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Presented by Dannise Jangyoung Marcus Bongsoo Breast Cancer Diagnostics
Outline ,[object Object],[object Object],[object Object],[object Object]
Introduction ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],World Health Organization, American Cancer Society
Introduction ,[object Object],[object Object],Normal breast Breast cancer Fine Needle Aspiration Surgical biopsy
Introduction ,[object Object],[object Object],[object Object],[object Object]
Data characteristics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Mangasarian, et al (1994) Wolberg, et al. (1994)
SVM (Support vector machine)  ,[object Object],[object Object]
SVM  ,[object Object],[object Object],[object Object]
SVM  ,[object Object],[object Object],[object Object]
Logistic Regression  ,[object Object],[object Object],[object Object]
Logistic Regression  Estimate Std. Error z value Pr(>|z|)  (Intercept) 7.35952 12.85259 0.573 0.5669  radius  2.04930 3.71588 0.551 0.5813  texture -0.38473 0.06454 -5.961 2.5e-09 *** perimeter 0.07151 0.50516 0.142 0.8874  area -0.03980 0.01674 -2.377 0.0174 *  smoothness -76.43227 31.95492 -2.392 0.0168 *  compactness 1.46242 20.34249 0.072 0.9427  concavity -8.46870 8.12003 -1.043 0.2970  concave_points -66.82176 28.52910 -2.342 0.0192 *  symmetry -16.27824 10.63059 -1.531 0.1257  fractal_dimension 68.33703 85.55666 0.799 0.4244  --- Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
SVM ,[object Object],[object Object],[object Object]
SVM Results ,[object Object],[object Object],Type Benign Malign Correct (%) 96.92 90.57 Type Benign Malign Correct (%) 96.63 89.85
Conclusion & Discussion ,[object Object],Type Benign Malign Mean model 99.43 97.63 Cross Validation (80%) 94.80 91.66 The reduced model (Full Dataset) 96.62 90.57 The reduced model (Bootstrap) 96.63 89.85
Conclusion & Discussion ,[object Object],[object Object],[object Object]
Conclusion & Discussion ,[object Object],Lasfargues, EY et al. 1958. Cultivation of human breast carcinomas.  Borras, M et al. 1997. Estrogen receptor negative/progesterone receptor-positive evsa-T mammary tumor cells: a model  for assessing the biological property of this peculiar phenotype of breast cancers. Cell line Origin of cell Estrogen  receptors Progesterone receptors ERBB2 Amplification BT-20 Primary No No No BT-474 Primary Yes Yes Yes MCF-7 Metastasis Yes Yes No SK-BR-3 Metastasis No No Yes
Conclusion & Discussion ,[object Object],[object Object],Britta Weigelt, Mina J. Bissell. 2008 Unraveling the microenvironmental influences on the normal  mammary gland and breast cancer. Seminar in Cancer Biology. (18) 311-321
Thank you very much ! Any questions ?

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2010 Spring, Bioinformatics II Presentation

  • 1. Presented by Dannise Jangyoung Marcus Bongsoo Breast Cancer Diagnostics
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.
  • 7.
  • 8.
  • 9.
  • 10.
  • 11. Logistic Regression Estimate Std. Error z value Pr(>|z|) (Intercept) 7.35952 12.85259 0.573 0.5669 radius 2.04930 3.71588 0.551 0.5813 texture -0.38473 0.06454 -5.961 2.5e-09 *** perimeter 0.07151 0.50516 0.142 0.8874 area -0.03980 0.01674 -2.377 0.0174 * smoothness -76.43227 31.95492 -2.392 0.0168 * compactness 1.46242 20.34249 0.072 0.9427 concavity -8.46870 8.12003 -1.043 0.2970 concave_points -66.82176 28.52910 -2.342 0.0192 * symmetry -16.27824 10.63059 -1.531 0.1257 fractal_dimension 68.33703 85.55666 0.799 0.4244 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
  • 12.
  • 13.
  • 14.
  • 15.
  • 16.
  • 17.
  • 18. Thank you very much ! Any questions ?

Hinweis der Redaktion

  1. 2 nd most common cancer, after lung cancer (and melanomas) (the WHO) Strongly related to age, less than 5% of cases are women under 40 yrs 1.3 million women diagnosed annually worldwide
  2. Cancer that forms in tissues of the breast, usually the ducts (tubes that carry milk to the nipple) and lobules (glands that make milk). It occurs in both men and women, although male breast cancer is rare. Risk factors
  3. After the mammogram… Or other disease such as mastitis
  4. Round, ellipse, moon, rough
  5. Primary tumor is a tumor growing at the anatomical site where tumor progression began and proceeded to yield a cancerous mass. Metastasis(Pleural effusion) is excess fluid that accumulates in the pleural cavity, the fluid-filled space that surrounds the lungs. Cancer cells can break away, leak, or spill from a primary tumor, enter lymphatic and blood vessels, circulate through the bloodstream. Metastasis is one of three hallmarks of malignancy.
  6. Fig. 2. Morphologies of breast cancer cell lines cultured in 2D and 3D. (Top) Images of 4 representative breast cancer cell lines cultured as 2D monolayer, (middle) and in 3D lrBM grouped by 3D morphological classification: Round, Mass, Grape-like and Stellate. (Bottom) 3D cultures were stained for F-actin and nuclei were counterstained with DAPI. Scale bars: top panel, 100$m; middle panel, 50$m; bottom panel, 20$m. Adapted from ref. [77].