Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae
The Rosaceae contains many economically valuable crop genera, including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage maps for these species, with a view to marker-assisted selection to assist breeding programs and, recently, in the development of transferable markers to permit syntenic comparisons of maps of different rosaceous genera. In this investigation, a set of Malus cDNA sequences were downloaded from the European Molecular Biology Laboratory database. The sequences were aligned with homologous full-length Arabidopsis genomic DNA sequences to identify putative intron–exon junctions and conserved flank…
Association Between Tumor Egfr and Kras Mutation Status and Clinical Outcomes in Nsclc Patients Randomized to Sorafenib Plus Best Supportive Care (BSC) or Bsc Alone: Subanalysis of the Phase III Mission Trial
ABSTRACT Background Tumor EGFR and KRas mutations are both predictive and prognostic biomarkers in patients with advanced NSCLC. We analyzed the correlation between these biomarkers and treatment outcomes in a phase III trial of 3rd/4th line sorafenib in patients with NSCLC. Methods The global, randomized, placebo-controlled MISSION trial enrolled 703 patients with advanced relapsed/refractory NSCLC of predominantly non-squamous histology. The primary study endpoint was overall survival (OS). EGFR and KRas mutations were analyzed in archival tumor samples and in circulating tumor DNA isolated from plasma. Results Tumor and/or plasma mutation data were available from 347 patients (49%). EGFR…
Progression-free survival as a surrogate for overall survival in advanced/recurrent gastric cancer trials: a meta-analysis.
The traditional endpoint for assessing efficacy of chemotherapies for advanced/recurrent gastric cancer is overall survival (OS), but OS requires prolonged follow-up. We investigated whether progression-free survival (PFS) is a valid surrogate for OS. Using individual patient data from the GASTRIC meta-analysis, surrogacy of PFS was assessed through the correlation between the endpoints and through the correlation between the treatment effects on the endpoints. External validation of the prediction based on PFS was also evaluated. Individual data from 4069 patients in 20 randomized trials were analyzed. The rank correlation coefficient between PFS and OS was 0.853 (95% confidence interval […
A genetic linkage map ofPhysocarpus, a member of the Spiraeoideae (Rosaceae), based on RAPD, AFLP, RGA, SSR and gene specific markers
Physocarpus opulifolius is a deciduous shrub native to North America belonging to the Spiraeoideae subfamily of the Rosaceae. The cultivars 'Luteus' and 'Diabolo' are grown in gardens for their ornamental foliage, golden and purple respectively. We developed a linkage map of P. opulifolius with a view to detecting markers for the leaf colour genes, which are under major gene control. A total of 162 molecular markers (128 RAPDs, 27 AFLPs, three RGA, three STS markers and one SSR) and the leaf colour genes Pur and Aur were scored in the Physocarpus progeny and used to create a linkage map covering 586.1 cM over nine linkage groups. There was an average of 18.2 markers per linkage group and a …
Simple Sequence Repeat Marker Development and Mapping Targeted to Previously Unmapped Regions of the Strawberry Genome Sequence
The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria ×ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physic…
The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing
A number of linkage maps have been previously developed in olive; however, these are mostly composed of markers that have not been characterized at the sequence level, supplemented with smaller numbers of microsatellite markers. In this investigation, we sought to develop a saturated linkage mapping resource for olive composed entirely of sequence characterized markers. We employed genotyping by sequencing to develop a map of a F2 population derived from the selfing of the cultivar Koroneiki. The linkage map contained a total of 23 linkage groups comprised of 1,597 tagged SNP markers in 636 mapping bins spanning a genetic distance of 1189.7 cM. An additional 6,658 segregating SNPs were asso…