What calling algorithm does Nexus Copy Number use?
A. Nexus Copy Number uses a proprietary algorithm called Rank Segmentation. It is based loosely on the CBS (Circular Binary Segmentation) algorithm developed by Adam Olshen. We have modified the CBS algorithm in a number of ways and significantly improved the processing speed by using a Normal distribution function for testing for change points as opposed to the non-parametric permutation based statistics used in the original CBS algorithm.
A. Nexus Copy Number offers the following algorithms for making calls. • Rank Segmentation: A robust variation of the well-known Circular Binary Segmentation (CBS) algorithm where the probe ranks are used to minimize the effect of outliers and drastically improve performance. • SNPRank Segmentation: An extension of the Rank Segmentation algorithm where B-Allele Frequency values are also included in the segmentation process generating both copy number and allelic event calls. • FASST Segmentation: A novel Hidden Markov Model (HMM) based approach that unlike other HMM methods does not aim to estimate the copy number state at each probe but uses many states to cover possibilities, such as mosaic events, and then make calls based on a second level threshold • SNP-FASST Segmentation: An extension of the FASST algorithm but adding many more states to cover events related to the B-Allele Frequency values to make copy number and allelic event calls.
