A review of cytogenetics and its automation

Journal of Medical Sciences

Volumn 7, Issue 1, 2007, Pages 1-18

  Prabhu Britto, A ^a   Ravindran, G ^a  

^a ANNA UNIVERSITY   (India)

Author keywords

Automated cytogenetics; Chromosome banding; Cytogenetics; Diagnosis; Medical imaging

Indexed keywords

PHYTOHEMAGGLUTININ;

ARTIFICIAL NEURAL NETWORK; CANCER; CELL CULTURE; CELL SUSPENSION; CHROMOSOMAL LOCALIZATION; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; CHROMOSOME BANDING PATTERN; CHROMOSOME G BAND; CHROMOSOME IDENTIFICATION; CHROMOSOME REARRANGEMENT; CHROMOSOME STRUCTURE; COMPUTER ANALYSIS; CYTOGENETICS; DIAGNOSTIC ACCURACY; DIAGNOSTIC VALUE; EARLY DIAGNOSIS; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENETIC DISORDER; HUMAN; IMAGE ANALYSIS; IMAGE PROCESSING; KARYOTYPING; LABORATORY AUTOMATION; METAPHASE; MOLECULAR IMAGING; PROCESS OPTIMIZATION; PROPHASE; QUANTITATIVE ANALYSIS; REVIEW; ROC CURVE; VALIDATION PROCESS;

EID: 33846453286     PISSN: 16824474     EISSN: 18125727     Source Type: Journal    
DOI: 10.3923/jms.2007.1.18     Document Type: Review

References (114)

1. Agam, G. and I. Dinstein, 1997. Geometric separation of partially overlapping nonrigid objects applied to automatic chromosome classification'. IEEE Trans. Pattern Anal. Mach. Intell., 19: 1212-1222.
2. Anderson, C.H., H. Greenspan and S. Akber, 2000. Image enhancement by nonlinear extrapolation in frequency space'. IEEE Trans. Image Process, 9: 1035-1048.
3. Butler, J.S., M.K. Butler and A. Stroud, 1964. Automatic Classification of Chromosomes'. In: Data Acquisition and Processing in Biology and Medicine 4, Enslein K. (Ed.) New York: Pergamon Press, pp: 47-57.
4. Bille, J., A. Erhardt, G. Johanssen and B. Ueberreiter, 1980. 'Biological dosimetry by aberration scoring using POLYP. Pattern Recognition, 14: 1200-1202.
5. Bresser, M., 1984. Automated Metaphase Finding. In: Report on Work Group Meeting on Automated Chromosome Analysis (Copenhagen, Oct. 11-113, 1984) Lundsteen C. (Ed.), Copenhagen: Rigshospitalet, pp: 9-11.
6. Caspersson, T., S. Farber, G.E. Foley, J. Kudynowski, E.J. Modest, E. Simonsson, U. Wagh and L. Zech 1968. Chemical differentiation along metaphase chromosomes'. Experimental Cell Rsearch 49: 219-222.
7. Castleman, K.R. and R.J. Wall, 1973. Automatic Systems for Chromosome Identification'. In: Proc. 23rd Nobel Symposium, T. Caspersson and Zech I. (Eds.), New York: Academic Press, pp: 77-84.
8. Castleman, K.R. and J.H. Melnyk, 1976. An Automated System for Chromosome Analysis: Final Report. Pasadena: JL Doc. Nr., 5040-30.
9. Carothers, A. and J. Piper, 1994. Computer-aided classification of human chromosomes: A review. Statistics and Computing, 4: 161-171.
10. Cho, J., 2000. Chromosome classification using backpropagation neural networks'. IEEE Eng. Med. Biol. Mag., 19: 28-33.
11. Corkidi, G., L. Vega, J. Marquez, E. Rojas and Ostrosky-Wegman, 1998. Roughness feature of metaphase chromosome spreads and nuclei for automated cell proliferation analysis'. Med. Biol. Eng. Comput., 36:679-685.
12. Cosio, F.A., L. Vega, A.H. Becerra, C.P. Melendez, G. Corkidi, 2001. Automatic identification of metaphase spreads and nuclei using neural networks. Med. Biol. Eng. Comput., 39: 391-396.
13. Drets, M.E., 1978. BANDSCAN-a computer program for on-line linear scanning of human banded chromosomes. Computer. Programs Biomed., 8: 283-294.
14. Drets, M.E. and H. Seuanez, 1973. Quantitation of heterogeneous human heterochromatin: Microdensitometric analysis of C-and G-bands'. In: Physiology and genetics of reproduction, Part A.Coutinho E.M., F. Fuchs (Eds.). Plenum, New York, pp: 29-52.
15. Drets, M.E. and F.J. Monteverde, 1987. Automated Cytogenetics with Modern Computerized Scanning Microscope Photometer Systems'. In: Cytogenetics, Obe G. and A. Basler (Eds.). Springer, Berlin, pp: 48-64.
16. Dudkin, A.K and D.A. Denissov, 1993. Visual object recognition via hypothesis construction/verification in chromosome analysis. Canadian Conf. on Electrical and Computer Engineering. 2: 1200-1203.
17. Drets, M.E., G.A. Folle and F.J. Monteverde, 1990. 'Quantitative detection of chromosome structures by computerized microphotometric scanning'. In: Chromosome aberrations. Obe,G. and A.T. Natarajan (Eds.). Basic and applied aspects. Springer, Berlin, pp: 1-12.
18. Delshadpour, S., 2003. Reduced size multi-layer perception neural network for human chromosome classification'. Proc. 25th Annual Intl. Conf. IEEE Engineering in Medicine and Biology Society. 3:2249-2252.
19. Errington, P. and J. Graham, 1993. Application of artificial neural networks to chromosome classification. Cytometry, 14: 627-639.
20. Ford, C.E. and J.L. Hamerton, 1956. The chromosomes of man. Nature, 178: 1020-1023.
21. Gallus, G. and G. Regliosi, 1974. A decisional model of recognition applied to the chromosome boundaries. J. Histochem. Cytochem., 22: 546-553.
22. Gaybay, C., 1986. Image structure representation: A discussion of some segmentation methods in cytology. IEEE Trans. Pattern Anal. Mach. Intell. 8: 140-146.
23. Graham, J. and J. Piper, 1994. Automated karyotype analysis Methods in Molecular Biology: Chromosome Analysis Protocols. Gosden, J.R.(Ed.) (Totowa, NJ: Humana Press).
24. Granlund, G.H., G.W. Zack, I.T. Young and M. Eden, 1976. A technique for multiple cell chromosome karyotyping. J. Histochem. Cytochemi., 24: 160-167.
25. Grasselli, A., 1969. Automatic Interpretation and Classification of Images. Academic Press, New York.
26. Green, D.K. and J. Cameron, 1972. Metaphase cell finding by machine. Cytogenetics, 11: 475-487.
27. Green, D.K., R. Bayley and D. Rutovitz, 1977. A cytogeneticist's microscope. Microscopica Acta, 79: 237-245.
28. Groen, F.C.A., 1977. Analysis of DNA-based measurement methods applied to human chromosome classification. Ph.D Thesis, Delft Univ. of Technology.
29. Guimaraes, L.V., A. Schuck and A. Elbern, 2003. Chromosome classification for karyotype composing applying shape representation on wavelet packet transform' Proc. 25th Annual Intl. Conf. of the IEEE Engineering in Medicine and Biology Society, 1: 941-943.
30. Harms, H. and H.M. Aus, 1984. Estimation of sampling errors in a high resolution TV microscope image processing system. Cytometry, 5: 228-235.
31. Harnden, D.G., H.P. Klinger, J.T. Jensen and M. Kaelbling, 1985. An international system for human cytogenetic nomenclature (ISCN 1985). Report of the Standing Committee on Human Cytogenetic Nomenclature. Basel, Switzerland: KAEGER.
32. Hilditch, J. and D. Rutovitz, 1972. Normalization of chromosome measurements. Comput. Biol. and Med., 2: 167-179.
33. Hoffbrand, V.A. and J.E. Pettit, 2000. Color Atlas of Clinical Hematology. 3rd Edn (St Louis, MO; Mosby).
34. Hsu, T.C., 1979. Human and Mammalian Cytogenetics: An Historical Perspective. Springer, New York.
35. Hutzler, P.J.S., 1981. Present and possible future applications of optical methods in karyotyping and metaphase search. In: Proc. 4th European Chromosome Analysis Workshop (Edinburg, March 25-27, 1981) Edinburgh: Medical Research Council p: 1.3.
36. Hungerford, D.A., A.J. Donelly, P.C. Nowell and S. Beck, 1959. The chromosome constitution of a human phenotypic intersex. Am. J. Hum. Genet., 11:215-236.
37. Ing, P.S., R.S. Ledley and H.A. Lubs, 1975. Chromosome Analysis at the National Biomedical Research Foundation. In: Proc. Asilomar Workshop on Automation of Cytogenetics, Mendelsohn, M.L. (Ed.), Pacific Grove CA: Enginering Foundation (751158) pp: 27-38.
38. Joyce-Loebl (Firm) (1985). Image Analysis: Principles and Practice. Gateshead, England: Joyce-Loebl, pp: 250.
39. Jain, A.K., 1989. Digital Image Processing. Prentice-Hall, Englewood Cliffs, NJ.
40. Keller, J.M., P. Gader, O. Sjahputera, C.W. Caldwell and H-M.T. Huang, 1995. A fuzzy logic rule-based system for chromosome recognition. Proc. 8th IEEE Symp. on Computer-Based Medi. Sys., pp: 125-132.
41. Korthof, G. and A.D. Carothers, 1991. Tests of performance of four semi-automatic metaphase-finding and karyotyping systems. Clin. Genet., 40:441-451.
42. Kyan, M.J., L. Guan, M.R. Amison and C.J. Cogswell, 1999. Feature extraction of chromosomes from 3D confocal microscope images. Intl. Conf. on Image Processing, 2: 843-847.
43. LeBeau, M.M. and J.D. Rowley, 1984. Recurring chromosomal abnormalities in leukemia and lymphoma. Cancer Survey 3 Edn. J. Rowley (Oxford: Oxford University Press), pp: 371-394.
44. Ledley, R.S., 1964. High speed automatic analysis of biomedical pictures. Science, 146: 216-223.
45. Ledley, R.S., L.S. Rotolo, T.J. Golab, J.D. Jacobsen, M.D. Ginsberg and J.B. Wilson, 1965. FIDAC-Film input to digital automatic computer and associated syntax directed pattern recognition system. In: Optical and electro-optical information processing, J.I. Tippett et al. (Eds.). Cambridge MA: MIT Press, pp: 591-631.
46. Ledley, R.S., H.A. Lubs and F.H. Ruddle, 1972. Introduction to chromosome analysis. Computers in Biol. Med., 2: 107-128.
47. Le Go, R., 1982. Automation in cytogenetics at C.E.A Paris. In: Biomedical Images and Computers, J. Sklansky and Bisconte, J.C. (Eds.) Berlin: Springer Verlag, pp: 66-77.
48. Lerner, B., H. Guterman, M. Aladjem, I. Dinstein and Y. Romem, 1996. Feature extraction by neural network nonlinear mapping for pattern classification. Proc. 13th Intl. Conf. on Pattern Recognition, 4: 320-324.
49. Liang, J., 1989. Intelligent splitting in the chromosome domain'. Pattern Recognition, 22: 519-532.
50. Lerner, B., M. Levinstein, B. Rosenberg, H. Guterman, L. Dinstein and Y. Romem, 1994. Feature selection and chromosome classification using a multi layer perception neural network. IEEE Conf. on Computational Intelligence, 6: 3540-3545.
51. Lu, Y. and Y. Yan, 1989. An expert system for banded chromosomes recognition'. Proc. Annual Int. Conf. IEEE Eng. Med. Biol. Soc., 6: 1789-1790.
52. Lundsteen, C., A.M. Lin and E. Granum, 1975. Visual classification of banded human chromosomes: Karyotyping compared with classification of isolated chromosomes. In: Proc. Asilomar workshop on automation of cytogenetics. Mendelsohn, M.L. (Ed.). Pacific Grove: Engineering Foundation (751158), pp: 110-116.
53. Lundsteen, C. and E. Granum, 1979. Description of chromosome banding patterns by band transition sequences. Clinical Genetics, 15: 418-429.
54. Lundsteen, C., J. Philip and E. Granum, 1980. Quantitative analyses of 6985 digitized trypsin G banded human metaphase chromosomes. Clin. Genet., 18: 355-370.
55. Lundsteen, C., 1986. Automated karyotyping systems'. In: Report on European Work Group on Automated Chromosome Analysis (Berlin, Sept.27-29, 1986).
56. Lundsteen, C. and A. Martin, 1989. On the selection of systems for automated cytogenetic analysis. Am. J. Med. Genet. 32: 72-80.
57. Lundsteen, C. and J. Piper, 1989. Automation of Cytogenetics. Springer-Verlag, Berlin, Heidelberg, New York.
58. Lundsteen, C., T. Gerdes, J. Maahr, 1991. Automated multiple-cell karyotyping: A clinical feasibility study. Clin. Genet., 39: 338-346.
59. Lundsteen, C., J., Maahr and T. Gerdes, 1992a. Automation of cytogenetics: Present state and the future. Springer-Verlag, Berlin.
60. Lundsteen, C., J. Maahr and T. Gerdes, 1992b. Automatic Assessment of the quality of G-banded metaphases. A preliminary study. J. Radiat. Res. 33: Suppl., 152-158.
61. Mascio, L.N., B.K. Yuen, W.P. Kegelmeyer, K. Matsumoto, J. Briner and A.J. Wyrobek, 1998. Advances in the automated detection of metaphase chromosomes labeled with fluorescence dyes. Cytometry, 33: 10-18.
62. Mendelsohn, M.L., 1966. Absorption Cytophotometry. Comparative Methodology for Heterogeneous Objects and the Two-Wavelength Method. In: Introduction to quantitative cytochemistry. Wied, G.L. (Ed.). Academic, New York, pp: 201-237.
63. Mitchell, T.M., 1997. Machine Learning. Boston, MA: WCB/McGraw-Hill.
64. Morrone, M.C. and D.C. Burr, 1988. Feature detection in human vision: A phase-dependent energy model. Proc. R. Soc. Lond. B 235: 221-245.
65. Mousavi, P., R.K. Ward and P.M. Lansdorp, 1999. Feature analysis and classification of chromosome 16 homologs using fluorescence microscopy image. IEEE Can. Conf. Electr. Comput. Eng., 2: 841846.
66. Neurath, P.W., B.L. Bablouzian, T.H. Warms, R.C. Serbagi and A. Falek, 1966. Human chromosome analysis by computer-an optical pattern recognition problem. Annals of the New York Academy of Sci., 128: 1013-1028.
67. Neurath, P.W., G. Gallus and W.D. Selles, 1970. Interactive Computer-aided Chromosome Analysis. J. Assoc. Advancement Medical Instrumentation, 4: 6-14.
68. Neurath, P.W., G. Gallus, J.B. Horton and W.D. Selles, 1975. Automatic Karyotyping: Progress, perspective and economics. In: Proc. Asilomar Workshop on Automation of Cytogenetics, Mendelsohn, M.L. (Ed.). Pacific Grove CA: Engineering Foundation (751158), pp: 17-26.
69. Oosterlinck, A., 1977. Een Geautomatiseerd Interactief Beeldherkenningssysteem met Toepassing in het Domein van Menselijke Chromosomeenclassificatie. Ph.D. Thesis Catholic Univ. Leuven. Leuven: Acco, pp: 244.
70. Painter, T.S., 1923. Studies in mammalian spermatogenesis II. The Spermatogenesis of man. J. Exp. Zool. 37: 291-321.
71. Pantaleao, C.H.Z., F.M. Azevedo, E.T. Pereira, M.C.M. Ribeiro and J.L.B. Marques, 2002. Development of a computerized system for cytogenetic analysis and classification. Proc. 2nd Joint 24th Annual Conf. and the Annual Fall Meeting of the Biomedical Engineering Soc., 3: 2211-2212.
72. Paris Conference, 1971 (1972). Standardization in Human Cytogenetics. Birth Defects: Original Article Series Vol. 8, No. 7 (The National Foundation, New York); also in Cytogenetics, 11: 313-362.
73. Patau, K., 1952. Absorption microphotometry of irregular-shaped objects. Chromosoma, 5: 341-362.
74. Piper, J. and C. Lundsteen, 1987. Human Chromosome Analysis by Machine. Trends Genet, 3: 309-313.
75. Piper, J., E. Granum, D. Rutovitz, H. Ruttledge, 1980. Automation of chromosome analysis. Signal Process, 2:203-221.
76. Piper, J., E. Granum, 1989. On fully automatic feature measurement for banded chromosome classification. Cytometry, 10: 242-255.
77. Pudney, C.J., M.J. Robins, B.J. Robins and P.D. Kovesi, 1996. Surface detection in 3D confocal microscope images via local energy and ridge tracing. J. Comput. Assist. Microsc, 8: 5-20.
78. Popescu, M., P. Gader, J. Keller, C. Klein, J. Stanley and C. Caldwell, 1999. Automatic karyotyping of metaphase cells with overlapping chromosomes. Comput. Biol. Med., 2: 61-82.
79. Ramstein, G., M. Bernadet, A. Kangoud and D. Barba, 1992. "Chromosome": A rule-based image analysis system for chromosome classification. Proc. Annual Int. Conf. IEEE Eng. Med. Biol. Soc., 3: 926-927.
80. Ruan, X., 2000. A classifier with the fuzzy Hopfield Network for human chromosomes, intelligent control and automation. Proc. 3rd World Congress on Intelligent Control and Automation. 2:1159-1164.
81. Rutovitz, D., D.K. Green, A.S.J. Farrow and D.C. Mason, 1978. Computer-assisted Measurement in the Cytogenetic Laboratory. In: Pattern Recognition, Batchelor, B.G. (Ed.) New York NY: Plenum, pp: 303-329.
82. Rutovitz, D. and E. Granum, 1981. Interaction or automation'. Proc. 4th European Chromosome Analysis Workshop (Edinburg, March 25-27, 1981) Edinburgh: Medical Research Council pp: 6.4ff.
83. Ryu, S.Y., J.M. Cho and S.H. Woo, 2001. A study for the feature selection to identify giemsa-stained human chromosomes based on artificial neural network'. Proc. 23rd Annual EMBS Int. Conf. (Istanbul, Turkey) 1: 691-692.
84. Sandberg, A.A. and S. Abe, 1980. Cytogenetic techniques in haematology. Clinics in Haematology, 9: 19-38.
85. Schwartzkopf, W., B.L. Evans and A.C. Bovik, 2001. Minimum Entropy segmentation applied to multi-spectral chromosome images. 2001 Int. Conf. on Image Processing, 2: 865-868.
86. Schwartzkopf, W., B.L. Evans and A.C. Bovik, 2002. Entropy estimation for segmentation of multi-spectral chromosome images. Proc. 5th IEEE Southwest Symp. On Image Analysis and Interpretation. pp: 234-237.
87. Shannon, C.E. and W. Weaver, 1949. The Mathematical Theory of Communication'. Urbana, IL: University of Illionois Press, pp: 125.
88. Sjahputera, O. and J.M. Keller, 1999. Evolution of a fuzzy rule-based system for automatic chromosome recognition. Proc. IEEE Intl. Conf. on Fuzzy Syst., 1: 129-134.
89. Stanley, R.J., J.M. Keller, P. Gader, C.W. Caldwell, 1998. Data-driven homologue matching for chromosome identification. IEEE Trans. Med. Image., 17:451-462.
90. Shoemaker, R.L., P.H. Bartels, D.W. Hillman J. Jonas D. Kessler, R.V. Shack and D. Vukobratovich, 1982. An ultrafast laser scanner microscope for digital image analysis. IEEE Trans. Biomed. Eng., 29:82-91.
91. Swets, J.A. and R.M. Pickett, 1982. Evaluation of Diagnostic Systems: Methods from Signal Detection Theory. Academic Press, New York, pp: 253.
92. Sweeney, W.P. and M.T. Musavi, 1993. Application of neural networks for chromosome classification. Proc. 15th Annual Intl. Conf. IEEE Engineering in Medicine and Biology Society. pp: 239-240.
93. Sweeney, N., R.L. Becker and B. Sweeney, 1997. A comparison of wavelet and Fourier descriptors for a neural network chromosome classifier. Proc. 19th Intl. Conf-IEEE/EMBS (Chicago IL, November 1997), pp: 1359-1362.
94. Tjio, H.J. and A. Levan, 1956. The Chromosome numbers of man. Hereditas, 42: 1-6.
95. Therman, E. and M. Susman, 1993. Human Chromosomes: Structure, Behavior and Effects. Springer Verlag, New York 3rd Edn.
96. Trask, B.J., 2002. Human Cytogenetics: 46 Chromosomes, 46 years and counting. Nat Rev Genet., 3: 769-778.
97. Van Daele, J., F. Dom, L. de Buysscher, A. Oosterlinck and H. van den Berghe, 1979. Metaphase finding using microprocessors. In: Proc. IEEE Conf. on Pattern Recognition and Image Processing (Chicago, IL, Aug. 6-8, 1979), pp: 460-465.
98. Vanderheydt, L., F. Dom, A. Oosterlinck and H. Berghe, 1981. Two-dimensional shape decomposition using fuzzy set theory applied to automated chromosome analysis. Pattern Recognition, 13: 147-157.
99. Vrolijk, J., P.L. Pearson and J.S. Ploem, 1980. LEYTAS, A system for the processing of microscopic images. Analytical and Quantitative Cytology, 2:41-48.
100. Vogel, F. and A.G. Motulsky, 1997. Human Genetics: Problems and Approaches. Springer-Verlag, Berlin 3rd Edn.
101. Wald, N., R.W. Ranshaw, J.M. Herron and J.G. Castle, 1970. Progress on an Automatic System for Cytogenetics Analysis. In: Human Population Cytogenetics, P.A. Jacobs, W.H. Price and P. Law, (Eds.) Edinburgh: Univ. Press, pp: 273-280.
102. Wang, Y-P., Q. Wu, K.R. Castleman and Z. Xiong, 2001. Image enhancement using multi scale differential operators. IEEE Intl. Conf. on Acoustics, Speech and Signal Processing (7-11 May 2001) 3: 1853-1856.
103. Wang, Y-P., Q. Wu, K.R. Castleman and Z. Xiong, 2003. Chromosome image enhancement using multi scale differential operators. IEEE Trans. Med. Imag., 22: 685-693.
104. Wang, X., B. Zheng, M. Wood, S. Li, W. Chen and H. Liu, 2005. Development and evaluation of automated systems for detection and classification of banded chromosomes: Current status and future perspectives. J. Phys. D: Applied. Phys. 38:2536-2542.
105. Watson, J.R.D. and F.H.C. Crick, 1953. A structure for deoxyribose nucleic acid. Nature, 171:737-738.
106. Weeks, A.R., H.R. Myler and H.G. Wenaas, 1993. Computer-generated noise images for the evaluation of image processing algorithms. Opt. Eng., 32:982-992.
107. Wu, Q., P. Suetens and A. Oosterlinck, 1989. On knowledge-based improvement of biomedical pattern recognition-a case study. Proc. 5th Conf. on Artificial Intelligence for Applications, pp: 239-244.
108. Wu, Q., P. Suetens and A. Oosterlinck, 1990. Chromosome classification using a multi-layer perception neural net'. Proc. 12th Annual Intl. Conf. IEEE Engineering in Med. Biol. Soc., pp: 1453-1454.
109. Wu, Q. and K.R. Castleman, 1996. Multi scale image enhancement of chromosome banding patterns. Proc. SPIE., 2825: 796-804.
110. Wu, Q., Y.-P. Wang, Z. Liu, T. Chen, K.R. Castleman, 2002. The effect of image enhancement on biomedical pattern recognition. Proc. 2nd Joint 24th Annual Conf. and the Annual Fall Meeting of the Biomedical Engineering Society, 2: 1067-1069.
111. Young, I.T., Balasubramanian, D.L. Dunbar, R.L. Peverini and R.P. Bishop, 1982. SSAM: Solid-state automated microscope. IEEE Trans. Biom. Eng., 29:70-81.
112. Yunis, J.J., 1980. Nomenclature for high resolution human chromosomes. Cancer Genet Cytogenet, 2: 221-229.
113. Yunis, J.J., 1981. Mid-prophase human chromosomes. The attainment of 2000 bands. Hum. Genet., 56:293-298.
114. Zimmerman, S.O., D.A. Johnston, F.E. Arrighi and M.E. Rupp, 1986. Automated homologue matching of human G-banded chromosomes. Comput. Biol. Med., 16:223-233.