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Cancer genome standards for long-read sequencing using cancer cell line mixtures
Jia Zhang1,2, Ho Yi Wong1,2, Lingchen Liu1,2
1QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
Gigascience
|April 4, 2026
Summary
Long-read sequencing (LRS) offers a promising approach for cancer variant detection, achieving recall rates comparable to short-read methods. Adequate sequencing depth in normal samples is crucial for accurate somatic variant identification using LRS.
Area of Science:
- Genomics
- Cancer Research
- Bioinformatics
Background:
- Long-read sequencing (LRS) enhances genome alignment and variant resolution in complex regions.
- LRS is a promising technology for cancer variant detection and biomarker discovery.
Purpose of the Study:
- To evaluate the performance of Oxford Nanopore LRS for detecting somatic variants in cancer.
- To compare LRS with short-read sequencing across various tumor purities and sequencing depths.
Main Methods:
- Generated experimental mixtures of cancer and normal cell lines simulating 10 tumor purities.
- Sequenced 22 samples using whole-genome LRS to 60x depth.
- Down-sampled data to determine optimal sequencing depth for variant detection.
Main Results:
- LRS variant calling tools demonstrated recall rates comparable to short-read gold standards.
- Tumor sequencing depth of 30x-60x is sufficient for common and structural variant detection.
- Adequate sequencing depth of matched normal samples is critical for accuracy.
Conclusions:
- LRS is effective for cancer variant detection, especially for structural variants.
- Optimizing sequencing depth and normal sample coverage are key for LRS implementation.
- LRS identified unique variants, suggesting potential for novel discoveries.
