Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
Chromosome evolution; Diversification; Ecogeography; Polyploidy; Repetitive DNA
Background and Aims
Changes in chromosome structure and number play an important role in plant evolution. A system well-suited to studying different modes of chromosome evolution is the genus Hypochaeris (Asteraceae) with its centre of species' diversity in South America. All South American species uniformly have a chromosome base number of x = 4 combined with variation in rDNA number and distribution, and a high frequency of polyploidy. The aim of this paper is to assess directions and mechanisms of karyotype evolution in South American species by interpreting both newly obtained and previous data concerning rDNA localization in a phylogenetic context.
Eleven Hypochaeris species from 18 populations were studied using fluorescence in situ hybridization (FISH) with 35S and 5S rDNA probes. A phylogenetic framework was established from neighbour-net analysis of amplified fragment length polymorphism (AFLP) fingerprint data.
A single 5S rDNA locus is invariably found on the short arm of chromosome 2. Using 35S rDNA loci, based on number (one or two) and localization (interstitial on the long arm of chromosome 2, but sometimes lacking, and terminal or interstitial on the short arm of chromosome 3, only very rarely lacking), seven karyotype groups can be distinguished; five of these include polyploids. Karyotype groups with more than one species do not form monophyletic groups.
Early evolution of Hypochaeris in South America was characterized by considerable karyotype differentiation resulting from independent derivations from an ancestral karyotype. There was marked diversification with respect to the position and evolution of the 35S rDNA locus on chromosome 3, probably involving inversions and/or transpositions, and on chromosome 2 (rarely 3) concerning inactivation and loss. Among these different karyotype assemblages, the apargioides group and its derivatives constitute by far the majority of species.
Asteraceae; fluorescence in situ hybridization; Hypochaeris; karyotype evolution; polyploidy; rDNA; South America
Hexaploid individuals of Senecio carniolicus (Asteraceae) predominantly occur in dense swards while diploids prevail in open vegetation. We test whether this habitat segregation is due to differential responses to competition. Linear regression models were used to relate biomass and maximum leaf length of adults to vegetation cover within radii of 20 cm around target individuals. Biomass differed between ploidy levels, but was independent from vegetation cover in both cytotypes. Maximum leaf length of diploids increased with vegetation cover, but remained constant in hexaploids. This suggests that at the adult stage diploids respond to increasing competition by changes in plant architecture rather than changes in resource utilization, while hexaploids are unaffected by competition. Consequently, other factors, such as competitive interactions at earlier life stages, likely are responsible for habitat segregation of diploid and hexaploid S. carniolicus.
Polyploidy; Competition; Alpine plants; Biomass; Vegetation cover
We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%–28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%–22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types.
next-generation sequencing; polyploidy; genome size; genome downsizing; transposable elements; LTR retrotransposons; Ty3/Gypsy; Orobanche; Phelipanche; Orobanchaceae
Reproductive interactions among cytotypes in their contact zones determine whether these cytotypes can co-exist and form stable contact zones or not. In autopolyploids, heteroploid cross-compatibilities might depend on parental ploidy, but tests of this hypothesis in autopolyploid systems with more than two ploidies are lacking. Here, we study Jacobaea carniolica, which comprises diploid, tetraploid, and hexaploid individuals regularly forming contact zones. Seeds obtained from in situ cross-pollinations within and among cytotypes were subjected to DNA flow cytometry and greenhouse germination experiments. Hybrid fitness and parental effects on hybrid fitness were tested with regression models comparing fitness parameters of early life stages. Irrespective of the direction of crosses, seed viability and seedling survival in diploid-polyploid crosses were substantially lower than in tetraploid-hexaploid crosses. In contrast, seedling growth traits indicated neither transgressive character expression nor any selection against hybrid offspring. Congruent with a model of genome dosage effects, these traits differed between reciprocal crosses, especially of diploids and tetraploids, where trait values resembled those of the maternal parent. The strong effect of parental ploidy on offspring fitness in heteroploid crosses may cause contact zones involving exclusively polyploid cytotypes to be less stable over longer terms than those involving diploids and polyploids.
Over the last few years, circulating microRNAs (miRNAs) have emerged as promising novel and minimally invasive markers for various diseases, including cancer. We already showed that certain miRNAs are deregulated in the plasma of breast cancer patients when compared to healthy women. Herein we have further explored their potential to serve as breast cancer early detection markers in blood plasma. Circulating miR-127-3p, miR-376a and miR-652, selected as candidates from a miRNA array-based screening, were found to be associated with breast cancer for the first time (n = 417). Further we validated our previously reported circulating miRNAs (miR-148b, miR-376c, miR-409-3p and miR-801) in an independent cohort (n = 210) as elevated in the plasma of breast cancer patients compared to healthy women. We described, for the first time in breast cancer, an over-representation of deregulated miRNAs (miR-127-3p, miR-376a, miR-376c and miR-409-3p) originating from the chromosome 14q32 region. The inclusion of patients with benign breast tumors enabled the observation that miR-148b, miR-652 and miR-801 levels are even elevated in the plasma of women with benign tumors when compared to healthy controls. Furthermore, an analysis of samples stratified by cancer stage demonstrated that miR-127-3p, miR-148b, miR-409-3p, miR-652 and miR-801 can detect also stage I or stage II breast cancer thus making them attractive candidates for early detection. Finally, ROC curve analysis showed that a panel of these seven circulating miRNAs has substantial diagnostic potential with an AUC of 0.81 for the detection of benign and malignant breast tumors, which further increased to 0.86 in younger women (up to 50 years of age).
Previous studies suggest that patients with chronic diseases, such as rheumatoid arthritis (RA), do not receive optimal preventive medical services including cancer screening tests. Few studies evaluated cancer screening in RA patients compared to non-RA.
Using data from a large US commercial insurance plan, we examined rates of screening tests for cervical, breast and colon cancer in patients with RA compared with non-RA. RA was defined as ≥ 2 diagnoses of RA and ≥ 1 prescription for a disease-modifying anti-rheumatic drug. Multivariable Cox models compared cancer screening test rates between RA and non-RA patients.
Both RA (n=13,314) and non-RA (n=212,324) patients were screened, on average, once every 3 years for cervical cancer and once every two years for breast cancer during the follow-up (mean: 2.3 years). In the age-adjusted Cox regression model, women with RA were more likely to receive ≥ 1 Papanicolaou smear (HR 1.21, 95% CI 1.17–1.24), mammogram (HR 1.49, 95% CI 1.45–1.53), and colonoscopy (HR 1.69, 95% CI 1.61–1.77) compared to non-RA. Men with RA, were also more likely to receive a colonoscopy (HR 1.52, 95% CI 1.40–1.64) than non-RA patients. The results were robust in multivariable analyses adjusted for age, physician visit numbers, percent of visits made to primary care physicians and comorbidity index.
Individuals with RA did not appear to be at risk for receiving fewer cancer screening tests than non-RA patients. The majority of both RA and non-RA patients were regularly screened for cervical, breast, and colon cancer as recommended.
TERT-locus single nucleotide polymorphisms (SNPs) and leucocyte telomere measures are reportedly associated with risks of multiple cancers. Using the iCOGs chip, we analysed ~480 TERT-locus SNPs in breast (n=103,991), ovarian (n=39,774) and BRCA1 mutation carrier (11,705) cancer cases and controls. 53,724 participants have leucocyte telomere measures. Most associations cluster into three independent peaks. Peak 1 SNP rs2736108 minor allele associates with longer telomeres (P=5.8×10−7), reduced estrogen receptor negative (ER-negative) (P=1.0×10−8) and BRCA1 mutation carrier (P=1.1×10−5) breast cancer risks, and altered promoter-assay signal. Peak 2 SNP rs7705526 minor allele associates with longer telomeres (P=2.3×10−14), increased low malignant potential ovarian cancer risk (P=1.3×10−15) and increased promoter activity. Peak 3 SNPs rs10069690 and rs2242652 minor alleles increase ER-negative (P=1.2×10−12) and BRCA1 mutation carrier (P=1.6×10−14) breast and invasive ovarian (P=1.3×10−11) cancer risks, but not via altered telomere length. The cancer-risk alleles of rs2242652 and rs10069690 respectively increase silencing and generate a truncated TERT splice-variant.
Our recent genome-wide association study identified a novel breast cancer susceptibility locus at 9q31.2 (rs865686).
To further investigate the rs865686–breast cancer association, we conducted a replication study within the Breast Cancer Association Consortium, which comprises 37 case–control studies (48,394 cases, 50,836 controls).
This replication study provides additional strong evidence of an inverse association between rs865686 and breast cancer risk [study-adjusted per G-allele OR, 0.90; 95% confidence interval (CI), 0.88; 0.91, P = 2.01 × 10–29] among women of European ancestry. There were ethnic differences in the estimated minor (G)-allele frequency among controls [0.09, 0.30, and 0.38 among, respectively, Asians, Eastern Europeans, and other Europeans; P for heterogeneity (Phet) = 1.3 × 10–143], but no evidence of ethnic differences in per allele OR (Phet = 0.43). rs865686 was associated with estrogen receptor–positive (ER+) disease (per G-allele OR, 0.89; 95% CI, 0.86–0.91; P = 3.13 × 10–22) but less strongly, if at all, with ER-negative (ER–) disease (OR, 0.98; 95% CI, 0.94–1.02; P = 0.26; Phet = 1.16 × 10–6), with no evidence of independent heterogeneity by progesterone receptor or HER2 status. The strength of the breast cancer association decreased with increasing age at diagnosis, with case-only analysis showing a trend in the number of copies of the G allele with increasing age at diagnosis (P for linear trend = 0.0095), but only among women with ER+ tumors.
This study is the first to show that rs865686 is a susceptibility marker for ER+ breast cancer.
The findings further support the view that genetic susceptibility varies according to tumor subtype.
Recent genome-wide association studies identified 11 single nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk. We investigated these and 62 other SNPs for their prognostic relevance. Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), rs3817198 (LSP1), rs889312 (MAP3K1), rs3803662 (TOX3), rs13387042 (2q35), rs4973768 (SLC4A7), rs6504950 (COX11) and rs10941679 (5p12) were genotyped for 25 853 BC patients with the available follow-up; 62 other SNPs, which have been suggested as BC risk SNPs by a GWAS or as candidate SNPs from individual studies, were genotyped for replication purposes in subsets of these patients. Cox proportional hazard models were used to test the association of these SNPs with overall survival (OS) and BC-specific survival (BCS). For the confirmed loci, we performed an accessory analysis of publicly available gene expression data and the prognosis in a different patient group. One of the 11 SNPs, rs3803662 (TOX3) and none of the 62 candidate/GWAS SNPs were associated with OS and/or BCS at P<0.01. The genotypic-specific survival for rs3803662 suggested a recessive mode of action [hazard ratio (HR) of rare homozygous carriers=1.21; 95% CI: 1.09–1.35, P=0.0002 and HR=1.29; 95% CI: 1.12–1.47, P=0.0003 for OS and BCS, respectively]. This association was seen similarly in all analyzed tumor subgroups defined by nodal status, tumor size, grade and estrogen receptor. Breast tumor expression of these genes was not associated with prognosis. With the exception of rs3803662 (TOX3), there was no evidence that any of the SNPs associated with BC susceptibility were associated with the BC survival. Survival may be influenced by a distinct set of germline variants from those influencing susceptibility.
Acute myocardial infarction; Epidemiology; Health policy and outcome research; Primary prevention; Secondary prevention; Resource utilization
Part D coverage gap entry is associated with a two-fold increased rate of drug discontinuation among beneficiaries now fully responsible for drug costs. Reduced adherence to drugs has been associated with adverse outcomes. We evaluated whether coverage gap entry is associated with risk of death or hospitalization for cardiovascular outcomes.
Prospective cohort study. Beneficiaries entered the study upon reaching the coverage gap spending threshold and were observed until an event, reaching the threshold for catastrophic coverage, or year’s end. Exposed patients were responsible for drug costs in the gap; unexposed patients received financial assistance. We matched 9,436 exposed patients to 9,436 unexposed patients based on propensity score (PS) or high-dimensional propensity score (hdPS).
Medicare Part D drug insurance.
303,978 Medicare beneficiaries aged 65+ in 2006 and 2007 with linked prescription and medical claims who enrolled in stand-alone Part D or retiree drug plans and reached the gap spending threshold.
Rates of death and hospitalization for any of 5 cardiovascular outcomes, including acute coronary syndrome+revascularization (ACS), after reaching the coverage gap spending threshold were compared using Cox proportional hazards models.
In PS-matched analyses, exposed beneficiaries had elevated but non-significant hazards of death (HR=1.25; 95% CI 0.98–1.59) and ACS (HR=1.16; 0.83–1.62) compared with unexposed patients. hdPS-matched analyses minimized residual confounding and confirmed results: death (HR=0.99; 0.78–1.24); ACS (HR=1.07; 0.81–1.41). Exposed beneficiaries were no more or less likely to experience other outcomes than were the unexposed.
During the short-term coverage gap period, having no financial assistance to pay for drugs was not associated with an increased risk of death or hospitalization for cardiovascular causes. However, long-term health consequences remain unclear.
Medicare Part D; coverage gap; adverse health outcomes; cardiovascular disease; drug discontinuation
Older‐generation anticonvulsants that highly induce cytochrome P450 enzyme system activity produce metabolic abnormalities that may increase cardiovascular risk. The objective of this study was to evaluate the risk of ischemic cerebrovascular and coronary events in adult new users of anticonvulsants that highly induce cytochrome P450 activity compared with other anticonvulsant agents, as observed in a routine care setting.
Methods and Results
This was a cohort study of patients 40 to 64 years old from the HealthCore Integrated Research Database who had initiated an anticonvulsant medication between 2001 and 2006 and had no recorded major coronary or cerebrovascular condition in the 6 months before treatment initiation. Propensity score (PS) matching was used to evaluate ischemic cerebrovascular and coronary risk among anticonvulsant new users. High‐dimensional propensity score (hdPS)–matched analyses were used to confirm adjusted findings. The study identified 913 events in 166 031 unmatched new treatment episodes with anticonvulsant drugs. In a PS‐matched population of 22 864 treatment episodes, the rate ratio (RR) for ischemic coronary or cerebrovascular events associated with highly inducing agents versus other agents was 1.22 (95% CI, 0.90‐1.65). The RR moved to 0.99 (95% CI, 0.73‐1.33) with adjustment for hdPS matching (RR, 1.47; 95% CI, 0.95‐2.28 for cerebrovascular events; RR, 0.70; 95% CI, 0.47‐1.05 for coronary events).
In this exploratory analysis, there was no evidence of a consistent and statistically significant effect of initiating anticonvulsants that highly induce cytochrome P450 activity on ischemic coronary or cerebrovascular outcomes compared with other agents, given routine care utilization patterns.
anticonvulsant drugs; claims data; cohort study; myocardial infarction; stroke
Several prior investigations demonstrate an improvement in bone mineral density associated with use of TNF inhibitors (TNFi). We compared the risk of osteoporotic fractures among patients with rheumatoid arthritis (RA) initiating a disease-modifying antirheumatic drug (DMARD).
A population-based cohort study was conducted using health care utilization data (1996–2008) from a Canadian province and a US commercial insurance plan. Patients with at least two RA diagnoses were identified and follow-up began with the first prescription for a DMARD. Drug regimens were categorized into three mutually exclusive hierarchical groups: 1) TNFi with or without non-biologic DMARDs (nbDMARD), 2) methotrexate (MTX) without a TNFi, or 3) other nbDMARD without a TNFi or MTX. Main outcomes were hospitalizations for fractures of the hip, wrist, humerus, or pelvis based on diagnoses and procedure codes.
The study cohort consisted of 16,412 RA patients with 25,988 new treatment episodes: 5,856 TNFi, 12,554 MTX, and 7,578 other nbDMARD. The incidence rate per 1,000 person-years for osteoporotic fracture were 5.11 (95% CI 3.50 – 7.45) for TNFi, 5.35 (95% CI 4.08–7.02) for MTX, and 6.38 (95% CI 3.78–10.77) for other nbDMARD. After multivariable adjustment for osteoporosis and fracture-related risk factors, the risk of non-vertebral osteoporotic fracture was not different in either TNFi (hazard ratio (HR) 1.07, 95% CI 0.57–1.98) or MTX (HR 1.18, 95% CI 0.60– 2.34) compared with nbDMARD.
Among subjects diagnosed with RA, the adjusted risk of non-vertebral fracture was similar across persons starting a TNFi, MTX, or other nbDMARD.
rheumatoid arthritis; fracture; disease modifying antirheumatic drugs
The AGO-ETC trial compared 5-year relapse-free survival of intense dose-dense (IDD) sequential chemotherapy with epirubicin (E), paclitaxel (T), and cyclophosphamide (C) (IDD-ETC) every 2 weeks vs conventional scheduled epirubicin/cyclophosphamide followed by paclitaxel (EC→T) (every 3 weeks) as adjuvant treatment in high-risk breast cancer patients. The objective of this study was to evaluate the safety and efficacy of epoetin alfa in a second randomization of the intense dose-dense arm.
One thousand two hundred eighty-four patients were enrolled; 658 patients were randomly assigned to the IDD-ETC treatment group. Within the IDD-ETC group, 324 patients were further randomly assigned to the epoetin alfa group, and 319 were randomly assigned to the non–erythropoiesis-stimulating agent (ESA) control group. Primary efficacy endpoints included change in hemoglobin level from baseline to Cycle 9 and the percentage of subjects requiring red blood cell transfusion. Relapse-free survival, overall survival, and intramammary relapse were secondary endpoints estimated with Kaplan-Meier and Cox regression methods. Except for the primary hypothesis, all statistical tests were two-sided.
Epoetin alfa avoided the decrease in hemoglobin level (no decrease in the epoetin alfa group vs –2.20g/dL change for the control group; P < .001) and statistically significantly reduced the percentage of subjects requiring red blood cell transfusion (12.8% vs 28.1%; P < .0001). The incidence of thrombotic events was 7% in the epoetin alfa arm vs 3% in the control arm. After a median follow-up of 62 months, epoetin alfa treatment did not affect overall survival, relapse-free survival, or intramammary relapse.
Epoetin alfa resulted in improved hemoglobin levels and decreased transfusions without an impact on relapse-free or overall survival. However, epoetin alfa had an adverse effect, resulting in increased thrombosis.
Dabigatran, an oral thrombin inhibitor, and rivaroxaban and apixaban, oral factor Xa inhibitors, have been found safe and effective in reducing stroke risk in patients with atrial fibrillation. We sought to compare the efficacy and safety of the 3 new agents based on data from their published warfarin-controlled randomized trials, using the method of adjusted indirect comparisons.
Methods and Results
We included findings from 44,535 patients enrolled in three trials of the efficacy of dabigatran (RE-LY), apixaban (ARISTOTLE), and rivaroxaban (ROCKET-AF), each compared with warfarin. The primary efficacy endpoint was stroke or systemic embolism; the safety endpoint we studied was major hemorrhage. To address a lack of comparability between trial populations caused by the restriction of ROCKET-AF to high risk patients, we conducted a subgroup analysis in patients with a CHADS2 score ≥3. We found no statistically significant efficacy differences among the three drugs, although apixaban and dabigatran were numerically superior to rivaroxaban. Apixaban produced significantly fewer major hemorrhages than dabigatran and rivaroxaban.
An indirect comparison of new anticoagulants based on existing trial data indicates that in patients with a CHADS2 score ≥3 dabigatran 150mg, apixaban 5mg, and rivaroxaban 20 mg resulted in statistically similar rates of stroke and systemic embolism, but apixaban had a lower risk of major hemorrhage compared to dabigatran and rivaroxaban . Until head-to-head trials or large-scale observational studies that reflect routine use of these agents are available, such adjusted indirect comparisons based on trial data are one tool to guide initial therapeutic choices.
Indirect comparison; anticoagulation; dabigatran; rivaroxaban; apixaban; warfarin; randomized controlled trial
Prospero (Hyacinthaceae) provides a unique system to assess the impact of genome rearrangements on plant diversification and evolution. The genus exhibits remarkable chromosomal variation but very little morphological differentiation. Basic numbers of x = 4, 5, 6 and 7, extensive polyploidy, and numerous polymorphic chromosome variants were described, but only three species are commonly recognized: P. obtusifolium, P. hanburyi, and P. autumnale s.l., the latter comprising four diploid cytotypes. The relationship between evolutionary patterns and chromosomal variation in diploids, the basic modules of the extensive cytological diversity, is presented.
Evolutionary inferences were derived from fluorescence in situ hybridization (FISH) with 5S and 35S rDNA, genome size estimations, and phylogenetic analyses of internal transcribed spacer (ITS) of 35S rDNA of 49 diploids in the three species and all cytotypes of P. autumnale s.l. All species and cytotypes possess a single 35S rDNA locus, interstitial except in P. hanburyi where it is sub-terminal, and one or two 5S rDNA loci (occasionally a third in P. obtusifolium) at fixed locations. The localization of the two rDNA types is unique for each species and cytotype. Phylogenetic data in the P. autumnale complex enable tracing of the evolution of rDNA loci, genome size, and direction of chromosomal fusions: mixed descending dysploidy of x = 7 to x = 6 and independently to x = 5, rather than successive descending dysploidy, is proposed.
All diploid cytotypes are recovered as well-defined evolutionary lineages. The cytogenetic and phylogenetic approaches have provided excellent phylogenetic markers to infer the direction of chromosomal change in Prospero. Evolution in Prospero, especially in the P. autumnale complex, has been driven by differentiation of an ancestral karyotype largely unaccompanied by morphological change. These new results provide a framework for detailed analyses of various types of chromosomal rearrangements and karyotypic variation in polyploids.
Chromosomal evolution; FISH; Genome size; Hyacinthaceae; ITS; Phylogeny; Prospero; rDNA
A recent two-stage genome-wide association study (GWAS) identified five novel breast cancer susceptibility loci on chromosomes 9, 10 and 11. To provide more reliable estimates of the relative risk associated with these loci and investigate possible heterogeneity by subtype of breast cancer, we genotyped the variants rs2380205, rs1011970, rs704010, rs614367, rs10995190 in 39 studies from the Breast Cancer Association Consortium (BCAC), involving 49,608 cases and 48,772 controls of predominantly European ancestry. Four of the variants showed clear evidence of association (P ≤ 3 × 10−9) and weak evidence was observed for rs2380205 (P = 0.06). The strongest evidence was obtained for rs614367, located on 11q13 (per-allele odds ratio 1.21, P = 4 × 10−39). The association for rs614367 was specific to estrogen receptor (ER)-positive disease and strongest for ER plus progesterone receptor (PR)-positive breast cancer, whereas the associations for the other three loci did not differ by tumor subtype.
breast cancer susceptibility; polymorphisms; genome wide association; risk factors; hormone receptor status; 11q13
A correctly-specified propensity score (PS) estimated in a cohort (“cohort PS”) should in expectation remain valid in a subgroup population. We sought to determine whether using a cohort PS can be validly applied to subgroup analyses and thus add efficiency to studies with many subgroups or restricted data. In each of 3 cohort studies we estimated a cohort PS, defined 5 subgroups, and then estimated subgroup-specific PSs. We compared difference in treatment effect estimates for subgroup analyses adjusted by cohort PSs versus subgroup-specific PSs. Then, 10M times, we simulated a population with known characteristics of confounding, subgroup size, treatment interactions, and treatment effect, and again assessed difference in point estimates. We observed that point estimates in most subgroups were substantially similar with the two methods of adjustment. In simulations, the effect estimates differed by a median of 3.4% (interquartile [IQ] range 1.3% to 10.0%). The IQ range exceeded 10% only in cases where the subgroup had <1000 patients or few outcome events. Our empirical and simulation results indicated that using a cohort PS in subgroup analyses was a feasible approach, particularly in larger subgroups.
Propensity Scores; Confounding Factors (Epidemiology); Multicenter Study [Publication Type]; Epidemiologic Methods; Effect Modifiers (Epidemiology); Comparative Effectiveness Research
High heterogeneity was observed among conserved domains of reverse transcriptase (rt)isolated from quinoa. Only one Ty1-copia rtwas highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes.
The heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.
Chenopodium quinoa; In situ hybridization; Reverse transcriptase; Ty1-copia and Ty3-gypsy retrotransposons
Prospective medical product monitoring is intended to alert stakeholders about whether and when safety problems are identifiable in a continuous stream of longitudinal electronic healthcare data. In comparing the performance of methods to generate these alerts, three factors must be considered: (1) accuracy in alerting; (2) timeliness of alerting; and (3) the trade-offs between the costs of false negative and false positive alerting. Using illustrative examples, we show that traditional scenario-based measures of accuracy, such as sensitivity and specificity, which classify only at the end of monitoring, fail to appreciate timeliness of alerting. We propose an event-based approach that classifies exposed outcomes according to whether or not a prior alert was generated. We provide event-based extensions to existing metrics and discuss why these metrics are limited in this setting because of inherent tradeoffs that they impose between the relative consequences of false positives versus false negatives. We provide an expression that summarizes event-based sensitivity (the proportion of exposed events that occur after alerting among all exposed events in scenarios with true safety issues) and event-based specificity (the proportion of exposed events that occur in the absence of alerting among all exposed events in scenarios with no true safety issues) by taking an average weighted by the relative costs of false positive and false negative alerting. This approach explicitly accounts for accuracy in alerting, timeliness in alerting, and the trade-offs between the costs of false negative and false positive alerting. Subsequent work will involve applying the metric to simulated data.
medical product monitoring; active surveillance; prospective safety monitoring; performance metrics; time-to-alerting; operating characteristics
Breast cancer is the most common cancer among women. To date, 22 common breast cancer susceptibility loci have been identified accounting for ~ 8% of the heritability of the disease. We followed up 72 promising associations from two independent Genome Wide Association Studies (GWAS) in ~70,000 cases and ~68,000 controls from 41 case-control studies and nine breast cancer GWAS. We identified three new breast cancer risk loci on 12p11 (rs10771399; P=2.7 × 10−35), 12q24 (rs1292011; P=4.3×10−19) and 21q21 (rs2823093; P=1.1×10−12). SNP rs10771399 was associated with similar relative risks for both estrogen receptor (ER)-negative and ER-positive breast cancer, whereas the other two loci were associated only with ER-positive disease. Two of the loci lie in regions that contain strong plausible candidate genes: PTHLH (12p11) plays a crucial role in mammary gland development and the establishment of bone metastasis in breast cancer, while NRIP1 (21q21) encodes an ER co-factor and has a role in the regulation of breast cancer cell growth.
Medicare Part D improved access to cardiovascular medications. Increased cardiovascular drug utilization and resulting health improvements could be derailed when beneficiaries enter the coverage gap and must pay 100% of drug costs. The coverage gap remains the subject of Congressional debate; evidence regarding its impact on cardiovascular drug use and health outcomes is needed.
Methods and Results
We followed 122,255 Medicare beneficiaries with cardiovascular conditions with linked prescription and medical claims who reached the coverage gap spending threshold in 2006 or 2007. Beneficiaries entered the study upon reaching the threshold and were followed until an event, the catastrophic coverage spending threshold, or year’s end. We matched 3,980 beneficiaries who reached the threshold and received no financial assistance (exposed) to 3,980 with financial assistance during the gap period (unexposed) using propensity score (PS) and high-dimensional PS (hdPS) approaches. We compared rates of cardiovascular drug discontinuation, drug switching, and death or hospitalization for acute coronary syndrome+revascularization (ACS), congestive heart failure, or atrial fibrillation. In PS-matched analyses, exposed beneficiaries were more likely to discontinue (HR=1.57; 95% CI, 1.39–1.79, RD=13.76; 95% CI, 10.99-16.54 drugs/100 person-years) but no more or less likely to switch cardiovascular drugs. There were no significant differences in rates of death (PS-matched HR=1.23; 0.89-1.71) or other outcomes.
Part D beneficiaries with cardiovascular conditions with no financial assistance during the coverage gap were at increased risk for cardiovascular drug discontinuation. However, the impact of this difference on health outcomes is not clear.
epidemiology; Part D coverage gap; cardiovascular drugs; cardiovascular morbidity and mortality
Under Medicare Part D, patient characteristics influence plan choice, which in turn influences Part D coverage gap entry. We compared pre-defined propensity score (PS) and high-dimensional propensity score (hdPS) approaches to address such ‘confounding by health system use’ in assessing whether coverage gap entry is associated with cardiovascular events or death.
We followed 243,079 Medicare patients aged 65+ with linked prescription, medical, and plan-specific data in 2005–2007. Patients reached the coverage gap and were followed until an event or year’s end. Exposed patients were responsible for drug costs in the gap; unexposed patients (patients with non-Part D drug insurance and Part D patients receiving a low-income subsidy (LIS)) received financial assistance. Exposed patients were 1:1 PS- or hdPS-matched to unexposed patients. The PS model included 52 predefined covariates; the hdPS model added 400 empirically identified covariates. Hazard ratios for death and any of five cardiovascular outcomes were compared. In sensitivity analyses, we explored residual confounding using only LIS patients in the unexposed group.
In unadjusted analyses, exposed patients had no greater hazard of death (HR=1.00; 95% CI, 0.84–1.20) or other outcomes. PS- (HR=1.29;0.99–1.66) and hdPS- (HR=1.11;0.86–1.42) matched analyses showed elevated but non-significant hazards of death. In sensitivity analyses, the PS analysis showed a protective effect (HR=0.78;0.61–0.98), while the hdPS analysis (HR=1.06;0.82–1.37) confirmed the main hdPS findings.
Although the PS-matched analysis suggested elevated though non-significant hazards of death among patients with no financial assistance during the gap, the hdPS analysis produced lower estimates that were stable across sensitivity analyses.
confounding; health services use; propensity score adjustment; high-dimensional propensity score; health policy
Usefulness of propensity scores and regression models to balance potential confounders at treatment initiation may be limited for newly introduced therapies with evolving use patterns.
To consider settings in which the disease risk score has theoretical advantages as a balancing score in comparative effectiveness research, because of stability of disease risk and the availability of ample historical data on outcomes in people treated before introduction of the new therapy.
We review the indications for and balancing properties of disease risk scores in the setting of evolving therapies, and discuss alternative approaches for estimation. We illustrate development of a disease risk score in the context of the introduction of atorvastatin and the use of high-dose statin therapy beginning in 1997, based on data from 5,668 older survivors of myocardial infarction who filled a statin prescription within 30 days after discharge from 1995 until 2004. Theoretical considerations suggested development of a disease risk score among non-users of atorvastatin and high-dose statins during the period 1995–1997.
Observed risk of events increased from 11% to 35% across quintiles of the disease risk score which had a C-statistic of 0.71. The score allowed control of many potential confounders even during early follow-up with few study endpoints.
Balancing on a disease risk score offers an attractive alternative to a propensity score in some settings such as newly marketed drugs and provides an important axis for evaluation of potential effect modification. Joint consideration of propensity and disease risk scores may be valuable.