SuperFreq: Integrated mutation detection and clonal tracking in cancer.

07:00 EST 13th February 2020 | BioPortfolio

Summary of "SuperFreq: Integrated mutation detection and clonal tracking in cancer."

Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that drive progression. Existing approaches for clonal tracking from sequencing data typically require the user to combine multiple tools that are not purpose-built for this task. Furthermore, most methods require a matched normal (non-tumour) sample, which limits the scope of application. We developed SuperFreq, a cancer exome sequencing analysis pipeline that integrates identification of somatic single nucleotide variants (SNVs) and copy number alterations (CNAs) and clonal tracking for both. SuperFreq does not require a matched normal and instead relies on unrelated controls. When analysing multiple samples from a single patient, SuperFreq cross checks variant calls to improve clonal tracking, which helps to separate somatic from germline variants, and to resolve overlapping CNA calls. To demonstrate our software we analysed 304 cancer-normal exome samples across 33 cancer types in The Cancer Genome Atlas (TCGA) and evaluated the quality of the SNV and CNA calls. We simulated clonal evolution through in silico mixing of cancer and normal samples in known proportion. We found that SuperFreq identified 93% of clones with a cellular fraction of at least 50% and mutations were assigned to the correct clone with high recall and precision. In addition, SuperFreq maintained a similar level of performance for most aspects of the analysis when run without a matched normal. SuperFreq is highly versatile and can be applied in many different experimental settings for the analysis of exomes and other capture libraries. We demonstrate an application of SuperFreq to leukaemia patients with diagnosis and relapse samples.


Journal Details

This article was published in the following journal.

Name: PLoS computational biology
ISSN: 1553-7358
Pages: e1007603


DeepDyve research library

PubMed Articles [23684 Associated PubMed Articles listed on BioPortfolio]

Breast cancer surveillance for BRCA1/2 mutation carriers - is "early detection" early enough?

Annual MRI screening is associated with a significant reduction in advanced-stage breast cancer diagnosis in BRCA1/2 mutation carriers. The impact that early detection has on subsequent oncological tr...

FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue.

With growing interest in monitoring mutational processes in normal tissues, tumor heterogeneity, and cancer evolution under therapy, the ability to accurately and economically detect ultra-rare mutati...

Longitudinal assessment of clonal mosaicism in humanhematopoiesis via mitochondrial mutation tracking.

Our ability to track cellular dynamics in humans over time in vivo has been limited. Here, we demonstrate how somatic mutations in mitochondrial DNA (mtDNA) can be used to longitudinally track the dyn...

Clonal hematopoiesis in hematological disorders.

Clonality studies can establish the single cell origin of tumors and thus differentiate clonal malignant and premalignant processes from reactive polyclonal processes. Detection of clonal cells may be...

Enrichment and Analysis of ctDNA.

ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity...

Clinical Trials [16454 Associated Clinical Trials listed on BioPortfolio]

Liquid Biopsy for Detection of Driver Mutation in NSCLC

The purpose of this study is to evaluate the diagnostic and prognostic efficacy of liquid biopsy in different specimens and in different methods compared with tissue detection .

Integrated Eye Tracking and Neural Monitoring for Enhanced Assessment of Mild TBI: Primary Study

This study was conducted to develop and validate integrated eye tracking and EEG measures for assessment of mild traumatic brain injury.

Next-generation Sequencing of Small Cell Lung Cancer to Identify Susceptibility Gene and to Assess Treatment

Participants will be consented into the study after they are found to meet the study inclusion criteria. The clinical staff will schedule a tissue biopsy and a blood draw for the participa...

Circulating Tumor DNA and Follow-up of BRCA1 Mutation Carriers (CirCa 01)

BRCA1 carriers who are at high risk of developing either a relapse and/or a new cancer growth will be included. These patients will be followed up during 30 months (2, 5 years) with mutate...

A Combination of Vemurafenib, Cytarabine and 2-chlorodeoxyadenosine in Children With LCH and BRAF V600E Mutation

Langerhans cell histiocytosis (LCH) is a disease caused by clonal expansion, proliferation, and dissemination of cells that are phenotypically close to Langerhans cells in different tissue...

Medical and Biotech [MESH] Definitions

Methods to identify and characterize cancer in the early stages of disease and predict tumor behavior.

The mechanism, in central lymphoid organs (THYMUS; BONE MARROW), that prevents immature lymphocytes from reacting to SELF-ANTIGENS. This is accomplished by CLONAL ANERGY and CLONAL DELETION.

Tumor suppressor genes located in the 5q21 region on the long arm of human chromosome 5. The mutation of these genes is associated with the formation of colorectal cancer (MCC stands for mutated in colorectal cancer).

A specialty which deals with the interrelationship of physical, psychological, social, behavioral, and ethical aspects of cancer. Psycho-oncology examines the behavioral and psychosocial factors that may influence the course of the disease, cancer risk, prevention, and detection.

LYMPHOCYTE ACTIVATION by a specific ANTIGEN thus triggering clonal expansion of LYMPHOCYTES already capable of mounting an immune response to the antigen.

Quick Search

DeepDyve research library

Relevant Topics

Cancer Disease
Cancer is not just one disease but many diseases. There are more than 100 different types of cancer. Most cancers are named for the organ or type of cell in which they start - for example, cancer that begins in the colon is called colon cancer; cancer th...

  Bladder Cancer Brain Cancer Breast Cancer Cancer Cervical Cancer Colorectal Head & Neck Cancers Hodgkin Lymphoma Leukemia Lung Cancer Melanoma Myeloma Ovarian Cancer Pancreatic Cancer ...

Searches Linking to this Article