Abstract 4976
Background
Recent studies have identified a complex but definitive role of germline DNA in cancer predisposition. Archived formalin-fixed paraffin-embedded (FFPE) samples from cancer patients are vital for several molecular and genomic studies. For retrospective studies investigating gene mutations, loss of heterozygosity and copy number changes, non-tumoral FFPE samples can be used as a source of germline DNA. The key challenge with FFPE DNA purification is usually due to the fixation process, which causes cross-linking and fragmentation of FFPE DNA. In spite of the development of several techniques for FFPE DNA extraction, automated extraction can provide efficient DNA purification with the least hands-on and the least contamination. We compared two different automated approaches with special focus on DNA yield and quality using the DNA integrity number (DIN) value.
Methods
The study was carried out on 48 non-tumoral FFPE samples from cancer patients. Two FFPE pretreatment methods were used simultaneously: GeneRead DNA FFPE Kit (removes cytosine deamination artifacts from FFPE) and QIAsymphony DSP DNA Kit. After the initial pretreatment, the extraction step was performed using the automated QIAsymphony SP instrument for both methods. Finally, the purified DNA was assessed using TapeStation for measuring the concentration and DIN value.
Results
The median DNA concentration using the GeneRead method was 13.85 ng/ul (1.13-111 ng/ul), while for QIAsymphony DSP the median DNA was 5.3 ng/ul (1.07-156 ng/ul). Of the total 48 FFPE samples, 40 purified by GeneRead and 29 purified by QIAsymphony DSP have DNA concentrations above the functional quantitative range of DIN. The median DIN value was 3.3 and 4.1 for GeneRead and QIAsymphony DSP, respectively.
Conclusions
This study demonstrates that the FFPE pretreatment step has an effect on automated DNA extraction. Highly efficient extraction of FFPE DNA based solely on quantity can be misleading as the DNA may be highly fragmented. The removal of cytosine deamination artifacts from FFPE samples can enhance DNA purification with less degradation. This may also have a crucial influence on the downstream molecular approaches such as DNA sequencing.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The author.
Funding
Has not received any funding.
Disclosure
The author has declared no conflicts of interest.
Resources from the same session
1054 - Safety, efficacy, and pharmacokinetic (PK) profile of cosibelimab, an anti‐PD‐L1 antibody, in patients (pts) with advanced cancers
Presenter: Philip Clingan
Session: Poster Display session 1
Resources:
Abstract
4264 - A Phase I study of tinostamustine in patients (pts) with advanced solid tumours
Presenter: Alain Mita
Session: Poster Display session 1
Resources:
Abstract
3811 - Lurbinectedin (LUR) in combination with Irinotecan (IRI) in patients (pts) with advanced solid tumors
Presenter: Santiago Ponce Aix
Session: Poster Display session 1
Resources:
Abstract
1311 - A phase I study of varlitinib (VAR; ASLAN001) an oral pan-HER tyrosine kinase inhibitor (TKI) combined with mFOLFIRI chemotherapy in advanced solid tumors
Presenter: Aaron Tan
Session: Poster Display session 1
Resources:
Abstract
3482 - Phase I study of lapatinib and trametinib in patients with KRAS mutant colorectal, non-small cell lung and pancreatic cancer
Presenter: Sanne Huijberts
Session: Poster Display session 1
Resources:
Abstract
4749 - Pharmacokinetic (PK) and updated survival data from the Canadian Cancer Trials Group IND.226 study of durvalumab ± tremelimumab in combination with platinum-doublet chemotherapy
Presenter: Desiree Hao
Session: Poster Display session 1
Resources:
Abstract
4530 - A Phase 2a clinical trial combining ALRN-6924 and palbociclib for the treatment of patients with tumors harboring wild-type p53 and MDM2 amplification or MDM2/CDK4 co-amplification
Presenter: Funda Meric-Bernstam
Session: Poster Display session 1
Resources:
Abstract
4280 - Updated Efficacy and Safety of Entrectinib in Patients with NTRK Fusion-Positive Tumors: Integrated Analysis of STARTRK-2, STARTRK-1 and ALKA-372-001
Presenter: Christian Rolfo
Session: Poster Display session 1
Resources:
Abstract
6144 - An international randomized cross-over bio-equivalence study of oral paclitaxel + HM30181 compared with weekly intravenous (IV) paclitaxel in patients with advanced solid tumors
Presenter: Christopher Jackson
Session: Poster Display session 1
Resources:
Abstract
4228 - Clinical Evaluation of Drug-Eluting Bead Transcatheter Arterial Chemoembolization(D-TACE) versus Conventional TACE in Treatment of unresectable Hepatocellular Carcinoma
Presenter: Yi Chen
Session: Poster Display session 1
Resources:
Abstract