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Oestrogen receptor (ER)-positive breast cancer (BC) is generally well responsive to endocrine therapy. Neoadjuvant endocrine therapy (NAET) is increasingly being used for downstaging ER-positive tumours. This study aims to analyse the effect of NAET on a well-characterised cohort of ER-positive BC with particular emphasis on receptor expression. This is a retrospective United Kingdom (UK) multicentre study of 391 patients who received NAET between October 2012 and October 2020. Detailed analyses of the paired pre- and post-NAET morphological changes and hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) expression were performed. The median duration of NAET was 86 days, with median survival and overall survival rates of 380 days and 93.4%, respectively. A total of 90.3% of cases achieved a pathological partial response, with a significantly higher rate of response in the HER2-low cancers. Following NAET, BC displayed some pathological changes involving the tumour stroma including central scarring and an increase in tumour infiltrating lymphocytes (TILs) and tumour cell morphology. Significant changes associated with the duration of NAET were observed in tumour grade (30.6% of cases), with downgrading identified in 19.3% of tumours ( p < 0.001). The conversion of ER status from positive to low or negative was insignificant. The conversion of progesterone receptor (PR) and HER2 status to negative status was observed in 31.3% and 38.1% of cases, respectively ( p < 0.001). HER2-low breast cancer decreased from 63% to 37% following NAET in the paired samples. Significant morphological and biomarker changes involving PR and HER2 expression occurred following NAET. The findings support biomarker testing on pre-treatment core biopsies and post-treatment residual carcinoma.

Introduction: Inflammatory breast cancer (IBC) is an aggressive form of breast cancer with a poorly characterized immune microenvironment., Methods: We used a five-colour multiplex immunofluorescence panel, including CD68, CD4, CD8, CD20, and FOXP3 for immune microenvironment profiling in 93 treatment-naïve IBC samples., Results: Lower grade tumours were characterized by decreased CD4+ cells but increased accumulation of FOXP3+ cells. Increased CD20+ cells correlated with better response to neoadjuvant chemotherapy and increased CD4+ cells infiltration correlated with better overall survival. Pairwise analysis revealed that both ER+ and triple-negative breast cancer were characterized by co-infiltration of CD20 + cells with CD68+ and CD4+ cells, whereas co-infiltration of CD8+ and CD68+ cells was only observed in HER2+ IBC. Co-infiltration of CD20+, CD8+, CD4+, and FOXP3+ cells, and co-existence of CD68+ with FOXP3+ cells correlated with better therapeutic responses, while resistant tumours were characterized by co-accumulation of CD4+, CD8+, FOXP3+, and CD68+ cells and co-expression of CD68+ and CD20+ cells. In a Cox regression model, response to therapy was the most significant factor associated with improved patient survival., Conclusion: Those results reveal a complex unique pattern of distribution of immune cell subtypes in IBC and provide an important basis for detailed characterization of molecular pathways that govern the formation of IBC immune landscape and potential for immunotherapy., (© 2022 S. Karger AG, Basel.)

Aims: Neoadjuvant endocrine therapy (NAET) is used in the management of oestrogen receptor (ER)-positive breast cancer. The optimal method for histological assessment of response and the effect of NAET on the tumour morphology, grade and molecular profile remain unclear. The aim of this study is to investigate the NAET effect on tumour type, grade and molecular profile by analysing a well-characterised cohort of breast cancer samples in a single large UK tertiary referral centre, and to provide guidance on the pathological assessment of those lesions to inform adjuvant management and prognosis., Methods and Results: A single large-institution cohort of 132 patients who received NAET over a 13-year period was identified. Comprehensive clinical, histopathological and follow-up data were collected. A detailed histological review of a subset with residual post-treatment carcinoma was undertaken. Two carcinomas (both of the lobular type) achieved complete pathological response. Central scarring was seen in 49.3% of tumours post-treatment. Significant changes in tumour type (41.6%), tumour grade (downgrading in one-third of tumours), and progesterone receptor (PR) expression (22.3%), with a switch to PR-negative status in 17.6% of cases, were observed. The last of these was associated with an absence of tumour-infiltrating lymphocytes (P = 0.005). Ten per cent of cases showed a change in HER2 expression (P = 0.002). The median patient survival was 60 months, and downgrading of tumours was associated with better overall survival (P = 0.05)., Conclusions: We propose a histological method for assessment of residual carcinoma following NAET, and recommend repeat ER/PR/HER2 testing to inform management and prognosis., (© 2021 The Authors. Histopathology published by John Wiley & Sons Ltd.)

Background: The optimal sequence of adjuvant chemotherapy and radiotherapy for breast cancer is unknown. SECRAB assesses whether local control can be improved without increased toxicity., Methods: SECRAB was a prospective, open-label, multi-centre, phase III trial comparing synchronous to sequential chemo-radiotherapy, conducted in 48 UK centres. Patients with invasive, early stage breast cancer were eligible. Randomisation (performed using random permuted block assignment) was stratified by centre, axillary surgery, chemotherapy, and radiotherapy boost. Permitted chemotherapy regimens included CMF and anthracycline-CMF. Synchronous radiotherapy was administered between cycles two and three for CMF or five and six for anthracycline-CMF. Sequential radiotherapy was delivered on chemotherapy completion. Radiotherapy schedules included 40 Gy/15F over three weeks, and 50 Gy/25F over five weeks. The primary outcome was local recurrence at five and ten years, defined as time to local recurrence, and analysed by intention to treat. ClinicalTrials.gov NCT00003893., Findings: Between 02-July-1998 and 25-March-2004, 2297 patients were recruited (1150 synchronous and 1146 sequential). Baseline characteristics were balanced. With 10.2 years median follow-up, the ten-year local recurrence rates were 4.6% and 7.1% in the synchronous and sequential arms respectively (hazard ratio (HR) 0.62; 95% confidence interval (CI): 0.43-0.90; p = 0.012). In a planned sub-group analysis of anthracycline-CMF, the ten-year local recurrence rates difference were 3.5% versus 6.7% respectively (HR 0.48 95% CI: 0.26-0.88; p = 0.018). There was no significant difference in overall or disease-free survival. 24% of patients on the synchronous arm suffered moderate/severe acute skin reactions compared to 15% on the sequential arm (p < 0.0001). There were no significant differences in late adverse effects apart from telangiectasia (p = 0.03)., Interpretation: Synchronous chemo-radiotherapy significantly improved local recurrence rates. This was delivered with an acceptable increase in acute toxicity. The greatest benefit of synchronous chemo-radiation was in patients treated with anthracycline-CMF., Funding: Cancer Research UK (CR UK/98/001) and Pharmacia., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

Background : Sarcomas are rare and heterogeneous tumours with a large proportion of patients requiring palliative intervention. They are regarded as relatively radioresistant and therefore achieving good palliation with radiation may require larger doses than for more common solid tumour types. Limited data is available regarding appropriate palliative radiotherapy dose fractionation. This case series aims to assess the effectiveness of radiotherapy in providing symptomatic improvement for advanced sarcomas. Method : Data was retrospectively collected for patients treated with palliative radiotherapy between July 2010 and April 2019 at one institution. The primary outcome was documented symptomatic improvement following radiotherapy. Secondary outcome was overall survival. Results : One hundred and five patients had a total of 137 sites treated using 25 different dose fractionation schedules. The median patient age was 54 (range 8-90) years. Treated sites included 114 soft tissue and 23 bone sarcomas. Data on symptomatic improvement was available in 56% and 67% of cases respectively. A total of 70% of soft tissue and 55% of bone sarcoma patients reported symptomatic improvement. Symptomatic response rates appeared to increase to a biological effective dose (BED) of 50Grey 4 (Gy 4 ) (alpha beta ratio (α/β) = 4 for tumour) but did not continue to improve with further rises in dose beyond this. C onclusion : Palliative radiotherapy offers symptomatic improvement for sarcoma patients with two-thirds of patients reporting reduction in symptoms. These results are limited by the heterogeneous study population including different sarcoma subtypes each with a probable different radio-sensitivity, treated with different radiotherapy schedules. Further prospective data collection is needed considering sarcoma subtype radio-sensitivity, to determine appropriate palliative dose fractionation schedules., Competing Interests: The authors declare no conflict of interest.

Our paper analyzes full plastid DNA sequence data of 202 wild and cultivated diploid potatoes, Solanum section Petota, to explore its phylogenetic utility compared to prior analyses of the same accessions using genome-wide nuclear SNPs, and plastid DNA restriction site data. The present plastid analysis discovered the same major clades as the nuclear data but with some substantial differences in topology within the clades. The considerably larger plastid and nuclear data sets add phylogenetic resolution within the prior plastid DNA restriction site data, highlight plastid/nuclear incongruence that supports hypotheses of hybridization/introgression to help explain the taxonomic difficulty in the section.

Background: Two national clinical trial groups, United Kingdom Children's Cancer and Leukaemia Group (CCLG) and the German Paediatric Oncology and Haematology Group (GPOH) together undertook a randomised trial, EICESS-92, which addressed chemotherapy options for Ewing's sarcoma. We sought the causes of unexpected survival differences between the study groups., Methods: 647 patients were randomised. Cox regression analyses were used to compare event-free survival (EFS) and overall survival (OS) between the two study groups., Results: 5-year EFS rates were 43% (95% CI 36-50%) and 57% (95% CI 52-62) in the CCLG and GPOH patients, respectively; corresponding 5-year OS rates were 52% (95% CI 45-59%) and 66% (95% CI 61-71). CCLG patients were less likely to have both surgery and radiotherapy (18 vs. 59%), and more likely to have a single local therapy modality compared to the GPOH patients (72 vs. 35%). Forty-five percent of GPOH patients had pre-operative radiotherapy compared to 3% of CCLG patients. In the CCLG group local recurrence (either with or without metastases) was the first event in 22% of patients compared with 7% in the GPOH group. After allowing for the effects of age, metastases, primary site, histology and local treatment modality, the risk of an EFS event was 44% greater in the CCLG cohort (95% CI 10-89%, p = 0.009), and the risk of dying was 30% greater, but not statistically significant (95% CI 3-74%, p = 0.08)., Conclusions: Unexpected differences in EFS and OS occurred between two patient cohorts recruited within an international randomised trial. Failure to select or deliver appropriate local treatment modalities for Ewing's sarcoma may compromise chances of cure. Trial registration Supported by Deutsche Krebshilfe (Grants No. DKH M43/92/Jü2 and DKH 70-2551 Jü3), and European Union Biomedicine and Health Programme (Grants No. BMH1-CT92-1341 and BMH4-983956), and Cancer Research United Kingdom. Clinical trial information can be found for the following: NCT0000251.

Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota. We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota, including 146 wild and 21 cultivated diploid potato accessions with a broad geographic distribution. Genome-wide genetic variation analysis showed that the diversity of wild potatoes is higher than that of cultivated potatoes, and much higher genetic diversity in the agronomically important disease resistance genes was observed in wild potatoes. Furthermore, by exploiting information about known quantitative trait loci (QTL), we identified 609 genes under selection, including those correlated with the loss of bitterness in tubers and those involved in tuberization, two major domesticated traits of potato. Phylogenetic analyses revealed a north-south division of all species in clade 4, not just those in the S. brevicaule complex, and further supported S. candolleanum as the progenitor of cultivated potato and the monophyletic origin of cultivated potato in southern Peru. In addition, we analyzed the genome of S. candolleanum and identified 529 genes lost in cultivated potato. Collectively, the molecular markers generated in this study provide a valuable resource for the identification of agronomically important genes useful for potato breeding., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

Premise of the Study: The species boundaries of wild and cultivated potatoes are controversial, with most of the taxonomic problems in the cultivated potato clade. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these problems., Methods: We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony-informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness-of-fit tests., Key Results: There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The results highlight a clade of species in South America not shown before, 'neocardenasii', sister to clade 1+2, that possesses key morphological traits typical of diploids in Mexico and Central America. Goodness-of-fit tests suggest potential hybridization between some species of the cultivated potato clade. However, we do not have enough phylogenetic signal with the data at hand to explicitly estimate such hybridization events with species networks methods., Conclusions: We document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support the recent reduction of species in this clade. The discovery of the neocardenasii clade forces a reevaluation of a hypothesis that section Petota originated in Mexico and Central America., (© 2018 Botanical Society of America.)

DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP) in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16-23) from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56) of the same 14 taxa. Intra-accession diversities were compared to those of a synthetic 'taxon-wide' population comprising a single individual from a variable number of available accessions of each sampled taxon. Results confirm the expected considerably lower levels of polymorphism within accessions of self-compatible as compared to self-incompatible taxa. We observed broadly similar levels of 'taxon-wide' polymorphism among self-compatible and self-incompatible species, with self-compatible taxa showing only slightly lower rates of polymorphism. The most diverse accessions were the two cultivated potato accessions examined, the least diverse being the Mexican allohexaploids Solanum demissum and S. iopetalum . Generally allopolyploid self-compatible accessions exhibited lower levels of diversity. Some purported self-incompatible accessions showed relatively low levels of marker diversity, similar to the more diverse self-compatible material surveyed. Our data indicate that for self-compatible species a single plant is highly representative of a genebank accession. The situation for self-incompatible taxa is less clear, and sampling strategies used will depend on the type of investigation. These results have important implications for those seeking novel trait variation (e.g., disease resistance) in gene banks as well as for the selection of individuals for genomics studies. We also show that AFLPs, despite having been largely replaced by other marker types, is highly suitable for the evaluation of within and between accession diversity in genebanks.

Premise of the Study: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences., Methods: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid ( Dc MP)., Key Results: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus . Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named Dc MP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations., Conclusions: Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus , (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid., (© 2017 Spooner et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons public domain license (CC0 1.0).)

Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex., Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic., Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.

We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR&#95;032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR&#95;032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.

The natural history of epiphytic plant species has been extensively studied. However, little is known about the physiology and genetics of epiphytism. This is due to difficulties associated with growing epiphytic plants and the lack of tools for genomics studies and genetic manipulations. In this study, tubers were generated from 223 accessions of 42 wild potato Solanum species, including the epiphytic species S. morelliforme and its sister species S. clarum. Lyophilized samples were analyzed for 12 minerals using inductively coupled plasma optical emission spectrometry. Mineral levels in tubers of S. morelliforme and S. clarum were among the highest for 10 out of the 12 elements evaluated. These two wild potato relatives are native to southern Mexico and Central America and live as epiphytes or in epiphytic-like conditions. We propose the use of S. morelliforme and S. clarum as model organisms for the study of mineral uptake efficiency. They have a short life cycle, can be propagated vegetatively via tubers or cuttings, and can be easily grown in controlled environments. In addition, genome sequence data are available for potato. Transgenic manipulations and somatic fusions will allow the movement of genes from these epiphytes to cultivated potato.

Crop wild relatives have a long history of use in potato breeding, particularly for pest and disease resistance, and are expected to be increasingly used in the search for tolerance to biotic and abiotic stresses. Their current and future use in crop improvement depends on their availability in ex situ germplasm collections. As these plants are impacted in the wild by habitat destruction and climate change, actions to ensure their conservation ex situ become ever more urgent. We analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota) with the aim of establishing priorities for further collecting to fill important gaps in germplasm collections. A total of 32 species (43.8%), were assigned high priority for further collecting due to severe gaps in their ex situ collections. Such gaps are most pronounced in the geographic center of diversity of the wild relatives in Peru. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, with only three species determined to be sufficiently represented currently. Priorities for further collecting include: (i) species completely lacking representation in germplasm collections; (ii) other high priority taxa, with geographic emphasis on the center of species diversity; (iii) medium priority species. Such collecting efforts combined with further emphasis on improving ex situ conservation technologies and methods, performing genotypic and phenotypic characterization of wild relative diversity, monitoring wild populations in situ, and making conserved wild relatives and their associated data accessible to the global research community, represent key steps in ensuring the long-term availability of the wild genetic resources of this important crop.

Premise of Study: Molecular phylogenetics of genome-scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. A companion phylogenomics analysis of Daucus using 94 conserved nuclear orthologs supported many of the traditional species but showed unexpected results that require morphological analyses to help interpret them in a practical taxonomic context., Methods: We evaluated character state distributions, stepwise discriminant analyses, canonical variate analyses, and hierarchical cluster analyses from 40 morphological characters from 81 accessions of 14 taxa of Daucus and eight species in related genera in an experimental plot., Key Results: Most characters showed tremendous variation with character state overlap across many taxa. Multivariate analyses separated the outgroup taxa easily from the Daucus ingroup. Concordant with molecular analyses, most species form phenetic groups, except the same taxa that are problematical in the molecular results: (1) the subspecies of D. carota, (2) D. sahariensis and D. syrticus, and (3) D. broteri and D. guttatus., Conclusions: Phenetic analyses, in combination with molecular data, support many Daucus species, but mostly by overlapping ranges of size and meristic variation. The subspecies of D. carota are poorly separated morphologically, are paraphyletic, and all could be recognized at the subspecies rank under D. carota. Daucus sahariensis and D. syrticus are so similar morphologically that they could be placed in synonymy. Combined molecular and morphological data support three species in accessions previously identified as D. broteri and D. guttatus. Molecular and morphological results support the new combination Daucus carota subsp. capillifolius., (© 2014 Botanical Society of America, Inc.)

Unlabelled: •, Premise of the Study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species.•, Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach.•, Key Results: Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of many different species as monophyletic with strong support, but failed to support other species. The single allele analysis gave slightly better topological resolution; trimming homopolymers failed to increase taxonomic resolution; the exonic data had a smaller proportion of parsimony-informative characters. Similar results demonstrating the same dominant topology can be obtained with many fewer markers. A Bayesian concordance analysis provided an overall similar phylogeny, but the coalescent analysis provided drastic changes in topology to all the above.•, Conclusions: Our research highlights some difficult species groups in Daucus and misidentifications in germplasm collections. It highlights a useful subset of markers and approaches for future studies of dominant topologies in Daucus., (© 2014 Botanical Society of America, Inc.)

Background: Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species., Results: We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs., Conclusions: The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies.

Premise of the Study: Taxonomists manage large amounts of specimen data. This is usually initiated in spreadsheets and then converted for publication into locality lists and indices to associate collectors and collector numbers from herbarium sheets to identifications (exsiccatae). This conversion process is mostly done by hand and is time-consuming, cumbersome, and error-prone. •, Methods and Results: We constructed a tool, 'exsic,' based on the statistical software R. The exsic function is part of the R package 'exsic' and produces specimen citations and exsiccatae conforming to four related formats. •, Conclusions: The tool increases speed, efficiency, and accuracy to convert raw spreadsheet tables to publication-ready content.

Premise of the Study: Analyses of genetic structure and phylogenetic relationships illuminate the origin and domestication of modern crops. Despite being an important worldwide vegetable, the genetic structure and domestication of carrot (Daucus carota) is poorly understood. We provide the first such study using a large data set of molecular markers and accessions that are widely dispersed around the world. •, Methods: Sequencing data from the carrot transcriptome were used to develop 4000 single nucleotide polymorphisms (SNPs). Eighty-four genotypes, including a geographically well-distributed subset of wild and cultivated carrots, were genotyped using the KASPar assay. •, Key Results: Analysis of allelic diversity of SNP data revealed no reduction of genetic diversity in cultivated vs. wild accessions. Structure and phylogenetic analysis indicated a clear separation between wild and cultivated accessions as well as between eastern and western cultivated carrot. Among the wild carrots, those from Central Asia were genetically most similar to cultivated accessions. Furthermore, we found that wild carrots from North America were most closely related to European wild accessions. •, Conclusions: Comparing the genetic diversity of wild and cultivated accessions suggested the absence of a genetic bottleneck during carrot domestication. In conjunction with historical documents, our results suggest an origin of domesticated carrot in Central Asia. Wild carrots from North America were likely introduced as weeds with European colonization. These results provide answers to long-debated questions of carrot evolution and domestication and inform germplasm curators and breeders on genetic substructure of carrot genetic resources.

Peripheral neuropathy is a well-recognised side effect of the cholesterol-lowering statins. Red yeast rice (RYR) is a traditional Chinese herb, widely available over-the-counter that has also been found to reduce cholesterol. Little data is available regarding its side effect profile. We report a case of a 60-year-old male receiving therapeutic imatinib for metastatic gastrointestinal tumour (GIST), who developed peripheral neuropathy while also taking RYR. The symptoms completely settled following withdrawal of the RYR and he has subsequently continued to take imatinib for over 2 years with no adverse effects. Further research into the safety profile of RYR is needed. The importance of questioning patients about over the counter medications and herbal remedies cannot be overemphasised.

Transfer of DNA between different compartments of the plant cell, i.e., plastid, mitochondrion and nucleus, is a well-known phenomenon in plant evolution. Six directions of inter-compartmental DNA migration are possible in theory, however only four of them have been previously reported. These include frequent cases of mitochondrion and plastid to nucleus transfer, plastid to mitochondrion transfer, and rare nucleus to mitochondrion migrations. The connection between the plastid and mitochondrial genomes in flowering plants has been viewed as a one way road. Contrary to these observations we found that a sequence widespread in the carrot mitochondrial genome, designated as Dc MP, was transferred to the plastid genome of a carrot ancestor. Interestingly, Dc MP was integrated into a tRNA promoter of the plastid trnV gene, replacing the original promoter sequence. The rearrangement of the plastid genome is specific for carrot and closely related species belonging Scandiceae clade. The structure of the sequence and the presence of a 6 nt target site duplication led us to speculate that the transfer was a result of a transposition event of a non-LTR retrotransposon. These findings open interesting questions about the evolution of organellar genomes and mobile genetic elements and provide a useful plastid marker to phylogenetically delineate species relationships within the Scandiceae clade.

Epithelioid haemangioendothelioma (EHE), first described in 1982, is an uncommon malignancy comprising of around 1% of all vascular tumors and accurate diagnosis relies on specialist review of histology. Cervical spinal primaries are very rare and standard treatment for localised disease is surgery. Data regarding management of localized but unresectable tumors are limited. We undertook a literature review in order to highlight its clinico-pathological features and we describe a first case of an unresectable cervical EHE, successfully treated with radical radiotherapy.

Purpose: MMT95 was the fourth of a series of International Society of Pediatric Oncology (SIOP) collaborations for children with high-risk nonmetastatic soft tissue sarcoma (STS). The principal objective was to explore survival advantage for an intensified chemotherapy strategy in a randomized trial., Patients and Methods: From July 1995 to June 2003, 457 previously untreated patients with incompletely resected embryonal rhabdomyosarcoma (RMS), undifferentiated sarcoma, and soft tissue primitive neuroectodermal tumor at all sites except paratesticular, vagina, and uterus, or with alveolar RMS were randomly assigned to receive either ifosfamide, vincristine, and dactinomycin (IVA) or a six-drug combination (IVA plus carboplatin, epirubicin, and etoposide) both delivered over 27 weeks. Cumulative doses were as follows: ifosfamide 54 g/m(2) (both arms), epirubicin 450 mg/m(2), etoposide 1,350 mg/m(2) (six-drug regimen). Poor responders after three courses of IVA were to be switched to the other arm. Delivery of radiotherapy was determined according to site and/or response to chemotherapy with or without surgery., Results: Overall survival (OS) for all patients was 81% (95% CI, 77% to 84%) at 3 years. No significant difference in outcome in either OS or event-free survival was noted between the two arms (3-year OS: 82% [95% CI, 76% to 86%] for IVA and 80% [95% CI, 74% to 85%] for the six-drug arm). Toxicity was significantly greater (infection, myelosuppression, and mucositis) in the six-drug arm. Overall burden of local therapy was consistent with data from previous SIOP studies and showed no difference between the two chemotherapy regimens., Conclusion: Intensification of chemotherapy for nonmetastatic RMS and other chemotherapy-sensitive STS provides no survival advantage or reduction in the intensity of local therapy and adds toxicity.

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2n = 2x = 24) to hexaploids (2n = 6x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes's series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAA(a)A(a) genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa.

Background: Recent genomic studies have drastically altered our knowledge of polyploid evolution. Wild potatoes (Solanum section Petota) are a highly diverse and economically important group of about 100 species widely distributed throughout the Americas. Thirty-six percent of the species in section Petota are polyploid or with diploid and polyploid cytotypes. However, the group is poorly understood at the genomic level and the series is ideal to study polyploid evolution. Two separate studies using the nuclear orthologs GBSSI and nitrate reductase confirmed prior hypotheses of polyploid origins in potato and have shown new origins not proposed before. These studies have been limited, however, by the use of few accessions per polyploid species and by low taxonomic resolution, providing clade-specific, but not species-specific origins within clades. The purpose of the present study is to use six nuclear orthologs, within 54 accessions of 11 polyploid species, 34 accessions of 29 diploid species of section Petota representing their putative progenitors, and two outgroups, to see if phenomena typical of other polyploid groups occur within wild potatoes, to include multiple origins, loss of alleles, or gain of new alleles., Results: Our results increase resolution within clades, giving better ideas of diploid progenitors, and show unexpected complexity of allele sharing within clades. While some species have little diversity among accessions and concur with the GBSSI and nitrate reductase results, such as S. agrimonifolium, S. colombianum, S. hjertingii, and S. moscopanum, the results give much better resolution of species-specific progenitors. Seven other species, however, show variant patterns of allele distributions suggesting multiple origins and allele loss. Complex three-genome origins are supported for S. hougasii, and S. schenckii, and one of the ten accessions of S. stoloniferum. A very unexpected shared presence of alleles occurs within one clade of S. verrucosum from Central America, and S. berthaultii from South America in six polyploid species S. demissum, S. hjertingii, S. hougasii, S. iopetalum, S. schenckii, and S. stoloniferum., Conclusions: Our results document considerable genomic complexity of some wild potato polyploids. These can be explained by multiple hybrid origins and allele losses that provide a clear biological explanation for the taxonomic complexity in wild potato polyploids. These results are of theoretical and practical benefit to potato breeders, and add to a growing body of evidence showing considerable complexity in polyploid plants in general.

Background: Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA., Results: Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome., Conclusions: This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select "model organisms", is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.

Background: The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility., Results: DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N., Conclusions: Our study represents the first phylogenetic analyses based on LCNGs in Pyrus. Ancient and recent duplications lead to a complex structure of Adh outparalogs and inparalogs in Pyrus and Malus, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, LFY2int2-N is the best nuclear marker for phylogenetic reconstruction of Pyrus due to suitable sequence divergence and the absence of lineage sorting.

Premise of the Study: An efficient alternative strategy to conventional cloning was needed to generate high-quality DNA sequences from a variety of nuclear orthologs for phylogenetic studies. This method would facilitate studies and minimize technical problems typically encountered in cloning methodologies., Methods: We tested a variety of single-strand conformation polymorphism (SSCP) protocols including purified and unpurified symmetric and asymmetric PCR, loading buffers, and electrophoresis conditions (buffers, matrix, running time, temperature). Results obtained from direct SSCP band sequencing were compared to those obtained from cloning., Key Results: Our optimized protocol uses asymmetric PCR, with the majority of the samples run in polyacrylamide gel electrophoresis (PAGE). It consistently separated PCR products from 450 to 1200 bp., Conclusions: Asymmetric PCR single-strand conformation polymorphism is an efficient alternative technique for isolating allelic variants of highly heterozygous individuals, with its greatest applications in sequencing allopolyploids. It eliminates two common problems encountered in cloning: PCR recombination and heteroduplex fixation. In addition, our protocol greatly lowers costs and time associated with procedures.

The concept that traits should be associated with related organisms and that nearby populations of the same species are likely to be more similar to each other than to populations spread far apart has long been accepted. Consequently, taxonomic relationships and biogeographical data are commonly believed to have the power to predict the distribution of disease resistance genes among plant species. In this study, we test claims of such predictivity in a group of widely distributed wild potato species. There was no clear association between resistance to soft rot and taxonomic relationships. However, we have found some associations between resistance to soft rot and environmental data such as annual precipitation and annual mean temperature. In addition, we have noted that high levels of resistance are mostly found in species with high levels of phenotypic plasticity. The three most resistant species were Solanum paucijugum, S. brevicaule, and S. commersonii.

Premise of the Study: The taxonomy of cultivated potatoes has been highly controversial, with estimates of species numbers ranging from 3 to 17. Ploidy level has been one of the most important taxonomic characters to recognize cultivated potato species, containing diploid (2n = 2x = 24), triploid (2n = 3x = 36), tetraploid (2n = 4x = 48), and pentaploid (2n = 5x = 60) cultivars. We tested the environmental associations of different ploidy levels in cultivated potato species that traditionally have been recognized as Linnaean taxa to see whether, in combination with prior morphological, molecular, and crossing data, some of the ploidy variants can be recognized as distinct taxa. •, Methods: We summarize 2780 chromosome counts of landrace cultivated potatoes, provide georeferences to 2048 of them, and analyze these data for 20 environmental variables at 10-min resolution using the randomForest algorithm to explore associations with taxa and ploidy variants. •, Key Results: Except for the S. tuberosum Chilotanum Group and extreme northern and southern range extensions of the Andigenum Group, it is impossible to find distinct habitats for the ploidy variants of the S. tuberosum Andigenum Group. •, Conclusions: Our distributional and ecological data, in combination with prior results from morphology, microsatellites, and crossing data, provide yet additional data to support a major reclassification of cultivated potato species. A rational, stable, and universally accepted taxonomy of this major crop plant will greatly aid all users of wild and cultivated potatoes from breeders to gene bank managers to ecologists and evolutionary biologists.

Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. The taxonomy of cultivated potatoes is particularly controversial. Using DNA sequence data of the waxy gene, we here infer relationships among the four species of cultivated potatoes accepted in the latest taxonomic treatment (S. ajanhuiri, S. curtilobum, S. juzepczukii and S. tuberosum, the latter divided into the Andigenum and Chilotanum Cultivar Groups). The data support prior ideas of hybrid origins of S. ajanhuiri from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. megistacrolobum; S. juzepczukii from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. acaule; and S. curtilobum from the S. tuberosum Andigenum Group (4x = S. tuberosum subsp. andigenum) × S. juzepczukii. For the tetraploid cultivar-groups of S. tuberosum, hybrid origins are suggested entirely within much more closely related species, except for two of three examined accessions of the S. tuberosum Chilotanum Group that appear to have hybridized with the wild species S. maglia. Hybrid origins of the crop/weed species S. sucrense are more difficult to support and S. vernei is not supported as a wild species progenitor of the S. tuberosum Andigenum Group.

Comparative genetic linkage mapping using a common set of DNA markers in related species is an important methodology in plant genome research. Here, we demonstrate a comparative fluorescence in situ hybridization (FISH) mapping strategy in plants. A set of 13 bacterial artificial chromosome clones spanning the entire length of potato chromosome 6 was used for pachytene chromosome-based FISH mapping in seven distantly related Solanum species including potato, tomato, and eggplant. We discovered one paracentric inversion and one pericentric inversion within specific lineages of these species. The comparative FISH mapping data revealed the ancestral structure of this chromosome. We demonstrate that comparative FISH mapping is an efficient and powerful methodology to study chromosomal evolution among plant species diverged for up to 12 million years.

Background: Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species., Results: Among potatoes, when total evidence is invoked, one single predominant history is highlighted with complete resolution within and among the three main clades. It also supports the hypothesis of the North and Central American B-genome origin of the tuber-bearing members of Solanum sect. Petota and shows a clear division between A genomes in clades 3 and 4, and B genomes in clade 1+2. On the other hand, when a prior agreement approach is invoked other potato evolutionary histories are revealed but with less support. These alternative histories could be explained by past hybridization, or fast rates of speciation. In the case of tomato, the analyses with all sequence data completely resolved 19 of 21 clades, for the first time revealed the monophyly of five clades, and gave further support for the recent segregation of new species from the former Solanum peruvianum. Concordance analyses revealed and summarized the extensive discordance among COSII markers. Some potential reasons for discordance could be methodological, to include systematic errors due to using a wrong model of sequence evolution, coupled with long branches, or mixtures of branch lengths within COSII, or undetected paralogy or alignment bias. Other reasons could be biological processes such as hybridization or lineage sorting., Conclusion: This study confirms and quantifies the utility of using DNA sequences from different parts of the genome in phylogenetic studies to avoid possible bias in the sampling. It shows that 11-18 loci are enough to get the dominant history in this group of Solanum, but more loci would be needed to discern the distribution of gene genealogies in more depth, and thus detect which mechanism most likely shaped the discordance.

DNA barcoding ("barcoding") has been proposed as a rapid and practical molecular method to identify species via diagnostic variation in short orthologous DNA sequences from one or a few universal genomic regions. It seeks to address in a rapid and simple way the "taxonomic impediment" of a greater need for taxonomic identifications than can be supplied by taxonomists. Using a complicated plant group, Solanum sect. Petota (wild potatoes), I tested barcoding with the most variable and frequently suggested plant barcoding regions: the internal nontranscribed spacer of nuclear ribosomal DNA (ITS) and the plastid markers trnH-psbA intergenic spacer and matK. These DNA regions fail to provide species-specific markers in sect. Petota because the ITS has too much intraspecific variation and the plastid markers lack sufficient polymorphism. The complications seen in wild potatoes are common in many plant groups, but they have not been assessed with barcoding. Barcoding is a retroactive procedure that relies on well-defined species to function, is based solely on a limited number of DNA sequences that are often inappropriate at the species level, has been poorly tested with geographically well-dispersed replicate samples from difficult taxonomic groups, and discounts substantial practical and theoretical problems in defining species.

Mutations in succinate dehydrogense-B (SDHB) and the von Hippel-Lindau (VHL) genes result in an increased risk of developing chromaffin tumours via a common aetiological pathway. The aim of the present retrospective study was to compare the clinical phenotypes of disease in subjects developing chromaffin tumours as a result of SDHB mutations or VHL disease. Thirty-one subjects with chromaffin tumours were assessed; 16 subjects had SDHB gene mutations and 15 subjects had a diagnosis of VHL. VHL-related tumours were predominantly adrenal phaeochromocytomas (22/26; 84.6%), while SDHB-related tumours were predominantly extra-adrenal paragangliomas (19/25; 76%). Median age at onset of the first chromaffin tumour was similar in the two cohorts. Tumour size was significantly larger in the SDHB cohort in comparison with the VHL cohort (P=0.002). Multifocal disease was present in 9/15 (60%) of the VHL cohort (bilateral phaeochromocytomas) and only 3/16 (19%) of the SDHB cohort, while metastatic disease was found in 5/16 (31%) of the SDHB cohort but not in the VHL cohort to date. The frequency of symptoms, hypertension and the magnitude of catecholamine secretion appeared to be greater in the SDHB cohort. Renal cell carcinomas were a feature in 5/15 (33%) of the VHL cohort and 1/16 (6%) of the SDHB cohort. These data indicate that SDHB-related tumours are predominantly extra-adrenal in location and associated with higher catecholamine secretion and more malignant disease, in subjects who appear more symptomatic. VHL-related tumours tend to be adrenal phaeochromocytomas, frequently bilateral and associated with a milder phenotype.

Purpose: To explore a strategy by which radiotherapy (RT) could be avoided in the treatment of young children with parameningeal rhabdomyosarcoma (PM RMS)., Patients and Methods: Fifty-nine children (median age, 2 years 3 months) with nonmetastatic cranial PM RMS were treated in the International Society of Pediatric Oncology MMT 89 and 95 trials between 1989 and 2003., Results: Five-year EFS and OS rates were 46% and 54%, respectively, for the whole group. No standard clinical or pathologic variables had prognostic impact. Fifty (85%) of 59 patients achieved complete local control either with (n = 28) or without (n = 22) RT administered as part of their primary treatment. Nine patients (15%) did not achieve local control (four of whom had had RT), and all died. Patients who received RT had a significantly superior 5-year EFS rate compared with patients who did not receive RT (59% v 28%, respectively). Twenty-three patients (48%) experienced relapse at a median interval of 15 months. Ultimately, only seven patients (12%) were cured without RT, although this represented 32% of those who achieved local control with initial chemotherapy., Conclusion: Despite concerns about the late effects of its use in young children, cure of PM RMS remains unlikely without systematic use of RT. The accurate prediction of the small subset of patients who achieve local control without RT and who do not experience relapse would provide an opportunity for a minority of patients to avoid RT.

Neo-Tuberosum refers to cultivated potato adapted to long-day tuberization and a syndrome of related morphological and physiological traits, developed by intercrossing and selection of short-day adapted potatoes of the Solanum tuberosum Andigenum Group, native from the Andes of western Venezuela to northern Argentina. This re-creation of the modern potato helped support the theory of an Andigenum Group origin of potato in temperate regions and the possibility to access the largely untapped diversity of the Andigenum Group germplasm by base broadening breeding. This Neo-Tuberosum derived theory, the re-creation of the modern potato from Andigenum germplasm, has been universally accepted for almost 40 years, and has had tremendous impact in planning some breeding programs and supporting phylogenetic conclusions in cultivated potato. We show, with microsatellite (simple sequence repeat, SSR) and plastid DNA marker data, that Neo-Tuberosum germplasm is closely related to Chilotanum Group landraces from lowland south-central Chile rather than to Andigenum Group germplasm. We interpret this quite unexpected result to be caused by strong rapid selection against the original Andigenum clones after unintended hybridization with Chilotanum Group germplasm. In addition, we show that Neo-Tuberosum and Andigenum Group germplasm did not serve to broaden the overall genetic diversity of advanced potato varieties, but rather that Neo-Tuberosum lines and lines not using this germplasm are statistically identical with regard to genetic diversity as assessed by SSRs. These results question the long-standing Neo-Tuberosum derived theory and have implications in breeding programs and phylogenetic reconstructions of potato.

Objective: Phaeochromocytomas and paragangliomas are familial in up to 25% of cases and can result from succinate dehydrogenase (SDH) gene mutations. The aim of this study was to describe the clinical manifestations of subjects with SDH-B gene mutations., Design: Retrospective case-series., Patients: Thirty-two subjects with SDH-B gene mutations followed up between 1975 and 2007. Mean follow-up of 5.8 years (SD 7.4, range 0-31). Patients seen at St Bartholomew's Hospital, London and other UK centres., Measurements: Features of clinical presentation, genetic mutations, tumour location, catecholamine secretion, clinical course and management., Results: Sixteen of 32 subjects (50%) were affected by disease. Two previously undescribed mutations in the SDH-B gene were noted. A family history of disease was apparent in only 18% of index subjects. Mean age at diagnosis was 34 years (SD 15.4, range 10-62). 50% of affected subjects had disease by the age of 26 years. 69% (11 of 16) were hypertensive and 80% (12 of 15) had elevated secretions of catecholamines/metabolites. 24% (6 of 25) of tumours were located in the adrenal and 76% (19 of 25) were extra-adrenal. 19% (3 of 16) had multifocal disease. Metastatic paragangliomas developed in 31% (5 of 16). One subject developed a metastatic type II papillary renal cell carcinoma. The cohort malignancy rate was 19% (6 of 32). Macrovascular disease was noted in two subjects without hypertension., Conclusion: SDH-B mutation carriers develop disease early and predominantly in extra-adrenal locations. Disease penetrance is incomplete. Metastatic disease is prominent but levels are less than previously reported. Clinical manifestations may include papillary renal cell carcinoma and macrovascular disease.

Purpose: The European Intergroup Cooperative Ewing's Sarcoma Study investigated whether cyclophosphamide has a similar efficacy as ifosfamide in standard-risk (SR) patients and whether the addition of etoposide improves survival in high-risk (HR) patients., Patients and Methods: SR patients (localized tumors, volume <100 mL) were randomly assigned to receive four courses of vincristine, dactinomycin, ifosfamide, and doxorubicin (VAIA) induction therapy followed by 10 courses of either VAIA or vincristine, dactinomycin, cyclophosphamide, and doxorubicin (VACA; cyclophosphamide replacing ifosfamide). HR patients (volume >or=100 mL or metastases) were randomly assigned to receive 14 courses of either VAIA or VAIA plus etoposide (EVAIA). Outcome measures were event-free survival (EFS; defined as the time to first recurrence, progression, second malignancy, or death) and overall survival (OS)., Results: A total of 647 patients were randomly assigned: 79 SR patients were assigned to VAIA, 76 SR patients were assigned to VACA, 240 HR were assigned to VAIA, and 252 HR patients were assigned to EVAIA. The median follow-up was 8.5 years. In the SR group, the hazard ratios (VACA v VAIA) for EFS and OS were 0.91 (95% CI, 0.55 to 1.53) and 1.08 (95% CI, 0.58 to 2.03), respectively. There was a higher incidence of hematologic toxicities in the VACA arm. In the HR group, the EFS and OS hazard ratios (EVAIA v VAIA) indicated a 17% reduction in the risk of an event (95% CI, -35% to 5%; P = .12) and 15% reduction in dying (95% CI, -34% to 10%), respectively. The effect seemed greater among patients without metastases (hazard ratio = 0.79; P = .16) than among those with metastases (hazard ratio = 0.96; P = .84)., Conclusion: Cyclophosphamide seemed to have a similar effect on EFS and OS as ifosfamide in SR patients but was associated with increased toxicity. In HR patients, the addition of etoposide seemed to be beneficial.

Thirty-six percent of the wild potato (Solanum L. section Petota Dumort.) species are polyploid, and about half of the polyploids are tetraploid species (2n = 4x = 48). Determination of the type of polyploidy and development of the genome concept for members of section Petota traditionally has been based on the analysis of chromosome pairing in species and their hybrids and, most recently, DNA sequence phylogenetics. Based on these data, the genome designation AABB was proposed for Mexican tetraploid species of series Longipedicellata Buk. We investigated this hypothesis with genomic in situ hybridization (GISH) for both representatives of the series, S. stoloniferum Schltdl. and S. hjertingii Hawkes. GISH analysis supports an AABB genome constitution for these species, with S. verrucosum Schltdl. (or its progenitor) supported as the A genome donor and another North or Central American diploid species (S. cardiophyllum Lindl., S. ehrenbergii (Bitter) Rydb., or S. jamesii Torrey) as the B genome donor. GISH analysis of chromosome pairing of S. stoloniferum also confirms the strict allopolyploid nature of this species. In addition, fluorescence in situ hybridization data suggest that 45S rDNA regions of the two genomes of S. stoloniferum were changed during coevolution of A and B genomes of this allotetraploid species.

Landrace potato cultivars are native to two areas in South America: the high Andes from eastern Venezuela to northern Argentina and the lowlands of south-central Chile. Potato first appeared outside of South America in Europe in 1567 and rapidly diffused worldwide. Two competing hypotheses suggested the origin of the "European" potato from the Andes or from lowland Chile, but the Andean origin has been widely accepted over the last 60 years. All modern potato cultivars predominantly have Chilean germplasm, explained as originating from breeding with Chilean landraces subsequent to the late blight epidemics beginning in 1845 in the UK. The Andean origin has been questioned recently through examination of landraces in India and the Canary Islands, but this evidence is inferential. Through a plastid DNA deletion marker from historical herbarium specimens, we report that the Andean potato predominated in the 1700s, but the Chilean potato was introduced into Europe as early as 1811 and became predominant long before the late blight epidemics in the UK. Our results provide the first direct evidence of these events and change the history of introduction of the European potato. They shed new light on the value of past breeding efforts to recreate the European potato from Andean forms and highlight the value of herbarium specimens in investigating origins of crop plants.

Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum. We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri, S. juzepczukii, and S. curtilobum. In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the cultivated potatoes into four species: (i) S. tuberosum, with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); (ii) S. ajanhuiri (diploid); (iii) S. juzepczukii (triploid); and (iv) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature.

Thomas Beatson's celebrated description in 1896 of bilateral oophorectomy as effective therapy for premenopausal breast cancer could be considered as the first demonstration of response of any cancer to a 'targeted therapy.' At that time, however, the understanding of the mechanism of the intervention was minimal. In recent years a host of new rationally designed, molecularly targeted cancer therapies have been introduced from both large pharmaceutic and small biotechnology companies, and the portfolio of new targeted treatments in the pipeline appears to be unending. The existence of this array of potential new therapies is the result of a prodigious effort in the researching and defining of the molecular components of the cancer phenotype, and the subsequent rational design of agents to target candidate pathways. Experience with endocrine therapy has shown that targeted therapies require the target to be not merely expressed in the cancer phenotype, but important in regulating growth of cancer cells. We may well look back at many of the current targeted therapy trials as unrealistically simplistic in failing to adequately and define the target phenotype. This approach risks rejecting highly active treatments for a small subgroup of a study population where minimal activity is present for the majority. The future for breast cancer therapy is promising, but it is important to be prepared for disappointment, as early success in animal models cannot guarantee a successful human therapy. Stunning results such as the adjuvant trastuzumab trials are likely to remain the exceptions rather that the rule, and most gains will be modest advances. A better understanding of the molecular biology of cancer may also aid in guiding the most appropriate use of existing therapies such as conventional chemotherapy. This knowledge will facilitate the rational selection of drug combinations and/or sequencing based on their mechanisms of action at a molecular level. The aim of this paper is to review the current state-of-the-art in novel targeted therapies for breast cancer based on an understanding of this disease at the molecular level, with particular reference to those agents entering the clinic.

Background: The National Epirubicin Adjuvant Trial (NEAT) and the BR9601 trial examined the efficacy of anthracyclines in the adjuvant treatment of early breast cancer., Methods: In NEAT, we compared four cycles of epirubicin followed by four cycles of cyclophosphamide, methotrexate, and fluorouracil (CMF) with six cycles of CMF alone. In the BR9601 trial, we compared four cycles of epirubicin followed by four cycles of CMF, with eight cycles of CMF alone every 3 weeks. The primary end points were relapse-free and overall survival. The secondary end points were adverse effects, dose intensity, and quality of life., Results: The two trials included 2391 women with early breast cancer; the median follow-up was 48 months. Relapse-free and overall survival rates were significantly higher in the epirubicin-CMF groups than in the CMF-alone groups (2-year relapse-free survival, 91% vs. 85%; 5-year relapse-free survival, 76% vs. 69%; 2-year overall survival, 95% vs. 92%; 5-year overall survival, 82% vs. 75%; P<0.001 by the log-rank test for all comparisons). Hazard ratios for relapse (or death without relapse) (0.69; 95% confidence interval [CI], 0.58 to 0.82; P<0.001) and death from any cause (0.67; 95% CI, 0.55 to 0.82; P<0.001) favored epirubicin plus CMF over CMF alone. Independent prognostic factors were nodal status, tumor grade, tumor size, and estrogen-receptor status (P<0.001 for all four factors) and the presence or absence of vascular or lymphatic invasion (P=0.01). These factors did not significantly interact with the effect of epirubicin plus CMF. The overall incidence of adverse effects was significantly higher with epirubicin plus CMF than with CMF alone but did not significantly affect the delivered-dose intensity or the quality of life., Conclusions: Epirubicin plus CMF is superior to CMF alone as adjuvant treatment for early breast cancer. (ClinicalTrials.gov number, NCT00003577 [ClinicalTrials.gov].)., (Copyright 2006 Massachusetts Medical Society.)