John J. Thomas, Ph.D. Email & Phone Number

Cambridge, Ma, Us

Provided strategic planning and wrote and reviewed data and documents to support large molecule development from candiate selection to late-stage development and regulatory filings.• Independent Analytical CMC Consulting Gene Therapy therapeutics o Spearheaded analytical gap analyses, method optimization and qualifications for Phase 1B AAV program and IND enabling reports for pre-IND AAV program Antigen capture nanoparticle therapeutics o Developed analytical strategy for antigen-capture nanoparticle company’s candidate selection process and coordinated early stability and characterization activities. Peptide nucleic acid therapeutics o Consultant with research process development on analytical purity analysis and consolidating labs sites. Instrument company o Provided direction on applications of novel instrumentation to benefit industry product development needs• DPS Group Global Consulting - Analytical CMC Gene Therapy therapeutics o Managed Analytical-CMC activities and provided guidance for Adenovirus gene therapy RTS- IL12 vector and small molecule gene activator for Glioblastoma program. Antibody-drug Conjugate Therapeutics o Directed CDMO and CRO analytical activities in preparation of phase III oncology program, developed CQA strategy and designed forced degradation plan.

Directed pre-IND Analytical and Purification Development for IND-readiness of first peptide nucleic acid (PNA) therapeutic candidate.• Oversaw method assay transfers to 2 CDMO’s and completed characterization and release method development from internal, academic and CROs.• Developed innovative purity, content and sequencing methods for first in-class PNA drugs. New release assays were successfully qualified for first planned large-scale manufacturing run.• Co-designed large scale drug substance purification development plans for the release of the first large scale lots and improvement in purity level.

Cambridge, Ma, Us

Cambridge, Massachusetts, Us

Group leader responsible for metabolite assay development and research support. Collaborated closely with clinical research, discovery research and pharmacology to characterize animal and patient metabolic profiles to assess product safety and efficacy.• Managed bioanalytical resources including CRO outsourcing and internal resources for 4 pre-clinical and 2 clinical programs.• Managed the successful development, qualification, transfer and validation of biomarker assays to 4 different CROs for Phase I phenylketonuria clinical trials using LC-MS/MS, HPLC_UV and qPCR methods.• Co-developed and implemented the first bioanalytical scientific report and protocol processes with QA.• Introduced and implemented new metabolomics discovery platforms that identified two new potential biomarkers for in-vitro and in-vivo bacterial strain characterization.

Group leader responsible for analytical development and product characterization of protein therapeutics. Also, provided broad cross-functional support for research, process development, quality control and regulatory filings.• Managed a group of 5 scientists and additional summer interns and co-ops in assay development and physicochemical, biophysical and activity characterization.• Implemented a Carbohydrate Center of Excellence to drive consensus-driven initiatives and goals.• Applied Design of Experiment (DOE) approaches for assay development and optimization that resulted in successful assay transfer, qualification and validation for four new release assays. • Directed research efforts to elucidate blood-brain barrier transport mechanisms that identified a key quality attributes.• Led the analytical support on the Kanuma CMC team that resulted in two new assay improvements as well as support of new formulation development with full stability and comparability studies.• Managed the design and early development of the LAL-D diagnostic assay for newborn screening. • Successfully designed a natural-like substrate with amenable MS response and comparable LAL enzyme activity

Lexington, Massachusetts, Us

Group leader responsible for analytical development and product characterization. Broad cross-functional analytical support for research, development, quality control, and regulatory filings.• Managed a group of 6 scientists responsible for supporting research and development programs.• Developed pre-clinical analytical strategy for ENPP1 program as the Analytical lead for ENPP1 program team. • Primary author for quality sections of Kanuma BLA filing and contributing author for SBC-103 IND filing.• Established statistical acceptance criteria for characterization assays and incorporated into clinical and Kanuma comparability studies.

Lexington, Massachusetts, Us

Planned and and executed analytical development and characterization activities for research and development.• Established critical carbohydrate and protein characterization assays as well as additional biophysical assays. Successfully incorporated new methods into one pre-clinical, one early-stage and one late- stage program. • Supervised a scientist and several student interns who were integrated into program teams• Analytical representative on research teams to investigate process methods to expand transgenic platform to new protein therapeutics.

Tokyo, Jp, Jp

Delivered advanced characterization data and new assays for early to late-stage products to define and monitor product attributes.• Phase II/III ARSA enzyme replacement neurodegenerative therapy program analytical lead on CMC team responsible for managing analytical assay development timelines.• Designed and led characterization studies of clinical and commercial enzyme therapeutic to identify and evaluate product attributes and degradation pathways. Determined key source of degradation for commercial VPRIV manufacturing investigation.• Successfully applied protein chemistry and carbohydrate chemistry approaches toward resolving manufacturing observations and pre-clinical biomarker method development.• Contributing author for CTA quality sections. Incorporated data from novel methodologies into one BLA and one IND filing. • Established strategies to establish theoretical toxicities, identify and levels of in-process additives for two clinical development programs.

North Chicago, Illinois, Us

Group leader responsible for antibody-drug conjugate characterization and method development. Lead efforts to implement new analytical technologies, method development and formulation development. • Managed a group of three scientists responsible for supporting biochemistry research, ADC purification development, quality control and formulation development of three clinical programs.• Managed method development to characterize the antibody-to-drug ratios, free drug levels and linker degradation using LCMS, 2D-HPLC, 1H-NMR, and UV-Vis to elucidate pathways for free drug and linkers.• Evaluated a new immortalized heptocyte cell line for in-vitro metabolism studies on the conjugated toxin molecules.

North Chicago, Illinois, Us

- Led Trastuzumab emtansine (Kadcyla) analytical development efforts in collaboration with Genentech Supported process development efforts to maximize antibody-to-drug ratios and purity for ADC for process development, formulation, quality control and stability.

Post-Doctoral Fellowship, Biological Chemistry And Molecular Biology

Ph.D., Bioanalytical Chemistry

M.S., Analytical Chemistry

B.S., Chemistry