Extended Data Fig. 9: Copy number profile derived from cfDNA of non-cancer controls and cancer patients.
From: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
(a, b) Log2 ratios estimated from the cfDNA of (a) n = 24 female and (b) n = 23 male control individuals. For each individual, the raw Log2 ratios were smoothed using a cubic spline. The two panels show the superimposed splines for all control samples according to gender. (c–e) Log2 ratios of tumor biopsies (top panels) and their corresponding matched cfDNA (bottom panel) for three cases (c) MSK-VB-0008, (d) MSK-VL-0056 and (e) MSK-VP-0004 where amplification of CCND1, FGFR1, EGFR and a homozygous deletion of BRCA2 were reported, respectively. The arrows point to the reported amplifications or deletions. The segmented Log2 ratios were used to compute the Pearson correlation coefficient comparing segments overlapping >75% in the tumor biopsies and cfDNA samples. In (a–e), the Log2 ratios are displayed according to their genomic coordinates. In (c-e), the grey dots show the raw estimates while the red lines represent the segmented values. (f) The association of the Pearson’s r against the ctDNA fraction and purity of the tumor biopsies. The cohort consists of n = 124 cancer patients with paired tumor biopsy and cfDNA samples. The p values were obtained using a permutation based one-sided Jonckheere-Terpstra test for increasing Pearson’s r with ctDNA fraction or tumor purity. The horizontal bars indicate the median and the boxes represent the interquartile range (IQR). The whiskers extend to 1.5 x IQR on either side. NE; not evaluable.
