Updating the genome: the CCL3L1 region of chr17q21

The CCL3L1 and CCL4L1 genes are found in a region of Human chromosome 17q12. These genes encode cytokines and the number of gene copies varies between individuals, with 0-4 copies in European individuals and 3-10 copies in African individuals. Copy number variations of these genes have been associated with various autoimmune diseases, possibly playing a role in rheumatoid arthritis susceptibility [PMID:17604289]. There are conflicting reports concerning how this region influences HIV infection and progression [PMID:15637236 and PMID:19812560].In the NCBI36 reference, this region was comprised of clones from different libraries, and thus different haplotypes. A user reported that it seemed likely that the selected tiling path, that also contained a gap, did not represent a valid structure at this biomedically important locus. We have tracked the work on this region in HG-75. Despite our best efforts, we could not resolve all problems in this region in time for the release of GRCh37.Because of the complexity of this region, we chose to produce a new tiling path using a BAC library that has been constructed from a hydatidiform mole library (CHORI-17). Complete hydatidiform moles are the result of a single sperm fertilizing an enucleated egg. The sperm reduplicates to generate two sets of the paternal chromosomes and thus contains DNA from a single haplotype. Clones from this resource have proven very useful for resolving highly duplicated genomic regions. The joins between...
Source: GenomeRef - Category: Genetics & Stem Cells Source Type: blogs