Marc Perry, Phd Email & Phone Number

Toronto, On, Ca

California, United States

Bioinformatics Sub-contractor at the UCSF Helen Diller Family Comprehensive Cancer Center• This project needed a robust data management system, so I created and implemented a logical, uniform, naming system for all of our samples and associated files. The result was a streamlined, navigable table showing all of the assays, and available analyses for each patient.• My team needed a way to access, explore, and query not only experimental data, but alsoclinical metadata, from this… Show more Bioinformatics Sub-contractor at the UCSF Helen Diller Family Comprehensive Cancer Center• This project needed a robust data management system, so I created and implemented a logical, uniform, naming system for all of our samples and associated files. The result was a streamlined, navigable table showing all of the assays, and available analyses for each patient.• My team needed a way to access, explore, and query not only experimental data, but alsoclinical metadata, from this large-scale genomic dataset. Therefore, I decided to install the popular cBioportal Data Analysis tool on a private server, and then taught myself how to reformat and transform the project's cumulative variant calls, gene expression levels, and copy number variants, so that I could load them into the MySQL database that drives the cBioportal Data Visualization GUI.• As the volume of WGS data increased, I undertook a comprehensive and in-depth cataloguing of recurrent SNVs, and structural variants (including Copy Number Variations, and Gene fusions) in both the coding AND non-coding regions for each patient. Our results culminated in the Cell paper we published in 2018.• Because valuable clinical data and metadata were inaccessible to most of the team, and because users who had access were maintaining separate versions of the data, we needed to harmonize all of this disparate information into a single, accessible, central repository. I decided to migrate the data that was being stored in the University's OnCore Clinical Trial Management System into a secure, open source, RDBMS called REDCap. I built nine Perl modules that parsed OnCore records—most tables included some fields with free text—and populated the new data dictionary for REDCap. Now, with this tool in place, researchers can generate reports, while CRAs can update patients' results. Show less

Toronto, Canada Area

TITLE: Biocuration Lead AT: Ontario Institute for Cancer Research (OICR)JOB DESCRIPTION: Bioinformatics Data Manager at the International Cancer Genome Consortium (ICGC)'s Data Coordination Center (DCC)• As part of the ICGC’s Pan-Cancer Analysis of Whole Genomes (PCAWG) sub-Project, I organized, tracked, managed, and repaired, the uploaded fastq, bam, and VCF files, and bam file QC reports, for all of the 2,843 matched tumor/normal pairs of WGS cancer genome datasets that were being… Show more TITLE: Biocuration Lead AT: Ontario Institute for Cancer Research (OICR)JOB DESCRIPTION: Bioinformatics Data Manager at the International Cancer Genome Consortium (ICGC)'s Data Coordination Center (DCC)• As part of the ICGC’s Pan-Cancer Analysis of Whole Genomes (PCAWG) sub-Project, I organized, tracked, managed, and repaired, the uploaded fastq, bam, and VCF files, and bam file QC reports, for all of the 2,843 matched tumor/normal pairs of WGS cancer genome datasets that were being submitted from around the globe.• As a member of the PCAWG Working group for RNA-Seq/Transcriptomics I created the Standard Operating Procedure (SOP) and Perl script so that participants could upload their RNA-Seq datasets into one of our six GNOS servers (Annai Systems) for uniform processing. I also coordinated both the mapping and homogenization of all this RNA-Seq metadata.• I continually extracted, collected, tabulated, and counted all of this flowing data to generate weekly reports for both our project teleconference calls and F2F team meetings.• To facilitate mapping of Donors, Specimens, Samples, and Clinical metadata, from PCAWG to the ICGC Datasets, I regularly extracted JSON data from the DCC Database and Data Portal and performed QA/QC Validation.• To update and improve the DCC's help desk Email queuing system, I configured, tested, and implemented the DCC’s brand new instance of Atlassian's JIRA Service Desk (which remains in use to this day) Show less

Department of Molecular and Medical Genetics

Ph.D., Biochemistry

Activities and Societies: President, Biochemistry Graduate Student's Union, 1984-1985 Nikyu, Aikido Yoshinkai I was the first person.

A.B., Biochemistry