Targeted sequencing of plasma cell-free DNA to predict response to PD1 inhibitors in advanced non-small cell lung cancer.

2019 ◽  
Vol 37 (8_suppl) ◽  
pp. 103-103
Author(s):  
Nicolas Guibert ◽  
Greg Jones ◽  
John F. Beeler ◽  
Clive D. Morris ◽  
Vincent Plagnol ◽  
...  
Keyword(s):  
Clinical Outcomes ◽  
Plasma Cell ◽  
Progressive Disease ◽  
Genetic Alterations ◽  
Targeted Sequencing ◽  
Cell Free Dna ◽  
Invasive Approach ◽  
Free Dna ◽  
Poor Outcomes ◽  
Immune Score

103 Background: Tumor mutational burden is an emerging biomarker of response to immune checkpoint inhibitors (ICI), whose clinical adoption is challenging, especially in liquid biopsies. We hypothesized that targeting limited but relevant genetic alterations in plasma cell-free DNA with next generation sequencing (NGS) along with early monitoring may represent a non-invasive approach to predict response to ICI. Methods: Plasma samples from responders (PFS > 6 months) and non-responders (progressive disease at first evaluation) patients collected before nivolumab (second line) initiation and at 1 month were tested using tagged amplicon sequencing of hotspots and coding regions from 36 genes, blinded to clinical outcomes and tumor genotype. Molecular profile of ctDNA, and its early kinetics (1 month) were analyzed as potential early indicators of response. Results: 98 patients were analyzed, of which 86 (39 responders, 47 non-responders) were evaluable for response. Alterations in ctDNA were detectable in 67/86 baseline samples (78%). The detection of a targetable oncogenic driver (5 EGFR, 1 ALK) was associated with progressive disease on the first CT-scan The presence of a PTEN and/or STK11 mutations (b-PS(+)) was correlated with poor outcomes (median PFS 1.5 months vs. 8 months in b-PS(-)) patients, p = 0.0007), while the presence of transversion mutations in KRAS and/or TP53 (b-KP-Tv(+)) predicted good outcomes (median PFS 11 months vs. 2 months in b-KP-Tv(-) patients, p = 0.0088). Combining these results, patients with a low “immune score” (driver and/or b-PS(+) and/or b-KP-Tv(-)) derived poor outcomes (PFS 2 months), compared with patients with a high immune score (no driver, b-PS(-) and b-KP-Tv(+), PFS 14 months, p = 0.0001, HR 2.96). Studying early changes in 65 specimens, molecular response was correlated with clinical outcomes (14 months PFS in patients with early ctDNA decrease compared to 2 months in patients with increase, p < 0.0001; HR 2.7). Using cut-off of 30% and 50% of plasma response increased the ability of ctDNA to predict response (HR 4 and 4.17, respectively). Conclusions: Targeted sequencing of plasma ctDNA and its early variations can predict response to anti-PD-1. Clinical trial information: NCT02827344.

Plasma cell-free DNA profiling of PI3K/Akt pathway aberrations in two multi-institutional independent metastatic castration-resistant prostate cancer (mCRPC) cohorts.

2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 159-159
Author(s):  
Edmond Michael Kwan ◽  
Chao Dai ◽  
Heidi Fettke ◽  
Christine Hauser ◽  
Patricia Bukczynska ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Clinical Outcomes ◽  
Plasma Cell ◽  
Akt Pathway ◽  
Castration Resistant Prostate Cancer ◽  
Cell Free Dna ◽  
Cox Regression Analysis ◽  
Pten Loss ◽  
Castration Resistant ◽  
Free Dna

159 Background: Tumour tissue from metastatic castration-resistant prostate cancer (mCRPC) harbors frequent copy number variations (CNVs) in the phosphatidylinositol-3-kinase (PI3K)/Akt-signaling pathway. However, identifying CNVs in plasma cell-free DNA (cfDNA) has proven challenging. With emerging data supporting Akt inhibition in PTEN-deficient mCRPC, cfDNA assays for robustly identifying PI3K/Akt pathway aberrations including CNVs are urgently required. Methods: In this multi-institutional prospective biomarker study, we used the Predicine cfDNA assay, optimised for CNV detection, to perform targeted sequencing in 231 mCRPC patients in two independent cohorts (Australian, n = 78; US, n = 153). Kaplan-Meier survival estimates and multivariable Cox regression analysis were used to assess associations between genomic aberrations and progression-free survival (PFS) and overall survival (OS). Results: PTEN loss and PIK3CA gain were detected in 37% (85/231) and 17% (39/231) of patients, respectively. Poorer outcomes were observed in patients with PI3K/Akt pathway aberrations, including those with dual PTEN loss and PIK3CA gain (HR 2.3, 95% CI 1.2-4.4). Similarly, cumulative CNV burden in the PI3K/Akt and AR pathways (0 vs 1 vs ≥2 CNVs in Australian cohort: median OS 33.5 vs 17.2 vs 9.7 months, p< 0.001; 0 vs 1 vs ≥2 CNVs in US cohort: median OS 35.5 vs 14.3 vs 9.2 months, p< 0.001) was associated with significantly worse clinical outcomes. Notably, 21% (31/146) of PTEN-neutral patients harbored other alterations in the PI3K/Akt pathway. Conclusions: Our cfDNA assay readily detected PI3K/Akt pathway CNVs, with the prevalence of PTEN loss comparable to prior tissue sequencing studies. CNVs in the PI3K/Akt pathway were associated with deleterious clinical outcomes, especially when concurrent with AR gain. Additional PI3K/Akt pathway aberrations were found in approximately one-fifth of PTEN-neutral mCRPC. Collectively, our data demonstrate the potential utility of profiling cfDNA to facilitate and optimize patient selection for treatment with Akt inhibitors in mCRPC. [Table: see text]

Targeted sequencing of plasma cell-free DNA to predict response to PD1 inhibitors in advanced non-small cell lung cancer

Lung Cancer ◽  
2019 ◽  
Vol 137 ◽  
pp. 1-6 ◽  
Author(s):  
Nicolas Guibert ◽  
Greg Jones ◽  
John F. Beeler ◽  
Vincent Plagnol ◽  
Clive Morris ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Plasma Cell ◽  
Cell Lung Cancer ◽  
Small Cell ◽  
Targeted Sequencing ◽  
Small Cell Lung ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Ultra-Deep Targeted Sequencing Reveals Cancer-Associated, Prognostically Significant Mutations in Circulating Cell-Free DNA in Treatment-Naive Patients with Follicular Lymphoma

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 20-21
Author(s):  
Tevfik Hatipoğlu ◽  
Esra Esmeray ◽  
Xiaozhou Hu ◽  
Hongling Yuan ◽  
Ayça Erşen Danyeli ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
Sanger Sequencing ◽  
Somatic Mutations ◽  
Progressive Disease ◽  
Tumor Tissue ◽  
Targeted Sequencing ◽  
Cell Free Dna ◽  
Free Dna ◽  
Treatment Naïve ◽  
Circulating Cell Free Dna

Background: Follicular lymphoma is the second most frequent non-Hodgkin lymphoma (NHL) accounting for 20-25% of NHL cases in western countries. Although it has an indolent character, progressive disease or relapse occurs within first two years following therapy initiation in ~20% of FL cases. Several somatic mutations were identified in genes of epigenetic regulation or other biological processes by sequencing of FL tumors. Current diagnostic and prognostic evaluations include invasive methodologies that may be less effective and more risky for the FL patients. Therefore, there is urgent need for development of non-invasive methods to improve diagnosis as well as risk stratification. Accumulating evidence has shown that circulating cell-free DNA (cfDNA) includes tumor-derived mutations in several cancer types; however, this possibility has not been comprehensively investigated in FL patients. Here we evaluated the potential diagnostic and prognostic value of cfDNA in FL cases by addressing the proportion by which cfDNA samples contains cancer-associated and prognosis-related mutations. Methods: Twenty FL cases with available clinic data were included in this study. Thirteen of these cases were symptomatic who were later treated with R-chemo whereas rest of the cases were asymptomatic who were in watchful-waiting. Plasma cfDNA, granulocyte DNA, and FFPE tumor tissue DNA samples were obtained from treatment-naive FL cases. A custom gene panel including exons and exon-intron boundaries of 110 FL-associated genes was constructed based on previously published studies for ultra-deep targeted sequencing. Paired-end sequencing of the captured regions were performed using a HiSeq system in Novogene, which generated 150 bp NGS reads. Targeted genomic regions were covered with &gt; 1500X average effective sequencing depth for identification of somatic variants with low variant allele fractions (VAF). Variants present in cfDNA and tumor tissue DNA but not in patient-matched granulocyte DNA were identified with the GATK pipeline including the MuTect2 variant caller. Somatic variants associated with hematopoietic and lymphoid tissues in the COSMIC database were chosen for further analyses. The final high-confident list of variants was determined by visual investigation and through additional filtering of each variant using Integrative Genomics Viewer. Selected variants were cross-validated with Sanger sequencing. Survival analyses were performed with Survival and Survminer R packages. Results: Ultra-deep targeted sequencing revealed 91 somatic variants (71 missense, 12 nonsense, 4 indel, 4 splice site) in 31 genes included in the panel. Consistent with previous reports, the most frequently mutated genes were CREBBP (40%), BCL2 (30%), STAT6 (25%), EZH2 (20%), and CARD11 (20%). In symptomatic cases, 41.5% of the variants was present in both cfDNA and tumor tissue DNA, whereas 52.3% and 6.2% of them was present only in tumor tissue DNA or in cfDNA samples, respectively. In asymptomatic cases, 11.5% of the detected variants was present in both cfDNA and tumor tissue DNA, while 84.6% and 3.8% of them were in only tumor tissue DNA or cfDNA samples. Mutations previously reported to be associated with FL pathogenesis (e.g. KMT2D R2417*) were in the list of common variants observed in both cfDNA and tumor tissue DNA. We observed high Ki67 staining, elevated LDH levels, presence of BCL2 or CCND3 mutations to be significantly associated with progression-free survival (Figure 1A, B). Importantly, survival analysis by stratifying patients based on BCL2 mutations present only in cfDNA also predicted poor prognosis (Figure 1C). One of the FL patient who had progressive disease contained histological transformation-associated gene (i.e. B2M and BTG1) mutations only in the cfDNA but not in tumor tissue DNA sample. Finally, we cross-validated the selected somatic variants with VAF &gt;20% using Sanger sequencing, which showed 100% consistency with NGS results. Conclusions: Tumor tissue-derived mutations can be detected in most FL patients albeit to a lesser extent than those in DLBCL. Plasma cfDNA genotyping may be useful for improving diagnosis and prognosis especially in symptomatic FL patients. Given that some somatic mutations associated with disease progression are detected only in plasma cfDNA samples, cfDNA genotyping may be useful for choosing appropriate therapy for high-risk FL patients. Disclosures No relevant conflicts of interest to declare.

scholarly journals Liquid Biopsies Using Plasma Exosomal Nucleic Acids and Plasma Cell-Free DNA Compared with Clinical Outcomes of Patients with Advanced Cancers

2017 ◽  
Vol 24 (1) ◽  
pp. 181-188 ◽  
Author(s):  
Lino Möhrmann ◽  
Helen J. Huang ◽  
David S. Hong ◽  
Apostolia M. Tsimberidou ◽  
Siqing Fu ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Clinical Outcomes ◽  
Plasma Cell ◽  
Liquid Biopsies ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Plasma Cell–Free DNA Profiling of PTEN-PI3K-AKT Pathway Aberrations in Metastatic Castration-Resistant Prostate Cancer

2021 ◽  
pp. 622-637
Author(s):  
Edmond M. Kwan ◽  
Chao Dai ◽  
Heidi Fettke ◽  
Christine Hauser ◽  
Maria M. Docanto ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Clinical Outcomes ◽  
Plasma Cell ◽  
High Risk Patient ◽  
Akt Pathway ◽  
Castration Resistant Prostate Cancer ◽  
Cell Free Dna ◽  
Pten Loss ◽  
Castration Resistant ◽  
Free Dna

PURPOSE Tumor tissue from metastatic castration-resistant prostate cancer (mCRPC) harbors frequent copy number variations (CNVs) in the PTEN-PI3K-AKT pathway. However, identifying CNVs in plasma cell–free DNA (cfDNA) has proven to be challenging. With emerging data supporting Akt inhibition in PTEN-deficient mCRPC, we profiled PTEN-PI3K-AKT pathway aberrations in patients with mCRPC using a novel cfDNA assay optimized for CNV detection. METHODS A next-generation sequencing–based cfDNA assay was used to profile 231 patients with mCRPC from two independent cohorts (Australian, n = 78; United States, n = 153). PTEN-PI3K-AKT pathway genomic aberrations were correlated with clinical outcomes, including progression-free survival and overall survival (OS). RESULTS PTEN loss and PIK3CA gain were detected in 37% (85 of 231) and 17% (39 of 231) of patients, respectively. Poorer outcomes were observed in patients with PTEN-PI3K-AKT pathway aberrations, including those with dual PTEN loss and PIK3CA gain (hazard ratio 2.3, 95% CI 1.2 to 4.4). Cumulative CNV burden in the PTEN-PI3K-AKT and androgen receptor (AR) pathways was associated with significantly worse clinical outcomes (0 v 1 v ≥ 2 CNVs in Australian cohort: median OS 33.5 v 17.2 v 9.7 months, P < .001; 0 v 1 v ≥ 2 CNVs in US cohort: median OS 35.5 v 14.3 v 9.2 months, P < .001). Notably, 21% (31 of 146) of PTEN-neutral patients harbored alternative PTEN-PI3K-AKT pathway aberrations. CONCLUSION PTEN-PI3K-AKT pathway CNVs were readily detected using our cfDNA assay, with the prevalence of PTEN loss comparable with tissue-based studies. Additional PTEN-PI3K-AKT pathway aberrations were found in one fifth of PTEN-neutral cases. Concurrent CNVs in the PTEN-PI3K-AKT and AR pathways portended poor survival, and identifying this high-risk patient subset for dual AR/Akt inhibition may optimize precision treatment with Akt inhibitors in mCRPC.

scholarly journals 5-Hydroxymethylcytosine Profiles in Plasma Cell-free DNA Reflect Molecular Characteristics of Diabetic Kidney Disease

2022 ◽  
Author(s):  
Jin-Lin Chu ◽  
Shu-Hong Bi ◽  
Yao He ◽  
Rui-Yao Ma ◽  
Xing-Yu Wan ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Plasma Cell ◽  
Diabetic Kidney Disease ◽  
Marker Genes ◽  
Hub Genes ◽  
Cell Free Dna ◽  
Invasive Approach ◽  
Diabetic Kidney ◽  
Non Invasive ◽  
Free Dna

Abstract Background: Complications of diabetes mellitus (DM) are the leading cause of DM-related disability and mortality. Notably, diabetic kidney disease (DKD), one of the main complications of DM, has become a frequent cause of end-stage renal disease. A clinically convenient, non-invasive approach for monitoring the development of DKD would benefit the overall life quality of patients with DM and contribute to lower medical burdens through promoting preventive interventions.Methods: We utilized 5hmC-Seal to profile genome-wide 5-hydroxymethylcytosines in plasma cell-free DNA (cfDNA). Candidate genes were identified by intersecting the differentially modified 5hmC marker genes (DMGs) and differentially expressed genes (DEGs) from the GEO datasets GSE30528 and GSE30529. Cytoscape software was used to construct the protein-protein interaction (PPI) network and identify the hub genes.Results: The final gene panel of 9 hub genes, including (CTNNB1, PTEN, MYD88, ITGAM, CD28, ITGB2, VCAM1, CXCR4, CD44) were confirmed. Further analysis indicated that this 9-gene signature showed a good capacity to distinguish between DKD and DM. Conclusions: The 5hmC-Seal assay was successfully applied to the cfDNA samples from a cohort of DM patients with or without DKD. Altered 5hmC signatures in plasma cfDNA indicate that 5hmC-Seal has the potential to be a non-invasive epigenetic tool for monitoring the development of DKD and be a part of diabetic care.

Genomic variations in plasma cell free DNA differentiate early stage lung cancers from normal controls

Lung Cancer ◽  
2015 ◽  
Vol 90 (1) ◽  
pp. 78-84 ◽  
Author(s):  
Shu Xia ◽  
Chiang-Ching Huang ◽  
Min Le ◽  
Rachel Dittmar ◽  
Meijun Du ◽  
...  
Keyword(s):  
Plasma Cell ◽  
Early Stage ◽  
Cell Free Dna ◽  
Lung Cancers ◽  
Genomic Variations ◽  
Free Dna ◽  
Normal Controls

scholarly journals PATH-27. MUTATION DETECTION USING PLASMA CELL-FREE DNA IN CHILDREN WITH CENTRAL NERVOUS SYSTEM TUMORS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii430-iii430
Author(s):  
Ross Mangum ◽  
Jacquelyn Reuther ◽  
Koel Sen Baksi ◽  
Ryan C Zabriskie ◽  
Ilavarasi Gandhi ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Plasma Cell ◽  
Pediatric Patients ◽  
Cns Tumors ◽  
Cell Free Dna ◽  
Pilot Studies ◽  
Dna And Rna ◽  
Free Dna ◽  
Initial Cohort

Abstract BACKGROUND The role of plasma cell-free DNA (cfDNA) as a cancer biomarker for tracking treatment response and detecting early relapse has been well described for solid tumors outside the central nervous system (CNS). However, the presence of a blood-brain barrier complicates the application of plasma cfDNA analysis for patients with CNS malignancies. METHODS cfDNA was extracted from plasma of pediatric patients with CNS tumors utilizing a QIAmp® MinElute® kit and quantitated with Qubit 2.0 Fluorometer. Extensive genomic testing, including targeted DNA and RNA solid tumor panels, exome and transcriptome sequencing, as well as copy number array, was performed on matched tumor samples as part of the Texas KidsCanSeq study. An Archer® Reveal ctDNA28 NGS kit was then used for assaying the sensitivity of detecting tumor-specific mutations in the plasma of these patients. RESULTS A median of 10.7ng cfDNA/mL plasma (Interquartile range: 6.4 – 15.3) was extracted from 78 patients at time of study enrollment. Longitudinal samples from 24 patients exhibited a median yield of 7.7ng cfDNA/mL plasma (IQR: 5.9 – 9.1). An initial cohort of 6 patients was identified with 7 somatic variants covered by the Archer® Reveal kit. Four of seven mutations identified in matched tumor specimens were detected in patient plasma at variant allele frequencies ranging from 0.2–1%. CONCLUSIONS While challenging, detection of cfDNA in the plasma of pediatric patients with CNS tumors is possible and is being explored in a larger patient cohort along with pilot studies investigating cerebrospinal fluid as an additional source for tumor-specific cfDNA.

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