<p>TABLE S1. Publication sources of mtDNA tumor mutation data. References are listed below the table and numbered independently of the main article.</p><p>No. Samples Total No. Tumor reported with Sequence Ref Samples Sample names Type somatic method queried mutation</p><p>1 Renal 7 15 DHPLC 1-7</p><p>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</p><p>Automated Ov8, Ov28, Ov30, Ov32, Ov34, 3 Ovarian 6 10 --ABI 310 Ov38</p><p>TTGE, Esophage E02, E05, E09, E10, E12, E14, 4 11 20 automated al E15, E16, E17, E18, E19 ABI 377</p><p>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 </p><p>Automated 105T, 123 A, 123 B, 123 C, 192 6 Renal 7 9 -LiCor T, 195 T, 94B 4200</p><p>7 Thyroid 6 14 dHPLC 1, 2, 4, 6, 9, 11</p><p>Automated 8 Renal 5 8 -LiCor 1177, 1282, 1604, 1608, 1627 4200</p><p>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, </p><p>9 Glioma 7 16 Microarray G2 , G4 , G5, G6 , G12, G13, -MitoAll G15, Resequenci ng</p><p>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</p><p>Manual BrCa24, BrCa27TL, BrCa27TR, and BrCa32, BrCa33, BrCa35, 10 Breast 11 18 Automated BrCa38, BrCa39, BrCa41, --ABI 3700 BrCa42, BrCa44</p><p>11 Prostate 3 16 Manual 32, PrCa1, PrCa46</p><p>Automated 12 Prostate 5 17 1N, 2H, 8N, 9N, 11N --ABI 377</p><p>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</p><p>*samples checked for redundancy</p><p>Head- 1565, 1637, 1680, 1684, He- 14 6 13 manual Neck Ne_Ca1678, He-Ne_Ca1708</p><p>14 Lung 6 14 manual 898, 902, 915, 1113, 1140, 1174</p><p>Automated --ABI PaCapx16, PaCapx17, 15 Pancreatic 4 5 1377, PaCapx19, PaCaPx27 Beckman CEQ2000</p><p> mitochip method paper-- samples Microarray 16 Lung 2 JHU_mito9, JHU_MITO_12 chosen for -MitoChip known somatic mutation</p><p>84, method paper, Microarray Head- samples -MitoChip, 17 13 1-13 neck chosen for salivary known rinse somatic mutation</p><p>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</p><p>CoCaV425, CoCaV429, 19 Colon 7 10 Manual CoCaV441, CoCaV456, CoCaV478, V410, V451</p><p>TTGE, 102, 104, 106, 108, 110, 112, 20 Breast 14 19 automated 114, 146, 152, 158, 176, 180, ABI 377 182, 184</p><p>TDGS, can't DGGE, 21 Thyroid 3 ThyCa1, ThyCa2, ThyCa3 determine Automated --ABI 373</p><p>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</p><p>697, 738, 773, 833, 844, 845, Automated 23 Breast 15 15 885, 898, 906, 911, 944, 954, --ABI 377 983, 988, 1026</p><p>1 Meierhofer, D., Mayr, J. A., Fink, K., Schmeller, N., Kofler, B., Sperl, W. et al. Mitochondrial DNA mutations in renal cell carcinomas revealed no general impact on energy metabolism. Br. J. Cancer 94, 268–274 (2006). </p><p>2 Jin, X., Zhang, J., Gao, Y., Ding, K., Wang, N., Zhou, D. et al. Relationship between mitochondrial DNA mutations and clinical characteristics in human lung cancer. Mitochondrion 7, 347–353 (2007). </p><p>3 Liu, V. W., Shi, H. H., Cheung, A. N., Chiu, P. M., Leung, T. W., Nagley, P. et al. High incidence of somatic mitochondrial DNA mutations in human ovarian carcinomas. Cancer Res. 61, 5998–6001 (2001). </p><p>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). </p><p>5 Tan, D. J., Chang, J., Chen, W. L., Agress, L. J., Yeh, K. T., Wang, B. et al. Somatic mitochondrial DNA mutations in oral cancer of betel quid chewers. Ann. N.Y. Acad. Sci. 1011, 310–316 (2004). 6 Nagy, A., Wilhelm, M. & Kovacs, G. Mutations of mtDNA in renal cell tumours arising in end-stage renal disease. J. Pathol. 199, 237–242 (2003). </p><p>7 Witte, J., Lehmann, S., Wulfert, M., Yang, Q. & Roher, H. D. Mitochondrial DNA mutations in differentiated thyroid cancer with respect to the age factor. World J. Surg. 31, 51–59 (2007). </p><p>8 Nagy, A., Wilhelm, M., Sukosd, F., Ljungberg, B. & Kovacs, G. Somatic mitochondrial DNA mutations in human chromophobe renal cell carcinomas. Genes Chromosomes Cancer 35, 256–260 (2002). </p><p>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). </p><p>10 Parrella, P., Xiao, Y., Fliss, M., Sanchez-Cespedes, M., Mazzarelli, P., Rinaldi, M. et al. Detection of mitochondrial DNA mutations in primary breast cancer and fine-needle aspirates. Cancer Res. 61, 7623–7626 (2001). </p><p>11 Jeronimo, C., Nomoto, S., Caballero, O. L., Usadel, H., Henrique, R., Varzim, G. et al. Mitochondrial mutations in early stage prostate cancer and bodily fluids. Oncogene 20, 5195–5198 (2001). </p><p>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). </p><p>13 Maximo, V., Soares, P., Lima, J., Cameselle-Teijeiro, J. & Sobrinho-Simoes, M. Mitochondrial DNA somatic mutations (point mutations and large deletions) and mitochondrial DNA variants in human thyroid pathology: a study with emphasis on Hurthle cell tumors. Am. J. Pathol. 160, 1857–1865 (2002). </p><p>14 Fliss, M. S., Usadel, H., Caballero, O. L., Wu, L., Buta, M. R., Eleff, S. M. et al. Facile detection of mitochondrial DNA mutations in tumors and bodily fluids. Science 287, 2017–2019 (2000). </p><p>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). </p><p>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). </p><p>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). </p><p>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). </p><p>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). </p><p>20 Tan, D. J., Bai, R. K. & Wong, L. J. Comprehensive scanning of somatic mitochondrial DNA mutations in breast cancer. Cancer Res. 62, 972–976 (2002). 21 Yeh, J. J., Lunetta, K. L., van Orsouw, N. J., Moore, Jr F. D. , Mutter, G. L., Vijg, J. et al. Somatic mitochondrial DNA (mtDNA) mutations in papillary thyroid carcinomas and differential mtDNA sequence variants in cases with thyroid tumours. Oncogene 19, 2060–2066 (2000). </p><p>22 Zhou, S., Kachhap, S., Sun, W., Wu, G., Chuang, A., Poeta, L. et al. Frequency and phenotypic implications of mitochondrial DNA mutations in human squamous cell cancers of the head and neck. Proc. Natl Acad. Sci. USA 104, 7540–7545 (2007). </p><p>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). </p>