Table 3

Frequency of loss of heterozygosity (LOH) in subclasses of breast cancersa

Chromosomal regionsClustersPbSubclassesPPcc
I (n = 22)II (n = 12)IA (n = 15)IB (n = 7)IIA (n = 4)IIB (n = 8)
1p3413d30NSe7290500.0580.055
4p14238NS7570130.04NS
4p15.33200.035f1371000.004NS
5q11.24100.011310000<0.00010.02
5q14418NS20862500.001NS
5q21–32418NS20862500.004NS
10q23–245025NS4071025NS
11q23–245933NS6057050NS
13q145025NS40712513NS
14q213217NS13712513NS
14q325033NS33862538NS
16q23–2432750.029g332950880.0530.001
17p135950NS47862563NS
17q11.2–126433NS53712538NS
17q2168250.029f608625250.046NS
18q22–23270NS1357000.032NS
Mean fractional LOH (%)21110.04h1437614<0.001h
  • a Subclasses defined by expression hierarchical clustering in Fig. 1 <$REFLINK> .

  • b P of Fisher’s exact test in comparing LOH frequencies for the individual chromosomal regions between two clusters or among four subclasses.

  • c P of exact score test of exact logistic regression adjusting for fractional LOH in comparing LOH frequencies for the individual chromosomal regions among four subclasses.

  • d Percentage of the tumors affected by LOH.

  • e P > 0.05; NS = not significant.

  • f P > 0.05 after adjusting for fractional LOH in exact score test of exact logistic regression.

  • g P = 0.005 after adjusting for fractional LOH in exact score test of exact logistic regression.

  • h P from Student’s t test.