Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer

Hennigan, S. Thomas; Trostel, Shana Y.; Terrigino, Nicholas T.; Voznesensky, Olga; Schaefer, Rachel; Whitlock, Nichelle C.; Wilkinson, Scott; Carrabba, Nicole V.; Atway, Rayann; Shema, Steven; Lake, Ross; Sweet, Amalia; Einstein, David J.; Karzai, Fatima; Gulley, James L.; Chang, Peter D.; Bubley, Glenn J.; Balk, Steven P.; Ye, Huihui; Sowalsky, Adam G.

doi:10.1101/655506

Cited by 18 publications

(17 citation statements)

References 46 publications

(52 reference statements)

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“…Based on pass-filter SNVs and indels identified from exome sequencing, 50 targets were selected randomly from 871 total calls for additional amplicon-based sequencing, with the exception of the TP53 Y236X nonsense alteration, which was subsequently included for verification 33,34 . Prior to nomination for targeted sequencing, each selected genomic coordinate was inspected in IGV and mutation calls falling in MAPQ < 10 were excluded.…”

Section: Methodsmentioning

confidence: 99%

“…edu/cgi-bin/hgPcr] to prevent production of unintended amplicons for each patient-specific batch of targets. The forward and reverse primer sequences identified above were appended with adaptor sequences 33 at the 5′ end, complementary to Illumina Nextera full-length primers (IDT). Dual-barcoded sequencing adaptors were modified 33 to contain longer regions of complementarity and were ordered with NGSO-4 purity from Sigma.…”

Section: Methodsmentioning

confidence: 99%

“…For the amplification of targets using the reverse primers, a mixture of reverse oligonucleotides was created with 1 μL of each 100 μM primer in a total volume of 100 μL TE, for a final concentration of 1 μM each primer. To 1.25 μL of this primer mix, 3.5 μL of 2.5 μM dUTP, 1 μL of TE, 8 μL of product from the terminal transferase reaction, 1.25 μL of a 2 μM stock of i5 barcoded sequencing adaptor 33 , and 15 μL of 2 × KAPA HiFi HotStart Uracil + ReadyMix were added. Samples were incubated in a thermal cycler at 98°C for 5 min initially and followed by 20 cycles of PCR (98°C-65°C-72°C for 30 s each with 7 min of final extension at 72°C).…”

Section: Methodsmentioning

confidence: 99%

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A case report of multiple primary prostate tumors with differential drug sensitivity

et al. 2020

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Localized prostate cancers are genetically variable and frequently multifocal, comprising spatially distinct regions with multiple independently-evolving clones. To date there is no understanding of whether this variability can influence management decisions for patients with prostate tumors. Here, we present a single case from a clinical trial of neoadjuvant intense androgen deprivation therapy. A patient was diagnosed with a large semi-contiguous tumor by imaging, histologically composed of a large Gleason score 9 tumor with an adjacent Gleason score 7 nodule. DNA sequencing demonstrates these are two independent tumors, as only the Gleason 9 tumor harbors single-copy losses of PTEN and TP53. The PTEN/TP53deficient tumor demonstrates treatment resistance, selecting for subclones with mutations to the remaining copies of PTEN and TP53, while the Gleason 7 PTEN-intact tumor is almost entirely ablated. These findings indicate that spatiogenetic variability is a major confounder for personalized treatment of patients with prostate cancer.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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A case report of multiple primary prostate tumors with differential drug sensitivity

et al. 2020

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“…The half-life of ctDNA is estimated to be up to 2 hours, and is dependent on factors including cell turnover, tumour size, excretion in bodily fluids and degradation rate by circulating nucleases [4]. Therefore, in non-metastatic cancer, concentration ranges of ctDNA, considered as fractions of total cell-free DNA, vary between tumour types, ranging from undetectable in prostate cancer [5] to 0.02-3.2% in non-small cell lung cancer (NSCLC) [6]. The historically poor sensitivity of ctDNA testing, has restricted its integration into routine clinical practice in non-metastatic disease [7].…”

Section: Introductionmentioning

confidence: 99%

Early circulating tumour DNA kinetics measured by ultra-deep next-generation sequencing during radical radiotherapy for non-small cell lung cancer: a feasibility study

Walls

McConnell²,

McAleese

et al. 2020

Radiat Oncol

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Background: The evaluation of circulating tumour DNA (ctDNA) from clinical blood samples, liquid biopsy, offers several diagnostic advantages compared with traditional tissue biopsy, such as shorter processing time, reduced patient risk and the opportunity to assess tumour heterogeneity. The historically poor sensitivity of ctDNA testing, has restricted its integration into routine clinical practice for non-metastatic disease. The early kinetics of ctDNA during radical radiotherapy for localised NSCLC have not been described with ultra-deep next generation sequencing previously. Materials and methods: Patients with CT/PET-staged locally advanced, NSCLC prospectively consented to undergo serial venepuncture during the first week of radical radiotherapy alone. All patients received 55Gy in 20 fractions. Plasma samples were processed using the commercially available Roche AVENIO Expanded kit (Roche Sequencing Solutions, Pleasanton, CA, US) which targets 77 genes. Results: Tumour-specific mutations were found in all patients (1 in 3 patients; 2 in 1 patient, and 3 in 1 patient). The variant allele frequency of these mutations ranged from 0.05-3.35%. In 2 patients there was a transient increase in ctDNA levels at the 72 h timepoint compared to baseline. In all patients there was a non-significant decrease in ctDNA levels at the 7-day timepoint in comparison to baseline (p = 0.4627). Conclusion: This study demonstrates the feasibility of applying ctDNA-optimised NGS protocols through specified time-points in a small homogenous cohort of patients with localised lung cancer treated with radiotherapy. Studies are required to assess ctDNA kinetics as a predictive biomarker in radiotherapy. Priming tumours for liquid biopsy using radiation warrants further exploration.

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“…This is because the levels of ctDNA observed in the BPH patients are extremely low, as reported in certain recent studies. Therefore, Hennigan and coworkers applied ultra-low-pass whole-genome sequencing to profile the cell-free DNA isolated from 112 patients with localized prostate cancer and concluded that the allele-specific alterations in ctDNA were below the threshold level required for detection [147].…”

Section: Prostate Cancermentioning

confidence: 99%

Detection of Circulating Tumor DNA in Solid Tumors

Testa¹,

Castelli²

2020

genetics

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Cancer is characterized by sequential and progressive genetic and epigenetic alterations in key proto-oncogenes and tumor suppressor genes, which ultimately lead to tumor development. Advances in the technology of analysis of molecular mechanisms have increased the efficiency of clinical management of cancer patients. Recent years have witnessed a progressive development in technologies that enable the detection of specific molecular abnormalities associated with various types of solid tumors in body fluids, a process that is globally known as "liquid biopsy". Liquid biopsy is largely based on the circulating free DNA (cfDNA) present in the plasma of healthy individuals and derived either from cell apoptosis or from the active secretion of microvesicles mediated by white blood cells (WBCs). The plasma of cancer patients contains DNA, which is referred to as circulating tumor DNA (ctDNA) and is released by the tumor cells in the form of DNA fragments of various sizes bearing the various types of genetic abnormalities specific to the tumors from which were derived. Sequencing studies conducted with several thousands of cancer patients have revealed that ctDNA accounts for only a fraction of the total DNA, and the size of this fraction varies in relation to tumor burden, tumor site, tumor subtypes, and several other biological properties of the tumor cells. Therefore, the levels of ctDNA are extremely low in several earlystage tumors, requiring highly sensitive methods for the detection of genetic alterations

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Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer

Abstract: Calagua. Portions of this research utilized the computational resources of the NIH HPC Biowulf cluster. 3 IN MEMORIAMThis work is dedicated to the memory of Dr. Valery Bliskovsky, who made invaluable contributions to this project.

Cited by 18 publications

References 46 publications

A case report of multiple primary prostate tumors with differential drug sensitivity

A case report of multiple primary prostate tumors with differential drug sensitivity

Early circulating tumour DNA kinetics measured by ultra-deep next-generation sequencing during radical radiotherapy for non-small cell lung cancer: a feasibility study

Detection of Circulating Tumor DNA in Solid Tumors

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