NEIGE. diagnosis In oncogenetics. Nicolas Sévenet 02 juillet
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1 NEIGE g for molecular NExt g generation sequencing diagnosis In oncogenetics Nicolas Sévenet 02 juillet 2012 n.sevenet@bordeaux.unicancer.fr t@b d i f
2 Reports 15 years
3 Next generation sequencing 06/2011 Earray (Agilent technologies) : targeted resequencing of 460 exons of 25 genes Database : Ensembl 62, GRChp37 Repeat Masker UCSC Oligos 120 mers, tiling 2X, +/- 50 bp around exons 2666 oligos duplicated 19 or 38 X oligos total) 0,187 Mb 10/ / experiments NEIGE 1 = 12 samples Positive controls 9 substitutions 5 delins Illumina GAIIX PGT-CGFB Bordeaux Illumina MiSeq GeT; INRA Toulouse NEIGE2 = 30 samples 16positive controls with «complex» mutations 14 samples double blind diagnostic series
4 Capture library selection BRCA1 uc002ict.22 BRCA2 uc001uub.1 BRIP1 uc002izk.1 PALB2 uc002dlx.1 ATM uc001pkb.1 BARD1 uc002veu.2 CHEK2 uc003adt.1 RAD51C uc002iwu.2 PTCH1 uc004avk.3 PTCH2 uc010olf.11 SUFU uc001kvy.1 PIK3CA uc003fjk.2 PTEN uc001kfb.2 MLH1 uc003cgl.2 MSH2 uc002rvy.1 MSH6 uc002rwd.3 MUTYH uc001cnh.2 PMS2 uc003spl.2 APC uc003kpy.33 EPCAM uc002rvx.2 CDH1 uc002ewg.1 STK11 uc002lrl.1 MRE11 uc001peu.2 RAD50 uc003kxi.2 TP53 uc002gij.2 Breast & Ovary cancers Transduction Colon Cancer Other
5 Integrative Genome Viewer (Broad Institute) BRCA2 exons dbsnp Coverage GAIIX reads MiSeq BRCA2 exons
6 Integrative Genome Viewer (Broad Institute) Substitutions BRCA2 3812C>G BRCA2 7759C>T MLH1 2041G>A PTEN 821G>A PTEN A>G PMS2 137G>T GAIIX MiSeq
7 Integrative Genome Viewer (Broad Institute) 1-bp deletion BRCA1 1390delA PTCH1 1299delC PTCH1 279delC GAIIX Number of reads MiSeq
8 Results of the first set of experiment 6 genes in 12 samples Variants attendus (total = 72) GAIIX (CASAVA) MiSeq (MiSeq Rep) polymorphismes substitutions délétions 3 3 insertions/2 1* 2 mutations faux sens 9 9 délétions 3 3 duplication 1 1 delétion insertion 1 1* Variants additionnels (total=151) GAIIX (CASAVA) MiSeq (MiSeq Rep) non vus par précriblage 3 3 nouveaux polymorphismes (hétérozygotes) substitutions délétions 6 6 insertions 4 4 nouveaux polymorphismes (homozygotes) nouveaux polymorphismes (hétérozygotes) en +/ nouveaux polymorphismes p (homozygotes) en +/ off Target (Nb de régions) 9 9 *: mal annoté
9 NEIGE2 16 positive controls with «complex» mutations 4 Gross gene rearrangement (GGR) 8 delins 4 point mutation 14 DNA sample from patients not previously screened Consultations : 07/2011 Double-blind blind study Gaëlle Geneste, Françoise Bonnet : EMMA-Sanger sequencing Delfine Lafon, Nicolas Sévenet : Next-Generation sequencing 100% of concordance NGS seems to be more sensitive than our current screening method (dhplc, EMMA, HRM) due to its detection and identification of homozygous variants Résultats BRCA1 : 1 GGR (del exons included), 2 Unknown Variant BRCA2 : 1 frameshift
10 Positive controls Gross Gene Rearrangement Del ex9 TACSTD1-Ex 1&2 MSH2 Del BRCA1
11 Positive controls delins PTCH1 PTEN MLH1 PTEN Exon 8 Exon 19 c.1807dupa c.2181_2182dupca p.tyr336x p.ile728thrfsx56 Exon 7 c.1019_1022dupagtt p.ile342valfsx96 Intron 4 c.254-1delg MLH1 Exon 16 c.1852_1853delinsgc p.lys618ala
12 Positive controls PTCH1 Mosaicism Germline Deleterious Mutation Exon 10; c.1453delc; p.leu485trpfsx6 Ratio Variant/WT = 98/908 10% Germline polymorphism Exon 12; c.1686c>t; p.ala562ala Reverse sequence Ratio Variant/WT = 322/304 50%
13 Double blind study BRCA1 del : c.5278-?_5592+?del Del BRCA
14 Double blind study Point mutations BRCA1 Exon 24 c g>a BRCA2 Exon 24 c.6209delaaag p.glu2070valfsx10
15 Capture statistics Targeted Bases with minimum 20X coverage (%) Uniquely aligned bases (%) Quality Control Manager, Genespring NGS, Agilent technologies High QC samples Bases of reads within targeted region +/- 200 bp (%) Bases of reads within targeted region (%) Duplicates (%) Low QC samples 10 samples
16 Capture statistics Uniquely aligned bases (%) Bases of reads within targeted region (%) Reads Bases Enrichment Coverage Low QC High QC Metrics 1F18_low 1K24_high Total reads Uniquely mapped reads (#) Unmatched reads (#) Avg read length(reads in targeted regions only) 149,96 150,05 Reads in targeted regions (#) Reads in targeted regions (%) 31,79 65,63 Total bases of reads (includes bases of unmatched reads)(#) Total bases of mapped reads(#) Uniquely Aligned Bases (#) Uniquely Aligned Bases (%) 82,14 87,12 Bases of reads within targeted regions (#) Bases of reads within targeted t regions (%) 28, ,36 Genome targeted (%) 0,01 0,01 Enrichment in targeted regions (fold) 5234, ,61 Average coverage (fold) 240,07 701,97 Median coverage (fold) Duplicates (%) Targeted regions (#) Targeted regions covered by at least 1 read (#) Targeted regions covered by at least 5 read (#) Targeted regions covered by at least 10 read (#) Targeted regions Targeted regions covered by at least 20 read (#) Targeted regions covered by at least 30 read (#) Targeted regions covered by at least 40 read (#) Zero Coverage Targeted Regions(#) 0 0 Zero Coverage Targeted Regions(%) 0 0 Duplicates Duplicates (#) Duplicates (%) 10,32 19,44 Targeted Bases with minimum 20X coverage (%) Bases in targeted regions Bases in targeted region Targeted bases with minimum 1x coverage (%) 99,97 99,99 Targeted bases with minimum 5x coverage (%) 99,87 99,9595 Targeted bases with minimum 10x coverage (%) 99,81 99,9 Targeted bases with minimum 20x coverage (%) 99,61 99,86 Targeted bases with minimum 30x coverage (%) 99,38 99,83 Targeted bases with minimum 40x coverage (%) 99,17 99,8 Targeted bases with minimum 1Kx coverage (%) 0 14,28
17 Molecular genetic lab, Institut Bergonié 200 m 2 technical platform 1 Covaris DNA fragmentation (Bx2 partner) 2 Sample qualification First steps before capture Post-PCR & sequencing area Pre-PCR/nucleic acid extraction PCR area DNA add 3 Library capture Amplification & indexing Multiplexing Library qualification 4 Sequencing by synthesis Primary analysis Secondary analysis PCR mix room
18 Molecular genetic lab, Institut Bergonié NGS : bioinformatic analysis workflow
19 Validation phase Experiments : Future 150 germline DNA samples double blind analyzed before 12/2012 Organization 10 samples multiplexed each week Analysis time < 2 weeks Developments Haloplex design & test (09/2012) V2 capture library design Enrichment for BAP1 & RAD51 family involved in HBOC Enrichment for DDB2 involved in Basal cell carcinoma syndrome Multiplexing of 25 samples with the 7Gb flowcell Expected NGS as the sole molecular diagnostic method from 02/2013
20 Acknowledgments Institut Bergonié Delfine Lafon Françoise Bonnet Équipe oncogénétique Michel Longy Nicolas Kihl Équipe informatique hôpital Integragen Francis Rousseau Bérengère Genin Agilent technologies Juliette Grégoire Hervé Chaulet Didier i Goidin i Florent Brun Plateforme Génome et transcriptome Univ. Bordeaux Segalen Christophe Hubert Jennifer Dupiot Plateforme Génome et transcriptome GeT Inra Toulouse Denis Milan Cécile Donnadieu Gérald Salin Fédéi Frédéric Escudié Jérôme Lluch Emeline Llhuillier Illumina Caroline Thureau Amélie Castro Tiphaine Godefroy
21 Bioinformatic infrastructure
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