scholarly journals Feasibility of Cell-Free DNA Collection and Clonal Immunoglobulin Sequencing in South African Patients With HIV-Associated Lymphoma

2021 ◽  
pp. 611-621
Author(s):  
Samantha L. Vogt ◽  
Moosa Patel ◽  
Atul Lakha ◽  
Vinitha Philip ◽  
Tanvier Omar ◽  
...  
Keyword(s):  
South Africa ◽  
Heavy Chain ◽  
Whole Blood ◽  
B Cell Lymphoma ◽  
Immunoglobulin Heavy Chain ◽  
Newly Diagnosed ◽  
Hiv Patients ◽  
Cell Free Dna ◽  
Low Resource ◽  
Free Dna

PURPOSE Diagnosis of AIDS lymphoma in low-resource settings, like South Africa, is often delayed, leaving patients with limited treatment options. In tuberculosis (TB) endemic regions, overlapping signs and symptoms often lead to diagnostic delays. Assessment of plasma cell-free DNA (cfDNA) by next-generation sequencing (NGS) may expedite the diagnosis of lymphoma but requires high-quality cfDNA. METHODS People living with HIV with newly diagnosed aggressive B-cell lymphoma and those with newly diagnosed TB seeking care at Chris Hani Baragwanath Academic Hospital and its surrounding clinics, in Soweto, South Africa, were enrolled in this study. Each participant provided a whole blood specimen collected in cell-stabilizing tubes. Quantity and quality of plasma cfDNA were assessed. NGS of the immunoglobulin heavy chain was performed. RESULTS Nine HIV+ patients with untreated lymphoma and eight HIV+ patients with TB, but without lymphoma, were enrolled. All cfDNA quantity and quality metrics were similar between the two groups, except that cfDNA accounted for a larger fraction of recovered plasma DNA in patients with lymphoma. The concentration of cfDNA in plasma also trended higher in patients with lymphoma. NGS of immunoglobulin heavy chain showed robust amplification of DNA, with large amplicons (> 250 bp) being more readily detected in patients with lymphoma. Clonal sequences were detected in five of nine patients with lymphoma, and none of the patients with TB. CONCLUSION This proof-of-principle study demonstrates that whole blood collected for cfDNA in a low-resource setting is suitable for sophisticated sequencing analyses, including clonal immunoglobulin NGS. The detection of clonal sequences in more than half of patients with lymphoma shows promise as a diagnostic marker that may be explored in future studies.

scholarly journals Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Brian C.-H. Chiu ◽  
Chang Chen ◽  
Qiancheng You ◽  
Rudyard Chiu ◽  
Girish Venkataraman ◽  
...  
Keyword(s):  
B Cell Lymphoma ◽  
Cell Free Dna ◽  
Invasive Approach ◽  
Non Invasive ◽  
Signature Genes ◽  
Non Hodgkin Lymphoma ◽  
Free Dna ◽  
Genome Wide ◽  
Circulating Cell Free Dna

AbstractThe 5-methylcytosines (5mC) have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the role of 5-hydroxymethylcytosines (5hmC) that are generated from 5mC through active demethylation, in lymphomagenesis is unknown. We profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 73 newly diagnosed patients with DLBCL and FL. We identified 294 differentially modified genes between DLBCL and FL. The differential 5hmC in the DLBCL/FL-differentiating genes co-localized with enhancer marks H3K4me1 and H3K27ac. A four-gene panel (CNN2, HMG20B, ACRBP, IZUMO1) robustly represented the overall 5hmC modification pattern that distinguished FL from DLBCL with an area under curve of 88.5% in the testing set. The median 5hmC modification levels in signature genes showed potential for separating patients for risk of all-cause mortality. This study provides evidence that genome-wide 5hmC profiles in cfDNA differ between DLBCL and FL and could be exploited as a non-invasive approach.

scholarly journals Clinical Utility of Comprehensive Cell-free DNA Analysis to Identify Genomic Biomarkers in Patients with Newly Diagnosed Metastatic Non–small Cell Lung Cancer

2019 ◽  
Vol 25 (15) ◽  
pp. 4691-4700 ◽  
Author(s):  
Natasha B. Leighl ◽  
Ray D. Page ◽  
Victoria M. Raymond ◽  
Davey B. Daniel ◽  
Stephen G. Divers ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Clinical Utility ◽  
Dna Analysis ◽  
Small Cell ◽  
Newly Diagnosed ◽  
Small Cell Lung ◽  
Cell Free Dna ◽  
Free Dna

Cell-free DNA as a biomarker in diffuse large B-cell lymphoma: A systematic review

2019 ◽  
Vol 139 ◽  
pp. 7-15 ◽  
Author(s):  
Javier Arzuaga-Mendez ◽  
Endika Prieto-Fernández ◽  
Elixabet Lopez-Lopez ◽  
Idoia Martin-Guerrero ◽  
Juan Carlos García-Ruiz ◽  
...  
Keyword(s):  
Systematic Review ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Cell Free Dna ◽  
Free Dna ◽  
Large B Cell Lymphoma ◽  
Large B Cell

scholarly journals 5-Hydroxymethylcytosines of Circulating Cell-Free DNA and Prognosis in Diffuse Large B-Cell Lymphoma

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2985-2985
Author(s):  
Brian C.-H. Chiu ◽  
Zhou Zhang ◽  
Qiancheng You ◽  
Elizabeth Stepniak ◽  
Paige Bracci ◽  
...  
Keyword(s):  
Overall Survival ◽  
B Cell ◽  
Cell Lymphoma ◽  
Prognostic Significance ◽  
B Cell Lymphoma ◽  
Cell Free Dna ◽  
Free Dna ◽  
Large B Cell Lymphoma ◽  
Large B Cell ◽  
Circulating Cell Free Dna

Abstract Background: Elevated levels of circulating cell-free DNA (cfDNA) have been associated with poor prognosis and relapse in patients with diffuse large B-cell lymphoma (DLBCL). However, the tumor-specific molecular targets in cfDNA that have prognostic significance remain unclear. We investigated the association between 5-hydroxymethylcytosine (5hmC), a mark of active demethylation and gene activation, in cfDNA from plasma and prognosis in DLBCL. Methods: We used the 5hmC-Seal, a highly sensitive chemical labeling technique integrated with next-generation sequencing (NGS), to profile 5hmC in plasma cfDNA samples from Caucasian patients at the University of Chicago who were newly diagnosed with DLBCL (n=43) or follicular lymphoma (FL, n=28), the two most common histological subtypes of non-Hodgkin lymphoma (NHL), in 2011-13. Baseline clinical, laboratory, and vital status data were abstracted from medical records. Patients were followed through December 31, 2017 and those who relapsed after completion of treatment, lost to follow-up, or died were censored. We profiled 5hmC with 1-2 ng of cfDNA extracted from ~2 ml of plasma for library construction and the NGS. We obtained ~25 million reads per sample, providing a depth of coverage ~600X in terms of gene bodies. We normalized read counts and identified differential 5hmC markers using DESeq2. Cox proportional hazards model were used to estimate the association between 5hmC markers and overall survival. Results: We found that in cfDNA from DLBCL patients, 5hmC markers were enriched within gene bodies and depleted in CpG islands. The cfDNA-based 5hmC profiles at diagnosis differed between DLBCL and FL, and in DLBCL, the 5hmC profiles differed between Ann Arbor stage (stage 1/2 vs stage 3/4), lactate dehydrogenase (LDH) level (normal vs elevated), and cell-of-origin (germinal center B-like and activated B-cell-like DLBCL). In addition, genome-wide 5hmC distribution patterns in cfDNA samples are highly correlated with those found in cfDNA-paired tumor tissues, supporting the tumor relevance of cfDNA in a patient. Next, we evaluated the prognostic significance of cfDNA-based 5hmC in DLBCL using a two-step approach. In the discovery phase (7 DLBCL patients with relapse and 12 age- and sex-matched patients without relapse within two years following treatment), a substantial number of 5hmC markers were associated with relapse (449 gene bodies at 5% false discovery rate [FDR]). These relapse-associated 5hmC signatures showed high sensitivity, specificity, and overall accuracy (area under curve [AUC]=0.91) in predicting relapse in the independent validation set (relapse=5, no relapse=13). Finally, we identified a panel of 128 5hmC markers (fold change >20% and p-value <0.05) that were associated with 4-year overall survival. Conclusion: These findings suggest that 5hmC signatures in cfDNA at the time of DLBCL diagnosis correlate with standard clinical prognostic indices and hold promise as non-invasive markers for prognosis and survival. Disclosures Smith: BMS: Consultancy; Portola: Honoraria.

scholarly journals Diagnosing Diabetes Mellitus With Glycated Haemoglobin in Newly Diagnosed HIV-positive Patients in Buffalo City Municipality, South Africa: A Cross-sectional Study

2019 ◽  
Vol 12 (1) ◽  
pp. 263-268
Author(s):  
Olufunso O. Sogbanmu ◽  
Larry O. Obi ◽  
Daniel T. Goon ◽  
Anthony Okoh ◽  
Benson Iweriebor ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
South Africa ◽  
Logistic Regression ◽  
Glycated Haemoglobin ◽  
Cross Sectional Study ◽  
Hiv Positive ◽  
Newly Diagnosed ◽  
Sectional Study ◽  
Hiv Patients ◽  
Cross Sectional

Background: The HbA1c estimates long-term glycaemic control in individuals. However, scanty data exist on the determination of Diabetes Mellitus (DM) in newly diagnosed HIV patients using the HbA1c screening tool in the South African context. Thus, this study examines the prevalence of diabetes mellitus in newly diagnosed HIV-positive patients in Buffalo City Municipality, East London, South Africa. Methodology: This was a cross-sectional study of 335 newly HIV-diagnosed patients between August 2016 and July 2017. Demographic (age, gender, residence, employment status and level of education) and behavioural variables (smoking and alcohol use (past 30 days)) were by self-reporting. Information on HbA1c and other clinical variables were obtained from the medical records of the patients. Diabetes mellitus was defined based on the Society for Endocrinology, Metabolism and Diabetes of South Africa (SEMDSA) 2017 guideline of HbA1c of above 6.5%. Weight and height were measured using standard protocols. Logistic regression analyses were applied to determine the predictors of abnormal glycated haemoglobin. Results: Majority of the participants were female (72%). The prevalence of patients with HbA1c greater than 6.5% was 6%. The multivariate analysis indicates only age (p=0.031) and race (0.019) significantly shows a correlation to increase the risk of development of DM in newly diagnosed HIV positive patients. The binary logistic regression analysis shows that age (above 46 years) (p=0.001; AOR (6.60); CI (2.08-20.9) was directly related to the development of DM. Conclusion: Consistent with other studies, the exclusive non-fasting HbA1c, which is a marker of glycaemic control, only underestimate glycemia in HIV patients with diabetes in this present study. Notwithstanding, HIV patients who are over 40 years are likely to develop DM. As such, screening older individuals diagnosed with HIV is crucial in offering a timely point of care and interventions.

scholarly journals Cell-free DNA in newly diagnosed patients with glioblastoma – a clinical prospective feasibility study

Oncotarget ◽  
2019 ◽  
Vol 10 (43) ◽  
pp. 4397-4406 ◽  
Author(s):  
Dorte Schou Nørøxe ◽  
Olga Østrup ◽  
Christina Westmose Yde ◽  
Lise Barlebo Ahlborn ◽  
Finn Cilius Nielsen ◽  
...  
Keyword(s):  
Feasibility Study ◽  
Newly Diagnosed ◽  
Cell Free Dna ◽  
Free Dna
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