DNAprint Genomics (DNAG)

[mingwan0]

Here's another project using SNPs to estimate ancestry:

http://www.ccc.columbia.edu/HICC_collaboration/projects/p20-joe.html

P20
2003-2004
The African-American grouping is a reasonably valid variable for conducting small-scale biological studies

Andrew Joe (PI, Columbia University), Nathan Consedine (Co-Pi, Long Island University)

We will identify and characterize two cohorts of African American (AA) individuals: US-born AAs and Jamaican individuals. The latter, presumably more homogenous cohort, will serve as the comparison group Using serum samples and polymerase chain reaction (PCR)-based methods, we will characterize the degree of genetic admixture of each group by determining the relative allelic frequency distributions of the D1S80 and HLA-DQA1 gene polymorphisms. We will demonstrate that the contribution of African alleles to both groups is not significantly different. There is an ongoing debate as to whether race is an appropriate and valid research variable for use in biological studies.

Specific Aim 1 was completed. The control population has been changed. Immigrants from many countries, including those from Africa, Europe, and Asia, have settled in Jamaica. Thus, ancestry analyses may not be too different from those conducted in the African-American population in the US. Nigerians from either the Yoruba or Ibo cultures will represent a more genetically homogeneous group and will therefore comprise the control population for this study. Specific Aim 2 project is based on the collection of human blood specimens and questionnaire data. Because the target study and comparison populations are very specific, three institutions – Columbia University Medical Center (CUMC), Harlem Hospital Center (HHC), and Long Island University (LIU) – will be required to complete the planned accrual. Thus, this protocol was presented to and is currently being reviewed by the Institutional Review Boards (IRBs) of the three institutions. Unfortunately, sample and data collection will not be possible until the protocol is approved. (a) Documents were reviewed and approved by the LIU IRB. (b) Documents were reviewed by the CUMC IRB [Protocol IRB-AAAA1500]. Revisions have been submitted. (c) Documents were reviewed by the HHC IRB. Revisions have been submitted. A 25-item questionnaire has been created that will investigate potential factors used by the study subjects to construct racial identity. The method of determining genetic admixture has been changed (Specific Aim 2) to allow a more reliable method for estimating racial ancestry. A panel of 50 SNPs will be studied, and these analyses will be conducted by Dr. Elad Ziv, Assistant Professor of Medicine at the University of California, San Francisco. An addendum to the IRB to include this SNP panel will be submitted.

Contribution of the P20 The results of these studies may help us to determine whether it is valid to study tumor biology using racial classifications.

Project-Generated Resources and Benefits: In this project, DNA and questionnaire data will be collected from the African-American and Nigerian cohorts.

Dr Elad Ziv was mentioned in this post yesterday where he collaborated with Shriver on a piece of work that used 52 Ancestry Informative Markers:

http://www.investorshub.com/boards/read_msg.asp?message_id=3040369

Coincidence?