COPY NUMBER ANALYSIS
This section provides details of copy number alterations detected in the tumour, including gains and losses and loss of heterozygosity (LOH). Look in this section for details about potentially relevant genes within the copy change regions and their associated expression metrics.
COPY NUMBER AND LOH
SUMMARY OF COPY NUMBER EVENTS
COPY NUMBER VARIANTS: GENOME DETAILS
CNVS OF POTENTIAL CLINICAL RELEVANCE
No copy number variants of clinical relevance were found from the analysis.
CNVS OF PROGNOSTIC OR DIAGNOSTIC RELEVANCE
No copy number variants of prognostic or diagnostic relevance were found from the analysis.
CNVS OF BIOLOGICAL RELEVANCE
Gene Copy Change LOH State CNV State Chr:band CNV Start CNV End Size (Mb) Expression (RPKM) Fold Change
vs. average
SARC
%ile
APC -1 NLOH Loss 5:q22.2 111520402 112184695 1 2.46 -2.25 36
COMMONLY AMPLIFIED ONCOGENES WITH COPY GAINS
Gene Copy Change LOH State CNV State Chr:band CNV Start CNV End Size (Mb) Expression (RPKM) Fold Change vs. average SARC %ile
AURKA +1 HET Gain 20:q13.2-q13.33 52545359 62821928 10.28 13.28 4.55 73
CCND2 +1 HET Gain 12:p13.32 4373073 4441890 0.07 100.32 3.86 98
CDK4 +1 HET Gain 12:p13.3-q14.1 58075229 58392623 0.32 67.73 3.13 14
FGFR1 +2 ALOH Gain 8:p11.23-p11.22 37597019 39231982 1.63 6.99 -1.43 1
HOMOZYGOUSLY DELETED TUMOUR SUPPRESSORS
No homozygous deleted tumour suppressors were found from the analysis.
HIGHLY EXPRESSED ONCOGENES WITH COPY GAINS
Gene Copy Change LOH State CNV State Chr:band CNV Start CNV End Size (Mb) Expression (RPKM) Fold Change vs. average SARC %ile
CCND +1 HET Gain 12:q13.32 4373073 4441890 0 100.32 3.86 98
HOXD11 +1 HET Gain 2:q31.1 176936995 177010532 0 16.52 13.52 94
HOXD13 +1 HET Gain 2:q31.1 176936995 177010532 0 59.93 49.76 100
HSP90AB1 +1 HET Gain 6:p21.1 44205590 44315036 0 1494.2 3.25 99
MYC +2 ALOH Gain 8:p24.21 128648140 128846228 0 60.13 2.67 86
TOP1 +1 HET Gain 20:q11.21-q13.13 30169985 48766874 19 108.32 3.17 100
LOWLY EXPRESSED TUMOUR SUPPRESSORS WITH COPY LOSSES
Gene Copy Change LOH State CNV State Chr:band CNV Start CNV End Size (Mb) Expression (RPKM) Fold Change vs. average SARC %ile
GPC3 -1 DLOH Loss X:p22.33-q28 182546 155260410 155.08 0.26 -19.69 14
KDM5C -1 DLOH Loss X:p22.33-q28 182546 155260410 155.08 2.83 -2.56 0
WT1 -1 DLOH Loss 11:p13 31270391 33703585 2.43 0.01 -4.93 14
CNV AND LOH FIGURES
Chr A Chr 1 Chr 2 Chr 3 Chr 4
Chr 5 Chr 6 Chr 7 Chr 8 Chr 9
Chr 10 Chr 11 Chr 12 Chr 13 Chr 14
Chr 15 Chr 16 Chr 17 Chr 18 Chr 19