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A somatic reference standard for cancer genome sequencing.

Craig DW, Nasser S, Corbett R, Chan SK, Murray L, Legendre C, Tembe W, Adkins J, Kim N, Wong S, Baker A, Enriquez D, Pond S, Pleasance E, Mungall AJ, Moore RA, McDaniel T, Ma Y, Jones SJ, Marra MA, Carpten JD, Liang WS - Sci Rep (2016)

Bottom Line: Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution.Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes.We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

View Article: PubMed Central - PubMed

Affiliation: Translational Genomics Research Institute, Phoenix, Arizona, USA.

ABSTRACT
Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

No MeSH data available.


Related in: MedlinePlus

Meta-analysis of the COLO829 somatic reference.(A) Mutational signature of all SNVs. All substitutions are referred to by the pyrimidine context of the mutated base pair. (B) Genomic evolution of COLO829. A schematic of unique somatic alterations across each truth set is shown. Separate lobes reflect the level of divergence demonstrated by each truth set as measured by the number of unique somatic SNVs and indels for that data set. Examples of unique events are shown. The Pleasance sample did not demonstrate unique coding SNVs or indels (chromosomal coordinates of unique intronic events are shown).
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f3: Meta-analysis of the COLO829 somatic reference.(A) Mutational signature of all SNVs. All substitutions are referred to by the pyrimidine context of the mutated base pair. (B) Genomic evolution of COLO829. A schematic of unique somatic alterations across each truth set is shown. Separate lobes reflect the level of divergence demonstrated by each truth set as measured by the number of unique somatic SNVs and indels for that data set. Examples of unique events are shown. The Pleasance sample did not demonstrate unique coding SNVs or indels (chromosomal coordinates of unique intronic events are shown).

Mentions: Evaluation of the somatic reference standard indicated that the most common somatic base substitution is C > T transitions (72.8%; Fig. 3A). 50.6% of all substitutions were comprised of C > T transitions occurring in a dipyrimidine context. This percentage falls short of the 60% threshold that characterizes the presence of the ultraviolet (UV) light signature reported in malignant cutaneous melanomas23242526, and that which was described originally in COLO82910, to indicate that changes to the UV signature accumulated in the separate lineages. The highest incidence of C > T transitions occurred in the T*A trinucleotide context (16.1% of all C > T transitions), followed by the T*C context (14.5% of all C > T transitions). The second most frequent base substitution was C > A transversions (10.9%), which is previously described to be associated with DNA damage caused by reactive oxygen species1027. Overall, the somatic reference has an average of 12 mutations per megabase, which falls within the prevalence range previously reported for melanoma28. CNVs (Fig. 2B; Supplementary Figure 3) were also widespread and thus indicate chromosomal instability in COLO829, as expected due to the highly mutated state of the line.


A somatic reference standard for cancer genome sequencing.

Craig DW, Nasser S, Corbett R, Chan SK, Murray L, Legendre C, Tembe W, Adkins J, Kim N, Wong S, Baker A, Enriquez D, Pond S, Pleasance E, Mungall AJ, Moore RA, McDaniel T, Ma Y, Jones SJ, Marra MA, Carpten JD, Liang WS - Sci Rep (2016)

Meta-analysis of the COLO829 somatic reference.(A) Mutational signature of all SNVs. All substitutions are referred to by the pyrimidine context of the mutated base pair. (B) Genomic evolution of COLO829. A schematic of unique somatic alterations across each truth set is shown. Separate lobes reflect the level of divergence demonstrated by each truth set as measured by the number of unique somatic SNVs and indels for that data set. Examples of unique events are shown. The Pleasance sample did not demonstrate unique coding SNVs or indels (chromosomal coordinates of unique intronic events are shown).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837349&req=5

f3: Meta-analysis of the COLO829 somatic reference.(A) Mutational signature of all SNVs. All substitutions are referred to by the pyrimidine context of the mutated base pair. (B) Genomic evolution of COLO829. A schematic of unique somatic alterations across each truth set is shown. Separate lobes reflect the level of divergence demonstrated by each truth set as measured by the number of unique somatic SNVs and indels for that data set. Examples of unique events are shown. The Pleasance sample did not demonstrate unique coding SNVs or indels (chromosomal coordinates of unique intronic events are shown).
Mentions: Evaluation of the somatic reference standard indicated that the most common somatic base substitution is C > T transitions (72.8%; Fig. 3A). 50.6% of all substitutions were comprised of C > T transitions occurring in a dipyrimidine context. This percentage falls short of the 60% threshold that characterizes the presence of the ultraviolet (UV) light signature reported in malignant cutaneous melanomas23242526, and that which was described originally in COLO82910, to indicate that changes to the UV signature accumulated in the separate lineages. The highest incidence of C > T transitions occurred in the T*A trinucleotide context (16.1% of all C > T transitions), followed by the T*C context (14.5% of all C > T transitions). The second most frequent base substitution was C > A transversions (10.9%), which is previously described to be associated with DNA damage caused by reactive oxygen species1027. Overall, the somatic reference has an average of 12 mutations per megabase, which falls within the prevalence range previously reported for melanoma28. CNVs (Fig. 2B; Supplementary Figure 3) were also widespread and thus indicate chromosomal instability in COLO829, as expected due to the highly mutated state of the line.

Bottom Line: Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution.Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes.We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

View Article: PubMed Central - PubMed

Affiliation: Translational Genomics Research Institute, Phoenix, Arizona, USA.

ABSTRACT
Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

No MeSH data available.


Related in: MedlinePlus