Biomedical subjects

Andrew Collins

Publications and source records attributed to Andrew Collins.

41 records · Page 3Linked to original sources

PubMed2002

The distinguishing sequence characteristics of mouse imprinted genes.

Sequence comparison analysis has been carried out for 31 imprinted mouse genes and a set of 150 control genes. The imprinted genes were found to be associated with significantly reduced numbers of short interspersed transposable elements (SINEs), in particular SINE Alu repeats. This is similar to recent analyses of human imprinted genes and supports the suggestion that there is either active selection against SINE elements in imprinted regions or a reduced rate of insertion of these elements. The reduction in numbers of SINEs was more consistent in paternally expressed genes, whereas for maternally expressed genes significantly reduced numbers of SINE-B2 elements were coupled with increased numbers of SINE-B4 and SINE-ID elements. Paternally expressed genes were also found to be associated with a lower GC content. Discriminant analysis revealed that the two sub-groups of imprinted genes can be cleanly separated from each other on the basis of their genomic sequence characteristics and that they tend to localize to different genomic compartments. The differences between the sequence characteristics of imprinted and control genes have also enabled us to develop a discriminant function that can be used in a genome-wide screen to identify candidate imprinted genes.

Animals↗

PubMed2002

PCR designer for restriction analysis of various types of sequence mutation.

Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.

Amidohydrolases↗

PubMed2002

Repair of oxidative DNA damage: assessing its contribution to cancer prevention.

DNA repair is a crucial factor in maintaining a low steady-state level of oxidative DNA damage and protecting us from cancer. Cancer case-control studies, using indirect assays in which chromosome breakage in lymphocytes is taken as a measure of failure to repair DNA, indicate an association between poor repair and cancer risk, but case-control studies can be misleading. Surprisingly little is known of the variations in repair capacity within healthy human populations. It is likely that differences in repair enzyme activity result from genetic polymorphisms in repair genes, which have been shown, in some cases, to be linked to cancer. There is a need for prospective studies, in which genotype is analysed (for a range of repair and related genes) and repair activity measured before cancer has developed. Using a new method to measure repair in an extract of lymphocytes, based on a modification of the comet assay, we are seeking answers to the following questions: what is the normal range of repair activities in healthy humans; do differences in repair capacity correlate with genetic variations; is low repair capacity associated with a high risk of cancer; how important is DNA repair rate in determining the steady-state level of damage; what is the extent of intra-individual variation; is repair modulated by environmental factors or induced by damage; are there differences in repair capacity between men and women; what is the association of DNA repair with ageing?

DNA↗

PubMed2002

Toward positional cloning with SNPs.

Efficient methods are available for positional cloning of major genes by linkage and linkage disequilibrium (LD). The application of these methods to complex diseases is more demanding, but advances in sequencing the human genome, SNP discovery, high-throughput genotyping techniques, LD maps, and haplotype annotation are revolutionizing positional cloning of oligogenes for common multifactorial disease.

Alleles↗

PubMedDate not supplied

Biomarkers.

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Amino Acids↗