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Supplementary Figure S2 from Complex Patterns of Genomic Heterogeneity Identified in 42 Tumor Samples and ctDNA of a Pulmonary Atypical Carcinoid Patient

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posted on 2023-04-04, 02:01 authored by Tamsin J. Robb, Peter Tsai, Sandra Fitzgerald, Paula Shields, Pascalene S. Houseman, Rachna Patel, Vicky Fan, Ben Curran, Rexson Tse, Jacklyn Ting, Nicole Kramer, Braden J. Woodhouse, Esther Coats, Polona Le Quesne Stabej, Jane Reeve, Kate Parker, Ben Lawrence, Cherie Blenkiron, Cristin G. Print

Supplementary Figure S2: Breakpoints in 10x Loupe software linked-reads view.

Each bar represents a sequencing read, and those joined with a horizontal line share the same barcode.

Reads are grouped by haplotype (green and purple), with unphased reads in grey. Vertical orange lines indicate putative breakpoints defined by the software. Given that the maximum region of the chromosome phased was significantly shorter than the length of Chr 11 (as indicated in the ‘phase block view’ plot), some breakpoints are assigned to different haplotypes, therefore haplotypes should not be compared between regions (the breakpoint appears in purple in some regions and in green in others).

The copy number patterns are consistent with all breakpoints occurring on the same copy of the chromosome.

Funding

Auckland Medical Research Foundation (AMRF)

Translational Medicine Trust

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ARTICLE ABSTRACT

DNA sequencing data from tumor samples and blood plasma from a single patient highlighted the critical early role of chromosomal alterations in atypical carcinoid tumor development. Common tumor variants were readily detected in the blood plasma, unlike emerging tumor variants, which has implications for using ctDNA to capture cancer evolution.

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