Large scale duplication of genetic material is a major force driving the evolution of genetic diversity. Gene duplication and subsequent divergence have been instrumental in the creation of new genes with specialized functional roles, a process that has been important for the creation of evolutionary diversity and speciation. The accumulating sequence of the human genome has revealed a class of genomic duplications that are chromosome-specific. Interestingly, these chromosome-specific sequence duplications or low copy repeats (LCRs) have been implicated in a number of human genetic disorders that are associated with recurrent genomic rearrangements. It has been proposed that illegitimate recombination facilitated by the highly homologous duplicated sequences give rise to deletions, duplications and inversions. Chromosome-specific LCRs on human chromosome 22q11 have been implicated in various constitutional rearrangements leading to genetic disease. Although the human 22q11 LCRs have been sequenced, very little is known about their evolution and amplification in the genome. Comparative analysis of the mouse genome has revealed an absence of LCRs at the orthologous loci. Examination of the 22q11 LCRs in non-human primates suggests that they have originated and evolved during primate evolution. We wish to investigate the mechanism responsible for chromosome-specific duplications and their role in the evolution of the primate genome. Toward this goal, we propose a comparative analysis of the organization and structure of the 22q11 LCRs in humans and non-human primates. We will analyze the 22q11 LCRs in various non-human primates at the chromosomal, gross structural and nucleotide sequence levels. The evolutionary analysis of the primate-specific 22q11 LCRs provide a unique opportunity to investigate the molecular mechanism underlying this form of genome evolution. We will also test the hypothesis that the processes responsible for the origin and spread of the chromosome-specific duplications are ongoing and may have resulted in genomic variability within the human population. We will perform a population-based analysis to look for genetic polymorphism in the structural organization of 22q11 LCRs within various human population groups. This will allow us to assess the involvement of LCRs in creating genetic variation that may lead to the genomic instability associated with human genetic disorders. Thus, the 22q11 LCRs provide a model system with which to gain a better understanding of the evolution of the human genome.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM064725-04
Application #
6830735
Study Section
Mammalian Genetics Study Section (MGN)
Program Officer
Eckstrand, Irene A
Project Start
2002-01-01
Project End
2007-12-31
Budget Start
2005-01-01
Budget End
2007-12-31
Support Year
4
Fiscal Year
2005
Total Cost
$249,900
Indirect Cost
Name
Children's Hospital of Philadelphia
Department
Type
DUNS #
073757627
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Jackson, Eric M; Shaikh, Tamim H; Gururangan, Sridharan et al. (2007) High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor. Hum Genet 122:117-27
Shaikh, Tamim H; O'Connor, Ronald J; Pierpont, Mary Ella et al. (2007) Low copy repeats mediate distal chromosome 22q11.2 deletions: sequence analysis predicts breakpoint mechanisms. Genome Res 17:482-91
Ming, Jeffrey E; Geiger, Elizabeth; James, Alison C et al. (2006) Rapid detection of submicroscopic chromosomal rearrangements in children with multiple congenital anomalies using high density oligonucleotide arrays. Hum Mutat 27:467-73
Inagaki, Hidehito; Ohye, Tamae; Kogo, Hiroshi et al. (2005) Palindromic AT-rich repeat in the NF1 gene is hypervariable in humans and evolutionarily conserved in primates. Hum Mutat 26:332-42
Morrissette, Jennifer J D; Medne, Livija; Bentley, Tyrone et al. (2005) A patient with mosaic partial trisomy 18 resulting from dicentric chromosome breakage. Am J Med Genet A 137:208-12