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PRF-DATA MANAGEMENT

Projahnmo AMNAHI Biobank

Biobank
AMANHI-Bangladesh Biobank
Biobank

As part of the Alliance for Maternal and Newborn Health Improvements (AMANHI) study funded by the Bill and Melinda Gates Foundation (BMGF) through WHO, we have established biorepositories and collected data on relevant phenotypes, clinical outcomes, and co-variates in a well characterized population-based cohorts of 3,000 pregnant women and their children in Sylhet, Bangladesh. The overarching goal of the biobank is to facilitate discoveries of biomarkers of adverse pregnancy outcomes (maternal, fetal and neonatal health outcomes) as new and more feasible methods become available. An additional goal is to identify biological mechanisms underlying the causes of the adverse outcomes including preeclampsia, spontaneous preterm birth (sPTB), stillbirth and intrauterine growth restrictions (IUGR) to create a platform to generate new approaches to treatment and prevention.

We have enrolled 3,000 pregnant women and followed them up-to 42 days post-partum. We have completed this part of the study and now the children of the pregnant women enrolled in the cohort are being followed up for physical growth and child development. All pregnant women were identified through pregnancy surveillance conducted by making home visits every 2 months by trained community health workers (CHWs). Pregnancies were confirmed via strip–based pregnancy tests and dated through ultrasound scans carried out by trained ultrasonologists before 19 weeks of gestation. The biobank contains maternal blood and urine specimens collected two times during pregnancy (8-19 weeks and 24-28 weeks or 32-36 weeks of gestation) and once during postpartum period (Day 42 postpartum) as well as delivery samples. Trained phlebotomists obtained maternal and umbilical cord blood samples and generated aliquots of serum, plasma, and buffy coat for storage. We also have collected and stored newborn stool, , placental samples (trimmed tissue and membrane), maternal stool, and umbilical cord blood (fresh/clotted), tissue and membrane. When cord blood (fresh/clotted) collection was not possible, saliva was collected from newborns. In addition, we collected infant blood & stool at 12 months of age and saliva samples from biological fathers of the enrolled newborns. All samples were processed and stored in -80°C freezers. CHWs collected detailed phenotypic and epidemiological data from the pregnant women four times during pregnancy (at 8-19 weeks, 24-28 weeks, 32-36 weeks, and 38-40 weeks of gestation), at delivery and twice during postpartum period (<7 days and at 42 days). The biospecimens and phenotypic data collected during pregnancy, delivery, and postpartum are a tremendously valuable resource for facilitating discoveries of biomarkers for adverse maternal, fetal, and neonatal health outcomes.

Table 1: Summary of AMANHI Biospecimen in Projahnmo Biobank
All Samples information of AMANHI study in PROJAHNMO Biobank
Sample collection timepoints Participant Sample type Total vial Shared Current vial in Biobank
Blood at antenatal-1_(24-28 weeks) Mother (n=2287) Serum 13545 3090 10447
Cytoff Tube 333 219 114
Buffy Coat 2287 15 2271
Plasma 17396 2324 17187
Blood at antenatal-2_(32-36 weeks) Mother (n=473) Plasma 3588 433 3588
Cytoff Tube 138 21 117
Buffy Coat 473 0 473
Serum 2755 0 2755
Blood at enrollment Mother(n=2999) Cytoff Tube 498 249 249
Plasma 21824 3452 21061
DNA Sample 2829 903 1926
Whatman Card 2999 0 2999
Buffy Coat 2056 1893 163
Serum 16696 228 16595
Blood at postnatal Mother(n=2529) Cytoff Tube 420 234 186
Buffy Coat 2529 0 2529
Serum 13308 0 13308
Plasma 18378 0 18376
Clotted cord blood at delivery Newborn(n=567) DNA Sample 414 121 293
Clotted Cord Blood Tube 429 405 15
Cord blood at delivery Newborn(n=1488) Buffy Coat 830 823 6
Whatman Card 1488 827 661
Plasma 8001 1455 7987
Serum 5082 0 5081
DNA Sample 1974 621 1353
Cytoff at 12month Mother (n=55) Cytoff Tube 165 165 0
Cytoff at 6month Mother(n=57) Cytoff Tube 171 171 0
Infant blood at 12 Month Infant(n=1158) Plasma 6487 0 6487
Buffy Coat 1158 0 1158
Serum 4987 0 4984
Whatman Card 331 0 331
Infant feces at 12 month Infant(n=1198) Infant Feces 1198 0 1198
Maternal stool at delivery Mother(n=2581) DNA Sample 230 115 115
Maternal Feces 2466 10 2448
Newborn blood within 72 hours of delivery Newborn(n=713) Whatman Card 713 550 163
Newborn saliva at postnatal Newborn(n=553) DNA Sample 312 38 274
Newborn Saliva 449 404 32
Newborn stool at postnatal Newborn(n=2217) DNA Sample 516 258 258
Newborn Feces 1959 0 1950
Paternal saliva Father(n=2183) Paternal Saliva 2431 10 2406
Placenta at delivery Mother(n=2532) Tissue with RNA Later (RNA8mmD2) 2304 1 2273
Flash Frozen Tissue (Sfreeze10mmABC) 2532 50 2462
Tissue with RNA Later (RNA8mmABC) 2304 0 2257
Cord with RNA Later (RNACords) 2304 0 2255
Flash Frozen Tissue (Sfreeze10mmD2) 2532 5 2508
Membrane with RNA Later (RNAMembrane) 2304 0 2274
Flash Frozen Cord (SfreezeCords) 2532 0 2511
Cord With Formalin (FormalinCord) 2532 0 2512
Tissue With Formalin (FormalinFullPunch) 2532 185 2306
Flash Frozen Membrane (SfreezeMembrane) 2532 0 2507
Membrane With Formalin (FormalinMembrane) 2532 0 2514
Tissue With RNA Later (RNA8mmD1) 2304 139 2133
Flash Frozen Tissue (Sfreeze10mmD1) 2532 199 2311
Urine at antenatal-1_(24-28 weeks) Mother(n=2292) Urine Sediment With RNA Later 2292 0 2224
Urine With Mineral oil 2292 0 2291
Raw Urine 11460 50 11404
Urine at antenatal-2_(32-36 weeks) Mother(n=475) Raw Urine 2375 0 2375
Urine With Mineral oil 475 0 475
Urine Sediment With RNA Later 475 0 472
Urine at enrollment Mother(n=3000) Urine Sediment With RNA Later 3000 0 2990
Urine With Mineral oil 2999 0 2999
Raw Urine 15000 130 14869
Urine at postnatal Mother(n=2534) Urine Sediment With RNA Later 2534 0 2497
Raw Urine 12665 0 12665
Urine With Mineral oil 2534 0 2534
Total 253720 19793 240162

Collaboration with national and international laboratories for assay

We have already established collaboration with several national and international laboratories for different assays of the stored biospecimens. Our current collaborators are as below:

1. Cincinnati Children’s Hospital Medical Center 2. University of California San Francisco 3. SERA Prognostics 4. Johns Hopkins University-Epigenetic study
5. Sapient Bioanalytics 6. Johns Hopkins University- Metal Study 7. The University of IOWA 8. Stanford University
9. Mayo Clinic 10. Johns Hopkins University- SGA Study 11. Virology lab at icddr,b 12. Immunobiology, Nutrition and toxicology lab at icddr,b
13. MAX-PLANCK institute of Biochemistry 14. The Aga Khan University

Maintenance of biobank

Maintenance of biobank in resource limited settings requires substantial care and efforts. To avoid unforeseen loss of specimens from power failure or mechanical freezer failure, or from natural disasters such as flood, earthquake, or hurricane that can cause great damage, we divided the specimens and stored them physically in two different locations: 1) in our Sylhet office in Bangladesh and 2) within the premises of our partner, North South University in Dhaka, Bangladesh. Half of the specimens of each study mother-child dyad are stored in Sylhet and the other half are stored in Dhaka. We have seven -80 freezers at our Sylhet cold room and six -80 freezers at our Dhaka cold room with two backup generators at each location. Moreover, each freezer has online UPS for uninterrupted power supply. In addition, we have standby liquid nitrogen cylinders for temporary storage of specimens if in case one or more freezers fail. Freezer rooms in both places have double air conditioner which continues 24/7 to prevent generating excess temperature in those rooms. Study staff physically check temperatures of all freezers and record them three times daily.