colo 829  (ATCC)

Journal: Cell Genomics

Article Title: Analysis of error profiles of indels and structural variants in deep-sequencing data

doi: 10.1016/j.xgen.2025.101082

Figure Lengend Snippet: Limit of detection of indels and SVs using COLO829 dilution experiment (A) Observed AFs of somatic alterations demonstrated a high correlation with designed dilution ladders across biological replicates (left and right). Gray shading indicates pure non-cancer cells. (B) Error rates are highly concordant between replicates. (C–D) SNV error rate ( y axis) for 12 substitution types ( x axis) calculated from a previously published dataset (C; see main text) and the deep-sequencing dataset of this study (D). Blue horizontal bars indicate the median error rate, which is also indicated on the top of the panels. (E) Error rate of spike-in indels and SVs in this study. Indels are further grouped into complex, simple, and repeat indels. Blue horizontal bars indicate the median error rate. (F) Error rate of repeat indels is highly correlated with the number of repeat units. In (A) and (B), symbols +, ×, and o represent SNV, SV, and indel, respectively. In (A), dark blue and red indicate detected and missed markers, respectively. Green markers with gray shading highlight error rate in non-cancer samples. In (A), 11 repeat indels are not included due to a high error rate as analyzed in (E) and (F). In (E), counts from both replicates are combined. In (F), all repeat indels have units with length of 1; thus, the homopolymer length equals the number of repeat units. Linear regression p values are shown in (A), (B), and (F). See also , , , and .

Article Snippet: Cell lines COLO829 and COLO829BL were purchased from ATCC (stock # CRL-1974 and # CRL-1980).

Techniques: Sequencing

Journal: Cell Genomics

Article Title: Analysis of error profiles of indels and structural variants in deep-sequencing data

doi: 10.1016/j.xgen.2025.101082

Figure Lengend Snippet: Limit of detection of indels and SVs using COLO829 dilution experiment (A) Observed AFs of somatic alterations demonstrated a high correlation with designed dilution ladders across biological replicates (left and right). Gray shading indicates pure non-cancer cells. (B) Error rates are highly concordant between replicates. (C–D) SNV error rate ( y axis) for 12 substitution types ( x axis) calculated from a previously published dataset (C; see main text) and the deep-sequencing dataset of this study (D). Blue horizontal bars indicate the median error rate, which is also indicated on the top of the panels. (E) Error rate of spike-in indels and SVs in this study. Indels are further grouped into complex, simple, and repeat indels. Blue horizontal bars indicate the median error rate. (F) Error rate of repeat indels is highly correlated with the number of repeat units. In (A) and (B), symbols +, ×, and o represent SNV, SV, and indel, respectively. In (A), dark blue and red indicate detected and missed markers, respectively. Green markers with gray shading highlight error rate in non-cancer samples. In (A), 11 repeat indels are not included due to a high error rate as analyzed in (E) and (F). In (E), counts from both replicates are combined. In (F), all repeat indels have units with length of 1; thus, the homopolymer length equals the number of repeat units. Linear regression p values are shown in (A), (B), and (F). See also , , , and .

Article Snippet: Melanoma cell line COLO829 , ATCC , # CRL-1974.

Techniques: Sequencing