Relation Between Hapmap Project And 1000Genomes Project

Question

[Matthew]

Why are there 2 projects, the HAPMAP and the 1000 Genomes Project?

Both projects provide ref panels, which can be used for imputations, so why wasnt the work of the HAPMAP project continued, providing the ref panel in the meantime with sequencing techniques?

Has the HAPMAP project ended?

On the website I find: (http://hapmap.ncbi.nlm.nih.gov/thehapmap.html.en) "The Project officially started with a meeting in October 2002 (http://genome.gov/10005336) and is expected to take about three years."

3 years from 2002 means it would have ended in 2005, whereas the latest release (#28) is from August 2010. Sorry, I dont get it! Will this (#28) be the latest HAPMAP release and is 1KG simply continuing the work of the HAPMAP Project? Or how are the 2 projects related to each other?

Would be nice if someone can bring light into my mental darkness ;)

Thank you, Matthew.

Answer 1

[Mitch Lokey]

I could be wrong but I believe this is the relation.

TL;DR HapMap did SNP genotyping whereas 1kGP did whole genome sequencing, and some of the individuals overlap.

First we have to establish a distinction. Genotyping vs Sequencing. Genotyping is the capture of a persons genetic identity at a defined locus. Sequencing is the capture of a persons "complete genome/segment of DNA" (https://www.biostars.org/p/5197/).

HapMap Phase 1: Released 2005, consisted of genotyping (not WGS) of several million known SNPs in 269 individuals. It included trio (individual and their parents) genotyping of individuals from Yoruba (YRI), Utah (CEU), Beijing (CHB), and Tokyo (JPT).

HapMap Phase 2: Released 2007. To increase the quality of Mapping ability the project had to identify more SNPs. Once they had several million more SNPs they conducted genotyping of the additional SNPs on the same populations.

HapMap Phase 3: Released 2009. Was an effort to expand the populations mapped. Using the SNPs from phase 1 & 2 they genotyped (not WGS) individuals from 11 populations (7 additional).

1000 Genomes Project (1kGP): Pilot released 2010. In an effort to make a more comprehensive map of human genetic variation sequencing (not genotyping) was carried out on 1029 individuals from 26 populations.

HERE is where the overlap is;

The 1kGP sought to make their data as useful as possible so they sequenced many individuals (but not all) from the HapMap project and some individuals from the ENCODE project.

Now in 2017 we have the beautiful Simons Genome Diversity Project (SGDP) and the Estonian Biocentre Human Genome Diversity Panel (EGDP) which both include more populations than the 1kGP and have better genomic coverage.

https://en.wikipedia.org/wiki/International_HapMap_Project https://en.wikipedia.org/wiki/1000_Genomes_Project https://en.wikipedia.org/wiki/Human_Genome_Project

Answer 2

[Alastair Kerr]

I have never quite worked out the demarcation between the 1000 genomes, HAPMAP & ENCODE. A bit muddied as some investigators have funding from more than one of these projects.

I am aware that HapMap (and ENCODE) are in version 3. There was a Nature paper late last year on HapMap: doi:10.1038/nature09298

Moreover HapMap and 1000 genomes are not in total isolation: at least in the QC stage. From the FAQ

The 1000 genomes project and HapMap share individuals and HapMap data has been used to help to both qc the data to ensure it is from the correct individual and to validate the early variant predictions to assess how accurate they were.