Ultrasensitive detection of TKI resistant mutations using Illumina NGS in chronic myeloid leukemia patients

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F18%3A00068763" target="_blank" >RIV/65269705:_____/18:00068763 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14740/18:00103392

Result on the web

<a href="http://phdretreat.ceitec.cz/ceitec-phd-and-postdoc-retreat-2018/" target="_blank" >http://phdretreat.ceitec.cz/ceitec-phd-and-postdoc-retreat-2018/</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Ultrasensitive detection of TKI resistant mutations using Illumina NGS in chronic myeloid leukemia patients

Original language description

The discovery of tyrosine kinase inhibitors (TKI) brought a revolution in the manage-ment of chronic myeloid leukemia (CML), increasing survival and life-quality of pa-tients. However, mutations in kinase domain (KD) of BCR-ABL1 may occur and result in therapy failure. Although KD mutation screening is routinely done by Sanger sequenc-ing (detection limit &gt;20%VAF), numerous studies showed enhanced sensitivity (&lt;15%) using next generation sequencing (NGS). Majority of NGS studies used two rounds of PCR to amplify KD sequence. Such approach may introduce PCR-based errors, restrict-ing the detection limit to &gt;1%. We aimed to develop new Illumina-based one-round PCR amplification protocol and bioinformatics pipeline (BI) with sensitivity LESS-THAN OR EQUAL TO1%. Our protocol was tested on 6 healthy controls (HC) and 34 retrospective samples from 13 CML patients with TKI resistant mutations (15 FUP samples at the time of SS muta-tion detection, 11 FUP samples collected 1-18 month before SS mutation detection, 8 diagnostic samples). The performance was assessed in comparison to routinely used SS. The BI was designed with respect to biological input (cDNA), allowing detection of SNVs with 0.1%VAF. Overall, no mutations were detected in ABL1 KD of HC, showing decreased background noise. NGS detected mutations in 100% of FUP samples previously positive by SS, showing high correlation of VAF (r2=0.96) and confirming its specificity. Due to high sensitivity, Illumina-based NGS analysis could detect mutations in 24% more samples than SS and proved to be suitable for earlier detection of TKI resistant mutations at very low frequencies (GREATER-THAN OR EQUAL TO0.1 %).

Czech name

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Czech description

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Type

O - Miscellaneous

CEP classification

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OECD FORD branch

10606 - Microbiology

Project

<a href="/en/project/NV17-30397A" target="_blank" >NV17-30397A: Mutational screening of primitive cell populations in chronic myeloid leukemia: BCR-ABL1 and beyond</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů