sequência de exomas nima forma familiar de cancro da tiróide: caracterização genética e funcional

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(1)SEQUENCIAÇÃO DE EXOMAS NUMA FORMA FAMILIAR DE CANCRO DA TIRÓIDE: CARACTERIZAÇÃO GENÉTICA E FUNCIONAL. CATARINA MIGUEL ALVES SALGADO. Dissertação de Mestrado em Oncologia. 2012.

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(3) CATARINA MIGUEL ALVES SALGADO. SEQUENCIAÇÃO DE EXOMAS NUMA FORMA FAMILIAR DE CANCRO. DA. TIRÓIDE:. CARACTERIZAÇÃO. GENÉTICA. E. FUNCIONAL. Dissertação de Candidatura ao grau de Mestre em Oncologia submetida ao Instituto de Ciências Biomédicas de Abel Salazar da Universidade do Porto. Orientador – Doutor Hugo Prazeres Categoria – Pós-Doc Afiliação – Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP) Co-orientador – Professora Doutora Paula Soares Categoria – Professor auxiliar Afiliação – Faculdade de Medicina da Universidade do Porto (FMUP).

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(5) Cancer Biology. Cancer Biology Group. Cancer Genetics.

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(7) C1q and tumor necrosis factor related protein 9 C2 calcium-dependent domain containing 3. Coding Sequence Centromere protein H. Corticotropin releasing hormone receptor 2 Cycle treshold DENN/MADD domain containing 1A Dulbecco’s Modified Eagle’s Medium Desoxyribonucleic acid Endonuclease/exonuclease/phosphatase family domain containing 1 Estrogen Receptor Fetal bovine serum G protein-coupled receptor 179 G protein-coupled receptor 65 Glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein1. Human acidic ribosomal protein Junctional sarcoplasmic reticulum protein 1 Laminin, alpha 5.

(8) Loss of heterozigosity Low-density lipoprotein-related protein 1B Large subunit GTPase 1 homolog Multinodular goiter Next-Generation Sequencing Neurotrophic Tyrosine Kinase receptor type 1 (ou TRK) Nuclear undecaprenyl pyrophosphate synthase 1 homolog Cyclin-dependent kinase inhibitor 1B Presequence translocase-associated motor 16 homolog Paired box 8 Polimerase Chain Reaction Proteinase K γ. Peroxisome Proliferator-Activated Receptor γ Papillary Thyroid Carcinoma RAS protein activator like 2 REarranged during Transfection Reverse Transcription-Polimerase Chain Reaction Sodium Dodecyl Sulphate Small interfering ribonucleic acid Single nucleotide variants. Tumors with Cell Oxyphilia Tumor protein p53 Thyroid Stimulating Hormone Uniparental Disomy UnTranslated Region.

(9) ABSTRACT. primers.

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(11) Next-Generation Sequencing. de novo Sanger. Sequencing. probably e possibly damaging GRID2IP in vitro GRID2IP GRID2IP. GRID2IP GRID2IP.

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(13) de novo. GRID2IP in vitro GRID2IP GRID2IP GRID2IP. GRID2IP.

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(15) Thyroid Stimulating Hormone feedback.

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(17) BRAF BRAF BRAF. BRAF. RAS. N-RAS. RAS RAS. N-RAS H-RAS RAS.

(18) RET/PTC1 RET/PTC3 NTRK1. PAX8/PPARγ PAX8/PPARγ et al γ PAX8/PPARγ wildtype PPARγ wildtype. TP53. TP53. TP53 TP53 RET RET. RET. BRAF p27KIP1.

(19) β TP53 microarrays MET FN1 LGALS3 KRT19, CITED1. PDGFA CITED1. IGFBP6 IGFBP6. CLDN10 CAV1. CAV2. mismatch repair MLH1. MSH2. Hereditary Non Polyposis Colorectal Cancer. BRCA1/2 RET. RET.

(20) RET. RET RET. RET RET RET. standard of care,. APC, PTEN, WRN e PRKAR1A.

(21) multinodular goiter. Espectro de alterações moleculares somáticas em tumores não-medulares da tiróide familiar (CNMTF). H-RAS BRAF. N-RAS. RAS linkage hits Loss. of. heterozigosity loci.

(22) NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 missense. GRIM-19). GRIM-19. Hurthle cell GRIM-19 Hurthle cell. GRIM-19 Tumors with Cell Oxyphilia. GRIM-19. versus low-density lipoprotein-related protein 1B. LRP1B. LRP1B. GRIM-19. LRP1B.

(23) locus PRN1 NMTC1. locus TCO1. locus MNG1. locus.

(24) next-generation second-generation sequencing. Polymerase Chain Reaction shotgun de novo Sanger Sequencing. insert,. primers. primers. round. primer. primer. primers.

(25) laser. second-generation. next-generation sequencing.

(26) et al second. next-. generation. bridge amplification, forward. primers. reverse array bridge PCR Bst cluster clusters clusters primer.

(27) base-call. wholegenome. whole-exome sequencing.

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(29) second-generation sequ in vitro second-generation arrays. polonies. array. base-calls base-calls. read depth.

(30) Whole-exome sequencing. whole-exome sequencing de novo SETBP1 exome sequencing MLL2 ASXL1 ANKRD11 exome sequencing. overgrowth. exome sequencing overgrowth. AKT1. et al.

(31) MAP3K1. TP53. MAP3K1 TP53 GATA3 next-generation sequencing. et al. ARID2 RAC1. BRAF. NRAS. PAK1. MLK3.

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(33) RET, RAS, BRAF status.

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(35) kit kit bridge amplification. μ. μ. clusters. kit. μ. mix. mix  μ. Clean-up. insert inserts kit. beads. beads. μ.

(36) beads. μ. μ μ. μ. primer. μ μ. Clean-up. Clean-up. insert. clusters. μ.

(37) inserts. primers. μ. Primer. μ. Clean-up. Clean-up. insert. chip. cocktail. Hibridização 1. μ. μ. μ.

(38) Captura de exões 1. beads μ. beads. beads. μ. μ. μ. μ. clusters. array. insert clusters. array,. clusters,. software software.

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(40) et al. pellet Sodium Dodecyl Sulphate.

(41) eppendorf. eppendorf.

(42) eppendorf. software. primers primer primers melting primers. primers. primer.

(43) primers. Polymerase Chain Reaction in vitro. primer forward primer reverse. kit. annealing. primers. et al primers.

(44) annealing. primers. kits. kit. primer forward. primer reverse. annealing primers. Touchdown. annealing. Touchdown. annealing. primers.

(45) annealing annealing primers. primers. primer. annealing. eppendorf. primer.

(46) short-spin. primer. annealing. primer. eppendorf. eppendorf pellet.

(47) pellet. reverse-transcriptase. Primer. GRID2IP. primers. .

(48) quencher. Real-Time GRID2IP housekeeping gene huPO GRID2IP. huPO. Δ cycle treshold. housekeeping gene Sequence Detection. System Applied Biosystems. Software. fetal bovine serum.

(49) real-Time.

(50) Terminal Deoxynucleotidyl Transferase Mediated dUTP Nick End Labeling. In. situ cell death detection kit, fluorescein citospins. µL. pellet. pellet citospin. μL.

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(52)

(53) Next-Generation Sequencing.

(54) Coding Sequence. missense nonsense nonsense. missense. splice sites. nonsense missense. splice sites. software missense Probably damaging. Possibly damaging.

(55) nonsense. PRIM2. PRAMEF1. nonsense PRIM2.  Wildtype nonsense PRIM2. primer PRAMEF1  Wildtype. primers Sanger. Sequencing PRAMEF1.

(56) PRAMEF1.

(57) Χ. nonsense. value. PRAMEF1 wildtype. nonsense. nonsense. Next-Generation. Sequencing. de novo. missense. nonsense. splice sites. PRAMEF1.

(58) nonsense. splice site. missense. de novo.

(59) nonsense missense splice sites. de novo. primers. Sanger Sequencing.

(60) Sanger Sequencing. Sanger Sequencing. → → → → → → → → → → → → → → →. de novo. Sanger. Sequencing. . primer.

(61) CENPH p.Q52H CFT. EEPD1 p.D422N CFT. Sangue. Sangue. C2CD3 p.Y1802H CFT Sangue. PAM16 p.R44Q CFT. NUS1 p.K214E CFT. GPR65 p.V156I CFT. JSPR1 p.G150A Sangue. CFT. Sangue. Sangue. LAMA5 p.T3126I Sangue. CFT. Sangue.

(62) Probably. → → → → → → → →. Possibly damaging.

(63) Χ. value. Χ. value. Χ. value. Χ. value. Χ. value.

(64) Χ. value. Χ. value. Χ. value.

(65) CRHR2 JSRP1 C1QTNF9 GPR179 GRID2IP DENND1A. CENPH. LAMA5. LSG1 GRID2IP. GRID2IP. GRID2IP BRAF. N-RAS GRID2IP,. BRAF. N-RAS GRID2IP. BRAF GRI2IP GRID2IP GRID2IP. GRID2IP.

(66) BRAF p.V600E. GRID2IP p.P753L Sangue. CFT. CPT-VF. Sangue. CFT. N-RAS p.Q61R CPT-VF. CFT. CPT-VF. → → →. . in vitro GRID2IP. primer. GRID2IP.

(67) GRID2IP. Real-Time PCR huPO. GRID2IP GRID2IP. GRID2IP GRID2IP.

(68) GRID2IP GRID2IP. GRID2IP Real-Time.

(69) GRID2IP. GRID2IP. GRID2IP GRID2IP. GRID2IP Deoxynucleotidyl Transferase Mediated dUTP Nick End Labeling. Terminal.

(70) GRID2IP. GRID2IP. GRID2IP. GRID2IP. GRID2IP.

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(73) nonsense. PRAMEF1. nonsense. wildtype PRAMEF1. DENND1A CENPH. LAMA5. de novo.

(74) Sanger sequencing. et al. et al. base-calls base-calls.

(75) Sanger Sequencing next-generation sequencing Sanger sequencing. Probably. Possibly damaging. DENND1A CENPH. LAMA5. PRAMEF1 de novo GRID2IP.

(76) GRID2IP. BRAF. N-RAS. BRAF GRID2IP. N-RAS. GRID2IP GRID2IP. GRID2IP. GRID2IP formin homology  Src homology 3 GRID2IP. GRID2IP. GRID2IP.

(77) GRID2IP. GRID2IP GRID2IP GRID2IP.

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(79) DENND1A. CENPH. LAMA5. Next-Generation Sequencing (Whole-Exome Sequencing),. de novo. GRID2IP. BRAF GRID2IP. GRID2IP. GRID2IP.

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(81) 1. 2. 3. 4. 5. 6.. 7. 8.. 9.. 10.. 11.. 12.. 13. 14. 15. 16. 17. 18.. 19.. 20.. Junqueira, L. and J. Carneiro, Histologia Básica. 2004, Guanabara Koogan, Rio de Janeiro. 407-412. DeLellis, R.A., et al. (2004) Pathology and genetics of tumours of endocrine organs. p. 320. Sobrinho-Simoes, M., et al. (2008) Intragenic mutations in thyroid cancer. Endocrinol Metab Clin North Am, 37(2), p. 333-62, viii. DeLellis, R.A. (2006) Pathology and genetics of thyroid carcinoma. J Surg Oncol, 94(8), p. 662-9. Sherman, S.I. (2003) Thyroid carcinoma. Lancet, 361(9356), p. 501-11. Couto, J.P., et al. (2009) How molecular pathology is changing and will change the therapeutics of patients with follicular cell-derived thyroid cancer. J Clin Pathol, 62(5), p. 414-21. Trovisco, V., et al. (2005) A new BRAF gene mutation detected in a case of a solid variant of papillary thyroid carcinoma. Hum Pathol, 36(6), p. 694-7. Adeniran, A.J., et al. (2006) Correlation between genetic alterations and microscopic features, clinical manifestations, and prognostic characteristics of thyroid papillary carcinomas. Am J Surg Pathol, 30(2), p. 216-22. Fugazzola, L., et al. (2006) Correlation between B-RAFV600E mutation and clinicopathologic parameters in papillary thyroid carcinoma: data from a multicentric Italian study and review of the literature. Endocr Relat Cancer, 13(2), p. 455-64. Nikiforova, M.N., et al. (2003) BRAF mutations in thyroid tumors are restricted to papillary carcinomas and anaplastic or poorly differentiated carcinomas arising from papillary carcinomas. J Clin Endocrinol Metab, 88(11), p. 5399-404. Trovisco, V., et al. (2005) Type and prevalence of BRAF mutations are closely associated with papillary thyroid carcinoma histotype and patients' age but not with tumour aggressiveness. Virchows Arch, 446(6), p. 589-95. Kim, T.Y., et al. (2006) The BRAF mutation is useful for prediction of clinical recurrence in low-risk patients with conventional papillary thyroid carcinoma. Clin Endocrinol (Oxf), 65(3), p. 364-8. Xu, X., et al. (2003) High prevalence of BRAF gene mutation in papillary thyroid carcinomas and thyroid tumor cell lines. Cancer Res, 63(15), p. 4561-7. Jin, L., et al. (2006) BRAF mutation analysis in fine needle aspiration (FNA) cytology of the thyroid. Diagn Mol Pathol, 15(3), p. 136-43. Xing, M., et al. (2005) BRAF mutation predicts a poorer clinical prognosis for papillary thyroid cancer. J Clin Endocrinol Metab, 90(12), p. 6373-9. Kim, K.H., et al. (2004) Mutations of the BRAF gene in papillary thyroid carcinoma in a Korean population. Yonsei Med J, 45(5), p. 818-21. Namba, H., et al. (2003) Clinical implication of hot spot BRAF mutation, V599E, in papillary thyroid cancers. J Clin Endocrinol Metab, 88(9), p. 4393-7. Trovisco, V., P. Soares, and M. Sobrinho-Simoes. (2006) B-RAF mutations in the etiopathogenesis, diagnosis, and prognosis of thyroid carcinomas. Hum Pathol, 37(7), p. 781-6. Kim, T.Y., et al. (2005) The BRAF mutation is not associated with poor prognostic factors in Korean patients with conventional papillary thyroid microcarcinoma . Clin Endocrinol (Oxf), 63(5), p. 588-93. Liu, R.T., et al. (2005) No correlation between BRAFV600E mutation and clinicopathological features of papillary thyroid carcinomas in Taiwan. Clin Endocrinol (Oxf), 63(4), p. 461-6..

(82) 21.. 22. 23. 24. 25.. 26. 27. 28. 29.. 30. 31.. 32.. 33.. 34.. 35.. 36. 37.. 38. 39.. 40.. Basolo, F., et al. (2000) N-ras mutation in poorly differentiated thyroid carcinomas: correlation with bone metastases and inverse correlation to thyroglobulin expression. Thyroid, 10(1), p. 19-23. Fukushima, T., et al. (2003) BRAF mutations in papillary carcinomas of the thyroid. Oncogene, 22(41), p. 6455-7. Garcia-Rostan, G., et al. (2003) ras mutations are associated with aggressive tumor phenotypes and poor prognosis in thyroid cancer. J Clin Oncol, 21(17), p. 3226-35. Manenti, G., et al. (1994) Selective activation of ras oncogenes in follicular and undifferentiated thyroid carcinomas. Eur J Cancer, 30A(7), p. 987-93. Quiros, R.M., et al. (2005) Evidence that one subset of anaplastic thyroid carcinomas are derived from papillary carcinomas due to BRAF and p53 mutations. Cancer, 103(11), p. 2261-8. Kondo, T., S. Ezzat, and S.L. Asa. (2006) Pathogenetic mechanisms in thyroid follicular-cell neoplasia. Nat Rev Cancer, 6(4), p. 292-306. Vasko, V., et al. (2003) Specific pattern of RAS oncogene mutations in follicular thyroid tumors. J Clin Endocrinol Metab, 88(6), p. 2745-52. Lazzereschi, D., et al. (1997) Oncogenes and antioncogenes involved in human thyroid carcinogenesis. J Exp Clin Cancer Res, 16(3), p. 325-32. Nikiforova, M.N., et al. (2003) RAS point mutations and PAX8-PPAR gamma rearrangement in thyroid tumors: evidence for distinct molecular pathways in thyroid follicular carcinoma. J Clin Endocrinol Metab, 88(5), p. 2318-26. Sugg, S.L., et al. (1999) Oncogene profile of papillary thyroid carcinoma. Surgery, 125(1), p. 46-52. Castro, P., et al. (2006) PAX8-PPARgamma rearrangement is frequently detected in the follicular variant of papillary thyroid carcinoma. J Clin Endocrinol Metab, 91(1), p. 213-20. Di Cristofaro, J., et al. (2006) Molecular genetic study comparing follicular variant versus classic papillary thyroid carcinomas: association of N-ras mutation in codon 61 with follicular variant. Hum Pathol, 37(7), p. 824-30. Zhu, Z., et al. (2003) Molecular profile and clinical-pathologic features of the follicular variant of papillary thyroid carcinoma. An unusually high prevalence of ras mutations. Am J Clin Pathol, 120(1), p. 71-7. Barril, N., A.B. Carvalho-Sales, and E.H. Tajara. (1999) Interphase cytogenetic analysis of normal tissue of thyroid gland by fluorescence in situ hybridization. Cancer Genet Cytogenet, 114(2), p. 162-4. Belge, G., et al. (1998) Cytogenetic investigations of 340 thyroid hyperplasias and adenomas revealing correlations between cytogenetic findings and histology . Cancer Genet Cytogenet, 101(1), p. 42-8. Castro, P., et al. (2005) Adenomas and follicular carcinomas of the thyroid display two major patterns of chromosomal changes. J Pathol, 206(3), p. 305-11. Criado, B., et al. (1995) Detection of numerical alterations for chromosomes 7 and 12 in benign thyroid lesions by in situ hybridization. Histological implications . Am J Pathol, 147(1), p. 136-44. van den Berg, E., et al. (1990) Cytogenetics of thyroid follicular adenomas. Cancer Genet Cytogenet, 44(2), p. 217-22. Roque, L., et al. (2003) Chromosome imbalances in thyroid follicular neoplasms: a comparison between follicular adenomas and carcinomas. Genes Chromosomes Cancer, 36(3), p. 292-302. Kroll, T.G., et al. (2000) PAX8-PPARgamma1 fusion oncogene in human thyroid carcinoma [corrected]. Science, 289(5483), p. 1357-60..

(83) 41.. 42.. 43. 44.. 45.. 46.. 47. 48. 49. 50.. 51.. 52. 53.. 54. 55.. 56.. 57.. 58. 59.. Dwight, T., et al. (2003) Involvement of the PAX8/peroxisome proliferator-activated receptor gamma rearrangement in follicular thyroid tumors. J Clin Endocrinol Metab, 88(9), p. 4440-5. Marques, A.R., et al. (2002) Expression of PAX8-PPAR gamma 1 rearrangements in both follicular thyroid carcinomas and adenomas. J Clin Endocrinol Metab, 87(8), p. 3947-52. Santoro, M., et al. (2002) RET activation and clinicopathologic features in poorly differentiated thyroid tumors. J Clin Endocrinol Metab, 87(1), p. 370-9. Tallini, G., et al. (1998) RET/PTC oncogene activation defines a subset of papillary thyroid carcinomas lacking evidence of progression to poorly differentiated or undifferentiated tumor phenotypes. Clin Cancer Res, 4(2), p. 287-94. Saltman, B., et al. (2006) Patterns of expression of cell cycle/apoptosis genes along the spectrum of thyroid carcinoma progression. Surgery, 140(6), p. 899-905; discussion 905-6. Soares, P., J. Cameselle-Teijeiro, and M. Sobrinho-Simoes. (1994) Immunohistochemical detection of p53 in differentiated, poorly differentiated and undifferentiated carcinomas of the thyroid. Histopathology, 24(3), p. 205-10. Zou, M., Y. Shi, and N.R. Farid. (1993) p53 mutations in all stages of thyroid carcinomas. J Clin Endocrinol Metab, 77(4), p. 1054-8. Donghi, R., et al. (1993) Gene p53 mutations are restricted to poorly differentiated and undifferentiated carcinomas of the thyroid gland. J Clin Invest, 91(4), p. 1753-60. Fagin, J.A., et al. (1993) High prevalence of mutations of the p53 gene in poorly differentiated human thyroid carcinomas. J Clin Invest, 91(1), p. 179-84. Ito, T., et al. (1992) Unique association of p53 mutations with undifferentiated but not with differentiated carcinomas of the thyroid gland. Cancer Res, 52(5), p. 136971. Park, K.Y., et al. (1998) Prevalences of Gs alpha, ras, p53 mutations and ret/PTC rearrangement in differentiated thyroid tumours in a Korean population. Clin Endocrinol (Oxf), 49(3), p. 317-23. Wright, P.A., et al. (1991) Mutation of the p53 gene in a differentiated human thyroid carcinoma cell line, but not in primary thyroid tumours. Oncogene, 6(9), p. 1693-7. Chiefari, E., et al. (1998) Analysis of RET proto-oncogene abnormalities in patients with MEN 2A, MEN 2B, familial or sporadic medullary thyroid carcinoma. J Endocrinol Invest, 21(6), p. 358-64. Dvorakova, S., et al. (2008) Somatic mutations in the RET proto-oncogene in sporadic medullary thyroid carcinomas. Mol Cell Endocrinol, 284(1-2), p. 21-7. Elisei, R., et al. (2008) Prognostic significance of somatic RET oncogene mutations in sporadic medullary thyroid cancer: a 10-year follow-up study. J Clin Endocrinol Metab, 93(3), p. 682-7. Eng, C. (1996) Seminars in medicine of the Beth Israel Hospital, Boston. The RET proto-oncogene in multiple endocrine neoplasia type 2 and Hirschsprung's disease . N Engl J Med, 335(13), p. 943-51. Eng, C., et al. (1996) The relationship between specific RET proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2. International RET mutation consortium analysis. JAMA, 276(19), p. 1575-9. Eng, C., et al. (1996) Heterogeneous mutation of the RET proto-oncogene in subpopulations of medullary thyroid carcinoma. Cancer Res, 56(9), p. 2167-70. Hofstra, R.M., et al. (1994) A mutation in the RET proto-oncogene associated with multiple endocrine neoplasia type 2B and sporadic medullary thyroid carcinoma . Nature, 367(6461), p. 375-6..

(84) 60.. 61.. 62.. 63.. 64.. 65.. 66. 67.. 68. 69. 70.. 71. 72. 73.. 74.. 75.. 76. 77.. 78.. Komminoth, P., et al. (1995) Analysis of RET protooncogene point mutations distinguishes heritable from nonheritable medullary thyroid carcinomas . Cancer, 76(3), p. 479-89. Matias-Guiu, X. (1998) RET protooncogene analysis in the diagnosis of medullary thyroid carcinoma and multiple endocrine neoplasia type II. Adv Anat Pathol, 5(3), p. 196-201. Cerutti, J.M., et al. (2004) A preoperative diagnostic test that distinguishes benign from malignant thyroid carcinoma based on gene expression. J Clin Invest, 113(8), p. 1234-42. Cheung, C.C., et al. (2001) Analysis of ret/PTC gene rearrangements refines the fine needle aspiration diagnosis of thyroid cancer. J Clin Endocrinol Metab, 86(5), p. 218790. Salvatore, G., et al. (2004) Analysis of BRAF point mutation and RET/PTC rearrangement refines the fine-needle aspiration diagnosis of papillary thyroid carcinoma. J Clin Endocrinol Metab, 89(10), p. 5175-80. Khoo, M.L., et al. (2002) Overexpression of cyclin D1 and underexpression of p27 predict lymph node metastases in papillary thyroid carcinoma. J Clin Endocrinol Metab, 87(4), p. 1814-8. Dobashi, Y., et al. (1994) Stepwise participation of p53 gene mutation during dedifferentiation of human thyroid carcinomas. Diagn Mol Pathol, 3(1), p. 9-14. Garcia-Rostan, G., et al. (2001) Beta-catenin dysregulation in thyroid neoplasms: down-regulation, aberrant nuclear expression, and CTNNB1 exon 3 mutations are markers for aggressive tumor phenotypes and poor prognosis. Am J Pathol, 158(3), p. 987-96. Ho, Y.S., et al. (1996) p53 gene mutation in thyroid carcinoma. Cancer Lett, 103(1), p. 57-63. Takeuchi, Y., et al. (1999) Mutations of p53 in thyroid carcinoma with an insular component. Thyroid, 9(4), p. 377-81. Hawthorn, L., et al. (2004) TIMP1 and SERPIN-A overexpression and TFF3 and CRABP1 underexpression as biomarkers for papillary thyroid carcinoma. Head Neck, 26(12), p. 1069-83. Huang, Y., et al. (2001) Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. Proc Natl Acad Sci U S A, 98(26), p. 15044-9. Jarzab, B., et al. (2005) Gene expression profile of papillary thyroid cancer: sources of variability and diagnostic implications. Cancer Res, 65(4), p. 1587-97. Wasenius, V.M., et al. (2003) Hepatocyte growth factor receptor, matrix metalloproteinase-11, tissue inhibitor of metalloproteinase-1, and fibronectin are upregulated in papillary thyroid carcinoma: a cDNA and tissue microarray study . Clin Cancer Res, 9(1), p. 68-75. Yano, Y., et al. (2004) Gene expression profiling identifies platelet-derived growth factor as a diagnostic molecular marker for papillary thyroid carcinoma. Clin Cancer Res, 10(6), p. 2035-43. Aldred, M.A., et al. (2004) Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J Clin Oncol, 22(17), p. 3531-9. Nose, V. (2011) Familial thyroid cancer: a review. Mod Pathol, 24 Suppl 2, p. S19-33. Burgess, J.R., et al. (1997) Two families with an autosomal dominant inheritance pattern for papillary carcinoma of the thyroid. J Clin Endocrinol Metab, 82(2), p. 3458. Christensen, S.B. and O. Ljungberg. (1983) Familial occurrence of papillary thyroid carcinoma. Br J Surg, 70(8), p. 508-9..

(85) 79.. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. 91. 92. 93. 94. 95. 96. 97. 98. 99.. 100. 101.. 102.. Cooper, D.S., et al. (1981) Congenital goiter and the development of metastatic follicular carcinoma with evidence for a leak of nonhormonal iodide: clinical, pathological, kinetic, and biochemical studies and a review of the literature. J Clin Endocrinol Metab, 52(2), p. 294-306. Couch, R.M., et al. (1986) An autosomal dominant form of adolescent multinodular goiter. Am J Hum Genet, 39(6), p. 811-6. Fischer, D.K., et al. (1989) Papillary carcinoma of the thyroid: additional evidence in support of a familial component. Cancer Invest, 7(4), p. 323-5. Gorson, D. (1992) Familial papillary carcinoma of the thyroid. Thyroid, 2(2), p. 131-2. Kraimps, J.L., et al. (1997) Familial papillary carcinoma of the thyroid. Surgery, 121(6), p. 715-8. Kwok, C.G. and I.R. McDougall. (1995) Familial differentiated carcinoma of the thyroid: report of five pairs of siblings. Thyroid, 5(5), p. 395-7. Lote, K., et al. (1980) Familial occurrence of papillary thyroid carcinoma. Cancer, 46(5), p. 1291-7. Marchesi, M., et al. (2000) Familial papillary carcinoma of the thyroid: a report of nine first-degree relatives of four families. Eur J Surg Oncol, 26(8), p. 789-91. Marchesi, M., et al. (2001) [Familial papillary carcinoma of the thyroid: biogenetic identification and clinical assessment of 4 families]. Ann Ital Chir, 72(3), p. 267-72. Nemec, J., et al. (1975) Familial occurrence of differentiated (non-medullary) thyroid cancer. Oncology, 32(3-4), p. 151-7. Ozaki, O., et al. (1988) Familial occurrence of differentiated, nonmedullary thyroid carcinoma. World J Surg, 12(4), p. 565-71. Phade, V.R., W.R. Lawrence, and M.H. Max. (1981) Familial papillary carcinoma of the thyroid. Arch Surg, 116(6), p. 836-7. Rios, A., et al. (2001) Familial papillary carcinoma of the thyroid: report of three families. Eur J Surg, 167(5), p. 339-43. Stoffer, S.S., et al. (1986) Familial papillary carcinoma of the thyroid. Am J Med Genet, 25(4), p. 775-82. Suzuki, S. and I. Watanabe. (1985) [Familial occurrence of papillary thyroid carcinoma]. Gan No Rinsho, 31(4), p. 414-9. Ito, Y., et al. (2008) Prevalence and prognosis of familial follicular thyroid carcinoma. Endocr J, 55(5), p. 847-52. Zivaljevic, V., et al. (2008) The incidence of familial nonmedullary thyroid cancer in a large case series. Acta Chir Belg, 108(3), p. 328-32. Ruben Harach, H. (2001) Familial nonmedullary thyroid neoplasia. Endocr Pathol, 12(2), p. 97-112. Dotto, J. and V. Nose. (2008) Familial thyroid carcinoma: a diagnostic algorithm. Adv Anat Pathol, 15(6), p. 332-49. Malchoff, C.D. and D.M. Malchoff. (2006) Familial nonmedullary thyroid carcinoma. Cancer Control, 13(2), p. 106-10. Prazeres, H.J., et al. (2008) Loss of heterozygosity at 19p13.2 and 2q21 in tumours from familial clusters of non-medullary thyroid carcinoma. Fam Cancer, 7(2), p. 1419. Prazeres, H., et al. (2010) The familial counterparts of follicular cell--derived thyroid tumors. Int J Surg Pathol, 18(4), p. 233-42. Lesueur, F., et al. (1999) Genetic heterogeneity in familial nonmedullary thyroid carcinoma: exclusion of linkage to RET, MNG1, and TCO in 56 families. NMTC Consortium. J Clin Endocrinol Metab, 84(6), p. 2157-62. Uchino, S., et al. (2002) Familial nonmedullary thyroid carcinoma characterized by multifocality and a high recurrence rate in a large study population. World J Surg, 26(8), p. 897-902..

(86) 103.. 104. 105.. 106.. 107.. 108.. 109. 110. 111.. 112.. 113. 114.. 115. 116. 117. 118.. 119.. 120.. 121.. Cavaco, B.M., et al. (2008) Familial non-medullary thyroid carcinoma (FNMTC): analysis of fPTC/PRN, NMTC1, MNG1 and TCO susceptibility loci and identification of somatic BRAF and RAS mutations. Endocr Relat Cancer, 15(1), p. 207-15. Stankov, K., et al. (2004) Allelic loss on chromosomes 2q21 and 19p 13.2 in oxyphilic thyroid tumors. Int J Cancer, 111(3), p. 463-7. Maximo, V., et al. (2005) Somatic and germline mutation in GRIM-19, a dual function gene involved in mitochondrial metabolism and cell death, is linked to mitochondrion-rich (Hurthle cell) tumours of the thyroid. Br J Cancer, 92(10), p. 1892-8. Kalakonda, S., et al. (2007) Tumor-suppressive activity of the cell death activator GRIM-19 on a constitutively active signal transducer and activator of transcription 3 . Cancer Res, 67(13), p. 6212-20. Gasparre, G., et al. (2007) Disruptive mitochondrial DNA mutations in complex I subunits are markers of oncocytic phenotype in thyroid tumors. Proc Natl Acad Sci U S A, 104(21), p. 9001-6. Lima, J., et al. (2003) Germline succinate dehydrogenase subunit D mutation segregating with familial non-RET C cell hyperplasia. J Clin Endocrinol Metab, 88(10), p. 4932-7. Liu, C.X., et al. (2000) LRP-DIT, a putative endocytic receptor gene, is frequently inactivated in non-small cell lung cancer cell lines. Cancer Res, 60(7), p. 1961-7. Liu, C.X., et al. (2000) Genomic organization of a new candidate tumor suppressor gene, LRP1B. Genomics, 69(2), p. 271-4. Liu, C.X., et al. (2001) The putative tumor suppressor LRP1B, a novel member of the low density lipoprotein (LDL) receptor family, exhibits both overlapping and distinct properties with the LDL receptor-related protein. J Biol Chem, 276(31), p. 28889-96. Prazeres, H., et al. (2011) Chromosomal, epigenetic and microRNA-mediated inactivation of LRP1B, a modulator of the extracellular environment of thyroid cancer cells. Oncogene, 30(11), p. 1302-17. Ron, E., et al. (1987) A population-based case-control study of thyroid cancer. J Natl Cancer Inst, 79(1), p. 1-12. Frich, L., E. Glattre, and L.A. Akslen. (2001) Familial occurrence of nonmedullary thyroid cancer: a population-based study of 5673 first-degree relatives of thyroid cancer patients from Norway. Cancer Epidemiol Biomarkers Prev, 10(2), p. 113-7. Galanti, M.R., et al. (1997) Parental cancer and risk of papillary and follicular thyroid carcinoma. Br J Cancer, 75(3), p. 451-6. Goldgar, D.E., et al. (1994) Systematic population-based assessment of cancer risk in first-degree relatives of cancer probands. J Natl Cancer Inst, 86(21), p. 1600-8. Hemminki, K. and C. Dong. (2000) Familial relationships in thyroid cancer by histopathological type. Int J Cancer, 85(2), p. 201-5. Pal, T., et al. (2001) Increased risk for nonmedullary thyroid cancer in the first degree relatives of prevalent cases of nonmedullary thyroid cancer: a hospital-based study. J Clin Endocrinol Metab, 86(11), p. 5307-12. Alsanea, O., et al. (2000) Is familial non-medullary thyroid carcinoma more aggressive than sporadic thyroid cancer? A multicenter series. Surgery, 128(6), p. 104350;discussion 1050-1. Cavaco, B.M., et al. (2008) Mapping a new familial thyroid epithelial neoplasia susceptibility locus to chromosome 8p23.1-p22 by high-density single-nucleotide polymorphism genome-wide linkage analysis. J Clin Endocrinol Metab, 93(11), p. 4426-30. He, H., et al. (2009) A susceptibility locus for papillary thyroid carcinoma on chromosome 8q24. Cancer Res, 69(2), p. 625-31..

(87) 122. 123. 124.. 125. 126. 127. 128. 129. 130. 131. 132. 133.. 134. 135. 136. 137. 138. 139. 140. 141. 142. 143.. 144.. 145.. Maxam, A.M. and W. Gilbert. (1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A, 74(2), p. 560-4. Sanger, F. and A.R. Coulson. (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol, 94(3), p. 441-8. Reddy, E.P., et al. (1982) A point mutation is responsible for the acquisition of transforming properties by the T24 human bladder carcinoma oncogene. Nature, 300(5888), p. 149-52. Tabin, C.J., et al. (1982) Mechanism of activation of a human oncogene. Nature, 300(5888), p. 143-9. Green, P. (1997) Against a whole-genome shotgun. Genome Res, 7(5), p. 410-7. Lander, E.S., et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409(6822), p. 860-921. DePristo, M.A., et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet, 43(5), p. 491-8. Eid, J., et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323(5910), p. 133-8. Mardis, E.R. (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet, 9, p. 387-402. Metzker, M.L. (2010) Sequencing technologies - the next generation. Nat Rev Genet, 11(1), p. 31-46. Shendure, J. and H. Ji. (2008) Next-generation DNA sequencing. Nat Biotechnol, 26(10), p. 1135-45. Sanger, F., S. Nicklen, and A.R. Coulson. (1977) DNA sequencing with chainterminating inhibitors. Proceedings of the National Academy of Sciences, 74(12), p. 5463-5467. Consortium., I.H.G.S. (2001) Initial sequencing and analysis of the human genome. . Nature, 409, p. 860-921. Haimovich, A.D. (2011) Methods, challenges, and promise of next-generation sequencing in cancer biology. Yale J Biol Med, 84(4), p. 439-46. Consortium., I.H.G.S. (2004) Finishing the euchromatic sequence of the human genome. Nature, 431, p. 931-45. Ley, T.J., et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456(7218), p. 66-72. Ng, S.B., et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461(7261), p. 272-6. Maher, C.A., et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458(7234), p. 97-101. Meyerson, M., S. Gabriel, and G. Getz. (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet, 11(10), p. 685-96. Ross, J.S. and M. Cronin. (2011) Whole cancer genome sequencing by nextgeneration methods. Am J Clin Pathol, 136(4), p. 527-39. Daniels, M., et al. (2012) Whole genome sequencing for lung cancer. J Thorac Dis, 4(2), p. 155-63. Fedurco, M., et al. (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res, 34(3), p. e22. Turcatti, G., et al. (2008) A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis . Nucleic Acids Res, 36(4), p. e25. Ding, L., et al. (2010) Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet, 19(R2), p. R188-96..

(88) 146. 147.. 148. 149. 150. 151. 152. 153. 154.. 155. 156. 157. 158. 159. 160. 161. 162. 163. 164.. 165. 166. 167. 168. 169.. Erlich, Y., et al. (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods, 5(8), p. 679-82. Campbell, P.J., et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet, 40(6), p. 722-9. Wang, K., et al. (2011) Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet, 43(12), p. 1219-23. Quail, M.A., et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods, 5(12), p. 1005-10. Rusk, N. (2011) Torrents of sequence. Nat Methods, 8, p. 44. Hoischen, A., et al. (2010) De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet, 42(6), p. 483-5. Ng, S.B., et al. (2010) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet, 42(9), p. 790-3. Hoischen, A., et al. (2011) De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome. Nat Genet, 43(8), p. 729-31. Sirmaci, A., et al. (2011) Mutations in ANKRD11 cause KBG syndrome, characterized by intellectual disability, skeletal malformations, and macrodontia. Am J Hum Genet, 89(2), p. 289-94. Lindhurst, M.J., et al. (2011) A mosaic activating mutation in AKT1 associated with the Proteus syndrome. N Engl J Med, 365(7), p. 611-9. Ellis, M.J., et al. (2012) Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 486(7403), p. 353-60. Berger, M.F., et al. (2012) Melanoma genome sequencing reveals frequent PREX2 mutations. Nature, 485(7399), p. 502-6. Nikolaev, S.I., et al. (2012) Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet, 44(2), p. 133-9. Pleasance, E.D., et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463(7278), p. 191-6. Wei, X., et al. (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet, 43(5), p. 442-6. Krauthammer, M., et al. (2012) Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet. Miller, S.A., D.D. Dykes, and H.F. Polesky. (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res, 16(3), p. 1215. Mullis, K., et al. (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol, 51 Pt 1, p. 263-73. Chamberlain, J.S., et al. (1988) Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res, 16(23), p. 1114156. Don, R.H., et al. (1991) 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res, 19(14), p. 4008. Rappolee, D.A., et al. (1988) Wound macrophages express TGF-alpha and other growth factors in vivo: analysis by mRNA phenotyping. Science, 241(4866), p. 708-12. Yamaguchi, H. and J. Condeelis. (2007) Regulation of the actin cytoskeleton in cancer cell migration and invasion. Biochim Biophys Acta, 1773(5), p. 642-52. Soares, P., et al. (2003) BRAF mutations and RET/PTC rearrangements are alternative events in the etiopathogenesis of PTC. Oncogene, 22(29), p. 4578-80. Miyagi, Y., et al. (2002) Delphilin: a novel PDZ and formin homology domaincontaining protein that synaptically colocalizes and interacts with glutamate receptor delta 2 subunit. J Neurosci, 22(3), p. 803-14..

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