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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