scholarly journals Selecting short DNA fragments in plasma improves detection of circulating tumour DNA

2017 ◽  
Author(s):  
Florent Mouliere ◽  
Anna M. Piskorz ◽  
Dineika Chandrananda ◽  
Elizabeth Moore ◽  
James Morris ◽  
...  
Keyword(s):  
Residual Disease ◽  
Dna Fragments ◽  
Copy Number Alterations ◽  
Chemotherapy Treatment ◽  
Genomic Changes ◽  
Size Selection ◽  
Non Invasive ◽  
Cancer Genomes ◽  
Circulating Tumour Dna ◽  
Tumour Origin

Introductory paragraphNon-invasive analysis of cancer genomes using cell-free circulating tumour DNA (ctDNA) is being widely implemented for clinical indications. The sensitivity for detecting the presence of ctDNA and genomic changes in ctDNA is limited by its low concentration compared to cell-free DNA of non-tumour origin. We studied the feasibility for enrichment of ctDNA by size selection, in plasma samples collected before and during chemotherapy treatment in 13 patients with recurrent high-grade serous ovarian cancer. We evaluated the effects using targeted and whole genome sequencing. Selecting DNA fragments between 90-150 bp before analysis yielded enrichment of mutated DNA fraction of up to 11-fold. This allowed identification of adverse copy number alterations, including MYC amplification, otherwise not observed. Size selection allows detection of tumour alterations masked by non-tumour DNA in plasma and could help overcome sensitivity limitations of liquid biopsy for applications in early diagnosis, detection of minimal residual disease, and genomic profiling.

Clinical validation of qPCR Target Selector™ assays using highly specific switch-blockers for rare mutation detection

2020 ◽  
Vol 73 (10) ◽  
pp. 648-655
Author(s):  
Lyle Arnold ◽  
Vassilios Alexiadis ◽  
Tim watanaskul ◽  
Vahid Zarrabi ◽  
Jason Poole ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Dna Amplification ◽  
Resistance Mutations ◽  
Tissue Samples ◽  
Patients With Cancer ◽  
Non Invasive ◽  
Dna Mutations ◽  
Substantial Risk ◽  
Specific Amplification ◽  
Circulating Tumour Dna

AimsThe identification of actionable DNA mutations associated with a patient’s tumour is critical for devising a targeted, personalised cancer treatment strategy. However, these molecular analyses are typically performed using tissue obtained via biopsy, which involves substantial risk and is often not feasible. In addition, biopsied tissue does not always reflect tumour heterogeneity, and sequential biopsies to track disease progression (eg, emergence of drug resistance mutations) are not well tolerated. To overcome these and other biopsy-associated limitations, we have developed non-invasive ‘liquid biopsy’ technologies to enable the molecular characterisation of a patient’s cancer using peripheral blood samples.MethodsThe Target Selector ctDNA platform uses a real-time PCR-based approach, coupled with DNA sequencing, to identify cancer-associated genetic mutations within circulating tumour DNA. This is accomplished via a patented blocking approach suppressing wild-type DNA amplification, while allowing specific amplification of mutant alleles.ResultsTo promote the clinical uptake of liquid biopsy technologies, it is first critical to demonstrate concordance between results obtained via liquid and traditional biopsy procedures. Here, we focused on three genes frequently mutated in cancer: EGFR (Del19, L858, and T790), BRAF (V600) and KRAS (G12/G13). For each Target Selector assay, we demonstrated extremely high accuracy, sensitivity and specificity compared with results obtained from tissue biopsies. Overall, we found between 93% and 96% concordance to blinded tissue samples across 127 clinical assays.ConclusionsThe switch-blocker technology reported here offers a highly effective method for non-invasively determining the molecular signatures of patients with cancer.

scholarly journals Development of circulating tumour DNA analysis for gastrointestinal cancers

ESMO Open ◽  
2020 ◽  
Vol 5 (Suppl 1) ◽  
pp. e000600 ◽  
Author(s):  
Yoshiaki Nakamura ◽  
Kohei Shitara
Keyword(s):  
Dna Analysis ◽  
Residual Disease ◽  
Turnaround Time ◽  
Resistance Mechanisms ◽  
Detection Methods ◽  
Comprehensive Genomic Profiling ◽  
Gi Cancers ◽  
Ctdna Analysis ◽  
Next Generation Sequencing Ngs ◽  
Circulating Tumour Dna

Comprehensive genomic profiling using next-generation sequencing (NGS) enables the identification of multiple genomic biomarkers established in advanced gastrointestinal (GI) cancers. However, tissue-based NGS has limitations, such as long turnaround time and failure to detect tumour heterogeneity. Recently, the analysis of circulating tumour DNA (ctDNA) using polymerase chain reaction-based or NGS-based methods has demonstrated the capability to detect genomic alterations with high accuracy compared with tumour tissue analysis with short turnaround time and identify heterogeneous resistance mechanisms. Furthermore, ctDNA analysis can be repeatedly performed on disease progression to clarify resistant clones. Clinical trials that test the outcome of a selected targeted therapy based on a ctDNA result are ongoing to prospectively evaluate the clinical utility of ctDNA analysis. Furthermore, the improvement of ctDNA analysis beyond current technical limits of mutation-based ctDNA detection methods has expanded the potential for detecting the presence of tumours in patients with no clinically evident disease, such as minimal residual disease and early cancer. Although a careful understanding of the advantages and limitations are required and further prospective studies are needed, the ctDNA analysis has the potential to overcome several challenges in the treatment of various types of cancers at all stages, including GI cancers.

Significance of Copy Number Alterations for Molecular Treatment Response in Childhood Acute Lymphoblastic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1434-1434
Author(s):  
Doris Steinemann ◽  
Gunnar Cario ◽  
Martin Stanulla ◽  
Leonid Karawajew ◽  
Marcel Tauscher ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Treatment Response ◽  
Copy Number ◽  
Array Cgh ◽  
Residual Disease ◽  
Lymphoblastic Leukemia ◽  
Individual Treatment ◽  
Copy Number Alterations ◽  
Childhood All ◽  
Significant Difference

Abstract In vivo response to initial therapy, as assessed by determination of minimal residual disease after five and 12 weeks of treatment, has evolved as one of strong prognostic factors in children with acute lymphoblastic leukemia (ALL) treated according to the BFM regime. It is currently not known if the individual treatment response might be influenced by copy number alterations (CNA) leading to altered gene expression. We compared leukemic genomic profiles of 25 treatment sensitive (MRD-SR) and 25 resistant (MRD-HR) childhood ALL patients by means of high-resolution array-CGH. CNA were found in 46 patients (92%) of both treatment response groups. Microscopic alterations affecting the whole or nearly whole chromosome arm were frequently found, e.g. gain of 21 in 11/50, loss of 9p in 5/50, loss of 8p in 3/50, loss of 20q in 3/50 and loss of 7p in 2/50 or gain of 1q in 2/50. The most significant difference was a gain of chromosome 1q23-qter due to an unbalanced t(1;19), found in 10/25 MRD-SR patients, but in none of the MRD-HR patients (p<0.002). The most frequent CNA in the MRD-HR group were deletions of genomic regions harboring the immunoglobulin genes (Ig), e.g. 2p11.2 in 15 of 25 cases (60%) compared to 7 of 25 in the MRD-SR group (28%) (p=0.045). Combining all Ig loci, significantly more MRD-HR than MRD-SR patients were affected with deletions (17 versus 8 patients, p=0.02). The frequency of other CNA, like loss of 9p21 or gains of 21q, did not differ strongly between the two patient groups. This is the first study evaluating the clinical significance of CNA as detected by array-CGH in childhood ALL and may lead to improved risk classification.

Non-Invasive Monitoring of Urinary KRAS Circulating Tumor DNA for Treatment Response and Minimal Residual Disease in Patients with Lung Adenocarcinoma.

2015 ◽  
Vol 33 (15_suppl) ◽  
pp. e19092-e19092 ◽  
Author(s):  
James Michael Randall ◽  
Mark G. Erlander ◽  
Cecile Rose T. Vibat ◽  
Saege Hancock ◽  
Vlada Melnikova ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Treatment Response ◽  
Minimal Residual Disease ◽  
Residual Disease ◽  
Circulating Tumor Dna ◽  
Invasive Monitoring ◽  
Non Invasive ◽  
Tumor Dna ◽  
Minimal Residual

scholarly journals Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes

2019 ◽  
Author(s):  
Ahmed Ibrahim Samir Khalil ◽  
Costerwell Khyriem ◽  
Anupam Chattopadhyay ◽  
Amartya Sanyal
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Simulated Data ◽  
Change Points ◽  
Copy Number Alterations ◽  
Biological Origin ◽  
Robust Detection ◽  
Cancer Data ◽  
Cancer Genomes ◽  
Low Coverage

AbstractMotivationDetection of copy number alterations (CNA) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales with distinct biological origin and function. Although several tools are available to identify CNAs using read depth (RD) of coverage, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. These tools are also affected by RD signal variations, pronounced in low-coverage data, which significantly inflate false detection of change points and inaccurate CNA calling.ResultsWe have developed CNAtra to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from whole-genome sequencing (WGS) data. CNAtra provides an analytical and visualization framework for CNV profiling using single sequencing sample. CNAtra first utilizes multimodal distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We utilized Savitzy-Golay filter and Modified Varri segmentation to capture the change points. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy number. Next, focal alterations were identified in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. We tested CNAtra calls using experimentally verified segmental aneuploidies and focal alterations which confirmed CNAtra’s ability to detect and distinguish the two alteration phenomena. We used realistic simulated data for benchmarking the performance of CNAtra against other detection tools where we artificially spiked-in CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall, and f-measure. CNAtra shows the highest sensitivity of 93% and 97% for detecting focal and large-scale alterations respectively. Visual inspection of CNAs showed that CNAtra is the most robust detection tool for low-coverage cancer data.Availability and implementationCNAtra is an open source software implemented in MATLAB, and is available at https://github.com/AISKhalil/CNAtra

scholarly journals Recovering rearranged cancer chromosomes from karyotype graphs

2019 ◽  
Author(s):  
Sergey Aganezov ◽  
Ilya Zban ◽  
Vitaly Aksenov ◽  
Nikita Alexeev ◽  
Michael C. Schatz
Keyword(s):  
Large Scale ◽  
Evolutionary Process ◽  
Copy Number Variations ◽  
Graph Representation ◽  
Covering Problem ◽  
Cancer Dataset ◽  
Decomposition Problem ◽  
Genomic Changes ◽  
Circular Structure ◽  
Cancer Genomes

AbstractMany cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time.We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged. CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.

scholarly journals Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing

2019 ◽  
Vol 20 (16) ◽  
pp. 3959 ◽  
Author(s):  
Juraj Gazdarica ◽  
Rastislav Hekel ◽  
Jaroslav Budis ◽  
Marcel Kucharik ◽  
Frantisek Duris ◽  
...  
Keyword(s):  
State Of The Art ◽  
Prenatal Testing ◽  
The State ◽  
Accurate Estimation ◽  
Special Focus ◽  
Dna Fragments ◽  
Sources Of Information ◽  
Non Invasive ◽  
Genomic Locations ◽  
Fetal Fraction

The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion.

scholarly journals Non-invasive diagnosis of retinoblastoma using cell-free DNA from aqueous humour

2019 ◽  
Vol 103 (5) ◽  
pp. 721-724 ◽  
Author(s):  
Amy Gerrish ◽  
Edward Stone ◽  
Samuel Clokie ◽  
John R Ainsworth ◽  
Helen Jenkinson ◽  
...  
Keyword(s):  
Aqueous Humour ◽  
Tumour Tissue ◽  
Retinal Cell ◽  
Chemotherapy Treatment ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Intravitreal Chemotherapy ◽  
Free Dna ◽  
Bilateral Retinoblastoma ◽  
Promising Source

Retinoblastoma is the most common eye malignancy in childhood caused by mutations in the RB1 gene. Both alleles of the RB1 gene must be mutated for tumour development. The initial RB1 mutation may be constitutional germline or somatic (originating in one retinal cell only). Distinguishing between these alternative mechanisms is crucial, with wider implications for management of the patient and family members. Bilateral retinoblastoma is nearly always due to a constitutional mutation; however, approximately 15% of unilateral cases also carry a germline mutation, and identifying these cases is important. This can be achieved by identifying both mutation types in tumour tissue and excluding their presence in blood. Modern eye-saving chemotherapy treatment (systemic, intra-arterial and intravitreal) has resulted in fewer enucleations. As a result, tumour tissue required to identify sporadic RB1 mutation(s) is not always available. Modern intravitreal chemotherapeutic techniques for retinoblastoma involve aspiration of aqueous humour (AH), providing a novel sample source for analysis. By analysing cell-free DNA present in the AH fluid of eyes affected with retinoblastoma, we have developed a screening test capable of detecting somatic RB1 mutations that is comparable to current tests on enucleated tumour tissue. The results obtained with fluid from enucleated eyes were concordant with tumour tissue in all 10 cases analysed. In addition, AH analysis from two patients undergoing intravitreal chemotherapy successfully identified somatic variants in both cases. Our findings suggest that AH fluid is a promising source of tumour-derived DNA in retinoblastoma for analysis.

scholarly journals Circulating Tumour DNA to Guide Treatment of Gastrointestinal Malignancies

2020 ◽  
Vol 36 (5) ◽  
pp. 388-396
Author(s):  
Yat Hang To ◽  
Belinda Lee ◽  
Hui-Li Wong ◽  
Peter Gibbs ◽  
Jeanne Tie
Keyword(s):  
Residual Disease ◽  
Disease Recurrence ◽  
Gastrointestinal Cancers ◽  
Prognostic Information ◽  
Gastrointestinal Malignancies ◽  
Metastatic Lesions ◽  
Apoptosis And Necrosis ◽  
Circulating Tumour Dna ◽  
Related Mortality

<b><i>Background:</i></b> Gastrointestinal cancers are among the most common cancers worldwide and account for a high proportion of cancer-related mortality. Advancements to improve outcomes are constrained by the lack of biomarkers that can offer early diagnostic and prognostic information as traditional serological tumour markers and conventional imaging approaches are not able to provide early information regarding disease recurrence and treatment outcomes. Recent advances in technology have allowed the detection of circulating tumour DNA (ctDNA) in plasma, nucleic acid fragments released into the circulation from primary or metastatic lesions undergoing apoptosis and necrosis. A growing body of evidence has emerged supporting the use of ctDNA in many aspects of cancer care. <b><i>Summary:</i></b> This review focuses on the potential role of ctDNA in the management of patients with gastrointestinal cancers including colorectal, pancreatic, and upper gastrointestinal cancers. In this review, we discuss its possible utility in screening, detection of minimal residual disease and prognostication, longitudinal surveillance, and identification of therapeutic targets and resistance incorporating recent literature and ongoing randomised clinical trials. <b><i>Key Messages:</i></b> ctDNA has substantial potential as a clinically useful marker in the management of gastrointestinal cancers from cancer screening through to treatment of advanced disease.

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