Supplemental data file 1. References used in ChromSorter PC

[1-15][16-41][42-74][75-107][108-149][150-192][193-223][224-250]

1. Atkin NB, Baker MC: Chromosome 7q deletions: observations on 13 malignant tumors. Cancer Genet Cytogenet 1993, 67(2):123-125.

2. Atkin NB, Baker MC: Chromosome study of five cancers of the prostate. Hum Genet 1985, 70(4):359-364.

3. Atkin NB, Baker MC: Chromosome 10 deletion in carcinoma of the prostate. N Engl J Med 1985, 312(5):315.

4. Astrom L, Weimarck A, Aldenborg F, Delle U, Hanson C, Verbiene I, Danielsson A, Hammarsten J, Kopf I: S-phase fraction related to prognosis in localised prostate cancer. No specific significance of chromosome 7 gain or deletion of 7q31.1. Int J Cancer 1998, 79(6):553-559.

5. Arps S, Rodewald A, Schmalenberger B, Carl P, Bressel M, Kastendieck H: Cytogenetic survey of 32 cancers of the prostate. Cancer Genet Cytogenet 1993, 66(2):93-99.

6. Alers JC, Rochat J, Krijtenburg PJ, Hop WC, Kranse R, Rosenberg C, Tanke HJ, Schroder FH, van Dekken H: Identification of genetic markers for prostatic cancer progression. Lab Invest 2000, 80(6):931-942.

7. Alers JC, Krijtenburg PJ, Vissers KJ, Bosman FT, van der Kwast TH, van Dekken H: Interphase cytogenetics of prostatic adenocarcinoma and precursor lesions: analysis of 25 radical prostatectomies and 17 adjacent prostatic intraepithelial neoplasias. Genes Chromosomes Cancer 1995, 12(4):241-250.

8. Alers JC, Krijtenburg PJ, Vissers CJ, Bosman FT, van der Kwast TH, van Dekken H: Cytogenetic heterogeneity and histologic tumor growth patterns in prostatic cancer. Cytometry 1995, 21(1):84-94.

9. Alers JC, Krijtenburg PJ, Vis AN, Hoedemaeker RF, Wildhagen MF, Hop WC, van Der Kwast TT, Schroder FH, Tanke HJ, van Dekken H: Molecular cytogenetic analysis of prostatic adenocarcinomas from screening studies : early cancers may contain aggressive genetic features. Am J Pathol 2001, 158(2):399-406.

10. Alers JC, Krijtenburg PJ, Rosenberg C, Hop WC, Verkerk AM, Schroder FH, van der Kwast TH, Bosman FT, van Dekken H: Interphase cytogenetics of prostatic tumor progression: specific chromosomal abnormalities are involved in metastasis to the bone. Lab Invest 1997, 77(5):437-448.

11. Alers JC, Krijtenburg PJ, Hop WC, Bolle WA, Schroder FH, van der Kwast TH, Bosman FT, van Dekken H: Longitudinal evaluation of cytogenetic aberrations in prostatic cancer: tumours that recur in time display an intermediate genetic status between non-persistent and metastatic tumours. J Pathol 1998, 185(3):273-283.

12. Alcaraz A, Takahashi S, Brown JA, Herath JF, Bergstralh EJ, Larson-Keller JJ, Lieber MM, Jenkins RB: Aneuploidy and aneusomy of chromosome 7 detected by fluorescence in situ hybridization are markers of poor prognosis in prostate cancer. Cancer Res 1994, 54(15):3998-4002.

13. Alcaraz A, Barranco MA, Corral JM, Ribal MJ, Carrio A, Mallofre C, Llopis J, Cetina A, Alvarez-Vijande R: High-grade prostate intraepithelial neoplasia shares cytogenetic alterations with invasive prostate cancer. Prostate 2001, 47(1):29-35.

14. Ahman AK, Jonsson BA, Damber JE, Bergh A, Emanuelsson M, Gronberg H: Low frequency of allelic imbalance at the prostate cancer susceptibility loci HPC1 and 1p36 in Swedish men with hereditary prostate cancer. Genes Chromosomes Cancer 2000, 29(4):292-296.

15. Afonso A, Emmert-Buck MR, Duray PH, Bostwick DG, Linehan WM, Vocke CD: Loss of heterozygosity on chromosome 13 is associated with advanced stage prostate cancer. J Urol 1999, 162(3 Pt 1):922-926.

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17. Badzioch M, Eeles R, Leblanc G, Foulkes WD, Giles G, Edwards S, Goldgar D, Hopper JL, Bishop DT, Moller P et al: Suggestive evidence for a site specific prostate cancer gene on chromosome 1p36. The CRC/BPG UK Familial Prostate Cancer Study Coordinators and Collaborators. The EU Biomed Collaborators. J Med Genet 2000, 37(12):947-949.

18. Bandyk MG, Zhao L, Troncoso P, Pisters LL, Palmer JL, von Eschenbach AC, Chung LW, Liang JC: Trisomy 7: a potential cytogenetic marker of human prostate cancer progression. Genes Chromosomes Cancer 1994, 9(1):19-27.

19. Baretton GB, Valina C, Vogt T, Schneiderbanger K, Diebold J, Lohrs U: Interphase cytogenetic analysis of prostatic carcinomas by use of nonisotopic in situ hybridization. Cancer Res 1994, 54(16):4472-4480.

20. Barranco MA, Alcaraz A, Corral JM, Sole M, Mallofre C, Llopis J, Rodriguez A, Ribal MJ, Alvarez-Vijande R, Carretero P: Numeric alterations in chromosomes 7 and 8 detected by fluorescent in situ hybridization correlate with high-grade localized prostate cancer. Eur Urol 1998, 34(5):419-425.

21. Beheshti B, Park PC, Sweet JM, Trachtenberg J, Jewett MA, Squire JA: Evidence of chromosomal instability in prostate cancer determined by spectral karyotyping (SKY) and interphase fish analysis. Neoplasia 2001, 3(1):62-69.

22. Bergerheim US, Kunimi K, Collins VP, Ekman P: Deletion mapping of chromosomes 8, 10, and 16 in human prostatic carcinoma. Genes Chromosomes Cancer 1991, 3(3):215-220.

23. Bergthorsson JT, Johannesdottir G, Arason A, Benediktsdottir KR, Agnarsson BA, Bailey-Wilson JE, Gillanders E, Smith J, Trent J, Barkardottir RB: Analysis of HPC1, HPCX, and PCaP in Icelandic hereditary prostate cancer. Hum Genet 2000, 107(4):372-375.

24. Bernardino J, Bourgeois CA, Muleris M, Dutrillaux AM, Malfoy B, Dutrillaux B: Characterization of chromosome changes in two human prostatic carcinoma cell lines (PC-3 and DU145) using chromosome painting and comparative genomic hybridization. Cancer Genet Cytogenet 1997, 96(2):123-128.

25. Berry R, Schaid DJ, Smith JR, French AJ, Schroeder JJ, McDonnell SK, Peterson BJ, Wang ZY, Carpten JD, Roberts SG et al: Linkage analyses at the chromosome 1 loci 1q24-25 (HPC1), 1q42.2-43 (PCAP), and 1p36 (CAPB) in families with hereditary prostate cancer. Am J Hum Genet 2000, 66(2):539-546.

26. Berry R, Schroeder JJ, French AJ, McDonnell SK, Peterson BJ, Cunningham JM, Thibodeau SN, Schaid DJ: Evidence for a prostate cancer-susceptibility locus on chromosome 20. Am J Hum Genet 2000, 67(1):82-91.

27. Berthon P, Valeri A, Cohen-Akenine A, Drelon E, Paiss T, Wohr G, Latil A, Millasseau P, Mellah I, Cohen N et al: Predisposing gene for early-onset prostate cancer, localized on chromosome 1q42.2-43. Am J Hum Genet 1998, 62(6):1416-1424.

28. Berube NG, Speevak MD, Chevrette M: Suppression of tumorigenicity of human prostate cancer cells by introduction of human chromosome del(12)(q13). Cancer Res 1994, 54(12):3077-3081.

29. Bishop DT, Kiemeney LA: Family studies and the evidence for genetic susceptibility to prostate cancer. Semin Cancer Biol 1997, 8(1):45-51.

30. Bock CH, Cunningham JM, McDonnell SK, Schaid DJ, Peterson BJ, Pavlic RJ, Schroeder JJ, Klein J, French AJ, Marks A et al: Analysis of the prostate cancer-susceptibility locus HPC20 in 172 families affected by prostate cancer. Am J Hum Genet 2001, 68(3):795-801.

31. Bova GS, Carter BS, Bussemakers MJ, Emi M, Fujiwara Y, Kyprianou N, Jacobs SC, Robinson JC, Epstein JI, Walsh PC et al: Homozygous deletion and frequent allelic loss of chromosome 8p22 loci in human prostate cancer. Cancer Res 1993, 53(17):3869-3873.

32. Bova GS, Isaacs WB: Review of allelic loss and gain in prostate cancer. World J Urol 1996, 14(5):338-346.

33. Bova GS, MacGrogan D, Levy A, Pin SS, Bookstein R, Isaacs WB: Physical mapping of chromosome 8p22 markers and their homozygous deletion in a metastatic prostate cancer. Genomics 1996, 35(1):46-54.

34. Bratt O, Anderson H, Bak-Jensen E, Baldetorp B, Lundgren R: Metaphase cytogenetics and DNA flow cytometry with analysis of S-phase fraction in prostate cancer: influence on prognosis. Urology 1996, 47(2):218-224.

35. Breitkreuz T, Romanakis K, Lutz S, Seitz G, Bonkhoff H, Unteregger G, Zwergel T, Zang KD, Wullich B: Genotypic characterization of prostatic carcinomas: a combined cytogenetic, flow cytometry, and in situ DNA hybridization study. Cancer Res 1993, 53(17):4035-4040.

36. Brothman AR: Cytogenetic studies in prostate cancer: are we making progress? Cancer Genet Cytogenet 1997, 95(1):116-121.

37. Brothman AR, Patel AM: Characterization of 10 marker chromosomes in a prostatic cancer cell line by in situ hybridization. Cytogenet Cell Genet 1992, 60(1):8-11.

38. Brothman AR, Peehl DM, Patel AM, MacDonald GR, McNeal JE, Ladaga LE, Schellhammer PF: Cytogenetic evaluation of 20 cultured primary prostatic tumors. Cancer Genet Cytogenet 1991, 55(1):79-84.

39. Brothman AR, Steele MR, Williams BJ, Jones E, Odelberg S, Albertsen HM, Jorde LB, Rohr LR, Stephenson RA: Loss of chromosome 17 loci in prostate cancer detected by polymerase chain reaction quantitation of allelic markers. Genes Chromosomes Cancer 1995, 13(4):278-284.

40. Brothman AR, Watson MJ, Zhu XL, Williams BJ, Rohr LR: Evaluation of 20 archival prostate tumor specimens by fluorescence in situ hybridization (FISH). Cancer Genet Cytogenet 1994, 75(1):40-44.

41. Brown JA, Alcaraz A, Takahashi S, Persons DL, Lieber MM, Jenkins RB: Chromosomal aneusomies detected by fluorescent in situ hybridization analysis in clinically localized prostate carcinoma. J Urol 1994, 152(4):1157-1162.

42. Cabeza-Arvelaiz Y, Sepulveda JL, Lebovitz RM, Thompson TC, Chinault AC: Functional identification of LZTS1 as a candidate prostate tumor suppressor gene on human chromosome 8p22. Oncogene 2001, 20(31):4169-4179.

43. Cancel-Tassin G, Latil A, Valeri A, Guillaume E, Mangin P, Fournier G, Berthon P, Cussenot O: No evidence of linkage to HPC20 on chromosome 20q13 in hereditary prostate cancer. Int J Cancer 2001, 93(3):455-456.

44. Carter BS, Ewing CM, Ward WS, Treiger BF, Aalders TW, Schalken JA, Epstein JI, Isaacs WB: Allelic loss of chromosomes 16q and 10q in human prostate cancer. Proc Natl Acad Sci U S A 1990, 87(22):8751-8755.

45. Carvalho-Salles AB, Mesquita JC, Tajara EH: Deletion (1)(q12) and double minutes in a metastatic adenocarcinoma of the prostate. Cancer Genet Cytogenet 2000, 116(1):50-53.

46. Chang GT, Steenbeek M, Schippers E, Blok LJ, van Weerden WM, van Alewijk DC, Eussen BH, van Steenbrugge GJ, Brinkmann AO: A novel gene on human chromosome 2p24 is differentially expressed between androgen-dependent and androgen-independent prostate cancer cells. Eur J Cancer 2001, 37(16):2129-2134.

47. Chang GT, Tapsi N, Steenbeek M, Blok LJ, van Weerden WM, van Alewijk DC, Eussen BH, van Steenbrugge GJ, Brinkmann AO: Identification of a gene on human chromosome 8q11 that is differentially expressed during prostate-cancer progression. Int J Cancer 1999, 83(4):506-511.

48. Chekmareva MA, Hollowell CM, Smith RC, Davis EM, LeBeau MM, Rinker-Schaeffer CW: Localization of prostate cancer metastasis-suppressor activity on human chromosome 17. Prostate 1997, 33(4):271-280.

49. Chekmareva MA, Kadkhodaian MM, Hollowell CM, Kim H, Yoshida BA, Luu HH, Stadler WM, Rinker-Schaeffer CW: Chromosome 17-mediated dormancy of AT6.1 prostate cancer micrometastases. Cancer Res 1998, 58(21):4963-4969.

50. Chen C, Brabham WW, Stultz BG, Frierson HF, Jr., Barrett JC, Sawyers CL, Isaacs JT, Dong JT: Defining a common region of deletion at 13q21 in human cancers. Genes Chromosomes Cancer 2001, 31(4):333-344.

51. Chen TR: Chromosome identity of human prostate cancer cell lines, PC-3 and PPC-1. Cytogenet Cell Genet 1993, 62(2-3):183-184.

52. Cheng L, Song SY, Pretlow TG, Abdul-Karim FW, Kung HJ, Dawson DV, Park WS, Moon YW, Tsai ML, Linehan WM et al: Evidence of independent origin of multiple tumors from patients with prostate cancer. J Natl Cancer Inst 1998, 90(3):233-237.

53. Cher ML, Bova GS, Moore DH, Small EJ, Carroll PR, Pin SS, Epstein JI, Isaacs WB, Jensen RH: Genetic alterations in untreated metastases and androgen-independent prostate cancer detected by comparative genomic hybridization and allelotyping. Cancer Res 1996, 56(13):3091-3102.

54. Cher ML, Ito T, Weidner N, Carroll PR, Jensen RH: Mapping of regions of physical deletion on chromosome 16q in prostate cancer cells by fluorescence in situ hybridization (FISH). J Urol 1995, 153(1):249-254.

55. Cher ML, Lewis PE, Banerjee M, Hurley PM, Sakr W, Grignon DJ, Powell IJ: A similar pattern of chromosomal alterations in prostate cancers from African-Americans and Caucasian Americans. Clin Cancer Res 1998, 4(5):1273-1278.

56. Cher ML, MacGrogan D, Bookstein R, Brown JA, Jenkins RB, Jensen RH: Comparative genomic hybridization, allelic imbalance, and fluorescence in situ hybridization on chromosome 8 in prostate cancer. Genes Chromosomes Cancer 1994, 11(3):153-162.

57. Chu LW, Pettaway CA, Liang JC: Genetic abnormalities specifically associated with varying metastatic potential of prostate cancer cell lines as detected by comparative genomic hybridization. Cancer Genet Cytogenet 2001, 127(2):161-167.

58. Cooney KA, McCarthy JD, Lange E, Huang L, Miesfeldt S, Montie JE, Oesterling JE, Sandler HM, Lange K: Prostate cancer susceptibility locus on chromosome 1q: a confirmatory study. J Natl Cancer Inst 1997, 89(13):955-959.

59. Cooney KA, Wetzel JC, Consolino CM, Wojno KJ: Identification and characterization of proximal 6q deletions in prostate cancer. Cancer Res 1996, 56(18):4150-4153.

60. Cooney KA, Wetzel JC, Merajver SD, Macoska JA, Singleton TP, Wojno KJ: Distinct regions of allelic loss on 13q in prostate cancer. Cancer Res 1996, 56(5):1142-1145.

61. Corral Molina JM, Alcaraz Asensio A, Barranco Sanz MA, Mallofre Gomez C, Ribal Caparros MJ, Cetina Herrando A, Beardo Villar P, Muntane Casasus J, Llopis Manzaneda J, Carretero Gonzalez P: [High incidence of chromosome 8 monosomy and chromosome 7 trisomy in prostatic primary tumor and its related lymphatic metastasis. Preliminary results]. Actas Urol Esp 1998, 22(10):811-817.

62. Crundwell MC, Arkell DG, Gearty J, Phillips SM: Genetic alterations in incidentally diagnosed, transitional zone prostate cancer: a seven year follow-up. J Urol 1997, 158(4):1568-1575.

63. Crundwell MC, Chughtai S, Knowles M, Takle L, Luscombe M, Neoptolemos JP, Morton DG, Phillips SM: Allelic loss on chromosomes 8p, 22q and 18q (DCC) in human prostate cancer. Int J Cancer 1996, 69(4):295-300.

64. Cui J, Deubler DA, Rohr LR, Zhu XL, Maxwell TM, Changus JE, Brothman AR: Chromosome 7 abnormalities in prostate cancer detected by dual-color fluorescence in situ hybridization. Cancer Genet Cytogenet 1998, 107(1):51-60.

65. Cunningham JM, Shan A, Wick MJ, McDonnell SK, Schaid DJ, Tester DJ, Qian J, Takahashi S, Jenkins RB, Bostwick DG et al: Allelic imbalance and microsatellite instability in prostatic adenocarcinoma. Cancer Res 1996, 56(19):4475-4482.

66. Dahiya R, Lee C, McCarville J, Hu W, Kaur G, Deng G: High frequency of genetic instability of microsatellites in human prostatic adenocarcinoma. Int J Cancer 1997, 72(5):762-767.

67. Dahiya R, McCarville J, Hu W, Lee C, Chui RM, Kaur G, Deng G: Chromosome 3p24-26 and 3p22-12 loss in human prostatic adenocarcinoma. Int J Cancer 1997, 71(1):20-25.

68. Dahiya R, McCarville J, Lee C, Hu W, Kaur G, Carroll P, Deng G: Deletion of chromosome 11p15, p12, q22, q23-24 loci in human prostate cancer. Int J Cancer 1997, 72(2):283-288.

69. Dahiya R, Yoon WH, Boyle B, Schoenberg S, Yen TS, Narayan P: Biochemical, cytogenetic, and morphological characteristics of human primary and metastatic prostate cancer cell lines. Biochem Int 1992, 27(4):567-577.