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Prenatal Diagnosis and Screening for Aneuploidy
Published in Vincenzo Berghella, Obstetric Evidence Based Guidelines, 2022
Sarah Harris, Angie Jelin, Neeta Vora
FTS with NT measurement. Cell-free DNA screening, although detection rates are unknown.Ultrasound findings in fetusCystic hygromaThickened nuchal fold (≥6 mm) at 16–23 weeksCHD (20%; usually left side: Coarctation, aortic stenosis, bicuspid aortic valve, left hypoplastic heart)Renal anomalies (60%)Hydrops or some hydropic changes (pleural effusion, ascites)Amniotic fluid: Occasionally oligohydramniosPlacenta: Normal
Approach to women with a previous child with a genetic disorder
Published in Minakshi Rohilla, Recurrent Pregnancy Loss and Adverse Natal Outcomes, 2020
The cell-free DNA test is a screening test best suited for women who have an escalated risk of having a child with a genetic disorder, such as women who already have a baby with a chromosomal disorder. This process has certain limitations. Any female carrying more than one baby is advised against undergoing this test. Second, it does not inspect for neural tube defects. To detect these disorders, an additional screening test is necessary. Also, although it is highly accurate in identifying chromosomal issues in high-risk women, it is not as accurate as diagnostic tests. Hence, it is advised to follow up a positive test result with a diagnostic test.
Investigation of DNA Methylation in Autosomal Dominant Polycystic Kidney Disease
Published in Jinghua Hu, Yong Yu, Polycystic Kidney Disease, 2019
Circulating cell-free DNA (ccfDNA) is DNA that is found in the bloodstream and can be captured as a biological sample, such as blood or serum, for diverse analysis. In healthy individuals, the quantity of ccfDNA is typically low,37 ranging from 1.8 to 44 ng/mL45 but these levels can increase following exercise.45,46 In diseased conditions, such as tumors, the levels of ccfDNA could increase depending on the stage of the disease.47 In addition, the amount of ccfDNA also depends on the activity of DNase enzymes in the circulatory system. In cancer studies for example, it has been shown that the increase in ccfDNA concentration is related to a decrease in DNase I enzyme activity.48
Updates on the profile of GenMark’s ePlex blood culture identification fungal pathogen panel
Published in Expert Review of Molecular Diagnostics, 2023
Masako Mizusawa, Karen C Carroll
Broad-range PCR and sequence-based assays use whole blood specimens and can identify a very wide range of fungal pathogens without waiting for culture growth. However, those tests are labor-intensive, often use expensive reagents and/or instrumentation and require technical expertise which is not yet suitable for routine clinical use. The direct detection of cell-free DNA in plasma by metagenomic next generation sequencing (mNGS) can also identify a very wide range of fungal pathogens and the test indications are not limited to blood stream infections. Current literature cites its use in the diagnosis of fungal pneumonia in adult and pediatric patients [58,59]. However, test interpretations are complex and require clinical context. The Karius cell-free DNA assay is also costly ($2500 per sample) and is only available through the manufacturer. Other mNGS methods currently require time-consuming and labor-intensive workflows. Other sequence-based assays including mNGS are making their way into academic institutions and reference labs that care for growing numbers of severely immunocompromised hosts such as patients with hematological malignancies and transplant recipients. The current major challenge with these approaches is in results interpretation, as the fungi detected may be saprophytes or could in fact be opportunistic pathogens causing disease. The other problem relates to not having an isolate for antifungal susceptibility testing.
Diagnostic accuracy of circulating-free DNA for the determination of hepatocellular carcinoma: a systematic review and meta-analysis
Published in Expert Review of Molecular Diagnostics, 2023
Wang Yinzhong, Wang Miaomiao, Tian Xiaoxue, Wang Qian, Qi Meng, Lei Junqiang
Recently, liquid biopsy-based cell-free DNA (cfDNA) has provided a noninvasive method to detect and diagnose cancer at an early stage [7]. Cell-free DNA is extracellular DNA released into the circulation by apoptotic or necrotic cancer cells that carries tumor genomic alterations and somatic gene mutations. Therefore, it can be used as a circulating marker to detect disease changes, treatment response, tumor burden, and disease recurrence [8–11]. This approach not only detects the molecular dynamics of disease and tumor development that cannot be identified by imaging but also reveals the characteristics of the entire tumor, whereas tissue biopsy is limited by heterogeneity within the tumor. Previous studies have shown that changes in cfDNA levels can be detected in the early stages of HCC [12,13]. Therefore, the analysis of abnormal cfDNA levels, gene mutations, abnormal methylation, and microsatellite alterations can provide valuable information about disease progression [14,15]. Numerous studies have demonstrated the potential of cfDNA as a routine diagnostic marker for HCC [16–18]. However, the results of published studies have not been standardized. Therefore, we retrospectively analyzed the relevant literature in the present study to systematically evaluate the diagnostic potential of cfDNA as a noninvasive biomarker for HCC that can be used to provide evidence-based clinical support to affected patients.
Creating standards for liquid biopsies: the BLOODPAC experience
Published in Expert Review of Molecular Diagnostics, 2022
Lauren C. Leiman, Jonathan Baden, Kevin D’Auria, C. Jimmy Lin, Kristen Meier
Working in collaboration with the FDA, BLOODPAC achieved a critical milestone when we published a set of recommended generic analytical validation protocols to help test developers address the challenges in evaluating Next-Generation Sequencing-Based ctDNA Assays [11]. These challenges include the limited amount of blood that can be drawn; the low frequency of tumor-derived DNA molecules in the blood, relative to the amount of nontumor-derived cell-free DNA; the extremely high level of sensitivity and specificity needed to detect ctDNA; the potential for false negatives in detecting these rare molecules; and the increased need for contrived samples to attain sufficient ctDNA for analytical validation. For example, the required types and numbers of samples evaluated in analytical validation studies is always reviewed on a case-by-case basis depending on the assay. Yet without guidance, it may still be unclear if a study such as an accuracy study should require tens or hundreds of samples. Our previously mentioned publication recommended ‘10 to 20 positive samples for each type of variant included in the assay’s Level 1 claims.’ Developers must still justify if this guideline is appropriate, yet its availability allows them to design their studies quickly and with confidence.