Implementation of BRCA Oncomine panel for germline and somatic variant analysis
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1 Tagliafico ESHG 2017.pptm 3.2% 03/03/2017 Implementation of BRCA Oncomine panel for germline and somatic variant analysis Enrico Tagliafico MD, PhD, Modena, Italy Center for Genome Research University of Modena and Reggio Emilia, Italy Clinical Genomics Laboratory University Hospital, Modena, Italy
2 Introduction Tagliafico ESHG 2017.pptm 6.5% 03/03/2017 The Lab # of samples processed/year Oncology (NGS) 500 Rare Diseases (NGS) 300 Microbiology/Virology (Sanger) 1700 Cytogenomics (CMA) 250 Personnel Biologists / Biotechnologist 5 Bioinformaticians 1 Physicians 3
3 Introduction Tagliafico ESHG 2017.pptm 9.7% 03/03/2017 The Lab Major Equipment: NGS: Ion Torrent PGM Ion Torrent S5 Illumina MiSeq DX Sanger: 3130xL Genetic Analyzer 3500xL Dx Genetic Analyzer Cytogenomics: Affymetrix GeneChip System Automation: IonChef 2x Hamilton Starlet 2x QIAgility
4 Workflow Tagliafico ESHG 2017.pptm 12.9% 03/03/2017 Sample Library and template preparation Ion HiQ TM Sequencing Data Analysis FFPE & Blood Ion Chef TM or manual + Ion One Touch Ion PGM TM System Ion Reporter TM Software
5 Ion BRCA Community panel vs Oncomine BRCA Tagliafico ESHG 2017.pptm 16.1% 03/03/2017 Total sample size Ion Ampliseq BRCA1 and BRCA2 Community panel ( ) Oncomine BRCA Research Panel (2017) Manual Manual + Ion Chef Ion Chef Manual Manual + Ion Chef Ion Chef Germline analysis Somatic analysis Tot samples Panel Characteristics Ion Ampliseq BRCA1 and BRCA2 Community panel Amplicons Pools 3 2 Library automation NO YES Template automation YES YES Oncomine BRCA Research Panel
6 Germline Analysis: Community Panel vs Oncomine Tagliafico ESHG 2017.pptm 19.4% 03/03/ % 75% Amplicons (%) 50% 25% BRCA1 and BRCA2 Community Panel Oncomine BRCA Research Assay 0% 20X 50X 100X 250X 500X 750X 1000X Mean coverage depth=500x
7 Germline Analysis: Community Panel vs Oncomine BRCA1 and BRCA2 Community panel (838 runs) Tagliafico ESHG 2017.pptm 22.6% 03/03/2017 Oncomine BRCA Research Panel (216 runs) 100% 100% 95% 95% 90% 90% 85% 85% Amplicons ( %) 80% 75% 70% Amplicons (% ) 80% 75% 70% 65% 65% 60% 60% 55% 55% 50% % Mean Coverage (#reads) Mean coverage (#reads) coverage>50x coverage>100x coverage >50X coverage >100X
8 Oncomine BRCA performances upon different experimental settings Tagliafico ESHG 2017.pptm 29% 03/03/2017 #samples/chip 8/316 16/316 8/318 16/318 32/318 #RUNS Analysis Germline Germline Somatic Germline Germline Library preparation Ion Chef Ion Chef Ion Chef Ion Chef Ion Chef Template+chip loading Ion Chef Ion Chef Ion Chef Ion Chef Ion Chef ISP loading 82% 85% 89% 92% 91% Total reads 3.36M 3.57M 5.28M 5.62M 5.56M Polyclonal 32% 31% 41% 42% 54% Usable reads 65% 67% 53% 54% 42% Statistics per sample Mapped Reads On Target 95.4% 95.6% 95.3% 95.3% 95.4% Amplicons>50X 99.9% 99.9% 100% 100% 100% Uniformity 98.4% 99.6% 99.5% 99.9% 99.9% Mean Depth
9 Oncomine BRCA performances upon different experimental settings Tagliafico ESHG 2017.pptm 29% 03/03/2017 #samples/chip 8/316 16/316 8/318 16/318 32/318 #RUNS Analysis Germline Germline Somatic Germline Germline Library preparation Ion Chef Ion Chef Ion Chef Ion Chef Ion Chef Template+chip loading Ion Chef Ion Chef Ion Chef Ion Chef Ion Chef ISP loading 82% 85% 89% 92% 91% Total reads 3.36M 3.57M 5.28M 5.62M 5.56M Polyclonal 32% 31% 41% 42% 54% Usable reads 65% 67% 53% 54% 42% Statistics per sample Mapped Reads On Target 95.4% 95.6% 95.3% 95.3% 95.4% Amplicons>50X 99.9% 99.9% 100% 100% 100% Uniformity 98.4% 99.6% 99.5% 99.9% 99.9% Mean Depth
10 Oncomine BRCA: somatic variant detection Tagliafico ESHG 2017.pptm 35.5% 03/03/2017
11 Oncomine BRCA: somatic variant detection Tagliafico ESHG 2017.pptm 38.7% 03/03/2017
12 Oncomine BRCA: somatic variant detection Tagliafico ESHG 2017.pptm 41.9% 03/03/2017 FORWARD REVERSE Test sample after Noise Subtraction & Submission Test sample (i.e. somatic) Control sample (i.e. normal germline)
13 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 45.2% 03/03/2017 Data from 3 runs with 40 samples from our lab (already tested by MLPA for CNV) were analyzed in blind by Thermofisher R&D using the new Ion Reporter CNV tool on germline samples RUN Nr. of samples Nr. of CNV Concordance with MLPA 2016_RUN42 16pz 3 100% 2017_RUN4 16pz 1 100% 2017_RUN7 8pz 2 100% TOTAL 40 6
14 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 48.4% 03/03/2017 Representative Normal Sample: 2016 Run42 Barcode 126
15 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 51.6% 03/03/ Run 42 Barcode 108: BRCA1 Exon18-20 Deletion
16 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 54.8% 03/03/ Run 42 Barcode 108: BRCA1 Exon18-20 Deletion: MLPA
17 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 58.1% 03/03/ Run 7 Barcode 122: BRCA1 Exon2 Deletion
18 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 61.3% 03/03/ Run 7 Barcode 122: BRCA1 Exon2 Deletion: MLPA
19 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 64.5% 03/03/ Run 7 Barcode 123: BRCA1 Exon 4-9 Deletion
20 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 67.7% 03/03/ Run 7 Barcode 123: BRCA1 Exon 4-9 Deletion: MLPA
21 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 71% 03/03/ Run 42 Barcode 105: BRCA2 Exon 4-26 Duplication
22 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 74.2% 03/03/ Run 42 Barcode 105: BRCA2 Exon 4-26 Duplication: MLPA
23 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 77.4% 03/03/ Run 42 Barcode 105: BRCA2 Exon 4-26 Duplication: The tandem duplication description
24 Oncomine BRCA: CNV detection Tagliafico ESHG 2017.pptm 80.6% 03/03/ Run 42 Barcode 105: BRCA2 Exon 4-26 Duplication: The tandem duplication description A B C D 4 kb 3 kb
25 Processing times Tagliafico ESHG 2017.pptm 83.9% 03/03/2017 Times to data (16 samples/2 chips) AmpliSeq BRCA1 and BRCA2 Community mpliseq BRCA1 and BRCA2 Community Panel (3 pools) (Manual+IonOneTouch) Panel (3 pools) (Manual+IonOneTouch) Day 1 Day 2 Day 3 Day 4 Night 4 AmpliSeq BRCA1 and BRCA2 Community AmpliSeq BRCA1 and BRCA2 Community Panel (3 pools) (Manual+Chef) Panel (3 pools) (Manual+IonChef) Day 1 Night 2 Day 3 & Night 3 Oncomine BRCA Research Research Assay (2 pools) Assay (Chef+Chef) (2 pools) (Chef+Chef) Day 1 & Night 1 Night 2 Day 3 & Night HOURS Library preparation Template enrichment & chip loading PGM cleaning, Sequencing run, Raw data processing Data Analysis & Variant calling
26 Processing times Tagliafico ESHG 2017.pptm 87.1% 03/03/2017 Hands-on times (16 samples/2 chips) AmpliSeq BRCA1 and BRCA2 Community Seq BRCA1 and BRCA2 Community Panel (3 pools) (Manual+IonOneTouch) Panel (3 pools) (Manual+IonOneTouch) AmpliSeq BRCA1 and BRCA2 Community AmpliSeq BRCA1 and BRCA2 Community Panel (3 pools) (Manual+Chef) Panel (3 pools) (Manual+IonChef) 9 0, Oncomine BRCA Oncomine BRCA Research Research Assay (2 pools) Assay (Chef+Chef) (2 pools) (Chef+Chef) 1 0, HOURS Library preparation Template enrichment & chip loading PGM cleaning, Sequencing run, Raw data processing Data Analysis & Variant calling
27 Processing times Tagliafico ESHG 2017.pptm 90.3% 03/03/2017 Times to report AmpliSeq BRCA1 and BRCA2 Community mpliseq BRCA1 and BRCA2 Community Panel (3 pools) (Manual+IonOneTouch) Panel (3 pools) (Manual+IonOneTouch) 4,5 0,5 2,5 1,5 0,5 AmpliSeq BRCA1 BRCA1 and BRCA2 and Community BRCA2 Panel (3 pools) Community (Manual+Chef) Panel (3 pools) (Manual+IonChef) 3,5 0,5 2,5 1,5 0,5 Oncomine BRCA Research Research Assay (2 pools) (Chef+Chef) Assay (2 pools) (Chef+Chef) 3,5 0,5 0,5 0, DAYS NGS Interpretation Sanger for low coverage and variant validation MLPA Reporting
28 Summary Tagliafico ESHG 2017.pptm 93.5% 03/03/2017 Oncomine TM BRCA Research Assay: High uniformity of coverage across all target regions (99.5%) 100% of target regions with at least 50X at low mean depth per sample Totally automated workflow (time saving and reproducibility) Suitable for both germline and somatic analysis Detection of 5% and below allele burden for somatic mutation Detection of CNV in germline sample Allow to report validated results within 5 days
29 Acknowledgements Tagliafico ESHG 2017.pptm 96.8% 03/03/2017 Elena Tenedini Isabella Bernardis Lucia Artuso Marco Marino Laura Cortesi Rosella Petraroli Andrea Lucchetti Chiara Magnanini Giorgio Pea Fabio Raffaldi Jon Sherlock Charles Scafe
30 Tagliafico ESHG 2017.pptm 100% 03/03/2017 Thermo Fisher Scientific and its affiliates are not endorsing, recommending, or promoting any use or application of Thermo Fisher Scientific products presented by third parties during this seminar. Information and materials presented or provided by third parties are provided as-is and without warranty of any kind, including regarding intellectual property rights and reported results. Parties presenting images, text and material represent they have the rights to do so.
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