Rhesus Macaque (Macaca mulatta) BAC Mapping Via PGI

(Version: PGI-MML.5)

Mapping Data Access
Rhesus PGI Paper

Pooled Genomic Indexing (PGI) is a method for mapping collections of Bacterial Artificial Chromosome (BAC) clones across species using a combination of clone pooling and DNA sequencing.1,2,3

PGI has been used to map a total of 16,495 unique rhesus BAC clones, gving 0.92X BAC clone coverage, to the positions of 18,035 homologous loci in the human genome NCBI Build 34. Approximately 57% of the human genome is covered by mapped BACs. A number of intrachromosomal rearrangements were detected by mapping multiple segments within the individual rhesus BACs onto multiple disjoint loci

This project is done in collaboration with the Baylor Human Genome Sequencing Center (HGSC) and is funded by grants from the NIH-NHGRI and NIH-NCRR to Aleksandar Milosavljevic.

PGI Method:

BACs are laid out in a transversal design array-pair. Pools are created from the rows and columns of the two arrays:

BAC Pooling

Following sequencing, pool reads are mapped to a genome. Coincident mapped pool reads form an index if their pools intersect (i.e. have a BAC in common). Thus the BAC is mapped to the location of the index:


PGI Performance Summary:

We applied PGI to a set of 22,776 BAC clones, contained in seven array pairs, from the CHORI-250 Rhesus macaque library. On average, 11 reads were deconvoluted to each BAC.

Access to the raw data, Genboree-browsable data, and other experiment-related files are available on the Data Access Page.

Posters and Presentations

PGI-related posters and presentations are available online.


1 Milosavljevic A, Harris RA, Sodergren EJ, Jackson AR, Kalafus KJ, Hodgson A, Cree A, Dai W, Csuros M, Zhu B, de Jong PJ, Weinstock GW, Gibbs RA (2005). Pooled genomic indexing of rhesus macaque. Genome Res, 15(2): 292-301.

2 Csuros M, Milosavljevic A (2004). Pooled Genomic Indexing (PGI): Analysis and Design of Experiments. J Comput Biol, 11(2): 1001-1021.

3 Csuros M, Milosavljevic A (2002). Pooled genomic indexing (PGI): mathematical analysis and experiment design, in Algorithms in Bioinformatics, Second International Workshop, WABI 2002, Guigo R. and Gusfield D. (eds.). Springer Verlag: Heidelberg, Germany. p. 10-28.