Developing Quality Programs for Cell-Free DNA (cfDNA) Extraction from Peripheral Blood

External proficiency testing for histocompatibility and immunogenetics in today and future

The Histocompatibility and Immunogenetics laboratories provide disease association and pharmacogenetic analyses as well as the tests required for transplantation immunology and transfusion medicine. They perform Human Leukocyte Antigen (HLA) genotyping in patients/recipients and potential donor candidates for solid organ and stem cell transplants using various molecular methods, and determine mismatches. In addition, they also perform HLA antibody tests to detect anti-HLA antibodies in patients and flow cross-matches to evaluate donor-recipient compatibility. Evidence-based clinical guidelines have emphasized the importance of laboratory tests in clinical practices for a long time. Understanding the principles of Quality Control and External Quality Assurance is a fundamental requirement for the effective management of Tissue Typing laboratories. When these processes are effectively implemented, errors in routine assays for transplantation are reduced and quality is improved. In this review, the importance of Quality Assurance, Quality control and proficiency testing in Histocompatibility and Immunogenetic testing, the necessity of external proficiency testing (EPT) for accreditation, and existing and potential EPT programmes will be reviewed and evaluated in the light of the literature.

Early diagnosis of ovarian cancer based on methylation profiles in peripheral blood cell-free DNA: a systematic review

Patients diagnosed with epithelial ovarian cancer (OC) have a 5-year survival rate of 49%. For early-stage disease, the 5-year survival rate is above 90%. However, advanced-stage disease accounts for most cases as patients with early stages often are asymptomatic or present with unspecific symptoms, highlighting the need for diagnostic tools for early diagnosis. Liquid biopsy is a minimal invasive blood-based approach that utilizes circulating tumor DNA (ctDNA) shed from tumor cells for real-time detection of tumor genetics and epigenetics. Increased DNA methylation of promoter regions is an early event during tumorigenesis, and the methylation can be detected in ctDNA, accentuating the promise of methylated ctDNA as a biomarker for OC diagnosis. Many studies have investigated multiple methylation biomarkers in ctDNA from plasma or serum for discriminating OC patients from patients with benign diseases of the ovaries and/or healthy females. This systematic review summarizes and evaluates the performance of the currently investigated DNA methylation biomarkers in blood-derived ctDNA for early diagnosis of OC. PubMed's MEDLINE and Elsevier's Embase were systematically searched, and essential results such as methylation frequency of OC cases and controls, performance measures, as well as preanalytical factors were extracted. Overall, 29 studies met the inclusion criteria for this systematic review. The most common method used for methylation analysis was methylation-specific PCR, with half of the studies using plasma and the other half using serum. RASSF1A, BRCA1, and OPCML were the most investigated gene-specific methylation biomarkers, with OPCML having the best performance measures. Generally, methylation panels performed better than single gene-specific methylation biomarkers, with one methylation panel of 103,456 distinct regions and 1,116,720 CpGs having better performance in both training and validation cohorts. However, the evidence is still limited, and the promising methylation panels, as well as gene-specific methylation biomarkers highlighted in this review, need validation in large, prospective cohorts with early-stage asymptomatic OC patients to assess the true diagnostic value in a clinical setting.

Methodology established for the detection of circulating tumor DNA by hybridization capture

Roche's AVENIO ctDNA analysis kits and bioinformatics analysis (the AVENIO system) are accessible to all NGS laboratories. We have developed an approach, namely the Sec-Seq system, and compared the accuracy, sensitivity, repeatability and economic cost between the AVENIO system and the Sec-Seq system. Both methods share the comparable accuracy and sensitivity in detecting the variant allele frequency of 0.0005, while the Sec-Seq system shows better accuracy in detecting the variant allele frequency of 0.001. Furthermore, the Sec-Seq system displays a much better detection sensitivity than the AVENIO system. The Sec-Seq system has satisfactory performance in detecting the rare genetic variants in ctDNA with lower economic cost compared with the AVENIO system.

A novel method for extracting circulating cell-free DNA from whole blood samples and its utility in the non-invasive prenatal test

OBJECTIVE

We verified a magnetic bead-based, simple, and fast method for circulating cell-free DNA (cfDNA) extraction from whole blood samples（CEWB） and characterized its utility in non-invasive prenatal testing (NIPT).

METHOD

We extracted cfDNA from both plasma and whole blood of the patients using CEWB and compared it to that extracted using a Qiagen extraction kit; ddPCR test was used to calculate the fragment size bias. In all, 304 samples were used for NIPT.

RESULTS

The CEWB group [mean ± standard deviation (SD): 4.34 ± 0.41 ng/mL plasma] reported less DNA weight yield than the Qiagen group (4.90 ± 0.50 ng/mL plasma). There was no significant difference between the CEWB group and the Qiagen group in the gene fragments (136 bp: p=0.064 and 420 bp: p=0.534). In a parallel cohort study to characterise the utility of the CEWB method in NIPT, the treatment group extracted by CEWB showed a sensitivity of 100%, a specificity of 99.65%, and a positive predictive value of 95%.

CONCLUSIONS

This study demonstrated that CEWB achieves an acceptable yield of DNA without contamination from genomic DNA. Subsequent clinical experiments in a parallel cohort indicated its utility for NIPT. This article is protected by copyright. All rights reserved.

Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics

While tissue biopsy has for the longest time been the gold-standard in biomedicine, precision/personalized medicine is making the shift toward liquid biopsies. Cell-free DNA (cfDNA) based genetic and epigenetic biomarkers reflect the molecular status of its tissue-of-origin allowing for early and non-invasive diagnostics of different pathologies. However, selection of preanalytical procedures (including cfDNA isolation) as well as analytical methods are known to impact the downstream results. Calls for greater standardization are made continuously, yet comprehensive assessments of the impact on diagnostic parameters are lacking. This study aims to evaluate the preanalytic and analytic factors that influence cfDNA diagnostic parameters in blood and semen. Text mining analysis has been performed to assess cfDNA research trends, and identify studies on isolation methods, preanalytical and analytical impact. Seminal and blood plasma were tested as liquid biopsy sources. Traditional methods of cfDNA isolation, commercial kits (CKs), and an in-house developed protocol were tested, as well as the impact of dithiothreitol (DTT) on cfDNA isolation performance. Fluorimetry, qPCR, digital droplet PCR (ddPCR), and bioanalyzer were compared as cfDNA quantification methods. Fragment analysis was performed by qPCR and bioanalyzer while the downstream application (cfDNA methylation) was analyzed by pyrosequencing. In contrast to blood, semen as a liquid biopsy source has only recently begun to be reported as a liquid biopsy source, with almost half of all publications on it being review articles. Experimental data revealed that cfDNA isolation protocols give a wide range of cfDNA yields, both from blood and seminal plasma. The addition of DTT to CKs has improved yields in seminal plasma and had a neutral/negative impact in blood plasma. Capillary electrophoresis and fluorometry reported much higher yields than PCR methods. While cfDNA yield and integrity were highly impacted, cfDNA methylation was not affected by isolation methodology or DTT. In conclusion, NucleoSnap was recognized as the kit with the best overall performance. DTT improved CK yields in seminal plasma. The in-house developed protocol has shown near-kit isolation performance. ddPCR LINE-1 assay for absolute detection of minute amounts of cfDNA was established and allowed for quantification of samples inhibited in qPCR. cfDNA methylation was recognized as a stable biomarker unimpacted by cfDNA isolation method. Finally, semen was found to be an abundant source of cfDNA offering potential research opportunities and benefits for cfDNA based biomarkers development related to male reproductive health.