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K K Kidd

Publications and source records attributed to K K Kidd.

At least 127 records · Page 7Linked to original sources
PubMed1991

Genotyping and haplotyping of polymorphisms directly from genomic DNA via coupled amplification and sequencing (CAS).

Coupled amplification and sequencing (CAS) allows a segment of DNA to be sequenced directly from genomic DNA. An initial PCR amplification stage selects and amplifies the target. During a subsequent stage both strands of the target segment are sequenced simultaneously and amplified further. We show that CAS can readily identify variant base pairs. Genotyping of a population for known sequence variation can be achieved simply and directly from genomic DNA of each organism by performing CAS only for the variant bases. The procedure supercedes development and optimization of alternative typing assays based on oligonucleotide hybridization or ligation. In addition, we show that competitive oligonucleotide priming with allelic primers can be readily performed in concert with the second stage of CAS. The combination of techniques allows sequencing of a single chromosome from a heterozygous genomic sample and direct haplotyping of the polymorphism at the priming site with any others encompassed within the amplified segment.

Animals↗
PubMed1991

No association between an allele at the D2 dopamine receptor gene (DRD2) and alcoholism.

OBJECTIVE: --We attempted to replicate a positive allelic association between the A1 allele of DRD2 (the D2 dopamine receptor locus) and alcoholism that has been reported. DESIGN: --We compared allele frequencies at the previously described Taq I restriction fragment length polymorphism system of DRD2 in alcoholics and random population controls. SUBJECTS: --The alcoholic subjects were 44 unrelated white individuals, diagnosed by direct structured interview to have alcohol dependence (by the Diagnostic and Statistical Manual of Mental Disorders, Revised Third Edition, criteria). The subjects in our random population control group (N = 68) were also white. RESULTS: --For the control group, allele frequencies at DRD2 were 0.20 (A1) and 0.80 (A2). For the alcoholic group overall, allele frequencies were 0.23 (A1) and 0.77 (A2). There were no significant differences in allele frequencies at the DRD2 locus between alcoholics and controls. The allele frequencies in both groups agreed closely with those observed in most previously described control populations. Subtyping the alcoholic group according to presence or absence of family history of alcoholism, presence or absence of antisocial personality disorder, age of onset, presence or absence of physical withdrawal symptoms, or recent alcohol consumption (as a measure of severity) did not in any case reveal significant differences in allele frequencies. CONCLUSION: --We were not able to replicate the results previously reported. We conclude that our data do not support an allelic association between the A1 allele at DRD2 and alcoholism.

Adult↗
PubMed1991

Coupled amplification and sequencing of genomic DNA.

Addition of dideoxyribonucleotides during the exponential phase of the PCR should result in the synthesis of two complementary sequence ladders. We have explored this hypothesis to develop coupled amplification and sequencing of genomic DNA. Coupled amplification and sequencing is a biphasic method for sequencing both strands of template as they are amplified. Stage I selects and amplifies a single target from the genomic DNA sample. Stage II accomplishes the sequencing as well as additional amplification of the target using aliquots from the stage I reaction mixed with end-labeled primer and dideoxynucleotides. We have successfully applied coupled amplification and sequencing to a 300-base-pair fragment 4 kilobases upstream from HOX2B directly from human whole genomic DNA.

Base Sequence↗
PubMed1991

Drift, admixture, and selection in human evolution: a study with DNA polymorphisms.

Accuracy of evolutionary analysis of populations within a species requires the testing of a large number of genetic polymorphisms belonging to many loci. We report here a reconstruction of human differentiation based on 100 DNA polymorphisms tested in five populations from four continents. The results agree with earlier conclusions based on other classes of genetic markers but reveal that Europeans do not fit a simple model of independently evolving populations with equal evolutionary rates. Evolutionary models involving early admixture are compatible with the data. Taking one such model into account, we examined through simulation whether random genetic drift alone might explain the variation among gene frequencies across populations and genes. A measure of variation among populations was calculated for each polymorphism, and its distribution for the 100 polymorphisms was compared with that expected for a drift-only hypothesis. At least two-thirds of the polymorphisms appear to be selectively neutral, but there are significant deviations at the two ends of the observed distribution of the measure of variation: a slight excess of polymorphisms with low variation and a greater excess with high variation. This indicates that a few DNA polymorphisms are affected by natural selection, rarely heterotic, and more often disruptive, while most are selectively neutral.

Animals↗
PubMed1991

No linkage between D2 dopamine receptor gene region and schizophrenia.

The dopamine hypothesis is one of the major etiological hypotheses of schizophrenia. The well-established role of genetic factors in schizophrenia together with reports of increased D2 dopamine receptor densities in untreated schizophrenic patients support the D2 dopamine receptor gene as a strong candidate gene for schizophrenia. The recent cloning of the D2 dopamine receptor gene made it possible to test the involvement of the D2 dopamine receptor locus (DRD2) in a large Swedish and a smaller Californian schizophrenia pedigree. Using multipoint linkage analysis between schizophrenia and a genetic map that includes the DRD2 locus and assuming a dominant mode of inheritance, we were able to exclude the DRD2 locus with a lod score of -4.14 for the penetrance of 0.72 and with a lod score of -3.05 for the lower bound penetrance of 0.56. The area of exclusion (lod score, less than -2.00) extended 27 centimorgans. These results provide strong evidence against linkage of the D2 dopamine receptor gene region to schizophrenia in the two pedigrees investigated. We conclude that the genetic predisposition to schizophrenia in these pedigrees is not due to aberrations in the DRD2 locus or the porphobilinogen deaminase locus. Our results do not support the D2 dopamine receptor hypothesis of schizophrenia. However, they cannot exclude the possibility that other genes regulating aspects of D2 dopamine expression might be involved in the etiology of schizophrenia, such as the expression of two D2 dopamine receptor subtypes by alternative RNA splicing.

California↗
PubMed1991

Parallelizing genetic linkage analysis: a case study for applying parallel computation in molecular biology.

Parallel computers offer a solution to improve the lengthy computation time of many conventional, sequential programs used in molecular biology. On a parallel computer, different pieces of the computation are performed simultaneously on different processors. LINKMAP is a sequential program widely used by scientists to perform genetic linkage analysis. We have converted LINKMAP to run on a parallel computer, using the machine-independent parallel programming language, Linda. Using the parallelization of LINKMAP as a case study, the paper outlines an approach to converting existing highly iterative programs to a parallel form. The paper describes the steps involved in converting the sequential program to a parallel program. It presents performance benchmarks comparing the sequential version of LINKMAP with the parallel version running on different parallel machines. The paper also discusses alternative approaches to the problem of "load balancing," making sure the computational load is shared as evenly as possible among the available processors.

Chromosome Mapping↗
PubMed1991

A linkage map spanning the locus for diastrophic dysplasia (DTD).

Diastrophic dysplasia (DTD) is an autosomal recessive osteochondrodysplasia. Patients have short-limbed short stature and suffer from generalized joint dysplasia. We have recently mapped DTD to the distal long arm of chromosome 5. Here we report the localization of DTD in relation to 16 polymorphic markers on distal 5q. No recombinations occurred with two loci, D5S72 and D5S66. One presumptive candidate gene, osteonectin (SPARC), could be excluded on the basis of three recombinations with the DTD locus. Multipoint linkage analysis performed against a fixed order of markers placed DTD between glucocorticoid receptor (GRL) and SPARC favored by the odds of 33:1 over the next best location of DTD between D5S72 and D5S55. The sex-averaged distance between the definite flanking markers, GRL and D5S55, is 17.5 cM. From previously reported data on the physical localization of markers, we conclude that the DTD locus is in 5q31-q34.

Alleles↗
PubMed1991

Progress towards completing the human linkage map.

Genetic linkage maps order polymorphic loci (markers) along a chromosome and provide a measure of distance that is an inherently statistical measure of the frequency of meiotic recombination and has no simple relationship to DNA length in Mb. Few accurate and dense maps now exist. Maps with markers spaced every 2 cM providing accurate estimates of distance should be available in the next few years, however.

Alleles↗
PubMed1991

Studies of three Amerindian populations using nuclear DNA polymorphisms.

Three Amerindian populations, two from Rondônia, Brazil (Karitiana and Rondônia Suruí), and one from Campeche, Mexico (Mayan), were typed for up to 30 nuclear restriction fragment length polymorphisms (RFLPs). Heterozygosities, both observed and expected, were compared with those of Europeans. Average heterozygosity is reduced among these Amerindians (relative to that of Europeans) by 7.0% (Mayan) to 27.1% (Karitiana). This amount of heterozygosity in the nuclear DNA is nevertheless high enough that it is unlikely that there was a severe or prolonged bottleneck.

Alleles↗
PubMed1991

Modeling uncertainty in a database for physical gene mapping data.

We are building a database for the storage, retrieval, and graphical display of physical gene mapping data. To allow this information to be analyzed robustly, such a database must confront the inherent uncertainty of the data as a central design issue. The paper describes the overall database design, the types of gene mapping data which the system will contain, the types of uncertainty in the data, and certain of the design issues involved in allowing the database to handle uncertainty in a comprehensive fashion. Only if a full appreciation of uncertainty is built into the system from its inception will a physical gene mapping database be truly robust and successful.

Chromosome Mapping↗