HARVARD COLLEGE, PRESIDENT & FELLOWS OF
The broad goals of the project are to identify determinants of susceptibility and resistance to infection by HIV-1 subtype C and of disease progression among people severely affected by the HIV/AIDS epidemic in southern Africa, and to reduce the burden of HIV1-C infection by identifying host targets for developing new intervention and prevention strategies. Most genome wide association studies (GWAS) have been conducted on males of European ancestry infected by HIV-1 subtype B. The burden of HIV is greatest in southern Africa where the HIV-1C epidemic has infected 16% of adults of whom >60% are women, and the dominant mode of viral transmission is heterosexual. This study represents the first GWAS for HIV-1C acquisition and control of viral replication, the first GWAS in the southern African population, and the first GWAS using the new 2.5 Illumina chip.
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| AWARD OVERVIEW |
| Award Number |
1RC4AI092715-01 |
Funding Agency |
Department of Health and Human Services |
| Total Award Amount |
$6,206,455 |
Project Location - City |
Boston |
| Award Date |
09/29/2010 |
Project Location - State |
MA |
| Project Status |
More than 50% Completed |
Project Location - Zip |
02115-6009
|
| Jobs Reported |
12.85 |
Congressional District |
07 |
| Project Location - Country |
US |
|
|
Recipient Information
(Grants)
| Recipient Information (Grants) |
|
Recipient Name
|
HARVARD COLLEGE, PRESIDENT & FELLOWS OF |
| Recipient DUNS Number |
149617367
|
| Recipient Address |
677 HUNTINGTON AVE |
| Recipient City |
BOSTON |
| Recipient State |
Massachusetts |
| Recipient Zip |
02115-6028 |
| Recipient Congressional District |
07 |
| Recipient Country |
USA |
Required to Report Top 5
Highly Compensated Officials |
No |
Projects and Jobs Information
| Projects and Jobs Information |
| Project Title |
GWAS on Determinants of HIV-1 Subtype C Infection |
| Project Status |
More than 50% Completed |
| Final Project Report Submitted |
No |
| Project Activities Description |
Colleges, Universities, and Professional Schools |
| Quarterly Activities/Project Description |
GWAS: Progress report. March 25, 2013 The goals of the GWAS project are to identify determinants of susceptibility and resistance to infection by HIV-1 subtype C, and disease progression among people severely affected by the HIV/AIDS epidemic in southern Africa. To achieve the goals, the following activities have been implemented between, December 21st, 2012 and March 25th, 2013: - The team finished processing of clinical samples at HSPH using the Infinium 2.5M chip protocol and data acquiring by iScan and QC. The obtained data was transferred from the lab to the biostatistical group for additional QC and analysis. - The QC and pre-processing optimization was performed. The data acquired by iScan were analyzed for single SNP and in population stratification analysis to infer about the association between SNPs and HIV susceptibility. Specifically, the association tests include qq-plots of the p-values, comparison of p-values across three data sets, Manhattan plots, and a check for relatedness. This is still work in progress. Here is the current summary of QC: INDIVIDUALS Remove: Total: Initial unique Sample IDs - 1,005 Exclusions due to low/failed genotyping 23 982 Exclusions due to duplications 50 932 Exclusions due to strange IBD patterns 3 929 Possible exclusions due to relatedness 70 859 SNPS Genotyped 2,443,179 Exclusions due to low call rate (<90%) 20,992 2,422,187 Exclusions due to MAD <0.01 548,667 1,873,520 Exclusions due to failed HWE (<0.0001) 2,756 1,870,764 - Viral genotyping was performed by targeting V1C5 region of HIV-1C env gp120. Viral sequences were obtained and analyzed in 52 subjects from Aim 1. In addition, sequencing is in progress for 38 subjects from Aim 1 and for 78 subjects from Aim 2. - There were three working group meetings between the lab and biostatistical groups, and two conference calls with an external Co-Investigator dedicated to data analysis and planning activities. |
| Jobs Created |
12.85 |
| Description of Jobs Created |
Research Associate; Research Assistant; Project Associate in the Department of Cancer Biology at the School of Public Health; Research Associate; Research Associate; Research Assistant; Postdoctoral Research Fellow; Research Fellow; Postdoctoral Research Fellow; Research Associate; Research Associate; Principal Research Scientist; (4) Home-Based Counselors
(1) Driver
(1) Lab Research Assistant
(1/2) Data Manager
|
Purchaser Information
(Grants)
| Purchaser Information |
| Contracting Office ID |
Not Reported |
| Contracting Office Name |
Not Available |
| Contracting Office Region |
Not Available |
| TAS Major Program |
75-0900 |
| Award Information |
| Award Date |
09/29/2010 |
| Award Number |
1RC4AI092715-01 |
| Order Number |
|
| Award Type |
Grants |
| Funding Agency ID |
75 |
| Funding Agency Name |
Department of Health and Human Services |
| Funding Office Name |
Not Available |
| Awarding Agency ID |
75 |
| Awarding Agency Name |
Department of Health and Human Services |
| Amount of Award |
$6,206,455 |
| Funds Invoiced/Received |
$4,171,737 |
| Expenditure Amount |
$4,223,463 |
| Infrastructure Expenditure Amount |
$0 |
| Infrastructure Purpose and Rationale |
Not Reported |
| Infrastructure Point of Contact Name |
Not Reported |
| Infrastructure Point of Contact Email |
Not Reported |
| Infrastructure Point of Contact Phone |
Not Reported |
| Infrastructure Point of Contact Address |
Not Reported |
| Infrastructure Point of Contact City |
Not Reported |
| Infrastructure Point of Contact State |
Not Reported |
| Infrastructure Point of Contact Zip |
Not Reported |
Product or Service Information
(Grants)
| Product or Service Information |
| Primary Activity Code |
611310 |
| Activity Description |
Colleges, Universities, and Professional Schools |
| Sub-Awards Information |
| Sub-awards to Organizations |
1 |
| Sub-award Amounts to Organizations |
$455,336 |
| Sub-Awards to Individuals |
0 |
| Sub-Award Amounts to Individuals |
$0 |
| Number of Sub-awards less than $25,000/award |
0 |
| Amount of Sub-awards less than $25,000/award |
$0 |
| Number of payments to vendors greater than $25,000 |
9 |
| Total Amount of payments to vendors greater than $25,000/award |
$1,307,580 |
| Number of payments to vendors less than $25,000/award |
850 |
| Total Amount of payments to vendors less than $25,000/award |
$304,155 |
Sub-award 109647-5034867 - BOTSWANA-HARVARD AIDS INSTITUTE
| Sub-Award Amount |
$455,336 |
| Sub-Award Date |
01/21/2011 |
| Sub-Awards Disbursed |
$455,336.00 |
| Project Location - City |
Gaborone |
| Project Location - State |
|
| Project Location - Zip Code |
|
| Project Location - Congressional District |
-- |
| Sub-Recipient DUNS Number |
538435473
|
| Sub-Recipient Address |
PRINCESS MARINA HOSPITAL, PLOT 1836 NORTH RING ROAD |
| Sub-Recipient City |
GABORONE |
| Sub-Recipient State |
GABORONE |
| Sub-Recipient Zip Code |
0000 |
| Sub-Recipient Congressional District |
-- |
Required To Report Top 5
Highly Compensated Officials |
No |
AXEQ TECHNOLOGIES INC - Award Number 1RC4AI092715-01 - AXEQ TECHNOLOGIES INC
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
966823432 |
| Vendor HQ Zip Code + 4 |
|
| Vendor Name |
AXEQ TECHNOLOGIES INC |
| Product and Service Description |
contract, exom sequencing; advanced analysis (genomic arrays) |
| Payment Amount |
$42,000 |
AXEQ TECHNOLOGIES INC - Award Number 1RC4AI092715-01 - AXEQ TECHNOLOGIES INC
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
966823432 |
| Vendor HQ Zip Code + 4 |
|
| Vendor Name |
AXEQ TECHNOLOGIES INC |
| Product and Service Description |
CONTRACT, EXOM SEQUENCING; ADVANCED ANALYSIS (GENOMIC ARRAYS) |
| Payment Amount |
$42,000 |
BGI AMERICAS CORPORATION - Award Number 1RC4AI092715-01 - BGI AMERICAS CORPORATION
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
272445508 |
| Vendor HQ Zip Code + 4 |
|
| Vendor Name |
BGI AMERICAS CORPORATION |
| Product and Service Description |
Whole Genome Resequencing. |
| Payment Amount |
$37,500 |
BGI AMERICAS CORPORATION - Award Number 1RC4AI092715-01 - BGI AMERICAS CORPORATION
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
272445508 |
| Vendor HQ Zip Code + 4 |
|
| Vendor Name |
BGI AMERICAS CORPORATION |
| Product and Service Description |
Whole Genome Resequencing. |
| Payment Amount |
$262,500 |
ILLUMINA, INC. - Award Number 1RC4AI092715-01 - ILLUMINA, INC.
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
033305264 |
| Vendor HQ Zip Code + 4 |
92122 |
| Vendor Name |
ILLUMINA, INC. |
| Product and Service Description |
illumina iscan system with universal starter kit; genomic arrays |
| Payment Amount |
$301,500 |
ILLUMINA, INC. - Award Number 1RC4AI092715-01 - ILLUMINA, INC.
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
033305264 |
| Vendor HQ Zip Code + 4 |
92122 |
| Vendor Name |
ILLUMINA, INC. |
| Product and Service Description |
illumina iscan system with universal starter kit; genomic arrays |
| Payment Amount |
$374,280 |
ILLUMINA, INC. - Award Number 1RC4AI092715-01 - ILLUMINA, INC.
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
033305264 |
| Vendor HQ Zip Code + 4 |
92122 |
| Vendor Name |
ILLUMINA, INC. |
| Product and Service Description |
HumanOmni2.5-8v1 Multi-Use DNA Analysis BeadChip (96 samples) Each HumanOmni2.5-8v1 Multi-use DNA Analysis BeadChip can process 8 samples and analyze ~2,500,000 loci. |
| Payment Amount |
$33,000 |
ILLUMINA, INC. - Award Number 1RC4AI092715-01 - ILLUMINA, INC.
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
033305264 |
| Vendor HQ Zip Code + 4 |
92122 |
| Vendor Name |
ILLUMINA, INC. |
| Product and Service Description |
illumina iscan system with universal starter kit; genomic arrays |
| Payment Amount |
$75,000 |
ILLUMINA, INC. - Award Number 1RC4AI092715-01 - ILLUMINA, INC.
| Award Number |
1RC4AI092715-01 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
033305264 |
| Vendor HQ Zip Code + 4 |
92122 |
| Vendor Name |
ILLUMINA, INC. |
| Product and Service Description |
HumanOmni2.5-8v1 Multi-Use DNA Analysis BeadChip (96 samples) Each HumanOmni2.5-8v1 Multi-use DNA Analysis BeadChip can process 8 samples and analyze ~2,500,000 loci. |
| Payment Amount |
$139,800 |
| Location Information |
| Latitude, Longitude |
42º 20' 8",
-71º 6' 3" |
| Congressional District |
07 |
| Address 1 |
|
| Address 2 |
|
| City |
Boston |
| County |
Suffolk |
| State |
MA |
| Zip |
02115-6009 |
|
 |