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Supplementary Tables from Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer

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posted on 2023-03-31, 00:41 authored by Natali Gulbahce, Mark Jesus M. Magbanua, Robert Chin, Misha R. Agarwal, Xuhao Luo, Jia Liu, Daniel M. Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li, Yanxiang Chen, Xingpeng Chen, Yuxiang Li, Rebecca Yu Zhang, Katharine Lee, Rick Tearle, Emily Park, Snezana Drmanac, Hope S. Rugo, John W. Park, Radoje Drmanac, Brock A. Peters

The following file contains Tables S1-12. The contents of these tables are referenced through the manuscript and contain the basis for the results summarized in the paper. The list of tables is as follows: S1. CNV. This table contains all the copy number gains and losses identified in the CTCs. S2. SNV. This table contains all of the somatic SNVs identified in the CTCs. S3. Indel. This table contains all of the somatic insertions and deletions identified in the CTCs. S4. NA12877 somatic. This table contains all of the somatic SNVs identified in NA12877. S5. Allele fraction. This table contains allele fraction calculations and compartment number filtering calculations. S6. Sanger and Miseq. This table contains all of the Sanger sequencing and Miseq validation for the 77 somatic SNVs validated in this study. S7. Mutational spectrum. This table contains the mutation spectrum analysis and the comparison of the CTC mutation spectrum to other tumor types. S8. Non-coding annotation. This table contains a list of potentially important somatic noncoding variants. S9. Splicing. This table contains somatic splicing variants. S10. MHC-II. This table contains the potential somatic coding changes which would result in MHC-II binding antigens. S11. Two hit. This table contains genes with two potential inactivating variants, this can include inherited and somatic variants. S12. Phasing. This table contains phased somatic and/or inherited variants that potentially inactivate a gene through a compound heterozygous mechanism.

Funding

Breast Cancer Research Foundation

Shenzhen Municipal Government of China

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ARTICLE ABSTRACT

Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA. WGS resulted in a read coverage of 23× per cell and an ensemble call rate of >95%. These barcoded reads enabled accurate detection of somatic mutations present in as few as 12% of CTCs. We found in CTCs a total of 2,766 somatic single-nucleotide variants and 543 indels and multi-base substitutions, 23 of which altered amino acid sequences. Another 16,961 somatic single nucleotide variant and 8,408 indels and multi-base substitutions, 77 of which were nonsynonymous, were detected with varying degrees of prevalence across the 34 CTCs. On the basis of our whole genome data of mutations found in all CTCs, we identified driver mutations and the tissue of origin of these cells, suggesting personalized combination therapies beyond the scope of most gene panels. Taken together, our results show how advanced WGS of CTCs can lead to high-resolution analyses of cancers that can reliably guide personalized therapy. Cancer Res; 77(16); 4530–41. ©2017 AACR.

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Computational Methods Gene Technologies Genome Biology Translational Research

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