iNDI FA13.1J Cell Lines Expansion and Distribution for the iPSC Neurodegenerative Disease Initiative (iNDI) Project

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs Page 1 of 8 STATEMENT OF WORK GENERAL INFORMATION Title of Project: iNDI FA13.1J cell lines expansion and distribution for the iPSC Neurodegenetive Disease Initiative (iNDI) project Statement of Need and Purpose: The National Institute on Aging (NIA), Center of Alzheimer’s Disease and Related Dementias (CARD) requires a contractor to generate a collection of up to 936 isogenic Alzheimer's disease and related dementias (ADRD) iPSC cell lines. Background Information and Objective: The iPSC Neurodegenerative Disease Initiative (iNDI) embedded within CARD, was established to apply genomic engineered iPSC-derived neuron models to the field of Alzheimer’s disease and related dementias (ADRD) research. The long-term, large-scale project demands well-validated pipelines to counter risks of outcome reliability and consistency, as well as maximizing throughput when dealing with a large number of cell lines. Period of Performance: Base Year : September 1, 2026- August 31, 2027 Option Year 1 : September 1, 2027- August 31, 2028 Option Year 2 : September 1, 2028- August 31, 2029 Option Year 3 : September 1, 2029- August 31, 2030 SCOPE OF WORK General Requirements: Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work below. Specific Requirements: Project Deliverables Gene-edited iPSC lines shall be expanded and quality controlled aligned with the -- 1 of 8 -- Version 11-30-2016-1 FAR Part 11—Describing Agency Needs Page 2 of 8 current iNDI cell line protocols using CRISPR-Cas12a technology. Once distribution lots have passed quality control they shall be made available for purchase to the scientific community. • FA13.1J female SNV lines (162 trios) totaling 486 iPSC lines (Appendix A) • 25 of the most relevant SNVs (trios) across six additional iPSC lines totaling 450 iPSC lines (Appendix B), enabling researchers to assess reproducibility across diverse genetic and APOE backgrounds Contractor shall have the option to engineer and expand iPSC lines via manual or automated process. Quality control procedures shall be specific for the manual and automated methods as noted below. Production Lot Quality Control Manual Expansion: • Post-thaw viability assessed by Trypan Blue exclusion. Acceptance criteria: Viability >80% • Non-viral agent panel testing via qPCR. Acceptance criteria: Negative • Viral (DNA) panel testing via qPCR. Acceptance criteria: Negative • Viral (RNA) panel testing via qPCR. Acceptance criteria: Negative • Yeast and fungal testing via inoculation and aerobic culture for 10 days.Acceptance criteria: Negative • Gram-negative bacterial testing via inoculation and aerobic culture for 48 hours. Acceptance criteria: Negative • Gram-positive bacterial testing via inoculation and aerobic culture for 48 hours. Acceptance criteria: Negative • Gene-edited variant sequence confirmation via PCR and Sanger sequencing of wild type and variant alleles. Acceptance criteria: Presence of intended gene edit(s) at the desired zygosity with no on-target mutations. Production Lot Quality Control Automated Expansion: • Post-Thaw Viable Cell Recovery: Cryotube thaw and plating into asingle well of a 12-well plate. Acceptance criteria: >50% confluency achieved within 10 days post-thaw • SNP-Based Digital Karyotyping: Illumina Infinium Global Diversity Array with Cytogenetics-8 (GDA-Cyto) add-on. Acceptance criteria: Normal karyotype, defined as no autosomal copy number variants (CNVs) >2.5Mb • Confirmation of Gene Edit: PCR, Sanger sequencing. Acceptance criteria: Presence of intended gene edit(s) at the desired zygosity with no on-target mutations • Identity Verification: Illumina Infinium Global Diversity Array with Cytogenetics-8 (GDA-Cyto) add-on. Acceptance criteria: Genotype matches parental and/or provided lead-clone reference sequence -- 2 of 8 -- Version 11-30-2016-1 FAR Part 11—Describing Agency Needs Page 3 of 8 • Pluripotency Expression Profile: RNA sequencing (Plasmidsaurus).Acceptance criteria: Expression of established pluripotency markers with absence of early differentiation markers • Reprogramming Vector Clearance: RNA sequencing (Plasmidsaurus). Acceptance criteria: Absence of Sendai virus expression • Sterility: Aerobic culture. Acceptance criteria: Negative • Mycoplasma: Mycoplasma qPCR (ABM Mycoplasma qPCR Kit, Cat. No. G240). Acceptance criteria: Negative Product & Web Content Creation: • Cell lines shall be made available for purchase by the scientific community through a Contractor created website that includes existing iNDI cell lines as well as newly created iPSC lines. • Quality control data and design files shall be curated and uploaded to website creating product pages for each iPSC line. Appendix A: Detailed list of FA13.1J female SNV iPSC lines to be expanded, QC’d and distributed for the scientific community. For each gene variant listed below, a heterozygous, a homozygous and a revertant iPSC line will be generated Number Parental Line Gene Variant 1 FA13.1J APOE C156R 2 FA13.1J TARDBP M337V 3 FA13.1J APOE R136S 4 FA13.1J APOE R158C 5 FA13.1J SNCA A53T 6 FA13.1J TARDBP Q331K 7 FA13.1J MAPT R406W 8 FA13.1J GBA1 N370S 9 FA13.1J LRRK2 G2019S 10 FA13.1J APP V717I 11 FA13.1J SOD1 A5V 12 FA13.1J GBA1 E326K 13 FA13.1J FUS R495* 14 FA13.1J APP A673T 15 FA13.1J PSEN1 E276A 16 FA13.1J PSEN2 N141I 17 FA13.1J GBA1 D448H 18 FA13.1J GRN Q125* 19 FA13.1J GBA1 D448V 20 FA13.1J SNCA E46K -- 3 of 8 -- Version 11-30-2016-1 FAR Part 11—Describing Agency Needs Page 4 of 8 21 FA13.1J APP E693G 22 FA13.1J GRN R493* 23 FA13.1J FUS P525L 24 FA13.1J MAPT V337M 25 FA13.1J PSEN1 M146I 26 FA13.1J UBQLN2 P506T 27 FA13.1J LRRK2 R1441H 28 FA13.1J MAT…