scholarly journals O9: DETECTION OF RELEVANT GENE MUTATIONS IN GLIOMA USING PLASMA CELL FREE DNA

2021 ◽  
Vol 108 (Supplement_1) ◽  
Author(s):  
M Ita ◽  
Y Nolan ◽  
A Toulouse ◽  
JH Wang ◽  
CH Lim ◽  
...  
Keyword(s):  
Human Brain ◽  
Somatic Mutation ◽  
Molecular Profiling ◽  
Genetic Profile ◽  
Beta Catenin ◽  
Genomic Profiling ◽  
Cell Free Dna ◽  
Surgical Interventions ◽  
Free Dna ◽  
Circulating Tumour Dna

Abstract Background Comprehensive molecular profiling of gliomas provide information essential for accurate biological classification beyond traditional histopathology. Genomic profiling utilizing tumour tissue samples inevitably involves obtaining tissues through potentially hazardous surgical procedures or stereotactic biopsies carrying risks of morbidity and mortality. Tissues from biopsies may also be insufficient or fail to capture a comprehensive picture of the tumours genetic profile due to tumour heterogeneity. In these contexts, complementary minimally invasive strategies are needed for molecular profiling of gliomas. Cell free DNA (cfDNA) has emerged as an easily accessible biomarker containing fragments of circulating tumour DNA (ctDNA) released into plasma through apoptosis. We explored its potential utility in genomic profiling of brain tumours. Method Plasma cfDNA from patients with radiographically suspected brain malignancies were extracted and quantified before planned surgical interventions. Cell free DNA was extracted using a QIAamp Circulating Nucleic Acid Kit (Qiagen), and was quantified (ng cfDNA/mL) using a DS-11 FX Spectrophotometer (DeNovix). Pathway focused profiling of somatic mutation status was performed using QBiomarker Somatic Mutation PCR Arrays for human brain cancers (Qiagen) through real time PCR (Roche). Result Somatic mutations in human brain cancer were evaluated in the following genes; BRAF, CTNNB1/beta-catenin, EGFR, IDH1, IDH2, KRAS, NF2, NRAS, PIK3CA, and PTEN. A total of 14 (70%) patients had greater than 1 somatic mutation detected in their plasma cfDNA. Conclusion We postulate that glioma derived circulating tumour DNA occur in plasma, and genomic analysis using cell free DNA may complement current methods of glioma genomic characterisation. Take-home message Glioma derived circulating tumour DNA occur in plasma.

Abstract 4593: Genomic profiling of cell free DNA (cfDNA) from patients with inflammatory breast cancer (IBC)

2018 ◽  
Author(s):  
Jianming Pei ◽  
Jacqueline Talarchek ◽  
Jennifer S. Winn ◽  
Katherine Alpaugh ◽  
Massimo Cristofanilli ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Inflammatory Breast Cancer ◽  
Genomic Profiling ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Genetic Variants Detected Using Cell-Free DNA from Blood and Tumor Samples in Patients with Inflammatory Breast Cancer

2020 ◽  
Vol 21 (4) ◽  
pp. 1290
Author(s):  
Jennifer S. Winn ◽  
Zachary Hasse ◽  
Michael Slifker ◽  
Jianming Pei ◽  
Sebastian M. Arisi-Fernandez ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Inflammatory Breast Cancer ◽  
Triple Negative ◽  
Genetic Profile ◽  
Cell Free Dna ◽  
Targeted Next Generation Sequencing ◽  
Pathogenic Variants ◽  
Free Dna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

We studied genomic alterations in 19 inflammatory breast cancer (IBC) patients with advanced disease using samples of tissue and paired blood serum or plasma (cell-free DNA, cfDNA) by targeted next generation sequencing (NGS). At diagnosis, the disease was triple negative (TN) in eleven patients (57.8%), ER+ Her2- IBC in six patients (31.6%), ER+ Her2+ IBC in one patient (5.3%), and ER- Her2+ IBC in one other patient (5.3%). Pathogenic or likely pathogenic variants were frequently detected in TP53 (47.3%), PMS2 (26.3%), MRE11 (26.3%), RB1 (10.5%), BRCA1 (10.5%), PTEN (10.5%) and AR (10.5%); other affected genes included PMS1, KMT2C, BRCA2, PALB2, MUTYH, MEN1, MSH2, CHEK2, NCOR1, PIK3CA, ESR1 and MAP2K4. In 15 of the 19 patients in which tissue and paired blood were collected at the same time point, 80% of the variants detected in tissue were also detected in the paired cfDNA. Higher concordance between tissue and cfDNA was found for variants with higher allele fraction in tissue (AFtissue ≥ 5%). Furthermore, 86% of the variants detected in cfDNA were also detected in paired tissue. Our study suggests that the genetic profile measured in blood cfDNA is complementary to that of tumor tissue in IBC patients.

scholarly journals Cell-free DNA in the supernatant of pleural effusion can be used to detect driver and resistance mutations, and can guide tyrosine kinase inhibitor treatment decisions

2019 ◽  
Vol 5 (1) ◽  
pp. 00016-2019 ◽  
Author(s):  
Karlijn Hummelink ◽  
Mirte Muller ◽  
Theodora C. Linders ◽  
Vincent van der Noort ◽  
Petra M. Nederlof ◽  
...  
Keyword(s):  
Pleural Effusion ◽  
Clinical Care ◽  
Molecular Profiling ◽  
Driver Mutation ◽  
Added Value ◽  
Pleural Effusions ◽  
Resistance Mutations ◽  
Cell Free Dna ◽  
Free Dna ◽  
Cell Pellet

ObjectivesMolecular profiling of tumours has become the mainstay of diagnostics for metastasised solid malignancies and guides personalised treatment, especially in nonsmall cell lung cancer (NSCLC). In current practice, it is often challenging to obtain sufficient tumour material for reliable molecular analysis. Cell-free DNA (cfDNA) in blood or other bio-sources could present an alternative approach to obtain genetic information from the tumour. In a retrospective cohort we analysed the added value of cfDNA analysis in pleural effusions for molecular profiling.MethodsWe retrospectively analysed both the supernatant and the cell pellet of 44 pleural effusions sampled from 39 stage IV patients with KRAS (n=23) or EGFR (n=16) mutated tumours to detect the original driver mutation as well as for EGFR T790M resistance mutations. Patients were diagnosed with either NSCLC (n=32), colon carcinoma (n=4), appendiceal carcinoma (n=2) or adenocarcinoma of unknown primary (n=1). Samples collected in the context of routine clinical care were stored at the Netherlands Cancer Institute biobank. We used droplet digital PCR for analysis.ResultsThe driver mutation could be detected in 36 of the 44 pleural effusions by analysis of both the supernatant (35 out of 44 positive) and the cell pellet (31 out of 44 positive). In seven out of 20 pleural effusions from patients with EGFR mutation-positive tumours, a T790M mutation was detected. All seven supernatants and cell pellets were positive.ConclusionscfDNA in pleural effusion can be used to detect driver mutations as well as resistance mechanisms like EGFR T790M in pleural effusion with high accuracy and is therefore a valuable bio-source.

scholarly journals Urine as a non-invasive alternative to blood for germline and somatic mutation detection in hepatocellular carcinoma

2021 ◽  
Author(s):  
Amy K. Kim ◽  
Selena Y. Lin ◽  
Surbhi Jain ◽  
Yixiao Cui ◽  
Terence Gade ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Somatic Mutation ◽  
Liquid Biopsy ◽  
Mononuclear Cells ◽  
Cell Free Dna ◽  
Genome Coverage ◽  
Non Invasive ◽  
Free Dna ◽  
Genotype Information ◽  
Targeted Ngs

AbstractCell-free DNA (cfDNA) from blood has become a promising analyte for cancer genetic liquid biopsy. Urinary cfDNA has been shown to contain mutations associated with non-genitourologic cancers including hepatocellular carcinoma (HCC). In this study, we evaluate urine as a noninvasive alternative to blood-based liquid biopsy in both germline and circulating tumor DNA (ctDNA) genotyping in HCC. Using quantitative PCR (qPCR), whole-genome sequencing (WGS), and targeted NGS, DNA isolated from blood or urine of patients with HCC was analyzed for overall genome coverage, HCC hotspot coverage, and germline or somatic mutation concordance. Targeted NGS of plasma and urine cfDNA was also performed for detection of somatic variants. We found urine cfDNA, similar to plasma cfDNA, showed a major mononucleosomal species of 150-180 bp in both healthy individuals and patients with HCC. By WGS, overall genome coverage breadth was similar between urine and plasma cfDNA, with higher fraction of covered cancer-associated mutation hotspots in urine cfDNA. qPCR analyses of HCC-associated mutations (TP53, CTNNB1, and TERT) in 101 patients with HCC revealed 78% overall concordance between plasma and urine. Targeted NGS of HCC-associated gene regions in additional 15 HCC patients showed a 97% overall position-level concordance between plasma and urine cfDNA. Collectively, urine DNA can potentially be used as a completely noninvasive liquid biopsy for HCC.Significance StatementHepatocellular carcinoma (HCC) is the most common liver cancer worldwide and the fastest growing gastrointestinal cancer in the U.S. Cell-free DNA (cfDNA) which originates from various cells undergoing apoptosis or necrosis including tumor cells, is present in all body fluids levels including urine. Urinary cfDNA isolated from patients with HCC showed a similar fragment size distribution, overall genome coverage, and comparable sensitivity for detecting HCC-associated variants compared to plasma cfDNA. Urine was also determined to be a reliable source of germline genotype information, similar to peripheral blood mononuclear cells in blood-based liquid biopsies. Urine cfDNA can be used as a completely non-invasive liquid biopsy in HCC.

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