NGS, a suitable approach for TP53 screening in CLL?

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1 NGS, a suitable approach for TP53 screening in CLL? Ferran Nadeu 2nd ERIC WORKSHOP ON TP53 ANALYSIS IN CHRONIC LYMPHOCYTIC LEUKEMIA 7-8 November 2017, Stresa (Italy)

2 The Sanger sequencing bottleneck 1 patient + TP53 4 PCR/case* = 20 patients + TP53 4 PCR/case* = 400 patients + TP53 4 PCR/case* = 4 PCRs 100 PCRs 1600 PCRs * Exon 4, exons 5-6, exon 7, exons 8-9.

3 The Sanger sequencing bottleneck 1 patient + TP53, SF3B1, BIRC3, NOTCH1 TP53 and ATM 75 4 PCR/case* PCR/case = 20 patients + TP53, SF3B1, BIRC3, NOTCH1 TP53 and ATM 75 4 PCR/case* PCR/case = 400 patients + TP53, SF3B1, BIRC3, TP53 NOTCH1 and ATM 4 PCR/case* 75 PCR/case = 75 4 PCRs PCRs PCRs Nadeu et al Blood 2016

4 Outline 1. NGS overcomes this Sanger sequencing bottleneck (focus on the Access-Array system) 2. NGS for TP53 analysis: a) Access-Array system b) Comparison of NGS libraries 3. Pros and cons of the use of NGS: a) Sensitivity b) Bioinformatic analysis c) Accuracy d) Possibility to study several genes simultaneously (i.e. panel of genes)

5 4-Primer Amplicon Tagging Access-Array system (Fluidigm) Quick overview Amplicon-based 15 amplicons of 180bp

6 Access-Array system (Fluidigm) Quick overview IFC controller AX 2304 individual reactions chambers (30 nl) Access Array IFC (Integrated Fluidic Circuit)

7 Access-Array system (Fluidigm) Quick overview IFC BioMark controller HDAX Access Array IFC (Integrated Fluidic Circuit)

8 Access-Array system (Fluidigm) Quick overview IFC controller AX Access Array IFC (Integrated Fluidic Circuit)

9 Access-Array system (Fluidigm) Quick overview Clean-up Access Array IFC (Integrated Fluidic Circuit)

10 Access-Array system Up to 480 amplicons Multiplexing 2nd PCR done in a 96-well plate in a or al ther ocycler Figures adapted from Access-Array System User Guide (Fluidigm).

11 Outline 1. NGS overcomes this Sanger sequencing bottleneck (Access-Array system) 2. NGS for TP53 analysis: a) Access-Array system b) Comparison of NGS libraries 3. Pros and cons of the use of NGS: a) Sensitivity b) Bioinformatic analysis c) Accuracy d) Possibility to study several genes simultaneously

12 Coverage/depth in NGS A T G C C T G A T G Coverage A T G C C T G T G C C T G A T G C C T G A G C C T G A T G C C T G A T A T G C C T G Spencer et al J Mol Diagn 2014

13 Access-Array system for TP53 analysis

14 Access-Array system (Fluidigm) Coverage Nadeu et al Blood 2016

15 Access-Array system (Fluidigm) Coverage A coverage >1000x was obtained in >85% of the sequence in 95% of the samples Nadeu et al Blood 2016

16 Comparison of NGS libraries for TP53 screening Capture hybridization-based Amplicon-based Acces-Array - Flluidigm AmpliSeq - ThermoFisher (Ion Torrent) Genereadv2/QIASeq - QIAgen Multiplicom - Agilent TruSeq Custom Amplicon - Agilent TruSeq Custom Amplicon DS Agilent NexteraXT - Illumina SureSelect - Agilent SeqCap EZ System -Nimblegen/Roche xgen Lockdown - IDT Haloplex Agilent Nextera XT - Illumina

17 Comparison of NGS libraries for TP53 screening Amplicon-based Capture hybridization-based

18 Outline 1. NGS overcomes this Sanger sequencing bottleneck (Access-Array system) 2. NGS for TP53 analysis: a) Access-Array system b) Comparison of NGS libraries 3. Pros and cons of the use of NGS: a) Sensitivity b) Bioinformatic analysis c) Accuracy d) Possibility to study several genes simultaneously

19 Pros and cons of NGS: Sensitivity Nadeu et al Blood 2016

20 Pros and cons of NGS: Sensitivity Rossi et al Blood 2014: 30% (15/50) patients carried only subclonal TP53 mutations 8% (4/50) patients carried isolated del(17p) NGS: 92% (46/50) of patients with TP53 alterations Sanger + FISH: 70% (35/50) of patients with TP53 alterations Nadeu et al Blood 2016: 34% (16/47) patients carried only subclonal TP53 mutations 9% (4/47) patients carried isolated del(17p) NGS: 91% (43/47) of patients with TP53 alterations Sanger + SNP array: 66% (31/47) of patients with TP53 alterations

21 Pros and cons of NGS: Bioinformatic analysis Spencer et al J Mol Diagn 2014 Sequencing error rate: Platform Chemistry Read length Genomic context...

22 Pros and cons of NGS: Bioinformatic analysis SVC Nadeu et al Blood 2016

23 Pros and cons of NGS: Bioinformatic analysis SVC Nadeu et al Blood 2016

24 VAF % VAF <12% Pros and cons of NGS: Accuracy (Sanger sequencing on 302 regions/genes detected 69 mutations) 100% specificity and 100% sensitivity (43 cases carrying high frequency mutations were subjected to a second round of NGS) 100% reproducibility 88 mutations verified by AS-PCR 77 mutations verified by a 2nd round of NGS 13/13 were also verified by AS-PCR Verification: AS-PCR or 2nd run of NGS After a non-stringent custom filtering 75% specificity < % of VAF Nadeu et al Blood 2016

25 Time Euros Benefit Pros and cons of NGS: Scalability n Genes targeted Precision medicine Cost Hands-on 0 1 n Number of genes targeted

26 Pros and cons of NGS: Panel of genes Nadeu et al Leukemia 2017

27 Pros and cons of NGS: Panel of genes Nadeu et al Leukemia 2017 Guièze et al Blood 2015

28 Take home messages NGS libraries and TP53 Easy design Short hands-on time Compatible with multiple sequencing platforms (Illumina, Ion Torrent, etc.) Percentage of amplification success 95%, and good accuracy (>90% mapping to target) Uniform coverage Highly sensitive and reproducible approach to detect mutations in TP53 and other genes in clinical samples NGS in the clinics Many different library approaches work well. We may face a CLL (or lymphoma) panel rather than analyzing an individual gene Which genes? How we validate it in larger cohorts? Should we sequence the normal DNA? It could be useful for the study of ATM mutations and for the variant calling. Bioinformatic approach (still not well defined) A gold-standard bioinformatic pipeline for deep-targeted NGS is not yet stablished. Limited accuracy in the detection of clinically relevant very low VAF mutations. Verification may be needed. Feasible identification of CNA [del(17p), del(11q)] from the same NGS data is still pending. should all this be uniform for the different centers?

29 Acknowledgment Elías Campo Cristina Capdevila Sara Guijarro Julio Delgado Guillem Clot Anna Enjuanes Magda Pinyol Helena Suárez-Cisneros Montse Sanchez Laura Pla Thank you for your attention!

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