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Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design
Helen I Field, Serena A Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M Dunning, Douglas F Easton, Paul DP Pharoah
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-180
Abstract: We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design.The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P < 1e-5).Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation.Seq4SNPs is available as a service at http://moya.srl.cam.ac.uk/oncology/bio/s4shome.html webcite and http://moya.srl.cam.ac.uk/cgi-bin/oncology/srl/ncbi/seq4snp1.pl webcite, currently for human SNPs, but easily extended to include any species in dbSNP.A survey of single nucleotide polymorphism (SNP) and primer design software reveals several packages that align EST or genome sequences to discover SNPs [1-6]. SNP-VISTA visualizes SNPs from aligned genome sequences [7]. Other packages take a chromosome region then use recorded SNP genotypes, and additional information, to reduce the set of SNPs that need genotyping [[8,9] and references therein]. SNP i
Common ERBB2 polymorphisms and risk of breast cancer in a white British population: a case–control study
Patrick R Benusiglio, Fabienne Lesueur, Craig Luccarini, Donald M Conroy, Mitul Shah, Douglas F Easton, Nick E Day, Alison M Dunning, Paul D Pharoah, Bruce AJ Ponder
Breast Cancer Research , 2005, DOI: 10.1186/bcr982
Abstract: We aimed to determine if common polymorphisms (frequency ≥ 5%) in ERBB2 were associated with breast cancer risk in a white British population. Five single-nucleotide polymorphisms (SNPs) were selected for study: SNP 1 near the promoter, SNP 2 in intron 1, SNP 3 in intron 4, SNP 4 in exon 17 (I655V), and SNP 5 in exon 27 (A1170P). We tested their association with breast cancer in a large case–control study (n = 2192 cases and 2257 controls).There were no differences in genotype frequencies between cases and controls for any of the SNPs examined. To investigate the possibility that a common polymorphism not included in our study might be involved in breast cancer predisposition, we also constructed multilocus haplotypes. Our set of SNPs generated all existing (n = 6) common haplotypes and no differences were seen in haplotype frequencies between cases and controls (P = 0.44).In our population, common ERBB2 polymorphisms are not involved in predisposition to breast cancer.Breast cancer is the most common cause of cancer in women in the United Kingdom and is, after lung cancer, the most common cause of cancer death (Office for National Statistics). Positive family history is a well-established risk factor for the disease: the risk to first-degree relatives of a breast cancer case is about twice the population risk [1]. Most of the excess familial risk associated with breast cancer is likely to be genetic in origin [2,3]. However, only about a third of this risk is accounted for by known genes, the most important being BRCA1 and BRCA2, while the remainder might be explained by a combination of weakly predisposing alleles [2-4]. A gene thought to be involved in low-level susceptibility to breast cancer is ERBB2 (HER2). This gene is located on chromosome 17q12–q21, spans 38 kilobases, and comprises 27 coding exons. It is a member of the ERBB family, a family of protein tyrosine kinases involved in cell division, migration, adhesion, differentiation, and apoptosis and consi
Common variation in EMSY and risk of breast and ovarian cancer: a case-control study using HapMap tagging SNPs
Patrick R Benusiglio, Fabienne Lesueur, Craig Luccarini, Joan McIntosh, Robert N Luben, Paula Smith, Alison Dunning, Douglas F Easton, Bruce AJ Ponder, Paul D Pharoah
BMC Cancer , 2005, DOI: 10.1186/1471-2407-5-81
Abstract: We used a genetic association study design to determine if common genetic variation (frequency ≥ 5%) in EMSY was associated with breast or ovarian cancer risk in the British population. Haplotype tagging single-nucleotide polymorphisms (htSNPs) were selected from the HapMap database and genotyped using Taqman? in two large study sets of white British women (n [breast set] = 2343 cases and 2284 controls, n [ovarian set] = 864 cases and 864 controls). HapMap data might be insufficient to tag genetic variation in EMSY comprehensively. We therefore screened the gene promoter and coding sequences with denaturing high performance liquid chromatography in order to identify additional SNPs that are most likely to be functional.HapMap data on 22 SNPs show that 4 htSNPs tag 4 common haplotypes: rs2282611 (5'up t>g), rs4245443 (IVS7 g>a), rs2513511 (IVS16 a>g), rs2155220 (3'down c>t). We observed no association between any of the genotypes or associated haplotypes and breast or ovarian cancer risk. Seventeen out of the 18 remaining HapMap polymorphisms (94%) were well tagged by the 4 selected htSNPs (r2s > 0.8). Genotype frequencies for two further SNPs identified by screening and located near exon-intron boundaries, rs2508740 (IVS9 a>g) and rs11600501 (IVS10 c>t), were also similar in cases and controls. In order to simulate unidentified SNPs, we performed the leave-one-out cross-validation procedure on the HapMap data; over 95% of the common genetic variation was well represented by tagging polymorphisms. We are therefore likely to have tagged any common, functional variants present in our population.We found no association between common genetic variation in EMSY and risk of breast or ovarian cancer in two large study sets of white British women.Breast and ovarian cancer are two of the most common causes of cancer in women in the United Kingdom (Office for National Statistics). Together, they account for about a third of all new cancer cases and a quarter of cancer deaths.
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.
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
Review of Scott Thumma & Edward R. Gray (Eds.), Gay Religion
Craig This
Journal of Men, Masculinities and Spirituality , 2007,
Abstract: Review of Scott Thumma & Edward R. Gray (Eds.), Gay Religion (Walnut Creek, CA: AltaMira Press, 2004), xvi + 376 pp.
Model-Based Forecasts of North American Forest Growth: A Review  [PDF]
Craig Loehle
American Journal of Climate Change (AJCC) , 2018, DOI: 10.4236/ajcc.2018.74032
Abstract: In the context of climate change, planning for forest management goals becomes more complicated. Possible changes in precipitation, temperature, and CO2 can affect tree growth substantially and potential effects differ by species and region. However, integration of potential forest growth responses to these factors can be achieved using models. Because of the need to understand the range of forest growth forecasts and the strengths and limitations of different modeling approaches, I summarized results from 25 studies of forecasted forest responses over coming decades. Some models used statistical relationships between tree rings and climate to forecast growth responses to future climate, some simulated net photosynthesis of a standard forest canopy, and many used tree or stand growth models at various levels of mechanistic detail. In general, models that included CO2 responses predicted enhanced forest growth by 2100 across most of the commercial timberland areas of the US and Canada. For modest warming, most models showed growth enhancement in most regions. For hotter scenarios, many models and regions showed even more growth enhancement, but some regions such as the Southwest, mountain West, and southwestern Canada were predicted to experience drought stress and increased fire incidence, although projections in these regions were variable. Young stands, angiosperms, and early-successional species were predicted to exhibit the most positive responses. As a result, commercial harvest ages might be accelerated by several years, depending on species. Some simulations for the Midwest and Northeast US predicted a doubling or more of net primary productivity although other studies show a lesser response. Model runs that did not include mechanisms of CO2 fertilization showed positive growth responses in only limited cases and generally showed growth declines. There also was some evidence indicating the potential spread of forest into woodland at shrub or prairie ecotones.
Studio pluriennale della segregazione sessuale nel Daino in ambiente mediterraneo
Simone Ciuti,Sara Davini,Siriano Luccarini,Marco Apollonio
Hystrix : the Italian Journal of Mammalogy , 2003, DOI: 10.4404/hystrix-14.0-4288
Abstract: Questa ricerca, condotta per 4 anni nella Tenuta di San Rossore (Pisa), ha analizzato il grado di segregazione sessuale tra 23 femmine e 25 maschi di daino (Dama dama) muniti di radiocollare, localizzati attraverso la tecnica della telemetria. Tre sono le ipotesi tradizionalmente supportate nell?interpretazione della segregazione sessuale: 1) ?the predation risk?, 2) ?the forage-selection? e 3) ?the activity budget?. La prima di queste è risultata una valida spiegazione della segregazione sessuale su larga scala, quando è stato comparato l?uso (espresso come percentuale di fix) da parte dei due sessi di aree caratterizzate dal disturbo antropico, presente solo di giorno, con quello di aree non interessate dalla presenza dell?uomo. Nei maschi è stato rilevato un uso maggiore delle aree disturbate, sia di giorno (73±8%) sia di notte (78±18%), eccezion fatta per la stagione autunnale (di giorno 29±22%, di notte 41±23%), quando i maschi raggiungono aree più remote con lo scopo di riprodursi (Wilcoxon, autunno contro estate, inverno e primavera, p≤0,018 di giorno, p≤0,021 di notte). Le distanze tra i centri di attività degli home range maschili ed il punto di massimo disturbo (l?ingresso principale della Tenuta) sono risultate nettamente minori di quelle rilevate nelle femmine (Mann-Whitney p≤0,01) ma, ovviamente, non in autunno (Mann-Whitney p>0,05). Durante il giorno l?uso da parte delle femmine di aree disturbate è risultato minimo durante tutte le stagioni (8±5%). Esse hanno frequentato tali aree solo di notte (35±13%, Wilcoxon giorno contro notte p≤0,028), eccezion fatta per il periodo estivo (3±1%, Wilcoxon giorno contro notte p>0,05) quando la presenza dei nuovi nati ne condiziona gli spostamenti limitandoli all?area più sicura. Mentre le altre due ipotesi considerate non sembrano essere valide spiegazioni della segregazione tra sessi su larga scala, non predicendo differenze nell?uso dello spazio tra il giorno e la notte, esse possono essere rimesse in gioco nell?analisi della partizione su piccola scala. Infatti, considerando ulteriori suddivisioni delle aree soggette a disturbo, i due sessi sono segregati anche di notte, pur frequentando lo stesso settore della Tenuta. Poiché di notte il disturbo antropico è assente, infatti, una segregazione su piccola scala non era attesa. Questo dimostra che, una volta scomparso il fattore determinante della segregazione diurna, possono entrare in gioco ulteriori fattori, come la differente velocità di foraggiamento dei due sessi (prevista dalla terza ipotesi), che porta i gruppi maschili e femminili a non riman
Spatial expression of DNA topoisomerase I genes during cell proliferation in Daucus carota
A Balestrazzi,G Bernacchia,L Pitto,G Luccarini
European Journal of Histochemistry , 2009, DOI: 10.4081/1611
Abstract: The spatial expression of carrot (Daucus carota L.) top1 genes encoding the two isoforms of the enzyme DNA topoisomerase I (EC was investigated. In situ hybridization analysis performed with a probe recognizing both top1 transcripts provided evidence that in explanted hypocotyls induced to proliferate in vitro by the addition of the growth regulator 2,4-dichlorophenoxyacetic acid (2,4-D), the mRNA accumulation parallels the proliferation of provascular cells of the stelar cylinder. During somatic embryogenesis, the histological distribution of top1 transcripts was strongly evident at the stage of torpedo-shaped embryos, but gene expression was not only restricted to meristematic regions. When the spatial localization was extended to carrot vegetative apices and the investigation was carried out with specific probes for top1a and top1b, both transcripts preferentially accumulated in tissues having mitotic activity.
Delayed intra-tumoural haemorrhage in pineal germinoma: Case report and review  [PDF]
Michael Colditz, Craig Winter
World Journal of Neuroscience (WJNS) , 2013, DOI: 10.4236/wjns.2013.33023

Intraparenchymal haemorrhage in a pineal germinoma is a very rare, though clinically significant event. We report the first case of a significantly delayed intraparenchymal haemorrhage in a pineal germinoma, 14 days after endoscopic third ventriculostomy (ETV), causing precipitous patient deterioration. We discuss potential contributing pathophysiological factors, and seek to illustrate that knowledge of its occurrence, and associated morbidity, is clinically significant in managing pineal germinoma patients with acute deterioration post obstructive hydrocephalus CSF diversion.

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