Fallbericht: Analyse der zirkulierenden Tumor-DNA-Fraktion mittels Ultra-Low-Pass Whole-Genome Sequencing korreliert bei kleinzelligem Stage-IV-Zervixkarzinom mit Ansprechen auf Radiochemotherapie und Rezidivierung – Eine Längsschnittstudie

2021 ◽  
pp. 1-6
Author(s):  
Ata Abbas ◽  
Morgan Gruner ◽  
Jennifer Karohl ◽  
Peter G. Rose ◽  
Amy Joehlin-Price ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Stage Iv ◽  
Cervix Uteri ◽  
Whole Genome ◽  
Aggressive Form ◽  
Radiologische Befunde ◽  
Low Pass ◽  
Tumor Dna

Das neuroendokrine Karzinom der Cervix uteri ist eine seltene und aggressive Form von Gebärmutterhalskrebs, die durch häufige Metastasierung schon bei Diagnosestellung und durch hohe Rezidivraten gekennzeichnet ist. Die Primärtherapie ist multimodal und beinhaltet oft eine Chemotherapie, zum Teil in Verbindung mit einer Strahlentherapie. Es liegen keine Daten vor, die Orientierung für das Vorgehen bei Rezidiven geben; Zweitlinientherapien werden aus Daten zum kleinzelligen Bronchialkarzinom abgeleitet. Die engmaschige Überwachung dieser Patientinnen im Hinblick auf Rezidive ist von größter Bedeutung. Dafür stellt die Bestimmung der zirkulierenden Tumor-DNA (ctDNA) im peripheren Blut eine attraktive, weil nicht-invasive Option dar. Mit dem ULP-WGS-Verfahren (<i>ultra-low-pass whole-genome sequencing</i>) lassen sich die Tumorlast und das Tumoransprechen beurteilen und Prognosen zur Rezidivierung abgeben; allerdings mangelt es bisher noch an Daten zur Rolle der ULP-WGS beim kleinzelligen Zervixkarzinom. Die vorliegende Arbeit stellt eine Patientin vor, deren Chemotherapie-Ansprechen und Tumor-Rezidivierung durch die ctDNA-Analyse korrekt überwacht wurden, wie radiologische Befunde bestätigten.

scholarly journals Case Report: Circulating Tumor DNA Fraction Analysis Using Ultra-Low-Pass Whole-Genome Sequencing Correlates Response to Chemoradiation and Recurrence in Stage IV Small-Cell Carcinoma of the Cervix - A Longitudinal Study

2021 ◽  
Vol 11 ◽  
Author(s):  
Ata Abbas ◽  
Morgan Gruner ◽  
Jennifer Karohl ◽  
Peter G. Rose ◽  
Amy Joehlin-Price ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Whole Genome Sequencing ◽  
Small Cell Carcinoma ◽  
Genome Sequencing ◽  
Circulating Tumor Dna ◽  
Small Cell ◽  
Response To Therapy ◽  
Whole Genome ◽  
Low Pass ◽  
Tumor Dna

Neuroendocrine carcinoma of the cervix is a rare and aggressive form of cervical cancer that presents with frequent metastasis at diagnosis and high recurrence rates. Primary treatment is multimodal, which often includes chemotherapy with or without radiation therapy. There are no data available to guide treatment for recurrence, and second-line therapies are extrapolated from small-cell lung carcinoma data. Close monitoring of these patients for recurrence is paramount. Evaluation of circulating tumor DNA (ctDNA) in the peripheral blood is an attractive approach due to its non-invasive nature. Ultra-low-pass whole-genome sequencing (ULP-WGS) can assess tumor burden and response to therapy and predict recurrence; however, data are lacking regarding the role of ULP-WGS in small-cell carcinoma of the cervix. This study demonstrates a patient whose response to chemotherapy and cancer recurrence was accurately monitored by ctDNA analysis using ULP-WGS and confirmed with radiologic imaging findings.

Abstract 2739: Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA

2017 ◽  
Author(s):  
Xiaoji Chen ◽  
Jill M. Spoerke ◽  
Kathryn Yoh ◽  
Walter C. Darbonne ◽  
Ling-Yuh Huw ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Circulating Tumor Dna ◽  
Copy Number Variations ◽  
Whole Genome ◽  
Low Pass ◽  
Tumor Dna

scholarly journals Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer

2019 ◽  
pp. 1-13 ◽  
Author(s):  
S. Thomas Hennigan ◽  
Shana Y. Trostel ◽  
Nicholas T. Terrigino ◽  
Olga S. Voznesensky ◽  
Rachel J. Schaefer ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Metastatic Prostate Cancer ◽  
Circulating Tumor Dna ◽  
Localized Prostate Cancer ◽  
Whole Genome ◽  
Aggressive Disease ◽  
Low Pass ◽  
Tumor Dna

PURPOSE Despite decreased screening-based detection of clinically insignificant tumors, most diagnosed prostate cancers are still indolent, indicating a need for better strategies for detection of clinically significant disease before treatment. We hypothesized that patients with detectable circulating tumor DNA (ctDNA) were more likely to harbor aggressive disease. METHODS We applied ultra-low-pass whole-genome sequencing to profile cell-free DNA from 112 patients diagnosed with localized prostate cancer and performed targeted resequencing of plasma DNA for somatic mutations previously identified in matched solid tumor in nine cases. We also performed similar analyses of data from patients with metastatic prostate cancer. RESULTS In all cases of localized prostate cancer, even in clinically high-risk patients who subsequently had recurrent disease, ultra-low-pass whole-genome sequencing and targeted resequencing did not detect ctDNA in plasma acquired before surgery or before recurrence. In contrast, using both approaches, ctDNA was detected in patients with metastatic prostate cancer. CONCLUSION Our findings demonstrate clear differences between localized and advanced prostate cancer with respect to the dissemination and detectability of ctDNA. Because allele-specific alterations in ctDNA are below the threshold for detection in localized prostate cancer, other approaches to identify cell-free nucleic acids of tumor origin may demonstrate better specificity for aggressive disease.

BIOM-23. A PILOT STUDY OF WHOLE GENOME SEQUENCING (WGS) OF PLASMA CELL-FREE DNA (cfDNA) FOR ULTRASENSITIVE DETECTION OF TUMOR DNA IN PATIENTS WITH GLIOBLASTOMA (GBM)

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi15-vi15
Author(s):  
Stephen J Bagley ◽  
Jacob Till ◽  
Aseel Abdalla ◽  
MacLean Nasrallah ◽  
Tomer Lauterman ◽  
...  
Keyword(s):  
Pilot Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tumor Tissue ◽  
Methylation Status ◽  
Tumor Burden ◽  
Whole Genome ◽  
Newly Diagnosed ◽  
Genome Wide ◽  
Tumor Dna

Abstract BACKGROUND Plasma circulating tumor DNA (ctDNA) is rarely detectable by traditional methods in patients with GBM. As a result, unlike in lung and other cancers, serial next generation sequencing of ctDNA for monitoring GBM tumor burden has been challenging. In light of the low tumor fraction (TF) of DNA fragments in GBM patient plasma and the urgent need to improve upon MRI for tracking GBM tumor burden, we conducted a pilot study in patients with newly diagnosed GBM using the C2 intelligence platform (C2i Genomics), which leverages genome-wide mutational integration for highly sensitive ctDNA detection. METHODS Plasma was collected pre- and post-operatively in patients with newly diagnosed GBM undergoing surgical resection/biopsy. cfDNA was extracted, quantified, and analyzed for fragment size. Genomic DNA (gDNA) was extracted from matched tumor tissue. Whole genome sequencing (WGS) was performed on both gDNA and cfDNA. A specific copy number alteration (CNA) compendium was created for each patient to generate a readout of TF (Zviran, Nat Medicine 2020). We assessed the association between TF at post-operative day 1 (a surrogate for residual disease) and OS, adjusting for other prognostic factors using Cox regression. RESULTS 37 patients were enrolled. For samples with high tumor fraction (n=5), a statistically significant (p&lt; 1e-4) correlation between CNA profiles of tumor tissue and plasma samples was observed. Post-operative TF above the median value was associated with inferior OS (median 7.7 vs. 19.3 months, p=0.019). This association persisted after adjusting for age, O6-methylguanine-DNA methyltransferase methylation status, extent of resection, and performance status (adjusted HR 2.5, 95% CI 1.1-5.6, p=0.03). CONCLUSION Genome-wide mutational integration enables ultra-sensitive detection of ctDNA in GBM patient plasma. Post-operative TF measured by the C2i test is independently associated with OS in newly diagnosed GBM, providing the foundation to evaluate this technology for personalized prognostication and disease monitoring.

Copy‐Number Variants Detection by Low‐Pass Whole‐Genome Sequencing

2017 ◽  
Vol 94 (1) ◽  
Author(s):  
Zirui Dong ◽  
Weiwei Xie ◽  
Haixiao Chen ◽  
Jinjin Xu ◽  
Huilin Wang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Copy Number Variants ◽  
Whole Genome ◽  
Low Pass

iStopCancer: A database of 6,016 low pass whole genome sequencing of minimal invasive samples from 21 cancer types of Chinese population.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 7062-7062
Author(s):  
Min Yuan ◽  
Qian Ziliang ◽  
Juemin Fang ◽  
Zhongzheng Zhu ◽  
Jianguo Wu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Cancer Patients ◽  
Genome Sequencing ◽  
Minimal Invasive ◽  
The Body ◽  
Whole Genome Sequencing Data ◽  
Low Grade ◽  
Whole Genome ◽  
Low Pass ◽  
Low Coverage

7062 Background: Cancer is a group of genetic diseases that result from changes in the genome of cells in the body, leading them to grow uncontrollably. Recent researches suggest Chromosome instability (CIN), which is defined as an increased rate of chromosome gains and losses, manifests as cell-to-cell karyotypic heterogeneity and drives cancer initiation and evolution. Methods: In the past two years, we initiated iStopCancer project, and characterized 4515 ‘best available’ minimal-invasive samples from cancer patients and 1501 plasma samples from non-tumor diseases by using low-pass whole genome sequencing. DNA from ‘best available’ minimal-invasive samples, including peripheral plasma, urines, pancreatic juice, bile and effusions were analyzed by low coverage whole genome sequencing followed by the UCAD Bioinformatics workflow to characterize the CINs. In total, 32T bp nucleotide (coverage =1.7X for each sample) were collected. All the data can be visualized on website: http://www.istopcancer.net/pgweb/cn/istopcancer.jsp . Results: 3748(83%) of tumors present detectable CIN (CIN score>1000) in minimal-invasive samples. The missed cancer patients were majorly from patients with either tumor size less than 2cm or less-aggressive cancers, including thyroid cancer, low-grade urothelial carcinoma, lung cancer in-situ, et al. Of the 1501 non-tumor individuals, 30(2.0%) present detectable CIN (|Z|>=3) at the time of sample collection, 24(80.0%) was diagnosed as tumor patient in 3-6 months follow-up. There were 9 (0.59%) of non-cancer individuals without detectable CIN were also reported as tumor patients during 6-month following up. In summary, the positive and negative prediction value is 80.0% and 99.4% respectively. The false alarms were majorly from patients with EBV activations, which indicates virus may interference chromosome stability and drove virus-associated carcinogenesis. For the patient with repeated detections, plasma cfDNA CIN dynamics predicted clinical responses and disease recurrences. Quick clearance of plasma cfDNA CIN in 2-3 weeks was found in 153 (83.6%) patients. Meanwhile, no quick clearance was found in majority of SDs/PDs (73/88=83.0%). Furthermore, cfDNA CIN predicts clinical response 2-8 weeks ahead of traditional biomarkers (CEA, CA15-3, CA199, AFP et al). Conclusions: Large-scale low coverage whole genome sequencing data provides useful information for cancer detection and managements.

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