Estimating cancer survival and clinical outcome based on genetic tumor progression scores

Jörg Rahnenführer 1,*, Niko Beerenwinkel 1, , Wolfgang A. Schulz 2, Christian Hartmann 3, Andreas

von Deimling 3, Bernd Wullich 4 and Thomas Lengauer 1

Presented by Rahul Jawa

Motivation Prediction of time to death or relapse is

important for tumor classification and selecting appropriate therapies

Survival Prediction based on clinical and histological parameters

Accumulation of genetic alterations during tumor progression can be used for the Assessment of the genetic status of the tumor

Evolutionary tree models have been applied for modeling dependences between the genetic events

Methods

• Oncogenetic Tree Models Describes order of genetic events in the

course of human tumor development Genetic events are gains or losses of

parts of chromosomes Oncogenetic tree T = (V, E, r, p) Problem: Fixed pattern, therefore some

samples are assigned probability zero

Methods (contd) Oncogenetic trees mixture models

Contains a star topology which models spontaneous and independent occurrence of genetic events

And arbitrary trees estimated from the observed data

This model is learned by an EM-like fashion by iteratively estimating the responsibilities of the different tree components for the data and the structure and parameters of the tree models are inferred from the weighted data

Methods (contd)

Methods (contd)

Genetic progression scores (3) Determines the progression status of

human tumors They are defined for tumor samples

that are represented by binary vectors indicating the occurrence of a list of genetic events(x1,…,xl)

Methods (contd)

A. Count Statistic• Measure of genetic progression = number

of events that have occurred• All events are independent and impact on

progression is cumulative

Methods (contd)

B. Weighted count statistic All genetic events are not equally important High frequent events occur early Less frequent events indicates more advanced

progression

Methods (contd)C. Genetic progression score

Used via Oncogenetic trees mixed model to integrate dependences between ordered events

A timed oncogenetic tree is obtained by assuming independent Poisson processes for the occurrence of events on the tree edges

Expected waiting time of a pattern is finally estimated as the average of all waiting times at which pattern is observed

Methods (contd) Survival analysis

Survival time starts at time of treatment and the endpoint is the death or relapse

If patient drops out before endpoint, the Cox proportional hazard model can be used to calculate risk of death

Hazard rate at a time t is the instantaneous rate of death during the next instant of time among survivors to time t

Lambda0 is the baseline hazard function B = (B1,…,Bp) is the vector of regression coefficients z = (z1,…zp) is a p-dimensional vector of covariates

that are potential predictors for the survival time

Data Sets Glioblastomas (Brain Tumor)

Survival time based on death Contained 75 patients with 5 censored Genetic events were chromosome

changes on the p-arm or q-arm of single chromosomes

Selected the events that were observed in at least 15% of the tumor samples

10q, 10p, 9p, 19q, 17p, 13q and 22q

Data Sets (contd) Prostate cancer

Survival time based on tumor relapse Contained 54 patients and 34 censored Genetic events were gains and losses of

chromosome parts on the p-arm or q-arm of all chromosomes

Selected the events that were observed in at least 10% of the tumor samples

3q+, 4q+, 6q+, 7q+, 8p-, 8q+, 10q-, 13q+ and Xq+

Results Estimated oncogenetic tree model for

Glioblastomas

Results (contd) Estimated oncogenetic tree model for

Prostate cancer

Results (contd)

Cox proportional hazard models Is used to identify genetic markers

that are relevant for estimating clinical outcome

Hazard ratio quantifies the relative risk of death

Results (contd) GPS for Glioblastomas Table 1 Glioblastoma data set: pattern of observed LOH

measurements for selected events, frequency of pattern and GPS calculated from oncogenetic tree model

Table 2 Glioblastoma dataset: genetic events defined by LOH on single chromosomes, frequencies and p-values in Cox models (original and false discovery rate adjusted in univariate and original in multivariate model)

Table 3 Glioblastoma dataset: GPS with hazard ratios, 95% confidence intervals and p-values in univariate and bivariate Cox regression model

Results (contd)

Results (contd)

GPS for Prostate cancer Gleason score is a prostate cancer grading system on scale 1-10 Table 4 Prostate cancer dataset: pattern of observed CGH

measurements for selected events, frequency of pattern and GPS calculated from oncogenetic tree model

Table 5 Prostate cancer dataset: genetic events defined by CGH on single chromosomes, frequencies and p-values in Cox models (original and false discovery rate adjusted in univariate and original in multivariate model)

Table 6 Prostate cancer dataset: genetic progression scores with hazard ratios, 95% confidence intervals and p-values in univariate and bivariate Cox regression model

Results (contd)

Results (contd)

Conclusion The GPS of a tumor gave the estimated average waiting

time of its observed genetic pattern in the timed oncogenetic tree

GPS was able to differenciate patient subgroups with respect to expected clinical outcome

GPS was applied to two different tumor types which shows that it could become a universal approach

For Gleason score of 7, GPS was able to further identify subgroups