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Table 2 Summary of clonality tests for the methylation cohort (n = 8)

From: Clonal relatedness in tumour pairs of breast cancer patients

  Patients BM1 BM7 BS7 BS8 IM4 IM9 IS1 IS4
Laterality Bilateral Bilateral Bilateral Bilateral Ipsilateral Ipsilateral Ipsilateral Ipsilateral
Synchronicity Metachronous Metachronous Synchronous Synchronous Metachronous Metachronous Synchronous Synchronous
Group BM BM BS BS IM IM IS IS
aCGH data Similarity Index
 SI 0.261 0.580 0.323 0.571 0.402 0.237 0.217 0.200
PSI 25.600 66.450 39.810 65.930 51.650 17.890 10.510 2.710
P 0.183 0.005 0.087 0.005 0.032 0.269 0.359 0.434
Clustering (Euclidean distance, single linkage)
 Clustering different similar different similar similar different different different
Distance measure
 Euclidean 46.801 19.823 59.036 16.362 43.821 60.220 63.932 66.099
 5th percentile not sign. significant not sign. significant not sign. not sign. not sign. not sign.
Shared segments
 Segments 34 37 10 32 24 3 53 38
 95th percentile significant significant not sign. significant significant not sign. significant significant
Clonality package
 LR2 0.044 135.409 0.011 34,945,440 0.008 0.006 0.000 0.001
P 0.262 0.009 0.455 0.000 0.519 0.552 0.912 0.879
Methylation data
Beta values
Similarity Index for methylation
 SImet 0.879 0.880 0.685 0.815 0.868 0.871 0.911 0.833
PSI 8.510 8.610 0.000 1.240 7.350 7.660 11.710 3.410
P 0.018 0.018 0.947 0.526 0.018 0.018 0.018 0.333
Clustering (Euclidean distance, single linkage)
 Clustering similar different different different similar different similar different
Distance measure
 Euclidean 87.969 86.972 228.809 125.860 92.508 90.574 71.300 134.247
 5th percentile significant significant not sign. not sign. not sign. not sign. significant not sign.
Methylation data
Intensity values
Similarity Index
 SI 0.578 0.573 0.439 0.594 0.517 0.565 0.648 0.467
PSI 20.360 19.770 0.000 22.520 11.010 18.650 29.070 1.410
P 0.018 0.018 0.737 0.018 0.088 0.018 0.018 0.456
Clustering (Euclidean distance, single linkage)
 Clustering similar similar different similar similar similar similar similar
Distance measure
 Euclidean 148.829 130.060 194.202 158.604 160.988 147.229 124.268 171.320
 5th percentile significant significant not sign. significant significant significant significant not sign.
Shared segments
 Segments 64 14 9 18 6 11 47 7
 95th percentile significant significant not sign. significant not sign. not sign. significant not sign.
Clonality package
 LR2 4.53 28.46 0.00 241,461,300 300,802.20 1.63 34,907,040,000,000 0.15
P 0.080 0.036 0.795 0.000 0.009 0.107 0.000 0.241
Consensus in clonality: 7/13 12/13 0/13 10/13 8/13 4/13 9/13 2/13
  1. PSI percentage of similarities between two tumours that are not due to recurrent chromosomal aberrations or randomness, LR2 final likelihood ratio with individual comparisons. Statistically significant variables (P < 0.05) are displayed in bold text