Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content
Abstract Background Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. Molecular profiling of ctDNA is often...
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| Format: | Article |
| Language: | English |
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BMC
2022-01-01
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| Series: | BMC Cancer |
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| Online Access: | https://doi.org/10.1186/s12885-021-09160-1 |
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| author | Devika Ganesamoorthy Alan James Robertson Wenhan Chen Michael B. Hall Minh Duc Cao Kaltin Ferguson Sunil R. Lakhani Katia Nones Peter T. Simpson Lachlan J. M. Coin |
| author_facet | Devika Ganesamoorthy Alan James Robertson Wenhan Chen Michael B. Hall Minh Duc Cao Kaltin Ferguson Sunil R. Lakhani Katia Nones Peter T. Simpson Lachlan J. M. Coin |
| author_sort | Devika Ganesamoorthy |
| collection | DOAJ |
| description | Abstract Background Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. Molecular profiling of ctDNA is often performed using targeted sequencing or low-coverage whole genome sequencing (WGS) to identify tumour specific somatic mutations or somatic copy number aberrations (sCNAs). However, these approaches cannot efficiently detect all tumour-derived genomic changes in ctDNA. Methods We performed WGS analysis of cfDNA from 4 breast cancer patients and 2 patients with benign tumours. We sequenced matched germline DNA for all 6 patients and tumour samples from the breast cancer patients. All samples were sequenced on Illumina HiSeqXTen sequencing platform and achieved approximately 30x, 60x and 100x coverage on germline, tumour and plasma DNA samples, respectively. Results The mutational burden of the plasma samples (1.44 somatic mutations/Mb of genome) was higher than the matched tumour samples. However, 90% of high confidence somatic cfDNA variants were not detected in matched tumour samples and were found to comprise two background plasma mutational signatures. In contrast, cfDNA from the di-nucleosome fraction (300 bp–350 bp) had much higher proportion (30%) of variants shared with tumour. Despite high coverage sequencing we were unable to detect sCNAs in plasma samples. Conclusions Deep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples, which were not detected in matched tumour samples. Sequencing of di-nucleosome bound cfDNA fragments may increase recovery of tumour mutations from plasma. |
| first_indexed | 2024-12-23T19:33:27Z |
| format | Article |
| id | doaj.art-7c33650a162849c0917d3be7602f54e8 |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-12-23T19:33:27Z |
| publishDate | 2022-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-7c33650a162849c0917d3be7602f54e82022-12-21T17:33:51ZengBMCBMC Cancer1471-24072022-01-0122111310.1186/s12885-021-09160-1Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour contentDevika Ganesamoorthy0Alan James Robertson1Wenhan Chen2Michael B. Hall3Minh Duc Cao4Kaltin Ferguson5Sunil R. Lakhani6Katia Nones7Peter T. Simpson8Lachlan J. M. Coin9Institute for Molecular Bioscience, University of QueenslandInstitute for Molecular Bioscience, University of QueenslandInstitute for Molecular Bioscience, University of QueenslandInstitute for Molecular Bioscience, University of QueenslandInstitute for Molecular Bioscience, University of QueenslandCentre for Clinical Research, Faculty of Medicine, The University of QueenslandCentre for Clinical Research, Faculty of Medicine, The University of QueenslandQIMR Berghofer Medical Research InstituteCentre for Clinical Research, Faculty of Medicine, The University of QueenslandInstitute for Molecular Bioscience, University of QueenslandAbstract Background Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. Molecular profiling of ctDNA is often performed using targeted sequencing or low-coverage whole genome sequencing (WGS) to identify tumour specific somatic mutations or somatic copy number aberrations (sCNAs). However, these approaches cannot efficiently detect all tumour-derived genomic changes in ctDNA. Methods We performed WGS analysis of cfDNA from 4 breast cancer patients and 2 patients with benign tumours. We sequenced matched germline DNA for all 6 patients and tumour samples from the breast cancer patients. All samples were sequenced on Illumina HiSeqXTen sequencing platform and achieved approximately 30x, 60x and 100x coverage on germline, tumour and plasma DNA samples, respectively. Results The mutational burden of the plasma samples (1.44 somatic mutations/Mb of genome) was higher than the matched tumour samples. However, 90% of high confidence somatic cfDNA variants were not detected in matched tumour samples and were found to comprise two background plasma mutational signatures. In contrast, cfDNA from the di-nucleosome fraction (300 bp–350 bp) had much higher proportion (30%) of variants shared with tumour. Despite high coverage sequencing we were unable to detect sCNAs in plasma samples. Conclusions Deep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples, which were not detected in matched tumour samples. Sequencing of di-nucleosome bound cfDNA fragments may increase recovery of tumour mutations from plasma.https://doi.org/10.1186/s12885-021-09160-1Cell-free DNACell-free tumour DNASomatic mutationsMutational signatures |
| spellingShingle | Devika Ganesamoorthy Alan James Robertson Wenhan Chen Michael B. Hall Minh Duc Cao Kaltin Ferguson Sunil R. Lakhani Katia Nones Peter T. Simpson Lachlan J. M. Coin Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content BMC Cancer Cell-free DNA Cell-free tumour DNA Somatic mutations Mutational signatures |
| title | Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content |
| title_full | Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content |
| title_fullStr | Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content |
| title_full_unstemmed | Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content |
| title_short | Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content |
| title_sort | whole genome deep sequencing analysis of cell free dna in samples with low tumour content |
| topic | Cell-free DNA Cell-free tumour DNA Somatic mutations Mutational signatures |
| url | https://doi.org/10.1186/s12885-021-09160-1 |
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