Study Primer

The following is a brief primer on the NNTC study. Further details on study procedures can be found according to domain under the Research menu tab above. Tabs below detail in a general sense how samples are collected, post-mortem procedures, processing of CNS tissues, and limitations of the resource.

Horizontal Tabs

Sample Collection
There are two pathways by which NNTC sites collect samples:

Pathway 1
  • Recruitment - live volunteers are prospectively recruited from clinics, hospitals, and local communities
  • Screening - volunteers are assessed for study eligibility
  • Informed Consent - volunteers and/or their legal guardians are assessed for ability to provide informed consent
  • History - participants and/or informants provide a medical, neurological, medication, psychiatric, and/or substance abuse history by administration of standardized questionnaires and medical records, if any
  • Examinations - participants receive a neurological exam, neuropsychological tests, a psychiatric assessment that includes the CIDI and BDI (in earlier years of the study PRISM was used in lieu of the CIDI), and medication adherence/Activities of Daily Living questionnaires
  • Laboratory - blood is collected for CBC, CD4+ T cell enumeration, plasma HIV load, and research samples of PBMC, serum, and plasma are stored. Urine toxicology is run, and optional CSF is collected for WBC count, total protein, glucose, and HIV load. Most participants also receive a RPR, serum albumin, and HCV antibody at entry. Additional labs may be available but are generally culled from the medical charts
  • Tiering: Medical history updates, examinations, and laboratory are repeated every 6-24 months depending on the participants’ health and/or likelihood of loss to followup. Some may be followed by telephone only.
  • Upon the participant's demise, a post-mortem exam is conduced and tissue is stored.
Pathway 2
  • The NNTC is contacted after an individual expires.
  • The decedent's family/legal guardian provides informed consent for tissue donation and release of medical records, if any.
  • A post-mortem exam is performed and tissue is stored.
Post-Mortem Procedures

The following lists both the ideal and not ideal conditions that exist on this study for collection of specimens:


  1. Post Mortem Interval (PMI) is <24 hours
  2. Ideal tissue collection minimally includes brain, spinal cord, peripheral nerve, muscle, thymus (if available) lymph node, and spleen. Tissue is suitable for freezing and formalin fixation
  3. Post mortem fluid collection includes cardiac aspiration of clot and serum ( if possible) and CSF
  4. Some sites may also collect samples of other tissues such as tumor, heart, lungs, gut, skin, endocrine, etc., on a case by case basis.

Not Ideal

  1. Prolonged PMI because pt. is found dead at home, uncertain time of death, legal or transport problems in retrieving remains
  2. Tissue is not available or is seriously damaged by prolonged PMI, hypoxia/ischemia, prolonged period on respirator, herniation, radiation etc. Only formalin fixation can be used.
  3. Clotting/lysis begins in perimortem period. Cardiac fluid (if extracted), may contain debris and hemolytic products. Cannot extract intact WBCs. CSF is extracted from brain or spine by use of a needle and syringe. Frequently such CSF contains tissue, blood or cellular debris. Usually has to be centrifuged to remove RBC so CSF WBC rarely collected/stored.
  4. Tissues such as gut are particularly fragile; family may refuse to donate certain organs
CNS Tissue Processing

After the brain is removed, the autopsy technician and/or pathologist will visually inspect this tissue for obvious abnormalities. In some cases, a pre-mortem MRI or CT may indicate unilateral brain pathology. In either case, visible lesions are sampled, fixed in formalin, and made into slides for diagnostic studies. If known unilateral pathology is present, that hemisphere is usually reserved for formalin fixation and the opposite hemisphere is selected for freezing. Otherwise the entire brain is hemi-sected; one hemisphere is immersed in formalin and the other is flash frozen. If there is a prolonged PMI and/or the tissue is highly friable, the entire brain will be placed in formalin and no frozen tissue will be available. The hemi-brain that is selected for freezing is chilled briefly, then sectioned in 1.0 to 0.5 cm sections which are sequentially numbered, placed in labeled plastic bags, and frozen. The spinal cord is divided into cervical, thoracic, and lumbosacral segments of approximately 1 cm each and alternately fixed or frozen. As requests are approved, brain sections are removed from the freezer, placed in a laminar flow hood, and tissue samples are dissected out by the neuropathologist, using either a scalpel or a Dremel tool (analogous to a dental drill).

Resource Limitations
  • Many requesters prefer one or more of a few small anatomical structures such as the basal ganglia, or hippocampus. As frequently requested cases and anatomic regions are repeatedly sampled, anatomical landmarks may become more difficult to locate and select regions may be completed depleted. Repetitive cutting, freezing, and thawing may damage surrounding areas, rendering them unusable for research.
  • It is not uncommon for individuals to expire on evenings, weekends, or holidays. The current protocol was designed to minimize the harvest- to- freezer time and to be performed by a non-neuropathologist on a 24/7/365 basis; hence, we rarely dissect out individual anatomical regions at autopsy. Such an approach would be prohibitively expensive.
  • Many of the brains have been subject to distortion of anatomy due to destructive processes common in AIDS such as tumor, bleeding, or infection. For this reason, we cannot provide samples suitable for stereologic studies that demand well –preserved, bilateral anatomical integrity.
  • We cannot provide samples for studies that will deplete an entire anatomical region or that will render large portions of the surrounding tissues unusable.
  • We do not routinely provide the following samples although they may be available on a case by case basis:
    • Viable frozen PBMCs, due to cost (non-viable PBMCs are available on a case by case basis).
    • DNA sampling is not routinely supported by the grants, but such samples may be available on a case by case basis.
    • Frozen CSF white blood cells, due to the low concentration in CSF and high cost of processing
    • Fresh whole blood, due to the need for immediate shipping
    • Fresh tissue, due to the need for immediate shipping

Individual Banks may agree to fulfill non-standard requests for tissues and fluids providing:

1. The request is approved by the NNTC Steering Committee

2. Fulfilling the request does not interfere with the usual protocol of the Bank and does not interfere with normal sample collection procedures

3. The requester agrees to underwrite or reimburse in full the costs of collecting samples in a non-standard fashion (e.g., paying for on call time, IRB submission costs, special packing and shipping)