Transcript Next Generation Sequencing Approach to Desmoid Tumors

Next Generation Sequencing
Approach to Desmoid Tumors
Matt van de Rijn
Which questions do we hope to
address?
• Can we distinguish aggressive desmoids from
those that are indolent?
• Can we distinguish recurrent desmoid tumors
from scars?
What do we need to know about
biology?
• Each human cell contains a nucleus where the
information for >20,000 genes resides
• Previously we could study genes one at a time
• Now can look at all of them simultaneously
Matt’s (simple) view of the cell:
DNA
RNA
mRNA
protein
Matt’s (simple) view of the cell:
In each human cell:
DNA: 3 billion basepairs
mRNA: >20,000 genes
What is “next generation
sequencing”?
• New technology in molecular biology that
allows us to do work that used to take several
years in one week
– First human genome took 10 years to sequence at
a cost of >2 billion dollars
– Now can be done within a week at <$5,000
Dramatic shift in approach:
Rather than sequencing long stretches of DNA (~700 bases)
in relatively few experiments, we now sequence millions of
very short fragments and let the computer figure out the
overlap
3SEQ

Uses Illumina Genome Analyzer for precise
quantification of genome-wide mRNA expression
levels on both frozen tissues and paraffin blocks
PLoS One 2010, 5:e8768)
What’s a Paraffin Tissue
Block?
Gene expression profiling by 3SEQ
RNAseq
DNAseq
Applications of paraffin block-based
“3SEQ”
• Gene expression profiling
-Characterization of fibroblastic lesions
-Comparing desmoid tumors to scars
• Study of lncRNA expression as potential
biomarker
Fibromatosis
Elastofibroma
collagenous fibroma (6)
elastofibroma (4)
infantile digital fibromatosis (3)
palmar fibromatosis (8)
nasopharyngeal angiofibroma (6)
fibroma of tendon sheath (4)
nodular fasciitis (6)
dermatofibrosarcoma protuberans (4)
desmoid type fibromatosis (7)
solitary fibrous tumor (5)
Fibr Tendon Sheath
Sol Fibrous tumor
We no longer rely on rare frozen tissue specimens and can use readily available
paraffin blocks
Goal:
To generate a clinically relevant predictor of desmoid behavior
Plan:
Compare desmoids with known aggressive behavior with those that never recurred
and determine which markers can be used to distinguish them
Applications of paraffin block-based
“3SEQ”
• Gene expression profiling
-Characterization of fibroblastic lesions
-Comparing desmoid tumors to scars
• Study of lncRNA expression as potential
biomarker
Problem:
When a desmoid comes back, it is difficult to tell recurring desmoid
from the scar of the previous surgery
Preliminary studies
already identify possible
markers
Plan:
Extend these studies
and validate findings
Applications of paraffin block-based
“3SEQ”
• Gene expression profiling
-Characterization of fibroblastic lesions
-Comparing desmoid tumors to scars
• Study of lncRNA expression as potential
biomarker
Matt’s (simple) view of the cell:
lncRNA
DNA
RNA
mRNA
protein
lncRNA’s detected by 3SEQ as
specifically expressed in different
malignancies
Plan:
Include desmoid tumors in this
series to look for biologically relative
lncRNAs
Laboratory:
Xiangqian Guo
Sushama Varma
Shirley Zhu
Matt van de Rijn
Rob West
Santosh Gupta
Trip Sweeney
Erna Forgo
Stanford Oncology:
Kristen Ganjoo
Stanford Surgery:
Raffi Avedian
DANA-Farber Oncology:
Suzanne George
Thank you!