The Genographic Project

==The Genographic Project==
===Overview===
The Genographic Project was initiated by the National Geographic Society and IBM in 2005 under Dr. Spencer Wells (a anthropologist, geneticist, and National Geographic Explorer-in-Residence).  The project aims to genetically determine the roots of the human race; where we originated from and how we came to populate the earth.  To accomplish this, researchers have acquired DNA samples from a variety of peoples around the word and analyzed them using present DNA technology.  To date 524, 384 individuals from 140 countries have been evaluated. 
The Genographic Project also is a non-profit, non-medical endeavor with additional goals involving public education and indigenous people welfare.  A description of these additional goals include: 1. To acquire and collaboratively evaluate DNA samples from indigenous peoples, 2. To facilitate public education by inviting any person to purchase a Genographic Project Participation and DNA Ancestry Kit, Geno 2.0, 3. To use funds generated from the kit and legacy fund to assist in the conservation and revitalization of indigenous and traditional peoples. 
This project intends to release peer-reviewed publications of the data to public domains as they become available. Both scientific and popular press has been generated in light of this project.  Some of the lastest press releases include "Southern India's Caste System Predates the Arrival of the Indo-Europeans" (11/28/2012), "Genographic Project and Univeraity of Pennsylvania Scientists Illuminate the Ancient History of Circumarctic Peoples" (05/17/2012), and  "Basque Roots Revealed Through DNA Analysis" (03/6/2012). 
===The Science behind the Project===
Individuals will submit a cheek swab sample using the DNA Ancestry Kit, Geno 2.0 and researchers will evaluate the DNA of that sample.  Most genetic information is conserved through generations, however mutations will periodically appear.  Mutations that are passed on through generations can be designated as markers.  This study will assess about 150,000 markers in the acquired DNA samples.  They will look at the maternal lineage using markers withing the mitochondrial genome in males and females, the paternal lineage in males using markers in the Y chromosome, and 130,000 other markers within the genome.  Each of these markers have regional correlations and tracking the markers in different people groups, while ideally enable the researchers to determine migration patterns.
====How to look at the 150,000 markers?====
To look at these markers scientists will employ the "GenoChip."  The Genochip version used is in this project is an Illumina HD iSelect genotyping bead array composed of nearly 150,000 microscopic beads.   
Below is a description of one of Illumina 's genotyping bead arrays. 
After acquiring genomic DNA it is chemically treated to include a biotin label. The biotin label will then bind to a steptavidin coated paramagnetic bead (This is so the DNA can later be recovered from solution).  The bead bound genomic DNA is placed in solution with three oligonucleotides (single strands of DNA).   These oligonucleotides are designated for the detection of each SNP (single nucleotide polymorphism - the "markers" mentioned above). Two of the oligonucleotides are allele specific, meaning they are each associated with a unique SNP allele.  Both of these oligonucleotides will contain unique, but general primers, with "general" referring to the fact that the primers are not complementarty to the genomic DNA.  The third oligonucleotide is locus specific, meaning that it recognizes a specific region downstream from the SNP.  The locus specific oligonucleotide also contains its own general primer and a sequence known as the address. The address is a 3'- 29 base specific sequence created by Illumina for the purpose of detection. It often serves as the bridge between the bead and the oligonucleotide of interest.
Primers are added to the genomic DNA and oligo solution and each allele specific oligo will become elongated  (using genomic DNA as a template) and ligate to the locus specif oligo.  Additional general primers labeled for each allele specific oligonucleotide ( Cy5, the other with Cy3) are added to the mixture. PCR reactions amplify the genomic DNA that was presented.  Following PCR, the products of the reaction are separated from the rest of the material.
In genotyoing bead assays, the main "base" of the assay is often contains a plate (glass, fiber-optic material), that contains many etches in the surface, creating tiny wells.  Silicon beads are added and the wells enable one bead to rest in one well.  The bead stays in place with the help of van der Waal forces.  The bead is conjugated to an address sequence.  This address is complementary to the address descibed above in the locus-specific oligo descriprion. 
The PCR products are incubated with the silicon beads and the addresses hybridize to complementary sequences.  The labels are then detected.  Three detection options are possible, one green, one red, and one with no color.  As described above, each oligo's general primer has a specific label associated with it.  Should a person be homozygous for the allele of interest the assay will present only red or green in the wells.  If it is heterozygous, the wells will be red and green.  If it is neither, or there are no beads in a well, no color will be observed. 
These assays are computer run, so the computer knows where beads probing for different addresses and ultimately sequences exist through decoding. 
Sources
http://abstracts.ashg.org/cgi-bin/2012/ashg12s
http://www.ohsu.edu/xd/research/research-cores/gmsr/project-design/array-technology/illumina-bead-arrays.cfm
http://www.illumina.com/technology/beadarray_technology.ilmn
===The Current Generated Map===
So far a fair amount of the released data, focuses on specific populations.  General migration out of Africa is estimated to have started 60,000 and 70,000 years ago based on the genetic and paleontological record.