Lee Trani
Lee Trani has a total of 27 co-authors. Here are the top co-authors by number of shared publications:
- Katie M. Campbell
Department of Medicine, Division of Hematology-Oncology, University of California – Los Angeles (UCLA), Los Angeles, CA
2 shared publications - Kilannin Krysiak
Department of Pathology, Washington University School of Medicine, St. Louis, Missouri, USA
2 shared publications - Malachi Griffith
Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, USA
2 shared publications - Obi L. Griffith
Washington University School of Medicine
2 shared publications - Zachary L. Skidmore
Department of Medicine Washington University St. Louis Missouri USA
2 shared publications - Alex Handler Wagner
The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH
1 shared publication
Latest Publications
- Open Access
Standard operating procedure for somatic variant refinement of tumor sequencing data
Purpose: Manual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS). Despite widespread use in analyzing MPS data, there has been little attempt to describe methods for manual review, resulting in high inter- and intra-lab variability in somatic variant detection and characterization of tumors. Methods: Open source software was used to develop an optimal method for manual review setup. We also developed a systemic approach to visually inspect each variant during manual review. Results: We present a standard operating procedures for somatic variant refinement for use by manual reviewers. The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewer’s confidence in the somatic variant call and 19 annotation tags that contextualize commonly observed sequencing patterns during manual review. Representative examples provide detailed instructions on how to classify variants during manual review to rectify lack of confidence in automated somatic variant detection. Conclusion: Standardization of somatic variant refinement through systematization of manual review will improve the consistency and reproducibility of identifying true somatic variants after automated variant calling.
Open AccessStandard operating procedure for somatic variant refinement of tumor sequencing data
Purpose: Manual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS). Despite widespread use in analyzing MPS data, there has been little attempt to describe methods for manual review, resulting in high inter- and intra-lab variability in somatic variant detection and characterization of tumors. Methods: Open source software was used to develop an optimal method for manual review setup. We also developed a systemic approach to visually inspect each variant during manual review. Results: We present a standard operating procedures for somatic variant refinement for use by manual reviewers. The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewer’s confidence in the somatic variant call and 19 annotation tags that contextualize commonly observed sequencing patterns during manual review. Representative examples provide detailed instructions on how to classify variants during manual review to rectify lack of confidence in automated somatic variant detection. Conclusion: Standardization of somatic variant refinement through systematization of manual review will improve the consistency and reproducibility of identifying true somatic variants after automated variant calling.