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Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
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Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number
Stephanie B Greene1, Angel E Dago1, Laura J Leitz1
1Epic Sciences, Inc., San Diego, CA, United States of America.
Plos One
|November 17, 2016
Summary
Genomic instability in circulating tumor cells (CTCs) can now be assessed at the single-cell level. This new assay detects copy number variations and genomic instability in CTCs, offering insights into cancer heterogeneity and treatment resistance.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Genomic instability is a key cancer hallmark linked to poor prognosis and therapy resistance.
- Assessing genomic instability in bulk tumor samples faces challenges like heterogeneity and limited sample availability.
- Circulating tumor cells (CTCs) offer a minimally invasive source for understanding tumor biology.
Purpose of the Study:
- To develop and validate a single-cell Copy Number Variation (CNV) assay for evaluating genomic instability in patient CTCs.
- To assess the feasibility of detecting genomic alterations and instability in CTCs from metastatic castration-resistant prostate cancer (mCRPC) patients.
- To establish the minimum sequencing requirements for reliable detection of genomic alterations in single CTCs.
Main Methods:
- Developed a single-cell CNV assay for genomic profiling of individual CTCs.
- Utilized the Epic Sciences CTC platform for CTC enumeration and characterization from blood samples.
- Performed whole genome amplification and sequencing of isolated CTCs, followed by copy number variation and large-scale state transition (LST) analysis.
- Validated the assay using prostate cancer cell lines spiked into healthy blood and clinical samples from mCRPC patients.
Main Results:
- The single-cell CNV assay reproducibly measured genomic instability in prostate cancer cell lines, with higher scores than white blood cell controls.
- Significant genomic alterations, including PTEN loss and androgen receptor (AR) amplification, were identified in mCRPC patient CTCs.
- Genomic instability and copy number variations can be reliably detected with as few as 350,000 sequencing reads per cell.
- A wide spectrum of genomic instability was observed within and among mCRPC patient samples, highlighting tumor heterogeneity.
Conclusions:
- The developed single-cell CNV assay is feasible for detecting genomic instabilities in CTCs.
- Single-cell genomic profiling of CTCs provides valuable insights into cancer heterogeneity and clonal evolution.
- This approach holds potential for patient stratification and monitoring disease progression in cancer treatment.
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