Identifying somatic mutations in cell-free DNA of aggressive lymphoma patients: First cell-free DNA results from the molecular profiling for lymphoma (MaPLe) study

Abstract Brain somatic mutations are an increasingly recognized cause of epilepsy, brain malformations and autism spectrum disorders and may be a hidden cause of other neurodevelopmental and neurodegenerative disorders. At present, brain mosaicism can be detected only in the rare situations of autopsy or brain biopsy. Liquid biopsy using cell-free DNA derived from cerebrospinal fluid has detected somatic mutations in malignant brain tumours. Here, we asked if cerebrospinal fluid liquid biopsy can be used to detect somatic mosaicism in non-malignant brain diseases. First, we reliably quantified cerebrospinal fluid cell-free DNA in 28 patients with focal epilepsy and 28 controls using droplet digital PCR. Then, in three patients we identified somatic mutations in cerebrospinal fluid: in one patient with subcortical band heterotopia the LIS1 p. Lys64* variant at 9.4% frequency; in a second patient with focal cortical dysplasia the TSC1 p. Phe581His*6 variant at 7.8% frequency; and in a third patient with ganglioglioma the BRAF p. Val600Glu variant at 3.2% frequency. To determine if cerebrospinal fluid cell-free DNA was brain-derived, whole-genome bisulphite sequencing was performed and brain-specific DNA methylation patterns were found to be significantly enriched (P = 0.03). Our proof of principle study shows that cerebrospinal fluid liquid biopsy is valuable in investigating mosaic neurological disorders where brain tissue is unavailable.

Download Full-text

Abstract 3622: Complete workflow for detection of low frequency somatic mutations from cell-free DNA using Ion Torrent™ platforms

10.1158/1538-7445.am2016-3622 ◽

2016 ◽

Author(s):

Jian Gu ◽

Dumitru Brinza ◽

Ann Mongan ◽

Richard Chien ◽

Dalia Dhingra ◽

...

Keyword(s):

Somatic Mutations ◽

Low Frequency ◽

Ion Torrent ◽

Cell Free Dna ◽

Free Dna

Download Full-text

Abstract 3980: Molecular profiling of cell-free DNA and RNA in the blood of patients with non-small cell lung cancer

10.1158/1538-7445.am2019-3980 ◽

2019 ◽

Author(s):

Jordan Reese ◽

Leisa Jackson ◽

Hestia S. Mellert ◽

Gary Pestano

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Cell Lung Cancer ◽

Molecular Profiling ◽

Small Cell ◽

Small Cell Lung ◽

Cell Free Dna ◽

Dna And Rna ◽

Free Dna

Download Full-text

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

ERJ Open Research ◽

10.1183/23120541.00016-2019 ◽

2019 ◽

Vol 5 (1) ◽

pp. 00016-2019 ◽

Cited By ~ 9

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.

Download Full-text

Detection of somatic mutations in cell-free DNA in plasma and correlation with overall survival in patients with solid tumors

Oncotarget ◽

10.18632/oncotarget.21982 ◽

2017 ◽

Vol 9 (12) ◽

pp. 10259-10271 ◽

Cited By ~ 16

Author(s):

Meenakshi Mehrotra ◽

Rajesh R. Singh ◽

Sanam Loghavi ◽

Dzifa Yawa Duose ◽

Bedia A. Barkoh ◽

...

Keyword(s):

Overall Survival ◽

Solid Tumors ◽

Somatic Mutations ◽

Cell Free Dna ◽

Free Dna

Download Full-text

Somatic mutations in plasma cell-free DNA are diagnostic markers for esophageal squamous cell carcinoma recurrence

Oncotarget ◽

10.18632/oncotarget.11409 ◽

2016 ◽

Vol 7 (38) ◽

pp. 62280-62291 ◽

Cited By ~ 28

Author(s):

Masami Ueda ◽

Tomohiro Iguchi ◽

Takaaki Masuda ◽

Yujiro Nakahara ◽

Hidenari Hirata ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Plasma Cell ◽

Squamous Cell ◽

Somatic Mutations ◽

Diagnostic Markers ◽

Cell Free Dna ◽

Free Dna

Download Full-text

Detection of somatic mutations in circulating cell-free DNA from patients with esophageal squamous cell carcinoma

10.21203/rs.3.rs-51232/v1 ◽

2020 ◽

Author(s):

Zuyang Yuan ◽

Xinfeng Wang ◽

Xiao Geng ◽

Yin Li ◽

Juwei Mu ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Solid Tumor ◽

Somatic Mutations ◽

White Blood Cells ◽

Cell Free Dna ◽

Free Dna ◽

Circulating Cell Free Dna

Abstract Background: The aim of this study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in circulating cell-free DNA (cfDNA) from patients with esophageal squamous cell carcinoma (ESCC). Methods: Paired multi-regional tumor tissues, cfDNA and white blood cells (WBCs) collected from five ESCC patients before treatment from a prospective study (NCT02395705). Of them, samples from Cohort 1 (E102 and E110) were sequenced by whole-exome sequencing (WES) and those from Cohort 2 (E104, E111 and E121) were sequenced by targeted captured sequencing with a panel of 560 cancer-related genes respectively. To call somatic single nucleotide variations (SNVs) by comparing the solid tumor or cfDNA with matched WBCs, the minimal variant allele frequency (VAFmin) as 0.1% and P value <0.05 were allowed. Results: Genomic DNA (gDNA) and plasma-derived cfDNA from 26 samples were successfully sequenced. In Cohort 1, 596 (596/712, 83%) and 562 (562/796, 71%) were heterogeneous SNVs in E102 and E110 respectively. There was a statistically significant linear relationship between the VAFs for tumor and cfDNA (R2 = 0.78, P <0.0001). In Cohort 2, 296 (296/323, 92%), 384 (384/423, 91%) and 331 (331/357, 93%) were heterogeneous SNVs in E104, E111 and E121respectively. cfDNA could recover an average of 60.7% (31/51; range, 35.7%-76.2%) of somatic mutations present in matched solid tumors. The correlation of VAFs between cfDNA and matched solid tumor was significantly positive (r2 =0.92, P <0.0001).Conclusions: Both sequencing approaches revealed the highly intratumoral heterogeneity in ESCC and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA. Further validation in cfDNA is required to define its potential utility for ESCC in clinical practice. Trial registrationAll patients selected in this study were from the registered clinical trial from ClinicalTrials.gov (NCT02395705). Date of registration: March 24, 2015.

Download Full-text