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Search Results: 1 - 10 of 189865 matches for " Jean E Abraham "
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Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping
Jean E Abraham, Mel J Maranian, Inmaculada Spiteri, Roslin Russell, Susan Ingle, Craig Luccarini, Helena M Earl, Paul DP Pharoah, Alison M Dunning, Carlos Caldas
BMC Medical Genomics , 2012, DOI: 10.1186/1755-8794-5-19
Abstract: Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek?) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by Gen-Probe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed.Total DNA yields were lower from saliva (mean 24 μg, range 0.2–52 μg) than from blood (mean 210 μg, range 58–577 μg) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA.We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.
Tierras secas, desertificación y recursos hídricos
E.M. Abraham
Ecosistemas , 2008,
Abstract:
CYP2D6 gene variants: association with breast cancer specific survival in a cohort of breast cancer patients from the United Kingdom treated with adjuvant tamoxifen
Jean E Abraham, Mel J Maranian, Kristy E Driver, Radka Platte, Bolot Kalmyrzaev, Caroline Baynes, Craig Luccarini, Mitul Shah, Susan Ingle, David Greenberg, Helena M Earl, Alison M Dunning, Paul DP Pharoah, Carlos Caldas
Breast Cancer Research , 2010, DOI: 10.1186/bcr2629
Abstract: This was a population based case-cohort study. We genotyped known functional variants (n = 7; minor allele frequency (MAF) > 0.01) and single nucleotide polymorphisms (SNPs) (n = 5; MAF > 0.05) tagging all known common variants (tagSNPs), in CYP2D6 in 6640 DNA samples from patients with invasive breast cancer from SEARCH (Studies of Epidemiology and Risk factors in Cancer Heredity); 3155 cases had received tamoxifen therapy. There were 312 deaths from breast cancer, in the tamoxifen treated patients, with over 18000 years of cumulative follow-up. The association between genotype and BCSS was evaluated using Cox proportional hazards regression analysis.In tamoxifen treated patients, there was weak evidence that the poor-metaboliser variant, CYP2D6*6 (MAF = 0.01), was associated with decreased BCSS (P = 0.02; HR = 1.95; 95% CI = 1.12-3.40). No other variants, including CYP2D6*4 (MAF = 0.20), previously reported to be associated with poorer clinical outcomes, were associated with differences in BCSS, in either the tamoxifen or non-tamoxifen groups.CYP2D6*6 may affect BCSS in tamoxifen-treated patients. However, the absence of an association with survival in more frequent variants, including CYP2D6*4, questions the validity of the reported association between CYP2D6 genotype and treatment response in breast cancer. Until larger, prospective studies confirming any associations are available, routine CYP2D6 genetic testing should not be used in the clinical setting.Tamoxifen has been the standard treatment for oestrogen receptor (ER)-positive breast cancer for more than three decades. Indications for its use [1] include: metastatic disease in women (pre- and post-menopausal) and men; adjuvant therapy in pre- and post-menopausal women with breast cancer (lymph node positive and negative); preventative therapy in women at high risk of breast cancer; ductal carcinoma in situ post-resection; and for the prevention of contra-lateral breast cancer. There are proven benefits ass
Fragmentation associated to Levy processes using snake
Romain Abraham,Jean-Francois Delmas
Mathematics , 2005,
Abstract: We consider the height process of a Levy process with no negative jumps, and its associated continuous tree representation. Using Levy snake tools developed by Duquesne and Le Gall, with an underlying Poisson process, we construct a fragmentation process, which in the stable case corresponds to the self-similar fragmentation described by Miermont. For the general fragmentation process we compute a family of dislocation measures as well as the law of the size of a tagged fragment. We also give a special Markov property for the snake which is interesting in itself.
Changing the branching mechanism of a continuous state branching process using immigration
Romain Abraham,Jean-Francois Delmas
Mathematics , 2006, DOI: 10.1214/07-AIHP165
Abstract: We construct a continuous state branching process with immigration (CBI) whose immigration depends on the CBI itself and we recover a continuous state branching process (CB). This provides a dual construction of the pruning at nodes of CB introduced by the authors in a previous paper. This construction is a natural way to model neutral mutation. Using exponential formula, we compute the probability of extinction of the original type population in a critical or sub-critical quadratic branching, conditionally on the non extinction of the total population.
Asymptotics for the small fragments of the fragmentation at nodes
Romain Abraham,Jean-Fran?ois Delmas
Mathematics , 2006, DOI: 10.3150/07-BEJ6045
Abstract: We consider the fragmentation at nodes of the L\'{e}vy continuous random tree introduced in a previous paper. In this framework we compute the asymptotic for the number of small fragments at time $\theta$. This limit is increasing in $\theta$ and discontinuous. In the $\alpha$-stable case the fragmentation is self-similar with index $1/\alpha$, with $\alpha \in (1,2)$ and the results are close to those Bertoin obtained for general self-similar fragmentations but with an additional assumtion which is not fulfilled here.
Record process on the Continuum Random Tree
Romain Abraham,Jean-Fran?ois Delmas
Mathematics , 2011,
Abstract: By considering a continuous pruning procedure on Aldous's Brownian tree, we construct a random variable $\Theta$ which is distributed, conditionally given the tree, according to the probability law introduced by Janson as the limit distribution of the number of cuts needed to isolate the root in a critical Galton-Watson tree. We also prove that this random variable can be obtained as the a.s. limit of the number of cuts needed to cut down the subtree of the continuum tree spanned by $n$ leaves.
$β$-coalescents and stable Galton-Watson trees
Romain Abraham,Jean-Francois Delmas
Mathematics , 2013,
Abstract: Representation of coalescent process using pruning of trees has been used by Goldschmidt and Martin for the Bolthausen-Sznitman coalescent and by Abraham and Delmas for the $\beta(3/2,1/2)$-coalescent. By considering a pruning procedure on stable Galton-Watson tree with $n$ labeled leaves, we give a representation of the discrete $\beta(1+\alpha,1-\alpha)$-coalescent, with $\alpha\in [1/2,1)$ starting from the trivial partition of the $n$ first integers. The construction can also be made directly on the stable continuum L{\'e}vy tree, with parameter $1/\alpha$, simultaneously for all $n$. This representation allows to use results on the asymptotic number of coalescence events to get the asymptotic number of cuts in stable Galton-Watson tree (with infinite variance for the reproduction law) needed to isolate the root. Using convergence of the stable Galton-Watson tree conditioned to have infinitely many leaves, one can get the asymptotic distribution of blocks in the last coalescence event in the $\beta(1+\alpha,1-\alpha)$-coalescent.
Local limits of conditioned Galton-Watson trees I: the infinite spine case
Romain Abraham,Jean-Francois Delmas
Mathematics , 2013, DOI: 10.1214/EJP.v19-2747
Abstract: We give a necessary and sufficient condition for the convergence in distribution of a conditioned Galton-Watson tree to Kesten's tree. This yields elementary proofs of Kesten's result as well as other known results on local limit of conditioned Galton-Watson trees. We then apply this condition to get new results, in the critical and sub-critical cases, on the limit in distribution of a Galton-Watson tree conditioned on having a large number of individuals with out-degree in a given set.
Local limits of conditioned Galton-Watson trees II: the condensation case
Romain Abraham,Jean-Francois Delmas
Mathematics , 2013,
Abstract: We provide a complete picture of the local convergence of critical or subcritical Galton-Watson tree conditioned on having a large number of individuals with out-degree in a given set. The generic case, where the limit is a random tree with an infinite spine has been treated in a previous paper. We focus here on the non-generic case, where the limit is a random tree with a node with infinite out-degree. This case corresponds to the so-called condensation phenomenon.
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