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 |