Search PubMed⌕ Search

Biomedical subjects

A J Brookes

Publications and source records attributed to A J Brookes.

At least 37 records · Page 2Linked to original sources
PubMed2000

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.

There are great hopes that the most common form of human genetic variation, single nucleotide polymorphisms (SNPs), can be used to improve radically biological understanding and to advance medicine. However, considerable controversy exists over just how SNPs can be applied to gain these insights. The second international SNP meeting, held at Schloss Hohenkammer, Munich, Germany, brought together leading international scientists from academia and industry to look at these issues from a multidisciplinary perspective. Topics that were covered spanned SNP discovery, scoring technologies, population genetics, disease studies, commercial dimensions, pharmacogenomics, bioinformatics, and legal considerations. SNP discovery is picking up speed; The SNP Consortium (TSC) is set to produce 300,000 publicly available SNPs within 2 years. Improved technologies for scoring SNPs are reducing hands-on time and cost, although truly high-throughput methods are still lacking for genome-wide population-based studies. Large numbers of SNPs have already been analysed in diverse populations. The results emphasise the importance of considering population history when using SNPs to search for genetic risk factors. Opinions on the feasibility of extensive SNP-based analysis of complex disease vary. However, combining expertise from several fields will be key to achieving optimal utilization of SNPs.

Humans↗
PubMed1999

Identification of 167 polymorphisms in 88 genes from candidate neurodegeneration pathways.

Catalogs of intra-gene polymorphisms are needed to facilitate wide-ranging candidate gene-based association studies in common complex diseases. With this in mind, we have scanned multiple alignments of expressed sequence tags and of genomic DNA sequences (PCR products from four to eight unrelated individuals) to find polymorphisms in 195 genes putatively involved in neurodegenerative illness (including components of oxidative stress, excitotoxicity, inflammation, apoptosis and aging). This led to the discovery of 167 polymorphisms in 88 genes. These comprised 163 single nucleotide polymorphisms, one insertion/deletion, and three other variations involving more than one base pair. The polymorphisms were distributed in the exons (87), introns (70), and gene flanking regions (10). Of the exonic polymorphisms, 17 would give rise to non-synonymous amino acid substitutions. These findings now provide a valuable resource for association studies in neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease.

Evolution, Molecular↗
PubMed1999

The essence of SNPs.

Single nucleotide polymorphisms (SNPs) are an abundant form of genome variation, distinguished from rare variations by a requirement for the least abundant allele to have a frequency of 1% or more. A wide range of genetics disciplines stand to benefit greatly from the study and use of SNPs. The recent surge of interest in SNPs stems from, and continues to depend upon, the merging and coincident maturation of several research areas, i.e. (i) large-scale genome analysis and related technologies, (ii) bio-informatics and computing, (iii) genetic analysis of simple and complex disease states, and (iv) global human population genetics. These fields will now be propelled forward, often into uncharted territories, by ongoing discovery efforts that promise to yield hundreds of thousands of human SNPs in the next few years. Major questions are now being asked, experimentally, theoretically and ethically, about the most effective ways to unlock the full potential of the upcoming SNP revolution.

DNA↗
PubMed1999

A zinc finger truncation of murine WT1 results in the characteristic urogenital abnormalities of Denys-Drash syndrome.

The Wilms tumor-suppressor gene, WT1, plays a key role in urogenital development, and WT1 dysfunction is implicated in both neoplastic (Wilms tumor, mesothelioma, leukemias, and breast cancer) and nonneoplastic (glomerulosclerosis) disease. The analysis of diseases linked specifically with WT1 mutations, such as Denys-Drash syndrome (DDS), can provide valuable insight concerning the role of WT1 in development and disease. DDS is a rare childhood disease characterized by a nephropathy involving mesangial sclerosis, XY pseudohermaphroditism, and/or Wilms tumor (WT). DDS patients are constitutionally heterozygous for exonic point mutations in WT1, which include mutations predicted to truncate the protein within the C-terminal zinc finger (ZF) region. We report that heterozygosity for a targeted murine Wt1 allele, Wt1(tmT396), which truncates ZF3 at codon 396, induces mesangial sclerosis characteristic of DDS in adult heterozygous and chimeric mice. Male genital defects also were evident and there was a single case of Wilms tumor in which the transcript of the nontargeted allele showed an exon 9 skipping event, implying a causal link between Wt1 dysfunction and Wilms tumorigenesis in mice. However, the mutant WT1(tmT396) protein accounted for only 5% of WT1 in both heterozygous embryonic stem cells and the WT. This has implications regarding the mechanism by which the mutant allele exerts its effect.

Animals↗
PubMed1998

Point mutations (Thr240Arg and Gln311Stop) [correction of Thr240Arg and Ala311Stop] in the Parkin gene.

Autosomal recessive juvenile parkinsonism (AR-JP) is a distinct clinical and genetic entity characterized by selective degeneration of nigral neurons. Recently, the parkin gene responsible for AR-JP has been identified. To date, we found two different deletional mutations including single and multiple exonic deletions. In the present study, we identified two types of point mutations (Thr240Arg and Gln311Stop) involving exons 6 and 8 in the parkin gene of the AR-JP patients from two Turkish families. This is the first report on point mutations for the parkin gene. Furthermore, the Thr240Arg mutation was located on a consensus sequence for the site of phosphorylation by casein kinase II. Identification of its mutation provides an important clue as to the role of the Parkin protein in degeneration of the substantia nigra in the brain of AR-JP patients.

Adolescent↗
PubMed1998

The NIK protein kinase and C17orf1 genes: chromosomal mapping, gene structures and mutational screening in frontotemporal dementia and parkinsonism linked to chromosome 17.

Full exon-intron structures are presented for the NIK serine/threonine protein kinase gene and a novel gene termed C17orf1. By in situ hybridisation and radiation hybrid mapping, a cosmid (cDD-Z) that contains regions of both of these genes has been localised between markers D17S800 and D17S791 at chromosome 17q21. The two genes are thus positional candidates for the mutant locus underlying frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17), a disease for which NIK is also a good biological candidate. Using exon-intron maps, a genomic DNA sequencing based mutation screen has been performed for the NIK and C17orf1 genes in a chromosome 17-linked FTDP-17 pedigree. Two silent single-base variations were detected in C17orf1. No alterations were restricted to DNA samples from patients, thus excluding the C17orf1 and NIK genes as likely sites of mutation FTDP-17.

Carrier Proteins↗
PubMed1998

Intron based radiation hybrid mapping of 15 complex I genes of the human electron transport chain.

At least 34 complex I subunits of the electron transport chain are encoded by the nuclear genome, but only 14 of these have been mapped in the human. To rapidly map additional subunits, we have performed a combination of database mining and direct "wet" experimentation to identify intron and/or 5' upstream genomic DNA regions for 16 complex I genes. Wet experimentation was applied to 5 genes, and involved direct PCR amplification of introns by inter-exon PCR or splinkerette based PCR walking. Database mining was applied to 11 genes, and entailed the identification of incompletely spliced mRNAs and genomic CpG island clone sequences. This data was in files that carried no documentary description of the non-exon regions. Non-exon sequences were thus derived for 15 complex I genes and used to design functional gene specific PCR assays. Radiation hybrid mapping of these PCRs located 15 complex I genes to chromosomes l, 4, 5 (2 genes), 7 (2 genes), 8, 9 (2 genes), 11, 14, 16 (2 genes), 18, and 19.

Chromosome Mapping↗
PubMed1997

Novel transcribed sequences neighbouring a translocation breakpoint associated with schizophrenia.

A 1.3Mb chromosome 11-specific yeast artificial chromosome (YAC) that spans a t(1;11) translocation breakpoint associated with major psychosis has been used to enrich cDNAs that are encoded within it and expressed in the human foetal brain. Database analysis of the selected fragments led to the identification of 54 clones matching alpha-tubulin, 4 fragments matching two anonymous human expressed sequence tags (ESTs) and 8 fragments giving no database matches. The clones matching alpha-tubulin led to the identification of a novel alpha-tubulin locus located approximately 250 kb proximal to the translocation breakpoint. Extensive sequence and expression analysis of this locus suggests that this is a processed pseudogene, although a long open reading frame is maintained and the possibility that an abnormally acting protein may be expressed in a highly tissue or developmental specific manner cannot be discounted. The novel cDNA fragments map up to 700 kb proximal to the translocation breakpoint and are associated with potential CpG islands. Reverse transcriptase polymerase chain reaction (RT-PCR) expression analysis and high resolution genomic mapping suggest that they may comprise up to three novel genes. No major disruption of the identified fragments could be detected in the genomic DNA of translocation carriers. The psychosis associated with this translocation may therefore be due to position effects on the transcription of these genes or an involvement of translocated chromosome 1 sequences.

Chromosomes, Artificial, Yeast↗
PubMed1997

In situ hybridisation mapping of genomic clones for five human respiratory chain complex I genes.

Using human and bovine short cDNA sequences as probes we screened human cosmid and P1 libraries for components of the complex I multi-subunit enzyme of oxidative phosphorylation. We isolated genomic recombinants encoding cI-B8 (gene NDUFA2), cI-B14 (gene NDUFA6), cI-B14.5a (gene NDUFA7), cI-ASHI (gene NDUFB8) and cI-23kD (gene NDUFS8). Genomic versions of these genes have not been previously cloned in the human although they are represented as anonymous entries in public cDNA databases. By using the derived genomic clones for in situ hybridisation studies we determined the following chromosome locations: NDUFA2, 5q31; NDUFA6, 21q22; NDUFA7, 20p13; NDUFB8, 12q21; NDUFS8, 3q28.

Animals↗
PubMed1996

Novel transcribed sequences represented in the complex genomic region 5q13.

YACs from the complex repetitive human genomic region 5q13, spanning the spinal muscular atrophy (SMA) locus, have been searched for transcribed sequences using the method of End Ligation Coincident Sequence Cloning. Six transcripts (PT1-6) have been identified, three of which (PT4, PT5 and PT6) are novel. Five of these elements hybridise to multiple loci in 5q13, but PT5 is single copy and maps very close to markers that show linkage disequilibrium with SMA.

Base Sequence↗
PubMed1996

Coincidence cloning. Taking the coincidences out of genome analysis.

The term "coincidence cloning" encompasses a wide range of methodologies, the aim of which is to isolate DNA sequences which occur in both of two input DNA sources. The nature of these input DNAs may be genomic or cDNA, cloned or uncloned, and as such the far reaching applicability of the techniques can be imagined. If the input DNAs are genomic then the product will be enriched for useful markers co-occurring between the two. If the input DNAs comprise one genomic resource and one cDNA resource the product will contain genes mapping to that particular genomic region. In this review a comparative description of the range of coincidence cloning methods is given, together with a discussion of their applications. Finally, consideration is given to the general limitations of these techniques.

Cloning, Molecular↗
PubMed1995

Mapping of retrotransposon sequences in the unstable region surrounding the spinal muscular atrophy locus in 5q13.

The mutation that underlies the autosomal recessive disorder spinal muscular atrophy (SMA) is located on chromosome 5q13. Recent studies show that SMA patients frequently have deletions and rearrangements in this region compared to normal controls. During the isolation of candidate cDNAs for the disease, we identified a sequence that shows high homology to the THE-1 retrotransposon gene family. Using YAC fragmentation techniques, we have refined the localization of this sequence to the domain known to show instability in SMA patients. The implication of these results for the mechanism of the mutation in SMA is discussed.

Base Sequence↗
PubMed1995

Identifying genes within microdissected genomic DNA: isolation of brain expressed genes from a translocation region associated with inherited mental illness.

An improved protocol has been developed for physical enrichment of cDNA sequences by hybridization to genomic DNA. When applied to microdissection recombinants derived from a translocation breakpoint region associated with inherited mental illness, a single cycle of the procedure permitted enriched cDNAs to be visualized directly by agarose gel electrophoresis. Hybridization screening of a library of clones derived from the enriched cDNAs, employing the genomic resource as a probe, led to the identification of six novel gene fragments. This general approach to the isolation of regionally encoded genes could be applied to any subchromosomal interval as a first step towards global transcription map construction.

Animals↗
PubMed1995

Catch-linker + PCR labeling: a simple method to generate fluorescence in situ hybridization probes from yeast artificial chromosomes.

A simple and efficient method to generate hapten-labeled DNA fragments from a trace amount of YAC DNA isolated by PFGE is described. After agarase digestion of the gel slice containing the resolved YAC recombinant, the purified DNA is digested with Sau3Al and a compatible CL oligonucleotide duplex ligated on. A probe is generated by PCR amplification using a primer complementary to the CL with a single biotin moiety incorporated at the 5' end. When used as a FISH probe, this material yields mapping results superior to Alu-PCR or whole YAC labeling methods and allows sensitive detection of chimerism.

Base Sequence↗