Genomics Research Projects
Chromosome 6p Deletion
Molecular Characterisations of Human Chromosome 6p Anomalies
Chromosome 6p deletions
Chromosome 6p deletions are rare events with around 50 cases described in the literature so far. We have characterised a large proportion of the 6p monosomy cases in detail using Fluorescent in situ hybridisation (FISH) and the available BAC and PAC library resources. The extent of the deletion is always variable, but regional hotspots for breakpoints have been identified. Through the study of genotype-phenotype correlations we have defined two distinct 6p deletion syndromes: interstitial deletions within the 6p22-24 segment and terminal deletions within the 6p24-pter segment. Most clinical features associated with 6p deletions are readily apparent at birth indicating a key role of the deleted genes in embryonic development. Interstitial deletions often include orofacial clefting, short neck, clinodactyly or syndactyly, brain, heart and kidney defects. In contrast, 6p terminal deletions are associated with corneal opacity, iridogoniodysgenesis anomaly, various Rieger type anomalies, hypertelorism and deafness. Furthermore, the genetic basis of the syndromes is being investigated by using the heterozygote mouse model (Del13(Svea)36H) deleted for the region syntenic with 6p22-25. Mice are subjected to N-ethyl-N-nitrosurea (ENU) treatment in an effort to identify the mutations for the phenotypes in the recessive screen that bear resemblance to some of the human 6p deletion features.
Chromosome 6p duplications
Isolated chromosome 6p duplications are very uncommon, most 6p trisomy cases reported are the result of unbalanced chromosomal translocations. The breakpoints involving 6p duplications range from 6p11-6p25. In general, the larger segmental duplications cause a more severe phenotype, with associated growth retardation, facial anomalies, severe mental retardation. We have characterised around 4 cases involving only chromosome 6p using FISH. Of these cases, 3 are interstitial duplications whilst the 4th case is duplicated for chromosome 6p22-pter and is a mosaic. In conjunction with FISH, we are investigating the applicability of the Infinium TM whole genome genotyping platform (Illumina Inc.) with our cases to determine copy number changes and accurately characterise the breakpoints. We are also testing the platform to screen the genome for microdeletions that may not be detected by molecular cytogenetic technologies.
Example of FISH on a 6p terminal deletion case: Case3 (Mirza et al., 2004) has the breakpoint positioned within the proximal segment of 6p25 with YAC probe 663a12(shown in green, mapping proximally on 6p25) distal to PAC dJ155I9(shown in red,mapping on 6p24.3/25) proving negative on del (6)
Mouse Chromosome 6p Deletions: Introduction
We have employed a forward genetics approach in order to assign function to the genes located within the mouse syntenic region to human 6p. This 14MB region of mouse chromosome 13 is hemizygous in the Del13Svea36H mouse (Arkell, R. M. et al (2001) Mammalian Genome 12: 687-694) and a visible marker within this area of hemizygosity has enabled a region specific, two generation ENU mutagenesis screen to be performed.
Mutant Phenotypes Isolated
Eleven novel mouse mutant lines have been isolated. These mouse mutants reflect the clinical phenotypes observed in the human 6p deletion patients.
Summary of mutant phenotypes for each mutant line (from Bogani D. (2005) PNAS 102 (35): 12477-12482)
* Assay was performed on heterozygous carriers of the mutation
† Phenotype associated with human 6p deletion syndrome
Localisation of causative mutations
Mutation containing candidate regions for each of the mutant lines have been identified by following the progress of the mutated chromosome with a comprehensive genotyping panel and assessing whether the mutant phenotype is retained in recombinants.
Mutation location. The critical intervals identified for each mutant line from the positional cloning effort (from Bogani D. et al (2005) PNAS 102 (35): 12477-12482)
The genes within these critical intervals have been screened for causative mutations.
The work is now focussed on assessing the complex interactions between large chromosomal deletions, small deletions, point mutations and genetic background through a novel genetic cross set up to focus on these aspects.