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Absolute quantification of somatic DNA alterations in human cancer.

Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G - Nat. Biotechnol. (2012)

Bottom Line: We used ABSOLUTE to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs.This analysis identified both pervasive subclonal somatic point-mutations and a small subset of predominantly clonal and homozygous mutations, which were overrepresented in the tumor suppressor genes TP53 and NF1 and in a candidate tumor suppressor gene CDK12.ABSOLUTE will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.

View Article: PubMed Central - PubMed

Affiliation: The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. scarter@broadinstitute.org

ABSTRACT
We describe a computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. The method, named ABSOLUTE, can detect subclonal heterogeneity and somatic homozygosity, and it can calculate statistical sensitivity for detection of specific aberrations. We used ABSOLUTE to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs. This analysis identified both pervasive subclonal somatic point-mutations and a small subset of predominantly clonal and homozygous mutations, which were overrepresented in the tumor suppressor genes TP53 and NF1 and in a candidate tumor suppressor gene CDK12. We also used ABSOLUTE to infer absolute allelic copy-number profiles from 3,155 diverse cancer specimens, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression (for example, with recessive inactivation of NF1 being less common after genome doubling). ABSOLUTE will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.

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Incidence and timing of whole genome doubling events in primary cancersa, b, Ploidy estimates were obtained from ABSOLUTE. Mean homologue imbalance was calculated as the average difference in the homologous copy numbers at every position in the genome. Genome doubling status was inferred from the homologous copy numbers (Online Methods, Supplementary Fig. 9).c, MPD – myeloproliferative disease, ALL – acute lymphoblastic leukemia, GBM - Glioblastomamultiforme, RCC - renal cell carcinoma, HCC - hepatocellular carcinoma, HGS-OvCa - high-gradeserous ovarian carcinoma.d, LOH (loss of heterozygosity) was defined as 0 allelic copies. Amplification was defined as > 1allelic copy for samples with 0 genome doublings, and as > 2 allelic copies for those with 1genome doubling. Calls were made based on the modal allelic copy numbers of eachchromosome arm. Dashed lines indicate y=x.e, SCNAs, defined as regions differing from the modal absolute copy number of each sample,were binned at adaptive resolution to maintain 200 SCNAs per bin, and renormalized by binlength. The value in each bin was further divided by the number of tumor samples in eachgenome doubling class, indicated by color as in a. The black line indicates slope = −1. Linearregression models were fit independently for each class using SCNAs 0.5 < x < 20 Mb. Thisresulted in fitted slope values of -1.05, -0.96, and -0.88 for 0, 1, and > 1 genome doublings,respectively (not shown).
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Figure 6: Incidence and timing of whole genome doubling events in primary cancersa, b, Ploidy estimates were obtained from ABSOLUTE. Mean homologue imbalance was calculated as the average difference in the homologous copy numbers at every position in the genome. Genome doubling status was inferred from the homologous copy numbers (Online Methods, Supplementary Fig. 9).c, MPD – myeloproliferative disease, ALL – acute lymphoblastic leukemia, GBM - Glioblastomamultiforme, RCC - renal cell carcinoma, HCC - hepatocellular carcinoma, HGS-OvCa - high-gradeserous ovarian carcinoma.d, LOH (loss of heterozygosity) was defined as 0 allelic copies. Amplification was defined as > 1allelic copy for samples with 0 genome doublings, and as > 2 allelic copies for those with 1genome doubling. Calls were made based on the modal allelic copy numbers of eachchromosome arm. Dashed lines indicate y=x.e, SCNAs, defined as regions differing from the modal absolute copy number of each sample,were binned at adaptive resolution to maintain 200 SCNAs per bin, and renormalized by binlength. The value in each bin was further divided by the number of tumor samples in eachgenome doubling class, indicated by color as in a. The black line indicates slope = −1. Linearregression models were fit independently for each class using SCNAs 0.5 < x < 20 Mb. Thisresulted in fitted slope values of -1.05, -0.96, and -0.88 for 0, 1, and > 1 genome doublings,respectively (not shown).

Mentions: Using such information, we could classify samples into three groups, which we interpreted as corresponding to 0, 1 and > 1 genome doubling events in the clonal evolution of the cancer. These three groups had modal ploidy values of 1.75, 2.75, and 4.0, respectively (Fig. 6a), and also segregated into three clusters by ploidy and mean homologous copy-number imbalance (Fig. 6b). We interpreted this as evidence of SNCAs occurring with net losses, interspersed with the genome doublings. This process resulted in intermediate ploidy values for the doubled clones (2.2 – 3.4N), with pervasive imbalance of homologous chromosomes (Fig. 6b).


Absolute quantification of somatic DNA alterations in human cancer.

Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G - Nat. Biotechnol. (2012)

Incidence and timing of whole genome doubling events in primary cancersa, b, Ploidy estimates were obtained from ABSOLUTE. Mean homologue imbalance was calculated as the average difference in the homologous copy numbers at every position in the genome. Genome doubling status was inferred from the homologous copy numbers (Online Methods, Supplementary Fig. 9).c, MPD – myeloproliferative disease, ALL – acute lymphoblastic leukemia, GBM - Glioblastomamultiforme, RCC - renal cell carcinoma, HCC - hepatocellular carcinoma, HGS-OvCa - high-gradeserous ovarian carcinoma.d, LOH (loss of heterozygosity) was defined as 0 allelic copies. Amplification was defined as > 1allelic copy for samples with 0 genome doublings, and as > 2 allelic copies for those with 1genome doubling. Calls were made based on the modal allelic copy numbers of eachchromosome arm. Dashed lines indicate y=x.e, SCNAs, defined as regions differing from the modal absolute copy number of each sample,were binned at adaptive resolution to maintain 200 SCNAs per bin, and renormalized by binlength. The value in each bin was further divided by the number of tumor samples in eachgenome doubling class, indicated by color as in a. The black line indicates slope = −1. Linearregression models were fit independently for each class using SCNAs 0.5 < x < 20 Mb. Thisresulted in fitted slope values of -1.05, -0.96, and -0.88 for 0, 1, and > 1 genome doublings,respectively (not shown).
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Figure 6: Incidence and timing of whole genome doubling events in primary cancersa, b, Ploidy estimates were obtained from ABSOLUTE. Mean homologue imbalance was calculated as the average difference in the homologous copy numbers at every position in the genome. Genome doubling status was inferred from the homologous copy numbers (Online Methods, Supplementary Fig. 9).c, MPD – myeloproliferative disease, ALL – acute lymphoblastic leukemia, GBM - Glioblastomamultiforme, RCC - renal cell carcinoma, HCC - hepatocellular carcinoma, HGS-OvCa - high-gradeserous ovarian carcinoma.d, LOH (loss of heterozygosity) was defined as 0 allelic copies. Amplification was defined as > 1allelic copy for samples with 0 genome doublings, and as > 2 allelic copies for those with 1genome doubling. Calls were made based on the modal allelic copy numbers of eachchromosome arm. Dashed lines indicate y=x.e, SCNAs, defined as regions differing from the modal absolute copy number of each sample,were binned at adaptive resolution to maintain 200 SCNAs per bin, and renormalized by binlength. The value in each bin was further divided by the number of tumor samples in eachgenome doubling class, indicated by color as in a. The black line indicates slope = −1. Linearregression models were fit independently for each class using SCNAs 0.5 < x < 20 Mb. Thisresulted in fitted slope values of -1.05, -0.96, and -0.88 for 0, 1, and > 1 genome doublings,respectively (not shown).
Mentions: Using such information, we could classify samples into three groups, which we interpreted as corresponding to 0, 1 and > 1 genome doubling events in the clonal evolution of the cancer. These three groups had modal ploidy values of 1.75, 2.75, and 4.0, respectively (Fig. 6a), and also segregated into three clusters by ploidy and mean homologous copy-number imbalance (Fig. 6b). We interpreted this as evidence of SNCAs occurring with net losses, interspersed with the genome doublings. This process resulted in intermediate ploidy values for the doubled clones (2.2 – 3.4N), with pervasive imbalance of homologous chromosomes (Fig. 6b).

Bottom Line: We used ABSOLUTE to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs.This analysis identified both pervasive subclonal somatic point-mutations and a small subset of predominantly clonal and homozygous mutations, which were overrepresented in the tumor suppressor genes TP53 and NF1 and in a candidate tumor suppressor gene CDK12.ABSOLUTE will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.

View Article: PubMed Central - PubMed

Affiliation: The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. scarter@broadinstitute.org

ABSTRACT
We describe a computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. The method, named ABSOLUTE, can detect subclonal heterogeneity and somatic homozygosity, and it can calculate statistical sensitivity for detection of specific aberrations. We used ABSOLUTE to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs. This analysis identified both pervasive subclonal somatic point-mutations and a small subset of predominantly clonal and homozygous mutations, which were overrepresented in the tumor suppressor genes TP53 and NF1 and in a candidate tumor suppressor gene CDK12. We also used ABSOLUTE to infer absolute allelic copy-number profiles from 3,155 diverse cancer specimens, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression (for example, with recessive inactivation of NF1 being less common after genome doubling). ABSOLUTE will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.

Show MeSH
Related in: MedlinePlus