Efficient Maximum Likelihood Estimation for Pedigree Data with the Sum-Product Algorithm

Engelhardt, Alexander; Rieger, Anna; Tresch, Achim and Mansmann, Ulrich (2016): Efficient Maximum Likelihood Estimation for Pedigree Data with the Sum-Product Algorithm. In: Human Heredity, Vol. 82: pp. 1-15

Abstract

OBJECTIVE We analyze data sets consisting of pedigrees with age at onset of colorectal cancer (CRC) as phenotype. The occurrence of familial clusters of CRC suggests the existence of a latent, inheritable risk factor. We aimed to compute the probability of a family possessing this risk factor as well as the hazard rate increase for these risk factor carriers. Due to the inheritability of this risk factor, the estimation necessitates a costly marginalization of the likelihood. METHODS We propose an improved EM algorithm by applying factor graphs and the sum-product algorithm in the E-step. This reduces the computational complexity from exponential to linear in the number of family members. RESULTS Our algorithm is as precise as a direct likelihood maximization in a simulation study and a real family study on CRC risk. For 250 simulated families of size 19 and 21, the runtime of our algorithm is faster by a factor of 4 and 29, respectively. On the largest family (23 members) in the real data, our algorithm is 6 times faster. CONCLUSION We introduce a flexible and runtime-efficient tool for statistical inference in biomedical event data with latent variables that opens the door for advanced analyses of pedigree data.

• Item Type: Journal article
• Faculties: Medicine > Institute for Medical Information Processing, Biometry and Epidemiology
• Subjects: 600 Technology > 610 Medicine and health
• ISSN: 1423-0062
• Alliance/National Licence: This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.
• Language: English