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
4883 - A New Population Model Validated Pharmacokinetic Similarity of HLX01 and Rituximab in B-Cell Lymphoma
Presenter: Yuankai Shi
Session: Poster Display session 1
Resources:
Abstract
4908 - Efficacy of salvage therapy in the treatment of Helicobacter pylori-positive gastric low-grade mucosa-associated lymphoid tissue lymphoma
Presenter: Sung-Nam Lim
Session: Poster Display session 1
Resources:
Abstract
2360 - Mutational analysis of extranodal marginal zone lymphoma using next generation sequencing
Presenter: Seok Jae Huh
Session: Poster Display session 1
Resources:
Abstract
2430 - Clinical features, treatment and outcomes of colon and rectum mucosa-associated lymphoid tissue (MALT) lymphoma: Literature reviews published in English between 1993 and 2017
Presenter: Jeong Yeon Kim
Session: Poster Display session 1
Resources:
Abstract
4654 - Splenic marginal zone lymphoma: clinical characteristics and prognostic factors in a series of 52 patients
Presenter: Guldane Cengiz Seval
Session: Poster Display session 1
Resources:
Abstract
1732 - Safety and efficacy of Bendamustine and Rituximab (BR) regimen in Indian Chronic Lymphocytic Leukemia patients
Presenter: Ajay Gogia
Session: Poster Display session 1
Resources:
Abstract
5784 - N-terminal B-type natriuretic peptide (NT-proBNP) as an independed prognostic marker for patients with newly diagnosed multiple myeloma complicated by dialysis-dependent renal failure
Presenter: Sergey Semochkin
Session: Poster Display session 1
Resources:
Abstract
836 - The first-line effect of Bortezomib-based Therapy on Clinical Outcomes for Taiwanese Patients with multiple myeloma
Presenter: Ching-Liang Ho
Session: Poster Display session 1
Resources:
Abstract
2085 - Impact of Donor Lymphocyte Infusion in Relapsing Myeloid Neoplasms Post Allogeneic Hematopoietic Stem Cell Transplantation
Presenter: Hanafy Hafez
Session: Poster Display session 1
Resources:
Abstract
6079 - Invasive fungal diseases in patients with Hodgkin’s lymphoma before and after allogeneic hematopoietic stem cell transplantation
Presenter: Marina Popova
Session: Poster Display session 1
Resources:
Abstract