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Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy
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Assessing aneuploidy with repetitive element sequencing.

Christopher Douville1,2,3,4, Joshua D Cohen1,2,3,4,5, Janine Ptak1,2,3,4

  • 1Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287.

Proceedings of the National Academy of Sciences of the United States of America
|February 21, 2020
PubMed
Summary
This summary is machine-generated.

A new assay, RealSeqS, detects cancer aneuploidy in liquid biopsies with high sensitivity. Combining this with other markers improves early cancer detection in patients.

Keywords:
aneuploidycirculating tumor DNAearly cancer detectionliquid biopsy

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Area of Science:

  • Genomics
  • Molecular Biology
  • Oncology

Background:

  • Aneuploidy, an abnormal chromosome number, is a hallmark of cancer.
  • Early cancer detection is crucial for improving patient outcomes.
  • Sensitive molecular assays are needed for non-invasive cancer diagnosis.

Purpose of the Study:

  • To develop and validate a sensitive PCR-based assay for detecting cancer aneuploidy.
  • To assess the performance of the assay in liquid biopsies from various cancer types.
  • To evaluate the combined diagnostic potential of aneuploidy detection with other biomarkers.

Main Methods:

  • Developed the Repetitive Element AneupLoidy Sequencing System (RealSeqS) using a single primer pair.
  • Amplified approximately 350,000 genomic amplicons.
  • Analyzed liquid biopsies from 883 nonmetastatic cancer patients and 812 healthy controls.

Main Results:

  • RealSeqS detected aneuploidy in 49% of liquid biopsies across eight cancer types (colorectum, esophagus, liver, lung, ovary, pancreas, breast, stomach).
  • The assay requires as little as 3 pg of DNA.
  • Combining aneuploidy detection with somatic mutation analysis and protein biomarkers achieved 80% median sensitivity, with only 1% false positives in healthy controls.

Conclusions:

  • RealSeqS is a sensitive and effective method for detecting cancer aneuploidy in liquid biopsies.
  • The integration of aneuploidy detection with other biomarkers significantly enhances early cancer detection capabilities.
  • This approach holds promise for non-invasive cancer screening and diagnosis.