appendix vii correlative study specimen
plans for assuring data accuracy

DNA and Immunological Monitoring studies for Stem Cell Gene Therapy for HIV Mediated by  
Lentivector Transduced, Pre-selected CD34+ Cells in AIDS-lymphoma participants  
| Lentivector Transduced, Pre-selected CD34+ Cells in AIDS-lymphoma participants Tube Type,  Blood  Component  Needed, Whole  Blood  Collection  Volume, and  Aliquot Volume   |                                                                                     |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------|----------------|------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------|
| Biomarker  Name,  Laboratory  Conducting  Assay and  Laboratory  Director                                                                                                    | Tissue/Body  Fluid Tested and Timing of  Assay                                      |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| Assay                                                                                                                                                                        | Timing of Analysis,  (conducted during  the trial or after the  trial)              |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| Use and                                                                                                                                                                      | Funding  Source(s)                                                                  |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| (CLIA:  Y/N)                                                                                                                                                                 | Purpose                                                                             |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| Study T  Lymphocytes and  their subsets  Pollard, UC Davis                                                                                                                   | Flow  Cytometry CLIA: N                                                             | Exploratory    | Blood                                                                                                            | White blood cell  component  EDTA whole  blood, 2-mL,  purple top, and  (PBMCs), from  18-mL EDTA,  purple top | Analyses will be  performed during the  trial. Samples should  be shipped to the  Pollard lab upon  collection.                                                             | CIRM |
| To evaluate the  development of  normal T cell  subsets                                                                                                                      | Baseline, 3, 6,  12, 24 months  post-transplant,  Early Disc., and  Off-Study Disc. |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| Cytokine studies  using stored  plasma and serum,  Pollard, UC Davis                                                                                                         | ELISA                                                                               | Exploratory to |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| CLIA: N                                                                                                                                                                      | evaluate the level  of cytokines  related to a  chronic  inflammatory  status       | Blood          | Serum from 5  mL Red top,  stored as 0.5 mL  aliquots 10 mL Plasma  (from EDTA  blood), stored as  1 mL aliquots | Plasma and Serum  samples will be  aliquoted and stored  for delayed analysis                                  | CIRM                                                                                                                                                                        |      |
| Baseline, 3, 6,  12, 24 months  post-transplant,  Early Disc., and  Off-Study Disc.                                                                                          |                                                                                     |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| Functional  Responses Upon  Reconstitution of  T Cell Immunity Pollard, UC Davis                                                                                             | Flow  cytometry,  assessment  of response  to antigen CLIA: N                       | Exploratory    | Blood                                                                                                            | White blood cell  component  (PBMCs),  EDTA, purple  top, from 20 mL  aliquot                                  | Analyses will be  performed during the  trial. Samples should  be shipped to the  Pollard lab upon  collection.                                                             | CIRM |
| To evaluate the  development of  functional  immune cells                                                                                                                    | Baseline, 3, 6,  12, 24 months  post-transplant,  Early Disc., and  Off-Study Disc. |                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |
| Monitoring for  Insertional  Oncogenesis and  Clonality of  Hematopoiesis  after Gene  Therapy Anderson, UC  Davis                                                           | LAM-PCR                                                                             | Exploratory    | Blood                                                                                                            | White blood cell  component  (PBMCs),  EDTA, purple  top, 10 mL  aliquot                                       | Analyses will be  performed during the  trial. Samples should  be shipped to the  Pollard lab upon  collection and will be  transferred to the  Anderson lab for  analysis. | CIRM |
| CLIA: N                                                                                                                                                                      | To determine if  clones of  transduced cells  have developed                        | 1, 2, 4, 6, 8, 10,  12, 18, 24  months posttransplant,  Early Disc., and  Off-Study Disc.                |                                                                                                                  |                                                                                                                |                                                                                                                                                                             |      |  
| Tube Type,  Blood  Component                                                                                   |                                                                                                               |                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |
|----------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------|--------|--------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------|
| Needed, Whole  Blood  Collection  Volume, and  Aliquot Volume                                                  |                                                                                                               |                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |
| Biomarker  Name,  Laboratory  Conducting  Assay and  Laboratory  Director                                      | Tissue/Body  Fluid Tested and Timing of  Assay                                                                | Timing of Analysis,  (conducted during  the trial or after the  trial) |        |                                                                          |                                                                                                                                                                             |                                     |
| Assay                                                                                                          | Use and                                                                                                       | Funding  Source(s)                                                     |        |                                                                          |                                                                                                                                                                             |                                     |
| (CLIA:  Y/N)                                                                                                   | Purpose                                                                                                       |                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |
| DNA monitoring  studies Anderson, UC  Davis                                                                    | PCR, qPCR,  sequencing CLIA: N                                                                                | Exploratory                                                            | Blood  | White blood cell  component  (PBMCs),  EDTA, purple  top, 5 mL aliquot   | Analyses will be  performed during the  trial. Samples should  be shipped to the Pollard lab upon  collection and will be  transferred to the  Anderson lab for  analysis.  | CIRM                                |
| To evaluate in  vivo gene  marking, anti-HIV  gene expression,  sequence analysis,  vector stability  analysis | Baseline, 1, 2,  4, 6, 8, 10, 12,  18, 24 months  post-transplant,  Early Disc., and  Off-Study Disc.         |                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |
| Monitoring for  immune response  to TRIM5α Anderson, UC  Davis                                                 | ELISA                                                                                                         | Exploratory                                                            | Blood  | White blood cell  component  (PBMCs),  EDTA, purple  top, 10 mL  aliquot | Analyses will be  performed during the  trial. Samples should  be shipped to the  Pollard lab upon  collection and will be  transferred to the  Anderson lab for  analysis. | CIRM                                |
| CLIA: N                                                                                                        | To evaluate  whether any  immune response  is occurring with  the expression of  the chimeric  TRIM5α protein | 1, 2, 6, 12, 18,  24 months posttransplant,  Early Disc., and  Off-Study Disc.                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |
| Monitoring of  changes in the  HIV reservoir and  viral diversity Henrich, UC San  Francisco                   | Peripheral  blood and  leukapheresis  cells/plasma CLIA: N                                                                                                               | Exploratory                                                            | Blood; | Double spun  plasma and  EDTA PBMC  (2 x 107 )                           | Analysis during  study, shipped to the  Henrich Lab at UC  San Francisco                                                                                                    | Dr. Henrich  Lab  Internal  Funding |
| To characterize  changes in HIV  reservoir/diversity                                                           | baseline, 2 and  10 weeks then  6, 12- and 24- months posttransplant                                                                                                               |                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |
| Monitoring of  mixed lymphocyte  reactions Henrich, UC San  Francisco                                          | Peripheral  blood and  Leukapheresis CD34+  depleted  cells; PBMC CLIA: N                                                                                                               | Exploratory                                                            | Blood  | CD34+ depleted  leukapheresis  cells EDTA PBMC  (2 x 107 )               | Analysis during  study, shipped to the  Henrich Lab at UC  San Francisco                                                                                                    | Dr. Henrich  Lab Internal  Funding  |
| To monitor for  reaction to  transformed cells                                                                 | baseline, 2 and  10 weeks then  6, 12- and 24- months posttransplant                                                                                                               |                                                                        |        |                                                                          |                                                                                                                                                                             |                                     |  
| Tube Type,  Blood  Component                                              |                                                |                                                                                                                                                                                                                    |                                                                                                                                                                                             |                                                                                                                |                                                                                                                                                 |      |
|---------------------------------------------------------------------------|------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------|------|
| Needed, Whole  Blood  Collection  Volume, and  Aliquot Volume             |                                                |                                                                                                                                                                                                                    |                                                                                                                                                                                             |                                                                                                                |                                                                                                                                                 |      |
| Biomarker  Name,  Laboratory  Conducting  Assay and  Laboratory  Director | Tissue/Body  Fluid Tested and Timing of  Assay | Timing of Analysis,  (conducted during  the trial or after the  trial)                                                                                                                                             |                                                                                                                                                                                             |                                                                                                                |                                                                                                                                                 |      |
| Assay                                                                     | Use and                                        | Funding  Source(s)                                                                                                                                                                                                 |                                                                                                                                                                                             |                                                                                                                |                                                                                                                                                 |      |
| (CLIA:  Y/N)                                                              | Purpose                                        |                                                                                                                                                                                                                    |                                                                                                                                                                                             |                                                                                                                |                                                                                                                                                 |      |
| GI Biopsy                                                                 | IFA, PCR  and RT-PCR  and FACS,  IHC           | Exploratory to  evaluate the  response of  immune system  following  reconstitution of  new anti-HIV hematopoietic  cells. To evaluate  the persistence of  HIV in HIV  dormant  reservoirs  following  transplant | Endoscopy  biopsy samples  will be obtained  at 6 months  post-transplant for the group  that will not  undergo ART  withdrawal or  any time before  ART  withdrawal and  at 8 weeks later. | Separate samples  will be obtained  for IHC, snap  freezing or to put  on RNA later for  DNA and RNA  analysis | Fresh samples will be  run immediately after  receiving the samples  by courier. Frozen  samples will be  stored at UC Davis  for future tests. | CIRM |
| Bone Marrow                                                               | CFU                                            | assay,                                                                                                                                                                                                             |                                                                                                                                                                                             |                                                                                                                |                                                                                                                                                 |      |
| Aspirate                                                                  | DNA  extraction,  quantitative  PCR CLIA:N     | To evaluate the in  vivo gene marking  of human CD34+  cells                                                                                                                                                       | Residual  Samples of  Bone marrow  aspirate                                                                                                                                                 | Two 10.0 ml  EDTA / (Purple  top tubes)                                                                        | 3- and 12-months post-transplant,  treatment  discontinuation                                                                                   | CIRM |
appendix vii correlative study specimen
specimen collection and processing instructions

The correlative studies can be divided into immunological and HIV studies, DNA monitoring studies, and monitoring for oncogenesis and hematopoietic clonality. The immunological studies will be done in 2 compartments: peripheral blood samples and endoscopy (gut mucosa) samples.
appendix vii correlative study specimen
1. blood samples

Samples will be collected via blood draws from participants (Maximum of 65 mL of blood collected). Blood samples for immunological studies A total of 45 mL of blood will be collected for immunological studies:  
- 40 mL EDTA anti-coagulated whole blood specimens and divided into four 10 mL
tubes. Whole blood (for PBMCs) is required from each participant at each time point described in the clinical protocol.  
- 5mL of non-anticoagulated blood (processed for ~ 3 mL of serum) in one 5 mL tube red top tube
appendix vii correlative study specimen
processing procedures red top tube

- Collect 5 mLs of whole blood in a 5 mL red top tube.  
- After blood is drawn, invert collection tube 5 times and allow the blood to clot 60 minutes, leaving the tube in an upright position during the clotting process for immediate processing. If multiple samples are collected in one day, and the site would like to hold the sample for processing later the same day, store the sample between 28oc until ready to invert the tube and clot the sample.
Once clotted, the collection tube should not be allowed to sit at room temperature for more than 1 hour prior to centrifugation and separation of the serum from the clot. Centrifuge the collection tube for 10 minutes at 1000 g. After separation, the serum should be clear and free from all blood cells. Aliquot the serum in the 3 mL cryovial.  
- Separated sera aliquots must be stored refrigerated until ready for shipment to UC
Davis on next available business day (specimens should be shipped **MONDAY** through **THURSDAY)**.
Each sample tube should be labeled with GlobalTraceSM specimen labels using a Sharpie pen to include the following information:
- 11-digit Participant \#  
- Date and time of collection
- Specimen type: (i.e., WB=Whole Blood, S=Serum) - Specimen purpose: (i.e., Immunological Studies)
appendix vii correlative study specimen
blood samples for dna monitoring

A total of 20 mL of blood will be collected for DNA monitoring studies (see Section 2.5.4 for analyses to be performed):
AMC 097 (Version 9.0) 07FEB2022 128 NCI Version Date 07FEB2022 CLIENT CONFIDENTIAL  
- 20 mL of EDTA anti-coagulated whole blood specimens in two 10 mL tubes will be collected.
Each sample tube should be labeled with GlobalTraceSM specimen labels using a Sharpie pen to include the following information:
- 11-digit Participant \#  
- Date and time of collection
- Specimen type: (i.e., WB=Whole Blood)
- Specimen purpose: (i.e., DNA Monitoring Studies)
appendix vii correlative study specimen
blood samples for safety monitoring

A total of 30 mL of blood may be collected for safety monitoring studies, as determined with the protocol chair per Section 2.5.8. If determined to be required, 30 mL of EDTA anti-coagulated whole blood specimens in three 10 mL tubes will be collected and shipped to the Pollard lab as noted below for blood samples.  
Each sample tube should be labeled with GlobalTraceSM specimen labels using a Sharpie pen to include the following information:
- 11-digit Participant \#  
- Date and time of collection - Specimen type: (i.e., WB=Whole Blood) - Specimen purpose: (i.e., Safety Monitoring Studies)
appendix vii correlative study specimen
blood specimen shipment

All **Blood Samples** should be shipped by priority overnight express on **MONDAY** through Thursday to the UC Davis correlative study laboratory.  
Refrigerated Blood Specimen Protocol
- Apply a strip of Parafilm, around all vials, where the cap meets the tube.  
- Wrap all blood tubes individually with bubble wrap.  
- Place all specimens in the clear plastic biohazard bag with an absorbent pad and seal.  
- Place the clear plastic biohazard bag in the white Tyvek biohazard bag and seal. - Place the sealed white Tyvek biohazard bag in the inner cardboard box of the shipper.  
- Place the inner cardboard box in the Styrofoam cutout, put the notched flap down first, and fold across. Remove your gloves.  
- Place four frozen cold packs in the Styrofoam box, one on each side of the inner cardboard box. Thermal protective gloves are recommended.  
- Place the lid on the Styrofoam box and put the Styrofoam box in the outer cardboard shipper.  
- Place the shipping manifest on the top of the closed Styrofoam box.
AMC 097 (Version 9.0) 07FEB2022 129 NCI Version Date 07FEB2022 CLIENT CONFIDENTIAL  
- Close and tape the box along the center break and on the sides. Secure the shipping label to the top of the box.
NOTE: FedEx's "Priority Overnight" is required shipping method.  
- It is the responsibility of the Primary Investigator to ensure that all staff personnel who will be handling, packaging, and/or shipping clinical specimens act in conformance with International Air Transport Association (IATA) regulations (IATA Packing Instruction 650) relating to the handling and shipping of hazardous goods. (IATA Packing Instruction 650 is located on the AMC web site).  
- Use a federally approved shipper for biological substance shipment (Category B).  
Label the shipper with the "Infectious substance" diamond shaped label. On one side, in black marker write "Biological Substance, Category B, UN 3373", your name or name of responsible person, date of collection and phone number of the person responsible for the package. Package and label the shipment in accordance with the instructions provided for that specific shipper.
- A Shipper's Declaration for Dangerous Goods is not required.  
Please Note: The shipper will be mailed back to the AMC site. The STP-100 SAF-T-PAK
shipper (VWR Cat \# 11217-082) is a complete kit (bubble wrap, absorbent paper, labels, etc.) for specimen shipment. To reuse the shipper, you will need new labels, wrap, etc. There is a refurbishment kit with extra bubble wrap and absorbent material (Fisher Scientific Cat \# 19-038-301E). Sample receipt and processing are performed Tuesday through Friday, unless other arrangements have been made for with the lab. Avoid collecting specimens for shipment on Fridays, and on days before an observed UC Davis holiday. All specimens should be shipped to:
Dr. Joseph Anderson University of California Davis 2921 Stockton Blvd., Room 1300 Sacramento, CA 95817 Tel: (916) 703-9300 Email: jsanderson@ucdavis.edu
appendix vii correlative study specimen
2. blood plasma and leukapheresis

Samples will be sent same day by special courier by arrangement of Dr. Henrich and sent to:
Henrich Laboratory University of California, San Francisco 1001Potrero Ave., Bldg. 3, Rm 603 San Francisco, CA 94110 Email: Timothy.Henrich@ucsf.edu
appendix vii correlative study specimen
3. endoscopy samples participants will

Participants are sedated with IV Benadryl, versed, and Demerol to achieve conscious sedation while being monitored for vital signs and comfort levels (heart rate and rhythm, blood pressure, O2 saturation). When participants are adequately sedated, an Olympus upper endoscope is passed to the small intestines where 24 biopsies are obtained using Boston Scientific biopsy forceps (large 2.8 mm). This typically requires 12 passes to acquire adequate samples for subsequent studies.
appendix vii correlative study specimen
sample disposition during the procedure

A total of 24 endoscopy (gut mucosa) samples will be collected. Endoscopy samples for RNA & DNA analysis
- A total of 8 biopsy specimens should be collected and **snap frozen**:  
o Six of the eight biopsy specimen should be transferred overnight on dry ice to UC
Davis.  
o Two of the eight biopsy specimen should be placed in 1 mL of RNAlater Qiagen and sent over night to UC Davis with chilled packaging.
Endoscopy samples for IHC and in situ staining
- A total of 3 biopsies should be collected and placed in formalin per clinical practice.  
- These are transported to the Pathology laboratory for paraffin embedding per clinical practice.
Endoscopy samples for vector frequency, immunologic flow cytometry analysis, and cellular HIV DNA measurement  
- A total of 13 biopsies are collected and placed in chilled 30 mL of RPMI media and transported overnight with chilled packaging to UC Davis.  
- These are transported to the UC Davis immunology laboratory for collagenase digestion and single cell suspension.
Each sample tube should be labeled with GlobalTraceSM specimen labels using a Sharpie pen to include the following information:
- 9-digit Participant \# - Date and time of collection  
- Specimen type: (i.e., WB=Whole Blood)
- Specimen purpose: (i.e., DNA Monitoring Studies)
Participants are monitored in the Endoscopy Suites recovery area and are released to a companion for transport home with specific instructions about who to contact from the study team should any concerns or side effects arise. Endoscopy Samples obtained at UC Davis Medical Center will be transported directly from the endoscopy suite to the laboratory. Samples from UC San Francisco will be transported by special courier as has been performed by previous clinical protocols. This is achieved by car from San Francisco and air from San Diego.
appendix vii correlative study specimen
endoscopy specimen shipment

Frozen endoscopy specimen protocol  
- Apply a strip of Parafilm, around all vials, where the cap meets the tube.  
- Place all specimens in the inner plastic biohazard bag with an absorbent pad and seal.  
- Place the clear plastic inner biohazard bag in the white Tyvek biohazard bag and seal.  
- Place the sealed white Tyvek biohazard bag in the inner cardboard box of the shipper.  
- Place the inner cardboard box in the Styrofoam cutout, put the notched flap down first, and fold across. Remove your gloves.  
- Using thermal protective gloves place the dry ice in the Styrofoam box and spread it evenly around each side of the inner cardboard box.  
- Place the lid on the Styrofoam box and put the Styrofoam box in the outer cardboard shipper. - Place the shipping manifest on the top of the closed Styrofoam box.
Close and tape the box along the center break and on the sides. Secure the shipping label to the top of the box.  
NOTE: FedEx's "Priority Overnight" is required shipping method  
- It is the responsibility of the Primary Investigator to ensure that all staff personnel who will be handling, packaging, and/or shipping clinical specimens act in conformance with International Air Transport Association (IATA) regulations (IATA Packing Instruction 650) relating to the handling and shipping of hazardous goods. (IATA Packing Instruction 650 is located on the AMC web site).  
- Use a federally approved shipper for biological substance shipment (Category B). Label the shipper with the "Infectious substance" diamond shaped label. On one side, in black marker write "Biological Substance, Category B, UN 3373," your name or name of responsible person, date of collection and phone number of the person responsible for the package. Package and label the shipment in accordance with the instructions provided for that specific shipper.  
- A Shipper's Declaration for Dangerous Goods is not required. However, for all dry ice shipments, the following information must be shown in sequence on the airway bill in the "Nature and Quality of Goods" box: Dry Ice, 9, UN1845, number of boxes being shipped, net weight of dry ice per box.
Please Note: The shipper will be mailed back to the AMC site. The STP-100 SAF-T-PAK
shipper (VWR Cat \# 11217-082) is a complete kit (bubble wrap, absorbent paper, labels, etc.) for specimen shipment. To reuse the shipper, you will need new labels, wrap, etc. There is a refurbishment kit with extra bubble wrap and absorbent material (Fisher Scientific Cat \# 19038-301E). Sample receipt and processing are performed Tuesday through Friday, unless other arrangements have been made for with the lab. Avoid collecting specimens for shipment on Fridays, and on days before an observed UC Davis holiday. All specimens should be shipped to:
Dr. Joseph Anderson University of California Davis 2921 Stockton Blvd., Room 1300 Sacramento, CA 95817 Tel: (916) 703-9300 Email: jsanderson@ucdavis.edu
appendix vii correlative study specimen
billing

Bill the FedEx \# available on the AMC member's only website. This number is supplied by the AMC Operations and Data Management Center. It is only to be used for billing shipment of specimens to the lab where the sample is processed and/or stored.
appendix vii correlative study specimen
record of blood and endoscopy

This study will track specimens via GlobalTraceSM, a component of the AMC AdvantageEDCSM system. The GlobalTraceSM shipment manifest must accompany all specimen shipments.
appendix vii correlative study specimen
technical questions

Study Team University of California, Davis Comprehensive Cancer Center 4501 X Street, Suite 3016 Sacramento, CA 95817 Tel: 916-703-9118 Fax: 916-734-1895 Email: HS-CELLULARTHERAPYRESEARCH@UCDAVIS.EDU
appendix vii correlative study specimen
4. bone marrow aspirate samples

Processing procedures
- Two 10.0 ml EDTA / Purple top tubes  
- Collect specimen per site's institutional SOP - Immediately transfer and if possible, completely fill two 10 ml EDTA (purple top tubes) with the bone marrow aspirate.
AMC 097 (Version 9.0) 07FEB2022 134 NCI Version Date 07FEB2022 CLIENT CONFIDENTIAL
Each sample tube should be labeled with GlobalTraceSM specimen labels using a Sharpie pen to include the following information:  
- 9-digit Participant \#
- Date and time of collection
- Specimen type: (i.e., BMA "Bone Marrow Aspirate")
- Specimen purpose: (i.e., DNA Studies)
All Bone Marrow Aspirate **Samples** should be shipped by priority overnight express on MONDAY through **Thursday** to the UC Davis correlative study laboratory.
appendix vii correlative study specimen
cool bone marrow aspirate specimen

- Apply a strip of Parafilm, around all vials, where the cap meets the tube.  
- Wrap all tubes individually with bubble wrap. - Place all specimens in the clear plastic biohazard bag with an absorbent pad and seal.  
- Place the clear plastic biohazard bag in the white Tyvek biohazard bag and seal.  
- Place the sealed white Tyvek biohazard bag in the inner cardboard box of the shipper.  
- Place the inner cardboard box in the Styrofoam cutout, put the notched flap down first, and fold across. Remove your gloves.  
- Place four cool gel packs in the Styrofoam box, one on each side of the inner cardboard box.  
- Place the lid on the Styrofoam box and put the Styrofoam box in the outer cardboard shipper.  
- Place the shipping manifest on the top of the closed Styrofoam box.  
- Close and tape the box along the center break and on the sides. Secure the shipping label to the top of the box.
NOTE: FedEx's "Priority Overnight" is required shipping method.  
- It is the responsibility of the Primary Investigator to ensure that all staff personnel who will be handling, packaging, and/or shipping clinical specimens act in conformance with International Air Transport Association (IATA) regulations (IATA Packing Instruction 650) relating to the handling and shipping of hazardous goods. (IATA Packing Instruction 650 is located on the AMC web site).  
- Use a federally approved shipper for biological substance shipment (Category B).
Label the shipper with the "Infectious substance" diamond shaped label. On one side, in black marker write "Biological Substance, Category B, UN 3373", your name or name of responsible person, date of collection and phone number of the person responsible for the package. Package and label the shipment in accordance with the instructions provided for that specific shipper.  
- A Shipper's Declaration for Dangerous Goods is not required.  
Please Note: The shipper will be mailed back to the AMC site. The STP-100 SAF-T-PAK
shipper (VWR Cat \# 11217-082) is a complete kit (bubble wrap, absorbent paper, labels, etc.) for specimen shipment. To reuse the shipper, you will need new labels, wrap, etc. There is a refurbishment kit with extra bubble wrap and absorbent material (Fisher Scientific Cat \# 19-038-301E). Sample receipt and processing are performed Tuesday through Friday, unless other arrangements have been made for with the lab. Avoid collecting specimens for shipment on Fridays, and on days before an observed UC Davis holiday. All specimens should be shipped to:
Dr. Joseph Anderson University of California Davis 2921 Stockton Blvd., Room 1300 Sacramento, CA 95817 Tel: (916) 703-9300 APPENDIX VIII: INTERNATIONAL PROGNOSTIC INDEX (AGE-ADJUSTED)  
| Characteristic          | Prognostic Factor (1 point for each)                  |
|-------------------------|-------------------------------------------------------|
| Ann Arbor Stage         | Stage III or IV                                       |
| Serum LDH level         | Elevated                                              |
| ECOG performance status | 2, 3 or 4 (patients with PS 3 or 4 are not  eligible) |
appendix vii correlative study specimen
appendix ix ccr5-tropism assay

1. Monogram Biosciences Assays:
GenoSure ArchiveSM DNA Sequencing - Test Code: R6000 Trofile® DNA - Test Code: E3600 2. This sample is to be collected within 8 weeks prior to study enrollment. 3. Draw 4mL of whole blood in 1 lavender top EDTA tube.
appendix vii correlative study specimen
4. do not centrifuge.

5. Freeze *immediately* at -20°C. Sample needs to be FULLY frozen before shipping. 6. Call Monogram Biosciences Client Services to schedule specimen pick-up at 800-7770171 by 1:00 p.m. to ensure next day delivery.  
7. Upon arrival of courier, please place frozen specimen tube into the secondary container offered by the courier.  
8. Ensure there is enough bubble wrap and absorbency sheets inside to contain any spills.  
9. Close container and give back to the courier for shipment to Monogram Biosciences.  
| APPENDIX X: RISK LIST FOR BEAM COMMON                       |       |
|-------------------------------------------------------------|-------|
| CTCAE Term                                                  | Grade |
| BEAM Neutrophil count decreased                             | 1-2   |
| Platelet count decreased                                    | 1-2   |
| Lymphocyte count decreased                                  | 1-2   |
| Febrile Neutropenia                                         | 3     |
| Nausea                                                      | 1-2   |
| Vomiting                                                    | 1-2   |
| Mucositis oral,                                             | 1-2   |
| Esophageal ulcer, esophagitis                               | 1-2   |
| Abdominal pain                                              | 1-2   |
| Diarrhea                                                    | 1-2   |
| Anorexia, dysphagia                                         | 1-2   |
| Alopecia                                                    | 1-2   |
| Fatigue                                                     | 1-2   |
| Infusion of Unmodified Cells Presyncope, dizziness          | 1-2   |
| Syncope                                                     | 3     |
| Hypoxia                                                     | 2     |
| Fever                                                       | 1-2   |
| OCCASIONAL                                                  |       |
| BEAM Blood Bilirubin increased                              | 1-2   |
| Alanine aminotransferase (ALT) increased                    | 1-2   |
| Aspartate aminotransferase (AST) increased                  | 1-2   |
| Pneumonitis                                                 | 1-2   |
| Hypotension                                                 | 1-2   |
| Hyperuricemia                                               | 1-2   |
| Maculopapular Rash                                          | 1-2   |
| Chills                                                      | 1-2   |
| Infusion of Unmodified CellsAMC 097 (Version 9.0) 07FEB2022 | 139   |
| NCI Version Date 07FEB2022                                  |       |
appendix vii correlative study specimen
appendix xi ati risk mitigation

Participant ID Number:
Date ¦__¦__¦/l__|__|/l__|__|__| (DD/MMM/YYYY)
Visit Type: ¦__¦__¦__¦__¦  
| Pre-ATI Risk Mitigation Counseling                  |          |          |
|-----------------------------------------------------|----------|----------|
| Procedure                                           | Initials | Comments |
| Partner assessment: Ask whether the volunteer       |          |          |
| has regular sex partner(s), casual partner(s), or   |          |          |
| both, and the gender of their sex partner(s):       |          |          |
| including but not limited to: cisgender male and/or |          |          |
| female, and/or transgender partners                 |          |          |
| Assess whether HIV status of partner(s) is known    |          |          |
| Assess the volunteer's current understanding of     |          |          |
| HIV transmission risk to partner(s)                 |          |          |
| Assess if the volunteer has other risk factors for  |          |          |
| transmitting HIV, such as sharing needles           |          |          |
| Describe the expected viral rebound during the ATI  |          |          |
| and the rationale for HIV-negative partners to use  |          |          |
| condoms and/or PrEP                                 |          |          |
| Ask whether the volunteer has heard of PrEP         |          |          |
| Describe PrEP and its potential benefits            |          |          |
| Provide and review the HIV Treatment                |          |          |
| Interruption Study Participation Disclosure         |          |          |
| Sheet                                               |          |          |
| Provide the PrEP for Partners information sheet     |          |          |
| If cisgender female partners are involved, provide  |          |          |
| PrEP for Cisgender Female Partners supplement       |          |          |
| Review the resources for accessing PrEP provided    |          |          |
| on the information sheets                           |          |          |
| Offer to follow up with the volunteer and/or their  |          |          |
| partner(s) if requested                             |          |          |  
Participant ID Number:
Date ¦__¦__¦/l__l__l__l/l__l__l__l (DD/MMM/YYYY)
Visit Type: ¦__¦__¦__¦__  
| Ongoing Risk Mitigation Counseling                    |                     |                        |          |
|-------------------------------------------------------|---------------------|------------------------|----------|
| f                                                     | Procedure           | Initials               | Comments |
| Has volunteer previously reported any sex partners    |                     |                        |          |
| on study?                                             | Yes                 | No                     |          |
| Is there a protection plan for partners? Yes No       |                     |                        |          |
| If no, offer shared study visit and navigation        |                     |                        |          |
| assistance.                                           |                     |                        |          |
| Has volunteer had new sex partners since last visit   |                     |                        |          |
| and/or anticipate change in sex partners:             |                     |                        |          |
| No                                                    | Yes, new partner(s) | Yes, anticipate change |          |
| If Yes, describe type of partners (cis/trans          |                     |                        |          |
| male/female), context (travel, event/party, sex work, |                     |                        |          |
| etc.), and plans for protecting partners.             |                     |                        |          |
| Offer shared study visit and navigation assistance.   |                     |                        |          |
| Review that viral rebound can occur at any time       |                     |                        |          |
| during the treatment interruption and may occur       |                     |                        |          |
| without any symptoms                                  |                     |                        |          |
| Review the risk that viral rebound poses to sexual    |                     |                        |          |
| partners                                              |                     |                        |          |
| Ask whether the participant wants to leave with       |                     |                        |          |
| condoms                                               |                     |                        |          |
| Ask whether the participant or their partners want to |                     |                        |          |
| discuss PrEP with a study team member                 |                     |                        |          |
| If PrEP has been discussed previously, follow up on   |                     |                        |          |
| whether action has been taken by the partner(s) and   |                     |                        |          |
| whether navigation assistance is needed               |                     |                        |          |
| Offer the HIV Treatment Interruption  Study           |                     |                        |          |
| Participation Disclosure Sheet, PrEP for              |                     |                        |          |
| Partners, and PrEP for Cisgender Female               |                     |                        |          |
| Partners , as applicable                              |                     |                        |          |
appendix xii hiv treatment interruption
hiv treatment interruption study participation

This document can help you talk with your partner(s) about the HIV treatment interruption study in which you are participating. You should take your time to decide if and who you want to tell. Telling others about your participation is a personal choice. You will need to find the right time and place to tell your partner(s). Below are a few points you can discuss with your partner(s).
appendix xii hiv treatment interruption
"undetectable means untransmittable" (u =

❏ I am a person living with HIV. I have been taking HIV medications. My virus has been undetectable for some time.  
❏ People who have taken their HIV medications and maintained an undetectable viral load for at least six months have no risk of sexually transmitting the virus to an HIV-negative partner according to the Centers for Diseases Control and Prevention (CDC).
appendix xii hiv treatment interruption
participation in an hiv treatment

❏ I am participating in a research study. ❏ Part of the study requires that I pause my HIV medications.  
❏ Stopping my HIV medications means that my virus could come back (rebound) at any time.  
❏ After pausing my medications, I will be tested frequently to see when my HIV comes back.  
❏ I may be off my HIV medications for as long as 12 weeks or morel. During this time, I may no longer be
"undetectable." I will restart my HIV medications if my virus remains detectable at high levels for weeks, months, if my CD4 count becomes too low, or if I develop symptoms or health problems.  
PrEP, HIV Testing and Counseling Information to Relay to Your Partners
❏ While I'm off my HIV medications, there is a risk of transmitting HIV to my partner(s).  
❏ The study staff can provide counseling about how to protect my partners against HIV transmission.  
❏ If you are HIV-negative, you should consider using PrEP to prevent HIV. The study team can provide a list of PrEP
resources available in the area. PleasePrEPme.org can also help you find a PrEP provider.  
❏ Using a condom may decrease the risk of transmitting HIV and other STIs during the treatment interruption period.  
❏ We do have the choice of not having sex during the HIV treatment interruption period, until I restart HIV
medications.  
❏ If you think you have been exposed to HIV, you should contact the study staff immediately. The research team can link you with HIV testing services that provide post-exposure prophylaxis (PEP) which may also prevent HIV
transmission. You should do this within 72 hours of being exposed to HIV. If you can't reach the study staff or don't want to call them, you should go to an Emergency Department within the 72 hour period.  
You should give your partner(s) time to process the information to ask questions.  
You should also be familiar with the partner-notification laws in your state. You can check with your state's Department of Health to find out more about the laws in your area. For the state of California, you can consult:
California HIV Laws (2019): http://www.californiaaidsresearch.org/topic-areas/hiv-laws_final.pdf If your partner(s) have any questions about the study, we are happy to discuss these issues with them. S/he/they should feel free to contact:
.  
Name:
Address: Phone:
appendix xiii prep information sheet
participation in an hiv treatment

PrEP is a medicine that prevents HIV.  We recommend that participants in our trial talk with their HIV-negative sexual partner(s) about PrEP.  This is because volunteers may no longer have "undetectable" HIV when they stop taking HIV
medications during part of the trial.  They may be able to transmit HIV to partner(s) during this period.  
  
The study team can provide information to help you or your partner(s) learn more about PrEP. If you or your partner(s) want more information, please ask!
appendix xiii prep information sheet
how can partners of study

There are several different ways to access PrEP.  The best way will depend on a partner's insurance and where they receive medical care. We can help figure out the best way to get PrEP.  
Partners should start by seeing whether their primary care doctor can prescribePrEP.
appendix xiii prep information sheet
where else can my partner

ww.PleasePrEPMe.org is a searchable online resource that can help find a PrEP provider according to specific geographic or insurance needs. PrEP can be accessed via telehealth through Nurx.com and PlushCare.com
prep for cisgender women what
where else can my partner

ls PrEP for you?  
  
We are happy to answer any questions you may have!
summary of changes a phase
where else can my partner

Version 9.0 NCI Protocol \#: AMC-097 Local Protocol \#: AMC-097 NCI Version Date: 07FEB2022 Protocol Date: 07FEB2022  
| I.                                                                                                                                                                                                                                                                                                                                                                          | Scientific and Substantive Changes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |                                                                                                                                                                        |                     |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------|
| #                                                                                                                                                                                                                                                                                                                                                                           | Section                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | Description of Change                                                                                                                                                  |                     |
| 1.                                                                                                                                                                                                                                                                                                                                                                          | How long will  I be in this  study                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | During years 3-15, participants will be contacted by a person from the  clinic rather than a person from the protocol team to collect information  about their health. |                     |
| 2.                                                                                                                                                                                                                                                                                                                                                                          | During the                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | The conditioning regimen prior to transplant                                                                                                                           | has been revised to |
| Study                                                                                                                                                                                                                                                                                                                                                                       | indicate that agents proven that have the same effects as rituximab  (biosimilars) may be used instead of ritixumab for participants with B  cell lymphoma. Participants will be informed of whether they will  receive rituximab or a similar agent. In addition, the duration that each  chemotherapy agent will be given has been removed. Both of these  changes are because instiutions are permitted to administer  conditioning regimens in accordance to their local guidelines and for  consistency with the protocol. In addition, allowing administration of agents similar to ritiumab will give participating centers an alternative  option for treatment if there is a supply shortage of rituximab. |                                                                                                                                                                        |                     |
| 3.                                                                                                                                                                                                                                                                                                                                                                          | Use of HIV-1  Medications  During the  Study                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | Additional information on the effects and risks of                                                                                                                     | stopping HIV        |
| medications have been added. In addition recommendations and  requirements to help reduce these risks have been added. Participants  will be informed that HIV levels will increase while immune function  may decrease and that it may take over 4-6 weeks for these levels to  return to baseline, increasing the risk of developing symptoms.  Additional risks include: |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |                                                                                                                                                                        |                     |
| Risk                                                                                                                                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |                                                                                                                                                                        |                     |
| Considerations  related to  COVID-19                                                                                                                                                                                                                                                                                                                                        | -                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Symptoms similar to those experienced upon initial HIV  infection                                                                                                      |                     |
| -                                                                                                                                                                                                                                                                                                                                                                           | Inflammation / heart problems                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                                                                                        |                     |
| -                                                                                                                                                                                                                                                                                                                                                                           | Resistence to HIV medications, increased risk of spreading HIV                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                        |                     |
| -                                                                                                                                                                                                                                                                                                                                                                           | Increased risk of infection of another strain of HIV                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |                                                                                                                                                                        |                     |
| Attachment 2                                                                                                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |                                                                                                                                                                        |                     |  
| #                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Section                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | Description of Change                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |           |    |     |       |    |          |     |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|----|-----|-------|----|----------|-----|
| -                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Risks related to COVID-19 have been added.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| Participants                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | will                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | be                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | counseled | on | the | risks | of | stopping | HIV |
| medications, and if sexually active, advised to use condoms and to refer  their partners for HIV testing and post-exposure treatment. Participants  will now be required to be tested for COVID-19 before stopping HIV  medications. In addition, participants will restart their HIV medications  if they development symptoms believed to be related to increased levels  of HIV, have been exposed to HIV infection, or become pregnant. A  calendar was added in Attachment 2 that outlines required assessment  required after stopping and restarting HIV medications. |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| 4.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | Use of HIV-1  Medications  During the  Study                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | The duration that HIV medications may be stopped post transplant has  been updated from 12 weeks to until the onset of criterion for  resumption to allow for additional assessment on the survival of the  anti-HIV gene. This is considered a safe duration as participants will be  closely monitored and HIV medications will be restarted if symptoms  develop.                                                                                                                                                                                 |           |    |     |       |    |          |     |
| Attachment 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| 5.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | Use of HIV-1  Medications  During the  Study                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | Requirements during the conditioning regimen were revised to indicate  that HIV medication may be held and that participants will be informed  by their study doctor whether holding HIV medications is necessary.  This change is consistent with the protocol requirements.                                                                                                                                                                                                                                                                        |           |    |     |       |    |          |     |
| 6.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | Optional  Sample                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| Collections                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | The consent has been revised to include information on the SCOPE  study being conducted by University of Califnornia San Franscico. The  SCOPE study includes optional GI biopsies at the same timepoints as  the optional GI biopsies in this study. Participants that join this study  and the SCOPE study at the same time and consent to optional studies  may have biopsy results from the SCOPE study used for this study. This  will minimize the number of biopsies taken for participants planning to  participate in both studies and that consent to optional GI biopsies. GI  biopsies were added to the study calendar to clarify timepoints and  collection. |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| Attachment 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| 7.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | How long will  I be in this  study                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Optional bone marrow collections have been added for research to  study the effects of the vector on participants' genetics and immune  system. Participants that consent to optional bone marrow biopsies will  have about 2 tablespoons (20mL) of bone marrow collected at 3,  months, 12 months, and at study discontinuation. Risks of participating  in optional bone marrow collection include discomfort, pain, bleeding,  scarring or infection at the site of the aspirate/biopsy and chance of  allergic reaction to the numbing medicine. |           |    |     |       |    |          |     |
| Optional Bone  Marrow  Biospies Optional  Sample                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |
| AMC-097 (Version 9.0) 07FEB2022                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | ii                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |           |    |     |       |    |          |     |  
AMC-097 (Version 9.0) 07FEB2022 ii NCI Version Date 07FEB2022  
| #                                                                                                                                                         | Section                            | Description of Change                                                                                                                                                                                                                                                                                                                                                                                                         |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Collections What is  Involved? Risks of bone  marrow  biopsies Samples for  Future  Research  Studies  Attachment 2                                       |                                    |                                                                                                                                                                                                                                                                                                                                                                                                                               |
| 8.                                                                                                                                                        | How long will  I be in this  study | Optional blood sample collections have been added to monitor HIV  levels and the vector. Participants that consent to optional blood  collections will have about 3 tablespoons (30mL) of blood collected  every 12 months for years 3-15 on study. Risks of bloow draws include  pain, a bruise or lump at the point where the blood is taken, redness and  swelling of the vein and infection, and a rare risk of fainting. |
| Optional                                                                                                                                                  |                                    |                                                                                                                                                                                                                                                                                                                                                                                                                               |
| Blood Sample  Collections Optional  Sample  Collections What is  Involved? Risk of blood  collections Samples for  Future  Research  Studies Attachment 2 |                                    |                                                                                                                                                                                                                                                                                                                                                                                                                               |
| 9.                                                                                                                                                        | Attachment 2                       | Required bone marrow biopsies to assess disease for staging were  added for consistency with the protocol                                                                                                                                                                                                                                                                                                                     |  
| II.   | Administrative and Editorial Changes   |                                                                                                                                               |
|-------|----------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|
| #     | Section                                | Description of Change                                                                                                                         |
| 10.   | Global                                 | The protocol version was changed to 9.0 and the date to 07FEB2022                                                                             |
| 11.   | Attachment 2                           | Optional GI biopsy collections were added to attachment 2 for  consistency with the optional study collections sections of the consent  form. |
amc-097 model informed consent form
where else can my partner

Study Title for Study Participants: **Stem Cell Gene Therapy for HIV-1 in AIDS Lymphoma**
Participants Official Study Title for Internet Search on http://www.ClinicalTrials.gov: A Phase I Study of Stem Cell Gene Therapy for HIV Mediated by Lentivector Transduced, Pre-selected CD34+ Cells
amc-097 model informed consent form
a clinical trial of the

You are being asked if you want to take part in a research study. The main goal of a research study is to learn things to help participants in the future. No one can guarantee that a research study will help you. Participating in research is voluntary. You have the right to know about the procedures, risks, and benefits of the research study. To participate in this study, you will need to give your written consent by signing this form. Please take your time to make your decision and discuss it with your family, friends, and caregivers. This study is being led by Mehrdad Abedi, MD from the Department of Hematology/Oncology at the University of California Davis, with AIDS Malignancy Consortium (AMC) sites at medical centers across the U.S.
amc-097 model informed consent form
what is the usual approach

You are being asked to take part in this study because you have human immunodeficiency virus (HIV) infection and a type of blood cancer called lymphoma. You have already been treated with chemotherapy and your disease is now growing. People who are not in a study are usually treated with an autologous peripheral blood stem cell transplant with high dose chemotherapy (for example BEAM, described below). An autologous peripheral blood stem cell transplant is when your own stem cells are collected from your blood, frozen, and then given back to you after you receive high dose chemotherapy. This transplant with high dose chemotherapy is intended to prevent your disease from coming back in the future.
amc-097 model informed consent form
what are my other choices

If you decide not to take part in this study, you have other choices. For example:
- You may choose to have the usual approach described above.  
- You may choose to take part in a different study, if one is available. - You may choose not to be treated for cancer, but you may want to receive comfort care to relieve symptoms. Comfort care, or palliative care, helps reduce pain, tiredness, appetite problems, and other issues caused by your disease. It does not treat the disease directly, but instead tries to improve how you feel. Comfort care tries to keep you as active and comfortable as possible.
amc-097 model informed consent form
why is this study being

The purpose of this study is to test the safety of combining the autologous stem cell therapy with gene therapy to treat your lymphoma. For gene therapy, researchers in a laboratory will add small AMC-097 (Version 9.0) 07FEB2022 1 NCI Version Date 07FEB2022 stretches of DNA called "anti-HIV genes" into your stem cells to make the gene therapy product used in this study. The type of anti-HIV genes and therapy in this study might make your immune cells more resistant to HIV.  
The goal of the study is to develop an immune system that can actively prevent new immune cells from getting infected with HIV, while the older cells die due to HIV. This new immune system might be able to fight the spread of HIV even without HIV medications. The gene therapy product in combination with your clinically indicated stem cell transplant in this study is considered experimental, because it has not been used in human clinical trials in the setting of an autologous transplant, and has not been approved by the Food and Drug Administration (FDA) for treatment of HIV. A similar gene therapy product has been used in other human clinical trials with stem cell therapy. Up to 18 people will take part in this study.
amc-097 model informed consent form
what are the study groups?

Study participants will get increasing amounts of stem cells with anti-HIV genes with autologous stem cell transplant.  
- The first group of study participants will receive equal amounts of the stem cells with anti-HIV
genes and stem cells without anti-HIV genes.  
- If gene therapy does not cause serious side effects, it will be given to the second group of study participants. The second group will receive more stem cells with anti-HIV genes and fewer stem cells without anti-HIV genes.  
- If the second group does not have serious side effects, the third group of participants will receive only stem cells with anti-HIV genes.  
- If there are issues with cells engrafting in the third group of participants, a fourth group will receive only stem cells with anti-HIV genes, but at a higher amount than the third group received.
If you are among the participants that receive only stem cells with anti-HIV-1 genes, some of the stem cells without anti-HIV genes will be stored and will only be used as a safety back up if you need them. This means that the backup cells would be used if the stem cells with the anti-HIV genes do not allow for recovery of your blood cells quickly enough.
amc-097 model informed consent form
how long will i be

You will receive a one-time infusion of stem cells with anti-HIV genes. The infusion goes into your vein like a blood transfusion over less than an hour. This is called an autologous transplant. You will have clinic visits to follow up on your transplant on this clinical trial for two years after your stem cell transplant. However, we would like to keep track of your medical condition for at least 15 years and maybe for the rest of your life. Additionally, every 12 months for years 3-15 we will request optional lab studies to monitor your HIV levels and to see how the vector is working in your body. A member of the research team at the clinic will contact you by phone or mail once a year for a short conversation and to ask if any new changes have occurred in your health.  
Keeping in touch with you and checking on your condition every year helps us look at the longterm effects of the study and the process of transplantation in general. Many transplant centers include this type of long-term follow-up as part of their regular medical care.
amc-097 model informed consent form
what extra tests and procedures

Most of the exams, tests, and procedures you will have are part of the usual approach for your cancer. However, there are some extra exams, tests, and/or procedures that you will need to have if you take part in this study.
amc-097 model informed consent form
before you begin the study

Your study doctor will review your past medical history to determine if you are eligible to participate. If you are eligible, you will have an opportunity to ask questions and review the study completely. If you agree to participate, you will sign the consent form. You will also be required to have certain tests performed prior to the start of the study to make sure you are eligible for this study. Most of these tests are standard of care for autologous transplant.  
You will have:  
- A review of your HIV status, which includes asking questions about behaviors related to risk factors for HIV,
- A physical examination,
- A chest x-ray,
- Pregnancy test for females who could become pregnant, - An EKG (basic heart test), - An echocardiogram (heart ultrasound) that assesses the heart function and heart valves, - A pulmonary function test to determine how well your lungs are working and how well you are breathing,
- Blood tests (several tablespoons will be taken from a vein in your arm).
If you recently had any of these tests, your doctor may decide it is not necessary to repeat them.  
You may be required to have:  
- A cardiac stress test that assess heart function when you are exercising for about 20 minutes,
- An imaging scan of your body called CT scan, to look at the location and size of your cancer and any possible source for infection,
- A bone scan if clinically indicated, and/or a bone marrow biopsy.
amc-097 model informed consent form
during the study

If the exams, tests, and procedures show that you can take part in the study, and you choose to take part, you will be admitted to the hospital as an inpatient only to give you the experimental stem cell therapy. If you experience sudden side effects or your lymphoma worsens during the study, an additional blood sample (about two tablespoons) may be drawn to study the causes.
amc-097 model informed consent form
the three parts of the

To collect your stem cells, you will get standard drugs to move stem cells from your bone marrow into your blood. This process is called stem cell mobilization. The treatment required for stem cell mobilization is called the mobilization regimen. This is a standard of care AMC-097 (Version 9.0) 07FEB2022 3 NCI Version Date 07FEB2022 procedure for all patients undergoing autologous transplant. Your transplant doctor will discuss the procedure with you. After the stem cells are in your blood, you will have a procedure called leukopheresis. This is where your blood is run through a machine to collect the stem cells. Leukopheresis will take about 4 hours for most people. You will have this procedure to collect stem cells each day until there are enough stem cells for a safe transplant. The stem cells that are collected will be split into two parts:  
- The first part will be used for stem cells with the anti-HIV genes. In a very clean laboratory, the anti-HIV genes will be put into your stem cells. Once the anti-HIV genes are in the stem cells, they will be frozen and stored until you are ready to receive them.  
- The second part of the stem cells will just be frozen and stored without the anti-HIV genes in them.  
Part 2: Conditioning Regimen
Starting six days before your stem cell transplant, you will get a high dose chemotherapy conditioning regimen called BEAM or R-BEAM through a vein in your arm to kill the lymphoma cells in your body. BEAM and R-BEAM are a mixture of several chemotherapy drugs that stop the growth of cancer cells. These chemotherapy drugs are widely used to treat lymphoma and for stem cell transplants. The name of the chemotherapy drugs in BEAM and R-BEAM regimens are:
- BCNU (also called carmustine) - Etoposide (also called VP-16) - Ara-C (also called cytarabine)
- Melphalan
- If you have a type of lymphoma called B cell lymphoma, you may receive rituximab or a drug proven to have the same effect. Rituximab or similar drug will be given before the transplant, and again after the transplant on day 21 and day 28. The study doctor will let you know if you will be given rituximab or a biological similar agent.  
Part 3: Reinfusion of Stem Cells (Transplantation)
One day after BEAM conditioning regimen is complete, the frozen stem cells that were previously collected from you will be thawed and re-infused into your veins through a catheter in your arm. As mentioned before, depending on the study group you are in, you may receive only anti-HIV gene treated stem cells, or a combination of anti-HIV gene treated stem cells and stem cells without anti-HIV genes. The stem cells with or without anti-HIV genes are supposed to travel to your bone marrow where they will begin making healthy, new blood cells. This step is necessary because the high doses of chemotherapy given to you during the conditioning regimen will not only destroy lymphoma cells, but also healthy cells in your bone marrow. Until the new stem cells begin producing healthy blood cells, you will be at an increased risk of excessive bleeding or developing an infection. You will stay in the hospital for about 3 to 4 weeks until your blood counts recover. The duration of hospital stay can be longer if any complication occurs or if your blood counts do not recover on time and you require additional stem cell infusion. During your transplant and AMC-097 (Version 9.0) 07FEB2022 4 NCI Version Date 07FEB2022 for about 6 months after transplant you will receive antibiotics to prevent some specific infections that can occur after transplant. Your transplant doctor will prescribe those medications for you based on the hospital's guidelines.
amc-097 model informed consent form
use of hiv-1 medications during

You are expected to take your anti-HIV medications during this study except for two occasions:
1. The anti-HIV medications you are currently taking may be stopped during BEAM
chemotherapy, and may be held immediately after that if you cannot tolerate taking oral medicines because of the side effects of BEAM chemotherapy. The anti-HIV medications will be resumed as soon as you are able to tolerate taking pills. The study doctor will let you know if any of your anti-HIV medications need to be stopped. In addition, some antiretroviral therapies may have effects on the bone marrow during its recovery (e.g., zidovudine) or may interact with BEAM chemotherapy causing side effects. The study doctor will let you know if any of your anti-HIV medications need to be changed.  
2. At a minimum of 6 months after transplant and only when we document that your immune system has recovered from the transplant, you will be asked if you would agree to stop all anti-HIV medications until you meet criteria for resuming your medications. This is to give an opportunity for the immune cells that have anti-HIV genes in them to increase in number; the cells that do not have anti-HIV genes will be eliminated. We will check your level of HIV-1 in the blood and its impact on your blood cells and your general health weekly.Your doctor will restart your anti-HIV medications if you or your doctor decides this is necessary, or you feel uncomfortable at any time. The decision to stop the anti-HIV medications during that time is voluntary and will not affect your follow up in this study. Even if the approach works, your virus is expected to come back (rebound) for several weeks before it comes under control. If the regimen works, the viral rebound will be temporary, meaning that it should go up and then down, but this is not guaranteed. Different participants might have different "patterns" of rebound - quick versus slow, high levels versus low levels, short versus prolonged. During this time, the study doctor will monitor you very carefully. Your capacity to transmit HIV will increase during this time, particularly when the virus rebounds, so we will ask you to protect your sexual partner(s). The study doctor will give you information on HIV testing sites and HIV prevention programs and will counsel you about risks related to stopping your HIV medications.  
If you choose to pause your HIV medications, you will be asked to get tested for the virus that causes COVID-19. If the test is positive, we will ask you to stay on your HIV medicines until you recover. During the period when you pause taking your HIV medications, if you experience COVID-19 symptoms you will be asked to get tested for the virus that causes COVID-19. If you test positive, you will need to resume your HIV medications. The follow-up study visits will be in an outpatient clinic. Your study doctor or a nurse will see you in the clinic to assess your health status. You will be requested to have blood tests on a periodic basis after you finish receiving the experimental treatment. These blood tests include:
- About three and a half tablespoons of blood will be taken from a vein in your arm for the blood tests to test the status of your health, and
- Approximately 4 large tablespoons of blood (60 mL) will be taken from a vein in your arm at several time points for studies of your immune system, genetic studies of the effect of introduced gene in your blood cells and HIV-1 studies.
amc-097 model informed consent form
optional intestinal biopsies

With your consent, we will collect optional biopsies from your upper intestine to see if combining the autologous stem cell therapy with gene therapy works to treat your lymphoma. More information about this optional study will be explained to you in the Additional Studies Section of this consent.
amc-097 model informed consent form
optional blood tests

With your consent, we will ask you have to have blood tests to monitor the levels of HIV in your blood. More information about this optional study will be explained to you in the Additional Studies Section of this consent.
amc-097 model informed consent form
optional bone marrow biopises

With your consent, we will collect optional bone marrow biospies to study the effects of the introduced gene on your genetics and immune systems. You can find more information about this optional study in the Additional Studies Section of this consent.
amc-097 model informed consent form
a study calendar that shows

You may have side effects while on this study. Everyone taking part in the study will be watched carefully for any side effects. However, the study doctor may not know or be able to predict all the side effects or risks. Side effects may be mild or very serious. The study doctors may give you medicines to help lessen side effects. In some cases, side effects can be serious, long lasting, or may never go away. There also is a risk of death. You should talk to the study doctor about any side effects that you have while taking part in the study. If you choose to take part in this study, there is a risk that:  
- You may lose time at work or home and spend more time in the hospital or doctor's office than usual
- You may be asked sensitive or private questions which you normally do not discuss. - The study approach may not be better, and could possibly be worse, than the usual approach for your cancer.
Here are important points about side effects:  
- The study doctors do not know who will or will not have side effects.  
- Some side effects may go away soon, some may last a long time, or some may never go away.  
- Some side effects may interfere with your ability to have children. - Some side effects may be serious and may even result in death.
Here are important points about how you and the study doctor can make side effects less of a problem:  
- Tell the study doctor if you notice or feel anything different so they can see if you are having a side effect.  
- The study doctor may be able to treat some side effects.
The study doctor may adjust the study drugs to try to reduce side effects. The tables below show the most common and the most serious side effects that researchers know about. There might be other side effects that researchers do not yet know about. If important new side effects are found, the study doctor will discuss these with you. The side effects associated with this study can be divided into side effects associated with autologous transplant that is the standard of care for the treatment of your lymphoma, and the side effect associated with gene therapy that is specific to your participation in this clinical trial. Potential Side Effects with Autologous Transplant with BEAM Chemotherapy Include
amc-097 model informed consent form
(but not limited to) common

In 100 people receiving BEAM, more than 20 and up to 100 may have:
- Low blood counts  
- Nausea/vomiting  
 - Mouth sores  
  
- Sores in esophagus  
  
  
- Difficulty eating  
  
- Hair loss
- Fatigue
amc-097 model informed consent form
occasional some may be serious

In 100 people receiving BEAM, from 4 to 20 may have:
- Liver problems  
  
  
- High levels of uric acid  
  
- Skin rash  
| -   | Chills   |
|-----|----------|
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occasional some may be serious

In 100 people receiving BEAM, 3 or fewer may have:  
  
  
- Severe allergic reactions
- Second cancers, including Myelodysplastic Syndromes (MDS) and leukemia
- Life-threatening infection  
- Disease of the peripheral nervous system - Sterility
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potential side effects with gene

As with any procedure, new adverse effects resulting in injury may be discovered. However, a similar gene therapy clinical trial for HIV-1 with a similar product given to five previous participants in a different institution was well tolerated. In the laboratory, no side effects have been seen. However, the potential side effects are:
- Failure of the stem cells to "take" and thrive in the bone marrow after infusion (this is known as engraftment). Back up stem cells will be saved if you are in the third group, and can be given to you if this happens.  
- Gene therapy could theoretically cause leukemia. This has not been seen with this gene therapy model in the laboratory in extensive testing and in limited human studies with a similar vector. Four instances of leukemia were reported in children who participated in an experimental gene therapy study conducted in France, not under the jurisdiction of the U.S. Food and Drug Administration (FDA). In that study, children were treated by gene therapy for a serious genetic disease.  
- Allergic Reactions: Proteins made from large amounts of non-human (protein) can sometimes lead to future allergic reactions. There is a small amount of a modified protein in the modified cells for which there is a small chance of allergic reaction, but it is unlikely to be harmful to you even if it occurs. If an allergic reaction occurs, it is more likely that the modified cells will be destroyed. After you receive the stem cells, your blood will be tested for any reaction that could affect the use of these agents in the future, but this reaction would not be directly harmful to you. This reaction is estimated to happen in about 4 out of 100 people.  
- Reproductive Risks: You should not get pregnant, breastfeed, or father a baby during stem cell transplant and for the first 3 months after the day of stem cell transplant. The stem cells with anti-HIV genes used in this study could be very damaging to an unborn baby. If you are a woman of childbearing age, you can only be admitted to the study if: a) you are not breast feeding; b) you are not pregnant (as determined by a pre-study blood test for pregnancy); c) you have been surgically sterilized or are using effective birth control.  
Since the effects of the proposed treatments on a fetus are unknown, any woman who becomes pregnant while on this study must immediately let the study doctor know and will be removed from the study. Another method of treatment will be suggested. If you are a male participant, you must practice effective birth control. You must immediately let the study doctor know if your partner becomes pregnant, and advise your partner to contact her physician. Check with the study doctor about what types of birth control, or pregnancy prevention, to use while in this study.  
- Unknown Risks: The experimental treatments may have side effects that no one knows about yet. In addition, there may be problems of gene therapy that are unexpected but which may occur. The special virus ("retroviral vector") that is used to modify your cells does not have the genes needed to reproduce itself, but it is possible in the future that it could combine with other genes in your body, or that it could activate an unknown virus in your body, to result in a known or unknown medical problem or disease, including the possibility of another cancer.
For more information about risks and side effects of the gene therapy transplant, ask your study doctor. Potential Side Effects with Stem Cell Infusion **Unrelated to the Gene Therapy**
COMMON, SOME MAY BE SERIOUS
In 100 people receiving Gene Therapy, more than 20 and up to 100 may have:  
- Low blood pressure
- Lightheadedness
- Fainting
- Fever - Decrease in oxygen in the blood
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occasional some may be serious

In 100 people receiving Gene Therapy, from 4 to 20 may have:
- Rapid heart rate  
- Chills  
| -   | Allergic reactions   |
|-----|----------------------|  
  
  
Additionally, while the cells are infused you may experience a garlic-like taste and a scratchy throat sensation. This is caused by the chemical used to preserve the cells and is usually a mild and temporary discomfort. Risk of Antiviral Therapy Withdrawal: Your doctor will ask if you would agree to stop taking your anti-HIV medications on at least two occasions as discussed above. Each time you stop your anti-HIV medications, there is a potential risk that HIV-1 infection become reactivated and suppress your immune system and make you susceptible to severe and potentially life threatening infections. The study doctors, including your HIV-1 doctor, will closely watch your immune system and will restart your anti-HIV medications if HIV viral reactivation and suppression of immune system reaches certain levels. However, restarting the anti-HIV medications may not completely stop the risk of complications. Your HIV viral load will increase several days to weeks after you stop your HIV medications. The viral load might increase to very high levels. If this happens, your CD4+ T cell counts will likely drop. It is important to realize that, in this study, the doctors will monitor you very closely and will restart your HIV medications as soon as it is clear that the viral load or T cell count puts you at high risk of developing any new clinical problems. Your viral load and immune function might take over 4-6 weeks to return back to levels comparable to where they were when you entered the study. When your HIV medications are stopped, you might have symptoms similar to when you first were infected with HIV, such as fever, rash, swollen glands, headache, sore throat, nausea, or vomiting. Other serious inflammation related symptoms, like increased buildup of plaque on artery walls which could possibly result in future heart attacks could happen. If you develop these symptoms, the study team will examine you and may restart your HIV medications if they believe the symptoms are due to increased HIV levels. Resistance to your HIV medications might occur once viral loads become detectable. However, because the study doctor will stop all of your HIV medications the same time, the risk of developing resistance to your HIV medications is lower. While you are off your HIV medications, you are at increased risk of transmitting HIV to sexual partners. You may also be at increased risk of becoming infected with a different HIV strain (called "superinfection"). Therefore, you should use male or female condoms at all times after HIV medications are stopped. If you feel you may have exposed someone to HIV, you should immediately refer them for testing and post-exposure prophylaxis (PEP). You should also seriously consider referring your HIV- negative sexual partner(s) for pre-exposure prophylaxis (PrEP) if you will be sexually active during the treatment interruption period. If you feel you have been exposed to HIV while off your HIV medications you may restart your medication this is recommended by your primary care provider. If you are a woman and become pregnant while not taking your HIV medications, the study team will ask you to restart your medications immediately because there is a chance that you could transmit HIV to your developing baby.
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considerations related to covid-19

There are additional risks of participation in this study due to the SARS-CoV-2 pandemic. SARSCoV-2 is the virus that causes COVID-19, which is an illness that affects each person differently.  
Some people have no symptoms at all, and some people have very severe symptoms that require hospitalization, oxygen, or support with a breathing machine. COVID-19 is a potentially deadly illness. The effects of COVID-19 in people with HIV are not fully known. It is currently thought that people with HIV on HIV medications are at similar risk of getting severe COVID-19 as people without HIV. The risk in people with HIV who are not taking HIV medications is unknown, but may very well be higher. This is important during the portion of the study when you will be asked to pause your HIV medications. If you choose to pause your HIV medications, you will be asked to get tested for the virus that causes COVID-19. If the test is positive, we will ask you to stay on your HIV medicines until you recover. Once you pause your HIV medications, you will be offered testing periodically or if you develop symptoms. If a test for the virus that causes COVID-19 returns positive, you may be asked to restart HIV medications.
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what possible benefits can i

You may not personally benefit from participating in this study. This study may help us learn things that may help people in the future.
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can i stop taking part

Yes. You can decide to stop at any time. If you decide to stop for any reason, it is important to let the study doctor know as soon as possible so you can stop safely. If you stop, you can decide whether or not to let the study doctor continue to provide your samples or your medical information to the organization running the study. If you decide you no longer want your samples to be used, any sample that remains will be destroyed and related health information will no longer be collected. Samples or related information that have already been given to or used by researchers will not be returned. The study doctor will tell you about new information or changes in the study that may affect your health or your willingness to continue in the study. The study doctor may take you out of the study:
- If your health changes and the study is no longer in your best interest  
- If new information becomes available
- If you do not follow the study rules
- If the study is stopped by the sponsor, IRB or FDA.
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what are my rights in

Taking part in this study is your choice. No matter what decision you make, and even if your decision changes, there will be no penalty to you. You will not lose medical care or any legal rights. For questions about your rights while in this study, call the ________________________ *(insert* name of center) Institutional Review Board at __________________ (insert telephone number).  
(Note to Local Investigator: Contact information for patient representatives or other individuals at a local institution who are not on the IRB or research team but take calls regarding clinical trial questions can also be listed here.)
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what are the costs of

The gene modified anti-HIV stem cells will be supplied at no charge while you take part in this study. The cost of getting a regular stem cell transplant as a standard of care for your disease is not paid by the study sponsor, so you or your insurance company may have to pay for this usually before transplant. You and/or your health plan/insurance company will need to pay for all the other costs of taking care of your cancer while in this study, including the cost of tests, procedures, or medicines to manage any side effects, unless you are told that certain tests are supplied at no charge. Before you decide to be in the study, you should check with your health plan or insurance company to find out exactly what they will pay for. You will not be paid for taking part in the mandatory part of this study. For the optional intestinal biopsy (upper endoscopy), a fee of $300 for each procedure completed will be paid to you.
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what happens if i am

If you are injured or hurt as a result of taking part in this study and need medical treatment, please tell your study doctor. The study sponsors will not offer to pay for medical treatment for injury.  
Your insurance company may not be willing to pay for study-related injury. If you have no insurance, you would be responsible for any costs. If you feel this injury was a result of medical error, you keep all your legal rights to receive payment for this even though you are in a study.
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who will see my medical

Your privacy is very important to us and the researchers will make every effort to protect it. Your information may be given out if required by law. For example, certain states require doctors to report to health boards if they find a disease like tuberculosis. However, the researchers will do their best to make sure that any information that is released will not identify you. Some of your health information, and/or information about your specimen, from this study will be kept in a central database for research. Your name or contact information will not be put in the database. There are organizations that may inspect your records. These organizations are required to make sure your information is kept private, unless required by law to provide information. Some of these organizations are:
- The AIDS Malignancy Consortium (AMC) - The Institutional Review Board, IRB, is a group of people who review the research with the goal of protecting the people who take part in the study.  
- The Food and Drug Administration and the National Cancer Institute in the U.S. - The drug manufacturers supporting the study (University of California Davis and University of Indiana).
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where can i get more

You may visit the NCI Web site at http://cancer.gov/ for more information about studies or general information about cancer. You may also call the NCI Cancer Information Service to get the same information at: 1-800-4-CANCER (1-800-422-6237). A description of this clinical trial will be available on http://www.ClinicalTrials.gov, as required by U.S. Law. This web site will not include information that can identify you. At most, the web site will include a summary of the results. You can search this web site at any time.
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who can answer my questions

You can talk to the study doctor about any questions or concerns you have about this study or to report side effects or injuries. Contact the study doctor __________________ (insert name of study doctor[s]) at __________________ *(insert telephone number).*
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additional studies section

This part of the consent form is about optional studies that you can choose to take part in. You will not get health benefits from any of these studies. The researchers leading this optional study hope the results will help other people with cancer in the future. The results will not be added to your medical records, but you or your study doctor will know the results if requested. You will not be billed for these optional studies. You can still take part in the main study even if you say 'no' to any or all of these studies. If you sign up for but cannot complete any of the studies for any reason, you can still take part in the main study. Circle your choice of "yes" or "no" for each of the following studies.
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optional sample collections for laboratory

Researchers are trying to learn more about cancer, HIV/AIDS, and other health problems. Much of this research is done using samples from your tissue, blood, urine, or other fluids. Through these studies, researchers hope to find new ways to prevent, detect, treat, or cure health problems. Some of these studies may be about genes. Genes carry information about features that are found in you and in people who are related to you. Researchers are interested in the way that genes affect how your body responds to treatment. If you choose to take part in this study, the study doctor for the main study would like to collect these specimen types:
- **Optional intestinal biopsy:** To obtain important information about the efficacy of this study, we would like to ask you to provide a biopsy sample from your upper intestine. Your doctor will discuss this with you 6 months after the transplant, or when your CD4 count is greater than 300 cells/ mm3. The endoscopy would be repeated 2 months after the first biopsy. If you agree to the intestinal biopsy 6 months and 8 months after the transplant, you will be asked to sign a separate consent at that time before those procedures. Our study partner at The University of California San Francisco is conducting a cohort study called SCOPE. There is also optional intestinal biopsies in this study. If you chose to coenroll in the SCOPE study, we will use their intestinal biopsy results for both studies. SCOPE is a separate study and requires a separate consent form. Participation in SCOPE is not a requirement of this study. If you agree to participate, you will be asked to sign a separate SCOPE consent form. We will give you the contact information for the SCOPE team if you are interested in learning more.  
- Optional bone marrow biopsies (for participants that do not have bone marrow involvement at baseline): If you agree to participate in the optional portion of the study, we will request a research bone marrow biopsy or aspirate performed for research studies at 3 months, 12 months after your stem cell infusion, and when you discontinue the study. These studies would normally be standard of care if there is lymphoma in your bone marrow. These samples will be used to monitor the effects of the introduced gene on your genetic and immune systems.  
- **Optional blood collections:** If you choose to take part in this study we will request optional lab studies every 12 months for years 3-15 to monitor your HIV levels and to see how the vector is working in your body.  
- Donation of left over **study specimens to the ACSR for all study participants:** If you choose to take part in this clinical trial, the researchers would like to collect unused blood and biopsy tissue left over after the study is done. The researchers ask your permission to store and use your samples and related health information (for example, your response to cancer treatment, results of study tests and medicines you are given) for medical research. The research that may be done is unknown at this time. Storing samples for future studies is called
"biobanking." The Biobank is being run by the **AIDS and Cancer Specimen Resource** and is supported by the National Cancer Institute.
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what is involved?

If you agree to take part, here is what will happen next:
1) Optional intestinal **biopsy:** An endoscopy will be performed to obtain small GI tissue samples. An endoscope (a small flexible tube) will be inserted into your stomach and a small tissue sample will be collected from your upper intestine using forceps. We will attempt to collect 24 very small tissue samples during each endoscopy session from you.  
2) **Optional bone marrow biopsies:** About 2 tablespoons (20mL) of your bone marrow will be collected. A bone marrow biopsy is performed using a hollow needle to remove a small sample of bone marrow. Before the biopsy, a local anesthetic is used to numb the area where the needle will be inserted.  
3) **Optional blood sample collections:** We will ask you to have about 3 tablespoons (30 mL) of blood collected. You will be seated in the lab or clinic and blood will be drawn by putting a needle into a vein in your arm.  
4) **Donation of left over study specimens to the ACSR for all study participants:** Your sample and some related health information will be stored in the ACSR Biobank, along with samples and information from other people who take part. The samples will be kept until they are used up. Information from your medical record may be updated after the study is over. Qualified researchers can submit a request to use the materials stored in the ACSR. A science committee at the ACSR will review each request. There will also be an ethics review to ensure that the request is necessary and proper. Researchers will not be given your name or any other information that could directly identify you. Neither you nor your study doctor will be notified when research will be conducted or given reports or other information about any research that is done using your samples. Some of your genetic and health information may be placed in central databases that may be public, along with information from many other people. Information that could directly identify you will not be included.  
Optional bone marrow biopsies, intestinal biopsy, and blood samples collected may be stored for up to 15 years to address research questions related to the treatment or the disease under study.
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what are the possible risks?

1) Endoscopy risks: The upper endoscopy is being performed as a part of a research project. The risks of endoscopy are remote, however, there can be pain, gagging, bleeding, infection, perforation (a hole through the bowel wall can occur) and rarely, death can occur.  
2) Sedation risks: The risks of intravenous sedation (putting someone to sleep) include bleeding, bruising, pain, infection from intravenous catheter, low blood pressure, decreased breathing, and allergic reaction to the medicine.  
3) Allergic reaction risks: Symptoms of allergic reaction may vary from individual to individual but often consists of generalized rash (red skin), itchiness, and a feeling of being excited or anxious.  
4) Very rarely swelling of the throat and/or difficulty breathing can accompany these symptoms.  
Occasionally (rare), midazolam (also called versed, a drug used for sedation) may cause a state of over excitement. The risks for small bowl biopsy are perforation and bleeding. These events have occurred in some patients though not with these physicians. These risks will be explained to you again by in detail prior to the endoscopy procedure by the gastroenterologist.  
5) Reproductive risks: You should not become pregnant or father a baby if having an upper endoscopy because the drugs used during the procedure can affect an unborn baby. Women should not breastfeed a baby if having an upper endoscopy. It is important to understand that you need to use birth control. Check with your study doctor about what kind of birth control methods to use and how long to use them. Some methods might not be approved for use in this study.
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risks of participating in the

The procedure may cause discomfort, pain, bleeding, scarring or infection at the site of the aspirate/biopsy. There is also a small chance that you could have an allergic reaction to the numbing medicine. After your skin heals, you may have a small scar where we took the sample.
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risks of participating in optional

The risks of taking blood include pain, a bruise or lump at the point where the blood is taken, redness and swelling of the vein and infection, and a rare risk of fainting.  
AMC-097 (Version 9.0) 07FEB2022 15 NCI Version Date 07FEB2022
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risks of donation of left

1) There is a risk that someone could get access to the personal information in your medical records or other information researchers have stored about you.  
2) There is a risk that someone could trace the information in a central database back to you. Even without your name or other identifiers, your genetic information is unique to you. The researchers believe the chance that someone will identify you is very small, but the risk may change in the future as people come up with new ways of tracing information.  
3) In some cases, this information could be used to make it harder for you to get or keep a job or insurance. There are laws against the misuse of genetic information, but they may not give full protection. There can also be a risk in knowing genetic information. New health information about inherited traits that might affect you or your blood relatives could be found during a study. The researchers believe the chance these things will happen is very small, but cannot promise that they will not occur.
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how will information about me

Your privacy is very important to the researchers and they will make every effort to protect it. Here are just a few of the steps they will take:  
1) When your sample(s) is sent to the researchers, no information identifying you (such as your name) will be sent. Samples will be identified by a unique code only.  
2) The list that links the unique code to your name will be kept separate from your sample and health information. The ACSR and AMC staff with access to the list must sign an agreement to keep your identity confidential.  
3) Researchers to whom the ACSR and the AMC send your sample and information will not know who you are. They must also sign an agreement that they will not try to find out who you are.  
4) Information that identifies you will not be given to anyone, unless required by law. 5) If research results are published, your name and other personal information will not be used.
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what are the possible benefits?

You will not benefit from taking part. The researchers, using the samples from you and others, might make discoveries that could help people in the future.
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are there any costs or

There are no additional costs to you or your insurance for these optional studies. You will not be paid for taking part in the mandatory part of this study. For the optional intestinal biopsy (upper endoscopy), a fee of $300 for each procedure completed will be paid to you. If any of the research leads to new tests, drugs, or other commercial products, you will not share in any profits.
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what if i change my

If you decide you no longer want your samples to be used, you can call the study doctor, _________________, *(insert name of study doctor for main trial)* at ________________________ (insert telephone number of study doctor for main trial) who will let the researchers know. Then, any sample that remains in the bank will no longer be used and related health information will no longer be collected. Samples or related information that have already been given to or used by researchers will not be returned.
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what if i have more

If you have questions about the use of your samples for research, contact the study doctor, ________________, *(insert name of study doctor for main trial)*, at _____________________
(insert telephone number of study doctor for main trial).  
Please circle your answer to show whether or not you would like to take part in each option: Samples for Future Research Studies: I agree to have an optional intestinal biopsy and/or have **biopsy results from the SCOPE** study used for this study **as described above.**
YES  NO Participant Initials: ____
I agree to have to have bone marrow biopsies as described above YES  NO Participant Initials: ____
I agree to have blood samples collected as described above.  
YES  NO Participant Initials: ____
My samples and related information may be donated to ACSR Biobank for use in future health research.  
YES  NO Participant Initials: ____
I agree to have my samples undergo genetic testing to learn about, prevent, diagnose, or treat HIV-related diseases and cancer.  
YES  NO Participant Initials: ____
This is the end of the section about optional studies__________________________________
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my signature agreeing to take

I have read the consent form or had it read to me and understand the information above. I have discussed it with the study doctor and my questions have been answered I understand that I will be given a signed and dated copy of this consent form. I agree to take part in the main study and any additional studies where I circled 'yes.' My signature below indicates that I understand my rights and want to take part in this study as a research participant. Participant's signature: ________________________________ Date of signature: _____________________________________ Signature of person(s) conducting the informed consent discussion: _______________________ Date of signature: _____________________________________
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attachment 1 amc certificate of

The NIH has given the AMC a Certificate of Confidentiality. The Certificate does not mean that the NIH or the U.S. Government recommend that you take part in this study. This Certificate helps us keep your health information private.  
Your records for this study will have information that may identify you. This Certificate lets us turn down legal demands for your study records. We can use the Certificate to turn down demands for records from a U.S. court. The Certificate can be used in any federal, state, or local legal matters. We will use the Certificate to turn down any demands for your study records. The cases where we cannot use the Certificate are explained below. We cannot use the Certificate to turn down a demand from the U.S. Government for study records. This applies to audits or reviews of the AMC. This also applies to study records that we have to report to the FDA. The Certificate does not stop you or your family members from sharing your health information. It does not stop you from talking about taking part in this study. You may give written permission for an insurer, employer, or other person to get copies of your study records. If you give permission, we cannot use the Certificate to say no to a request for your study records.  
AMC-097 (Version 9.0) 07FEB2022 21 NCI Version Date 07FEB2022  
ATTACHMENT 2: STUDY CALENDAR  
| Prior to study enrollment and treatment, the following tests will be performed:  Required Studies/Testing Within 8 weeks  prior to enrollment  (stem cell collection) Within 1 week prior to  On the day of admission  admission for transplant for transplant before start  of chemotherapy Medical history and physical  examination X X X  Infectious disease tests X Chest X ray X X Heart strip X Imaging for staging of your disease X Lung function test X Kidney function blood tests X Bone marrow biopsy X Tests for HIV-1 X X Heart tests X Review of your diagnosis slides X Tests of your immune systems X X X Future research blood sample X Pregnancy test for females of  childbearing potential X X  After you receive your stem cell transplant, you will have the following tests and follow up   |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|  
After you receive your stem cell transplant, you will have the following tests and follow up visits:  
| AMC-097 (Version 9.0) 07FEB2022       | 21               |    |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
|---------------------------------------|------------------|----|----|----|----|----|----|----|----|----|----|----|-----|----|----|----|----|--------------|
| Weeks after-HCT                       | Months After-HCT | Years  AfterHCT    |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| Study                                 |                  |    |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| Assessments/ Testing Post  Transplant | 3-15,            |    |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| 1                                     | 2                | 3  | 4  | 6  | 2  | 3  | 4  | 6  | 8  | 10 | 12 | 14 | 16, | 18 | 20 | 22 | 24 | once a  year |
| Blood count                           | X                | X  | X  | X  | X  | X  | X  | X  | X  | X  | X  | X  | X   | X  | X  | X  | X  | X            |
| History and  physical exam            | X                | X  | X  | X  | X  | X  | X  | X  | X  | X  | X  | X  | X   | X  | X  | X  | X  | X            |
| Imaging for  staging of               | X                | X  | X  | X  |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| your disease Required bone            | X                | X  | X  |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| marrow if you  have bone              |                  |    |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |  
| Weeks after-HCT                                                              | Months After-HCT   | Years  AfterHCT   |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
|------------------------------------------------------------------------------|--------------------|---|----|----|----|----|----|----|----|----|----|----|-----|----|----|----|----|--------------|
| Study                                                                        |                    |   |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| Assessments/ Testing Post  Transplant                                        | 3-15,              |   |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| 1                                                                            | 2                  | 3 | 4  | 6  | 2  | 3  | 4  | 6  | 8  | 10 | 12 | 14 | 16, | 18 | 20 | 22 | 24 | once a  year |
| marrow  involvement (for staging  your disease) Optional bone  marrow biopsy | X                  | X | X  |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| (for research) Optional GI  biospy                                           | X                  | X |    |    |    |    |    |    |    |    |    |    |     |    |    |    |    |              |
| Tests of your  immune                                                        | X                  | X | X  | X  | X  | X  | X  | X  | X  | X  | X* |    |     |    |    |    |    |              |
| system Tests for HIV1 activity                                                                              | X                  | X | X  | X  | X  | X  | X  | X  | X* |    |    |    |     |    |    |    |    |              |
| Genetic testing                                                              | X                  | X | X  | X  | X  | X  | X  | X  | X  | X* |    |    |     |    |    |    |    |              |  
Telephone contact with you or your health care provider for the follow up of HIV status and development of  
  
  
  
any other cancer X
Most of the tests above involve standard medical care. Standard care is what is normally done to prevent, diagnose, or treat a certain condition or illness. Other parts of this study, namely administration of stem cells with anti-HIV gene in them is investigational. Furthermore, the follow up visits and test for assessment of the side effects and the evaluation of your immune system will be a part of the study, and out of the standard of care boundaries, and the follow up blood work may involve that are being tested for a certain condition or illness.  
| Assessments                                | Within 1 Week  prior to stopping  HIV medications   | After   | stopping   |     |
|--------------------------------------------|-----------------------------------------------------|---------|------------|-----|
| your                                       | HIV                                                 |         |            |     |
| medications  (for about 12  weeks or more) | After you resume taking your HIV  medications       |         |            |     |
| Weekly                                     | When you start                                      | W4      | W8         | W24 |  
| your HIV  medications          |        |     |    |    |    |
|--------------------------------|--------|-----|----|----|----|
| COVID Testing                  | X      |     |    |    |    |
| Stop                           | taking | ART | X  |    |    |
| medication Clinical Assessment | X      | X   | X  | X  | X  |
| Tests on your immune           | X      | X   | X  | X  | X  |
| system HIV studies             | X      | X   | X  | X  | X  |
| Blood samples collected        | X      | X   | X  | X  |    |
| for research Couseling         | about  | not |    |    |    |
| taking                         | your   | HIV |    |    |    |
| medications                    | X      | X   |    |    |    |