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130314_bjori

To reveal the role of additional genetic variants in endometrial cancer of Lynch syndrome patients we used targeted exome sequencing. In our 480kB panel and a pilot of 15 patients we found 20 putative variants in exonic regions.
by

Balazs Jori

on 5 November 2013

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Transcript of 130314_bjori

High quality / quantity
Amplification
Purification
Hybridization
Fragmentation
Since wide variation in endometrial cancer risk
Additional rare genetic variants
HYPOTHESIS
Targeted Exome Sequencing
to Detect Additional Genetic Factors of Endometrial Cancer in Lynch Syndrome

Balázs Jóri
Maastricht University, The Netherlands
Lynch syndrome
25-70% colorectal cancer
25-70% endometrial cancer
3-28% ovarian cancer
Inherited condition
Autosomal dominant
Mutations in mismatch repair genes
Genetic counseling
Increased cancer risk
Germ line DNA biobank
Targeted Exome Capture
Capture of Region Of Interest
Next Generation Sequencing
Bioinformatic analysis
average per patient
Next Generation Sequencing
with Illumina HiSeq
with Haloplex
6.7M-20.2M seq./sample
89% High Quality
93% Duplicate reads
Targeted capture
90% of Region of Interest (ROI)
at least 20x with unique sequences
NextGene software package
Library
15 samples
150-650 bp dsDNA products
Incl. barcodes + sequencing motifs
Standardized for NGS
Strategy
CAPTURE
NGS
ANALYSIS
DESIGN
Results
Putative hits
Validation
Department of
Obstetrics and
Gynaecology
Department of Clinical
Genomics
Gynaecology
Endometrium Research Group
Clinical Genetics
Genome Centre
Roy Kruitwagen
Toon van Gorp
Andrea Romano
Bert Delvoux
Encarna Gómez-Carcía
Rien Blok
Rick Kamps
Bart de Koning
Fons Stassen
Thank you for your attention!
Founder origin of
MSH6 mutation
Conclusions
11
183
867
172
1050
found variants
rare variants
coding rare
non exonic
in dbSNP
capture properties: 480kB, 2069 regions, 154 genes
Future perspectives
Validation
technical (Sanger)
biological (relevance)
Other variants
splicing site
large deletions
Technical pipeline
20 putative coding variants
1 patient
11 rare coding
15 patients
37 rare coding
20
amino acid changing variants
Full transcript