The Leeds Teaching Hospitals NHS Trust

Sarcomas and Soft Tissue Tumours

Sarcoma and soft tissue tumour genetic studies

Soft tissue tumours are a diverse group of neoplasms affecting tissues which connect, support, or surround other structures and organs of the body. Classification is traditionally based on histology, although tumour location, size, growth pattern, recurrence risk, patient age, and distribution of metastases are also important. Most soft tissue tumours are either benign or malignant (i.e. sarcomas) but some are intermediate, ie locally aggressive with a potential to metastasise.

Although histopathology remains the gold standard for diagnosis, advances in genetic technology are reshaping approaches to diagnosis and disease management. The majority of soft tissue tumours contain acquired cytogenetic changes – many demonstrate disease-specific chromosome translocations, whilst some contain other molecular events such as oncogene amplifications. Cytogenetic and molecular testing plays an increasingly important role in aiding pathology diagnosis and providing information important to disease progression and outlook.

Cytogenetic testing and molecular genetic testing is performed by the Leeds Genetics/Histopathology Molecular Oncology team for an expanding number of soft tissue tumour types using a variety of techniques such as G-banding, FISH, and Sanger sequencing.


FISH showing PAX-FOXO1 amplification in alveolar rhabdomyosarcoma  

two                                   FISH showing 13q14 deletion in spindle cell lipoma


                                FISH showing EWSR1 rearrangement in Ewing’s sarcoma


 G-banding showing large marker chromosome containing MDM2 amplification in well-differentiated liposarcoma


Sanger sequencing showing KIT exon 9 mutation in a GIST

Sample Requirements - G-Banding

Whilst the great majority of genetic testing in soft tissue tumours involves the use of DNA-based tests, a cell culture and karyotyping service is available on fresh tissue for exceptional cases where this may be of clinical benefit.

Cell culture requires living cells. Please ensure that the sample reaches us as quickly as possible (within 24 hours). First class post is satisfactory.

Samples should be placed in sterile containers, containing sterile, fresh (i.e. less than one month since opening) culture medium - this should ideally be Ham’s F10, but any balanced salt solution is acceptable. Transport medium is available from the laboratory on request. On no account should samples be transported in formalin.

Samples from within St James’s should be sent in sealed plastic bags, with the request card protected from the sample.

Samples from other hospitals should be placed in taped absorbent boxes containing appropriate padding and packing.

Request cards should be protected from samples.

Where delays over 24 hours are unavoidable, e.g. for biopsies taken on Saturday afternoon or Sunday, samples should be refrigerated and sent to the laboratory to arrive on the next working day.

Open biopsies from the tumour itself are preferred.

Sample size is important, and the chances of obtaining a successful result increase with biopsies above 5mm in diameter.

Trucut biopsies and fine needle aspirates will also be accepted if no open biopsy is available, although smaller sized samples can result in a higher failure rate.

Where consent for research is available, surplus tumour tissue from paediatric patients will be stored for possible future research or development purposes, in line with the agreed St James’s Hospital Paediatric Oncology tumour storage pathway.

Where appropriate, other fluids where tumour infiltration is known or suspected may be sent. These include pleural effusions, cerebro-spinal fluid, bone marrow, blood and cystic fluid.

Cytogenetic analysis of blood or bone marrow may also be undertaken by the molecular oncology team where infiltration into blood or bone marrow is known or suspected. 

Sample Requirements - FISH

Fresh tumour biopsies for short-term (overnight) culture for interphase FISH studies should be sent to the lab as ‘urgent’ in transport medium, sterile saline or dry.

All Formalin fixed and paraffin wax embedded (FFPE) samples should be sent to the Leeds histopathology laboratory for entry onto the CoPath LIMS. Samples can either be sent as cut sections or as a block. Cut sections should be of 4µ thickness on positively charged coated superfrost slides, with an accompanying marked H&E stained slide with the tumour area marked on it to guide FISH analysis, along with the % tumour nuclei present.  If sending paraffin blocks, these will be cut and marked by the Leeds Histopathology team prior to genetic analysis. Blocks should contain >20% tumour, and will be returned once the analysis is complete.

Sample requirements - GISTs

See Molecular Oncology section on GIST tumour testing  here for more details.

Sample labelling and referral forms

All referrals must be sent with an appropriate referral form available here. Please use clear patient identifiers on the sample containers, slides and referral form. All patient samples must be labelled with at least three patient identifiers.

Sample transport

When sending samples by post a secure container should be used to conform to current postal regulations, i.e. P650 and UN3373 as applicable. See here for further information.

For the laboratory address and contact details, see the laboratory contacts page.

FISH analysis

FISH tests are available for a wide variety of soft tissue tumour types, mainly using validated commercially available probe sets:

Tumour type

Test type and method

Alveolar rhabdomyosarcoma

FOXO1 gene rearrangement – break apart FISH

FOXO1-PAX gene fusion – single fusion FISH

MYCN amplification – single copy FISH

PAX7 & PAX3 rearrangements – break apart FISH

Ewing’s sarcoma tumours

EWSR1 gene rearrangement – break apart FISH

EWSR1-FLI1 gene fusion – dual fusion FISH

EWSR1-ERG1 gene fusion – dual fusion FISH

Desmoplastic small round cell tumours (DSRCT)

EWSR1 gene rearrangement – break apart FISH

WT1 gene rearrangement – break apart FISH

Clear cell sarcoma

EWSR1 gene rearrangement – break apart FISH

Angiomatoid fibrous histiocytoma

EWSR1 gene rearrangement –break apart FISH

Extraskeletal myxoid chondrosarcoma

EWSR1 gene rearrangement – break apart FISH

NR4A3 gene rearrangement – break apart FISH

Other tumours with EWSR1 rearrangements –

Myoepitheloid tumour, occasional myxoid liposarcoma, slerosing epitheloid fibrosarcoma

EWSR1 gene rearrangement – break apart FISH

Nodular fasciitis, giant cell granulomas, aneurysmal bone cysts, and myositis ossificans

USP6 – break apart FISH

Endometrial stromal sarcoma

JAZF1 rearrangement (low grade tumours) – break apart FISH

YWHAE rearrangement (high grade tumours) - break apart FISH

PHF1 rearrangement - break apart FISH

SMARCB1 (INI1) deletion – single copy FISH

**Synovial sarcoma

SS18 gene rearrangement – break apart FISH

Well-differentiated and dedifferentiated liposarcoma

MDM2 amplification – single copy FISH


Myxoid liposarcoma

FUS-DDIT3 gene rearrangement – break apart FISH

Spindle cell lipoma and well differentiated spindle cell liposarcoma

13q deletion – single copy FISH

Cellular angiofibroma and mammary-type myofibroblastoma

13q deletion – single copy FISH

Alveolar soft part tumour

TFE3 gene rearrangement – break apart FISH

DFSP/giant cell fibroblastoma

COLIA1-PDGFB rearrangement – single fusion FISH

Low grade fibromyxoid sarcoma and sclerosing epitheloid sarcoma

FUS gene rearrangement – break apart FISH

Inflammatory myofibroblastic tumour

ALK gene rearrangement – break apart FISH

Rhabdoid tumours

SMARCB1 (INI1) deletion – single copy FISH

Mesoblastic nephroma/congenital fibrosarcoma

ETV6 gene rearrangement – break apart FISH


PLAG1 gene rearrangement - break apart FISH

Undifferentiated sarcoma/small round cell sarcoma

CIC rearrangement - break apart FISH

Spitzoid tumours

Break apart FISH for rearrangements of either ALK, ROS1, NTRK1 or NTRK3

Ossifying fibromyoid tumours

PHF1 rearrangement - break apart FISH

Myxoinflammatory fibroblastic sarcomas

TGFBR3 rearrangement - break apart FISH

** RNA based analysis using reverse transcriptase PCR (RT-PCR) is also available for detection of SSX2-SS18 rearrangements in FFPE tissue in synovial sarcoma.

Additional FISH probes are available for a number of carcinomas of soft tissues. These include:

TFE3 break apart probe for TFE3 associated renal cell carcinoma

MAML2 break apart probe for mucoepidermoid carcinoma, hidradenoma

ETV6 break apart probe for ETV6 rearrangements in mammary analogue secretory carcinoma

NUTM1 break apart probe for NUT midline carcinoma

FISH reports, turnaround times and prices

Reports can be e-mailed if you supply the Genetics laboratory with an address. A paper copy will only be posted if specifically requested.

The expected turnaround time for pre-labelled FFPE slides is 3 working days. This increases to 5 working days if just blocks are sent.

Prices are available on contact to

Further information on the Leeds Sarcoma Service is also available at:

Future developments, including RT-PCR

The laboratory is keen to introduce new tests as necessary. Newly available FISH probes can be ordered and validated where there is a clinical utility. We are also keen to expand our repertoire of RNA based testing for translocations.