Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

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 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

• 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

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 MATR3 S85C

29 FA13.1J PARK7 L166P

30 FA13.1J TBK1 E696K

31 FA13.1J LRRK2 R1441G

32 FA13.1J PFN1 C71G

33 FA13.1J FUS R521H

34 FA13.1J HNRNPA1 D262N

35 FA13.1J PSEN1 M135V

36 FA13.1J FUS R216C

37 FA13.1J SETX L389S

38 FA13.1J VCP R159H

39 FA13.1J ANXA11 G38R

40 FA13.1J PLCG2 P522R

41 FA13.1J TREM2 R47H

42 FA13.1J SOD1 D91A

43 FA13.1J LRRK2 R1441C

44 FA13.1J LRRK2 I2020T

45 FA13.1J PINK1 A217D

46 FA13.1J PRKN R275W

47 FA13.1J SNCA A30P

48 FA13.1J TMEM175 M393T

49 FA13.1J VCP R155H

50 FA13.1J ANXA11 R346C

51 FA13.1J HNRNPA2B1 D290V

52 FA13.1J TIA1 P351L

53 FA13.1J KIF5A N256S

54 FA13.1J VPS13D R4228Q

55 FA13.1J DCTN1 G59S

56 FA13.1J OPTN E478G

57 FA13.1J TMEM106B T185S

58 FA13.1J TMEM106B S185T

59 FA13.1J SORL1 T947M

60 FA13.1J CSF1R A781E

61 FA13.1J ABCA7 W1214*

62 FA13.1J ADAM10 R181G

63 FA13.1J ANG K41I

64 FA13.1J ATP13A2 c1306

65 FA13.1J CHMP2B Q165*

66 FA13.1J DNMT1 Y511C

67 FA13.1J VAPB P56S

68 FA13.1J ERBB4 R927Q

69 FA13.1J KCNA1 R239S

70 FA13.1J KIF5A R204Q

71 FA13.1J MATR3 T622A

72 FA13.1J PANK2 c.1413-1G>T

73 FA13.1J POLG G737R

74 FA13.1J PRNP Q160*

75 FA13.1J SNCB P123H

76 FA13.1J SYNJ1 R219Q

77 FA13.1J VAPB D130E

78 FA13.1J ANXA11 D40G

79 FA13.1J VCP R155C

80 FA13.1J UBQLN2 P497H

81 FA13.1J CHMP2B D148Y

82 FA13.1J MATR3 F115C

83 FA13.1J CHMP2B Q206H

84 FA13.1J PARK7 D149A

85 FA13.1J OPTN Q398E

86 FA13.1J APP A692G

87 FA13.1J PSEN2 M239I

88 FA13.1J CSF1R E633K

89 FA13.1J PFN1 G118V

90 FA13.1J TBK1 G217R

91 FA13.1J ATP13A2 T517I

92 FA13.1J TREM2 T66M

93 FA13.1J CLN5 W26*

94 FA13.1J CHMP2B I29V

95 FA13.1J ABCA7 E1679X

96 FA13.1J MAPT N279K

97 FA13.1J ADAM10 Q170H

98 FA13.1J MAPT Q336R

99 FA13.1J APP E693Q

100 FA13.1J SORL1 Y141C

101 FA13.1J EIF2B1 V183F

102 FA13.1J EIF2B3 I229M

103 FA13.1J EIF2B5 R195H

104 FA13.1J EIF4G1 A502V

105 FA13.1J SOD1 I113T

106 FA13.1J LRRK2 Y1699C

107 FA13.1J PINK1 P399L

108 FA13.1J PRKN T240M

109 FA13.1J PRKN R42P

110 FA13.1J LRRK2 N2081D

111 FA13.1J SNCA A30G

112 FA13.1J MAPT R317W

113 FA13.1J GRN A9D

114 FA13.1J PSEN1 A75V

115 FA13.1J PSEN2 A85V

116 FA13.1J GBA1 L444P

117 FA13.1J PINK1 L347P

118 FA13.1J BCAT1 E360K / F276L

119 FA13.1J CHCHD10 R15L

120 FA13.1J SERPINI1 S49P

121 FA13.1J SETX L1976R

122 FA13.1J SMN1 G279V

123 FA13.1J VPS13C c8445

124 FA13.1J TREM2 E151K

125 FA13.1J TUBA4A R320C

126 FA13.1J CACNA1A R583Q

127 FA13.1J DAO G331E

128 FA13.1J ATM K750K

129 FA13.1J ATP13A2 M854R

130 FA13.1J COQ2 M128V

131 FA13.1J FBXO7 I87T

132 FA13.1J GCH1 G201E

133 FA13.1J ITPR1 N602D

134 FA13.1J KCNA1 R417*

135 FA13.1J KCNC3 R420H

136 FA13.1J MAPT G300R

137 FA13.1J PLA2G6 K545R

138 FA13.1J PLEKHG4 c.-16C>T

139 FA13.1J PRKAR1B L50R

140 FA13.1J PRKCG F643L

141 FA13.1J RAB39B T168K

142 FA13.1J RNF216 R694C

143 FA13.1J SERPINI1 G392E

144 FA13.1J SIGMAR1 E102Q

145 FA13.1J SLC1A3 P290R

146 FA13.1J SPG11 Q1875*

147 FA13.1J SPTBN2 R480W

148 FA13.1J MAPT R5H

149 FA13.1J LRRK2 R793M

150 FA13.1J DCTN1 R785W

151 FA13.1J TREM2 Q33X

152 FA13.1J EPHA1 P460L

153 FA13.1J FUS R521G

154 FA13.1J SORL1 G1681D

155 FA13.1J TREM2 R62H

156 FA13.1J DNAJC6 S59G

157 FA13.1J EIF2AK2 A109V

158 FA13.1J CACNA1G R1274S

159 FA13.1J NKX6-2 K41*

160 FA13.1J PRKN P437L

161 FA13.1J BLOC1S1 H69P

162 FA13.1J PLAAT4 I14T

Appendix B: Detailed list of engineered gene variants in six additional iPSC lines that will be expanded, QC’d and distributed to scientific community. For each gene variant listed below, a heterozygous, homozygous and revertant iPSC line will be available in each of the six iPSC lines.

Number Gene & Variant

1 APOE C112R

2 APOE R136S

3 APOE R158C

4 SNCA A53T

5 TARDBP M337V

6 TARDBP Q331K

7 APP A673T

8 APP E693G

9 FUS R495X

10 GRN Q125X

11 PSEN1 E276A

12 PSEN2 N141I

13 SNCA E46K

14 FUS P525L

15 PSEN1 M135V

16 TREM2 R47H

17 ABCA7 E1679X

18 ABCA7 W1214X

19 UBQLN2_P497H

20 PSEN2 M239I

21 SORL1 T947M

22 GRN A9D

23 MAPT P301L

24 MAPT R317W

25 TREM2 Q33X

To accomplish these requirements, the Contractor shall provide dedicated senior PhD accredited project manager to develop cell lines.

GOVERNMENT RESPONSIBILITIES

The government will provide a list of selected mutations to vendor for cell line engineering.

DELIVERY OR DELIVERABLES

Contractor shall make cell lines 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.

REPORTING REQUIREMENTS

After completion of the expansion and quality control, the contractor shall provide a report for each cell line documenting quality control testing.

OTHER CONSIDERATIONS

Travel:

The principal place of performance is the contractor’s work site. Travel for contractor employees will not be necessary.

Key Personnel:

Not applicable.