCA20,

9 Glioma 7 16 Microarray G2 , G4 , G5, G6 , G12, G13, -MitoAll G15, Resequenci ng

HCT1, HCT2, HCT4, HCT5, HCT6, HCT7, HCT8, HCT9, HCT11, HCT16, HCT17, HCT18, HCT21, HCT23, HCT25, HCT26, HCT27, Microarray HCT28, HCT29, HCT30, -MitoAll 9 Thyroid 44 66 HCT31, HCT32, HCT33, Resequenci HCT36, HCT37, HCT38, ng HCT39, HCT40, HCT42, HCT43, HCT44, TC4, TC5, TC6, TC7, TC8, TC11, TC12, TC14, TC15, TC16, TC18, TC19, TC20

Manual BrCa24, BrCa27TL, BrCa27TR, and BrCa32, BrCa33, BrCa35, 10 Breast 11 18 Automated BrCa38, BrCa39, BrCa41, --ABI 3700 BrCa42, BrCa44

11 Prostate 3 16 Manual 32, PrCa1, PrCa46

Automated 12 Prostate 5 17 1N, 2H, 8N, 9N, 11N --ABI 377

ThyCa1, ThyCa2, ThyCa3, ThyCa4, ThyCa5, ThyCa6, ThyCa7, ThyCa8, ThyCa9, ThyCa10A, ThyCa10B, ThyCa11, ThyCa12A, ThyCa12b, ThyCa14, ThyCa15, ThyCa16a, ThyCa16B, Automated ThyCa17, ThyCa18, ThyCa19, 13 Thyroid 45 66 --ABI 377 ThyCa20, ThyCa21, ThyCa22, ThyCa23, ThyCa25, ThyCa27, ThyCa28, ThyCa30, ThyCa31, ThyCa32, ThyCa35, ThyCa39, ThyCa40, ThyCa41, ThyCa44, ThyCa46, ThyCa51, ThyCa53, ThyCa54, ThyCa56, ThyCa57, ThyCa59, ThyCa60, ThyCa62 580*, 716*, 799, 874, 899, 1124, 1127, Blad Ca884, Blad_Ca580*, Blad_Ca716*, 14 Bladder 12 14 manual Blad_Ca870, Blad_Ca884

*samples checked for redundancy

Head- 1565, 1637, 1680, 1684, He- 14 6 13 manual Neck Ne_Ca1678, He-Ne_Ca1708

14 Lung 6 14 manual 898, 902, 915, 1113, 1140, 1174

Automated --ABI PaCapx16, PaCapx17, 15 Pancreatic 4 5 1377, PaCapx19, PaCaPx27 Beckman CEQ2000

mitochip method paper-- samples Microarray 16 Lung 2 JHU_mito9, JHU_MITO_12 chosen for -MitoChip known somatic mutation

84, method paper, Microarray Head- samples -MitoChip, 17 13 1-13 neck chosen for salivary known rinse somatic mutation

18 Head- 12 84, Microarray 1-12* (checked for non- Neck method -MitoChip, redundancy with ref 17) paper, salivary samples rinse chosen for known somatic mutation

CoCaV425, CoCaV429, 19 Colon 7 10 Manual CoCaV441, CoCaV456, CoCaV478, V410, V451

TTGE, 102, 104, 106, 108, 110, 112, 20 Breast 14 19 automated 114, 146, 152, 158, 176, 180, ABI 377 182, 184

TDGS, can't DGGE, 21 Thyroid 3 ThyCa1, ThyCa2, ThyCa3 determine Automated --ABI 373

1017, 1063, 1164, 1280, 1356, 1493, 1535, 1565, 1680, 1691, 1736, 1809, 1817, 1836, 1858, 2008, 2018, 2039, 2043, 2051, Head- microarray 22 41 83 2075, 2105, 2126, 2195, 2232, Neck --mitochip 2382, 2444, 2455, 2550, 2553, 2555, 2702, 2704, 2714, 2717, 2760, 2778, 2818, 2828, 2907, 3538

697, 738, 773, 833, 844, 845, Automated 23 Breast 15 15 885, 898, 906, 911, 944, 954, --ABI 377 983, 988, 1026

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4 Tan, D. J., Chang, J., Liu, L. L., Bai, R. K., Wang, Y. F., Yeh, K. T. et al. Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer. BMC Cancer 6, 93 (2006).

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9 Gasparre, G., Porcelli, A. M., Bonora, E., Pennisi, L. F., Toller, M., Iommarini, L. et al. Disruptive mitochondrial DNA mutations in complex I subunits are markers of oncocytic phenotype in thyroid tumors. Proc. Natl Acad. Sci. USA 104, 9001–9006 (2007).

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12 Gomez-Zaera, M., Abril, J., Gonzalez, L., Aguilo, F., Condom, E., Nadal, M. et al. Identification of somatic and germline mitochondrial DNA sequence variants in prostate cancer patients. Mutat. Res. 595, 42–51 (2006).

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15 Jones, J. B., Song, J. J., Hempen, P. M., Parmigiani, G., Hruban, R. H., Kern, S. E. et al. Detection of mitochondrial DNA mutations in pancreatic cancer offers a ‘mass’-ive advantage over detection of nuclear DNA mutations. Cancer Res. 61, 1299–1304 (2001).

16 Maitra, A., Cohen, Y., Gillespie, S. E., Mambo, E., Fukushima, N., Hoque, M. O. et al. The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res. 14, 812–819 (2004).

17 Mithani, S. K., Smith, I. M., Zhou, S., Gray, A., Koch, W. M., Maitra, A. et al. Mitochondrial resequencing arrays detect tumor-specific mutations in salivary rinses of patients with head and neck cancer. Clin. Cancer Res. 13, 7335–7340 (2007).

18 Mithani, S. K., Taube, J. M., Zhou, S., Smith, I. M., Koch, W. M., Westra, W. H. et al. Mitochondrial mutations are a late event in the progression of head and neck squamous cell cancer. Clin. Cancer Res. 13, 4331–4335 (2007).

19 Polyak, K., Li, Y., Zhu, H., Lengauer, C., Willson, J. K., Markowitz, S. D. et al. Somatic mutations of the mitochondrial genome in human colorectal tumours. Nat. Genet. 20, 291–293 (1998).

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23 Zhu, W., Qin, W., Bradley, P., Wessel, A., Puckett, C. L., Sauter, E. R. et al. Mitochondrial DNA mutations in breast cancer tissue and in matched nipple aspirate fluid. Carcinogenesis 26, 145–152 (2005).