Abstract: Direct targeted sequencing (DTS) methods and a hidden Markov model (HMV) can be used to call the copy number of a segment of interest within a region of interest. Described herein are methods for calling a copy number variant or a copy number variant abnormality using an HMM, and methods for determining a copy number based on a copy number likelihood model, in a test sequencing library that has be sequenced using DTS methods. Also described herein are methods for determining a copy number of a segment, including accounting for spurious capture probes that may arise from the DTS methods.

Abstract: Direct targeted sequencing (DTS) methods and a hidden Markov model (HMM) can be used to call the copy number of a segment of interest within a region of interest. Described herein are methods for calling a copy number variant or a copy number variant abnormality using an HMM, and methods for determining a copy number based on a copy number likelihood model, in a test sequencing library that has be sequenced using DTS methods. Also described herein are methods for determining a copy number of a segment, including accounting for spurious capture probes that may arise from the DTS methods.

Abstract: Described herein are methods of assessing a sample-specific performance of a copy number variant model, a method for determining a copy number of an interrogated segment within a region of interest, and a method for determining a copy number variant abnormality within a region of interest. Sample-specific performance of the copy number variant caller is assessed by parameterizing a copy number variant model base on sequencing reads from a test sample, generating synthetic copy number variants using the sequencing read from the test sample, and calling the number of copies in the synthetic copy number variants using the copy number variant model and the sample-specific parameters. Calling a number of copies of an interrogated segment can include parameterizing a hidden Markov model using an analytic first derivative gradient and second derivative Hessian of one or more parameters in a copy number likelihood model.

Abstract: Direct targeted sequencing (DTS) methods and a hidden Markov model (HMM) can be used to call the copy number of a segment of interest within a region of interest. Described herein are methods for calling a copy number variant or a copy number variant abnormality using an HMM, and methods for determining a copy number based on a copy number likelihood model, in a test sequencing library that has be sequenced using DTS methods. Also described herein are methods for determining a copy number of a segment, including accounting for spurious capture probes that may arise from the DTS methods.

Abstract: A system for managing information in a laboratory is disclosed. The system can receive sample information, the sample information including at least one sample identifier and sample order information. The system can send movement information to one or more robotics units based on at least the sample identifier. The system can perform, on at least one identified sample, one or more analytical functions to generate results data. The system can organize the results data based on the sample order information.

Abstract: According to one aspect, systems and processes for managing stored genomic sequencing data are provided. In exemplary process, a trigger related to a call review event is detected, where at least one portion of a denormalized data structure is accessed based on the detected trigger. In response the accessing, the at least one portion of the denormalized data structure is transformed into a normalized data structure. A user request associated with the at least one portion of the denormalized data structure is received. The normalized data structure is accessed in response to the user request, and information contained within the normalized data structure is then displayed on a display screen.