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Completing a genomic characterisation of microscopic tumour samples with copy number.

ABSTRACT:

Background

Genomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously developed the DigiPico sequencing platform to accurately identify somatic mutations from such samples.

Results

Here, we complete this genomic characterisation with copy number. We present a novel protocol, PicoCNV, to call allele-specific somatic copy number alterations from picogram quantities of tumour DNA. We find that PicoCNV provides exactly accurate copy number in 84% of the genome for even the smallest samples, and demonstrate its clinical potential in maintenance therapy.

Conclusions

PicoCNV complements our existing platform, allowing for accurate and comprehensive genomic characterisations of cancers in settings where only microscopic samples are available.

SUBMITTER: Nulsen J

PROVIDER: S-EPMC10688092 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Completing a genomic characterisation of microscopic tumour samples with copy number.

Nulsen Joel J Hussain Nosheen N Al-Deka Aws A Yap Jason J Uddin Khalil K Yau Christopher C Ahmed Ahmed Ashour AA

BMC bioinformatics 20231130 1

<h4>Background</h4>Genomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously developed the DigiPico sequencing platform to accurately identify somatic mutations from such samples.<h4>Results</h4>Here, we complete this genomic characterisation with copy number. We present a novel protocol, PicoCNV, to call allele-specific somatic copy number alterations f ...[more]

PMID: 38036971

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