Radiopharmaceutical Therapy Practice Patterns Across Medicare Providers: An Opportunity for Growth in Radiation Oncology

PURPOSE/OBJECTIVE(S)

Given the recent explosion of research and development of novel targeted agents with improved specificity for delivery, we examined the providers administering radiopharmaceutical therapy (RPT) through analysis of U.S. Medicare payments. We further evaluated differences by specialties with respect to total distinct patients, total services billed, and average Medicare payment and submitted charge.

MATERIALS/METHODS

This retrospective study queried the Provider Utilization & Payment Data prepared by the Centers for Medicare & Medicaid Services for 2020. The Healthcare Common Procedure Coding System (HCPCS) codes used for analysis comprised: Radioactive material therapy into vein; Infusion/instillation of radioelement solution; Radioactive material therapy into artery; and Lu 177 dotatate therapeutic. Provider specialties for which there existed at least 5 entries were included. Outcome measurements included provider gender, practice region, total distinct patients, total services billed, average submitted charge, and average standardized Medicare payment. Descriptive and nonparametric statistics (Kruskal-Wallis Test, Dunn's test) were calculated by specialty.

RESULTS

A total of 171 providers were identified who billed for the above HCPCS codes within Diagnostic Radiology (DR) (n = 68, 39.8%), Nuclear Medicine (NM) (n = 59, 34.5%), Radiation Oncology (RO) (n = 24, 14.0%), and Interventional Radiology (IR) (n = 20, 11.7%). Geographically, 42.7% of providers were in the South, 23.4% in the West, 18.1% in the Midwest, and 15.8% in the Northeast. By gender, 21.1% identified as female, 78.9% as male. Descriptive statistics are summarized in Table 1. Total distinct patients was not significantly different across specialty (p = 0.872). Total services billed was significantly different for RO compared to IR (p<0.001), DR (p<0.001), and NM (p<0.001). There was no significant difference in average Medicare payment between RO and IR (p = 0.405), and between NM and DR (p = 0.063), though there was a significant difference in average submitted charge between NM and DR (p = 0.008).

CONCLUSION

The results of this study highlight the opportunity for growth in radiation oncologists' utilization of RPT. Given the upcoming demand, it is pivotal to recognize the critical role radiation oncologists play in careful oncologic decision making, appropriate dosing and delivery of therapies by clinical scenario, and considerable follow up necessitated in patients receiving these novel therapies.

High-Dose Rate Brachytherapy Alone for Treatment of Unfavorable Intermediate Risk Prostate Cancer: A Propensity-Score Matched Analysis

PURPOSE/OBJECTIVE(S)

To demonstrate the feasibility of high-dose rate brachytherapy (HDR BT) as monotherapy for unfavorable intermediate risk (UIR) prostate cancer by comparing survival outcomes of HDR BT alone against external beam radiation therapy (EBRT) + HDR BT boost, +/- androgen deprivation therapy (ADT) using propensity-score matched (PSM) data.

MATERIALS/METHODS

This retrospective study queried two data registries collecting patient data from 1991 to present. 633 patients with UIR prostate cancer treated with HDR BT alone, HDR BT+EBRT or HDR+EBRT+ADT were included. HDR BT patients received 42-45Gy/6 fractions (fx) or 27 Gy/2 fx. For HDR BT+EBRT, the HDR dose was 20-24 Gy/2 fx, 24 Gy/4 fx, or 15 Gy/1 fx. EBRT patients received 45 Gy/25 fx to the prostate +/- pelvic nodes. GU/GI toxicities were graded according to the Common Terminology Criteria for Adverse Events (CTCAE) v5.0. Time-to-event analyses were carried out to evaluate the relationship between treatments and five primary endpoints of interest: freedom from biochemical recurrence (FFBC), freedom from distant metastasis (FFDM), freedom from local failure (FFLF), cancer specific survival (CSS), and overall survival (OS) at 5 years. PSM was performed with one-to-n matching. Logistic regression was used to estimate the respective propensity scores. The five potential confounders identified were T-stage, Gleason score, pre-treatment PSA, age, and percent positive cores. Balance was checked using the standardized mean difference of covariates. Univariate and multivariate analyses were conducted on the matched data. Toxicity analysis was performed via association between a change in pre- and post-treatment GU/GI toxicity status and the treatment group, as well as incidence of post-treatment severe GI/GU toxicity (grade 3 or higher) and the treatment group.

RESULTS

Univariate analysis with Kaplan-Meier method and log rank test comparison between the three cohorts demonstrated no significant difference in all survival outcomes FFBC, FFDM, FFLF, CSS, OS (p = 0.15, 0.19, 0.29, 0.57, 0.28, respectively). Multivariate analysis with Cox proportional hazard regression showed no differences in HR for FFBC and OS (p = 0.95, 0.11) with addition of EBRT, or with EBRT+ADT (p = 0.17, 0.24); no fit was obtainable for FFDM, CSS, FFLF. Toxicities between the three cohorts were not significantly different when comparing post-treatment and baseline GI/GU symptoms (p = 0.53/1). No Grade 2 or 3 GI toxicities were identified, while 8%/1% HDR patients, 10%/1% HDR+EBRT patients, and 12%/2% HDR+EBRT+ADT patients experienced Grade 2/3 GU toxicities. The incidence of grade 3 or higher GU toxicities between the three groups was not significantly different (p = 0.91).

CONCLUSION

This propensity-score matched study demonstrates the feasibility of HDR BT alone for effective treatment of UIR prostate cancer when compared to HDR+EBRT or HDR+EBRT+ADT, while potentially minimizing the added toxicities of EBRT and the undesirable side effect profile of ADT.

A108 ARE INPATIENTS STILL MORE LIKELY TO FAIL BOWEL PREPARATION IN THE SPLIT-DOSE ERA? FINDINGS FROM 47, 292 COLONOSCOPIES IN THE SOUTHWEST ONTARIO COLONOSCOPY COHORT

Background

Prior studies before the widespread use of split-dose bowel preparation have shown a high rate of inadequate bowel preparation in hospitalized patients. Whether this is still true in the era of split-dose bowel preparation is unknown.

Aims

To determine the impact of inpatient status on bowel preparation quality in the contemporary era of split-dose bowel preparation.

Methods

The Southwest Ontario Colonoscopy cohort consists of all inpatient and outpatient colonoscopies performed between April 2017 and Oct 2018 at 21 hospitals serving a large geographic health region. Procedures done in patients &lt; 18 years of age or by an endoscopist performing &lt;50 colonoscopies/year were excluded. Data were collected through a mandatory quality assurance form that was completed by the endoscopist after each procedure. Pathology reports were manually reviewed. The primary outcome was adequate bowel preparation, defined on an ordinal scale as “good” or “fair” rather than “poor”. Secondary outcomes included adenoma detection rate (ADR), sessile serrated polyp detection rate (ssPDR), polyp detection rate (PDR), and cecal intubation rate (CIR).

Results

A total of 47,292 colonoscopies were performed by 75 physicians (36.2% by gastroenterologists, 60% by general surgeons, 4% others), of which 1,690 were inpatients (3.6%). Inpatients were older (mean 66.8 years vs 60.2 years, p&lt;0.0001), more co-morbid (≥ASA grade 3, 53.6% vs 23.7%, p&lt;0.0001), performed for symptomatic indications (95.7% vs 48.6%, p&lt; 0.0001), have trainee involvement (47% vs 11.6% p&lt;0.001), and less likely to receive split-dose bowel preparation (71.7% vs 91.6% p&lt;0.001). On crude analysis, inpatients were less likely to have adequate bowel preparation (86.2% vs 97.6% p&lt;0.001). On multi-variable analysis, inpatients had lower odds of achieving adequate bowel preparation (OR=0.41, 95% CI 0.33 - 0.50, p&lt;0.001), lower ADR (OR=0.47, 95% CI 0.40 - 0.55, p&lt;0.001), lower PDR (OR=0.54, 95% CI 0.47 - 0.61 p&lt;0.001) and lower CIR (OR = 0.43, 95% CI 0.35 - 0.54, p&lt;0.001).

Conclusions

In the era of split-dose bowel preparation, inpatient status is still an important predictor of inadequate bowel preparation with resultant lower quality outcome metrics.

Funding Agencies

None

A105 ENDOSCOPIC MUCOSAL RESECTION (EMR) OF LARGE SESSILE POLYPS: DATA FROM A MULTI-CENTER HEALTH ZONE

Background

EMR is the standard of care for management of large non-invasive colonic polyps. Current guidelines recommend repeat colonoscopy within 6 months after EMR of large sessile polyps to assess the EMR site for residual adenoma. We reviewed the outcomes and compliance to these guidelines in patients at the University of Alberta Hospital (UAH) and surrounding 7 hospitals.

Aims

The primary outcome was the proportion of patients who received a follow up colonoscopy within 180 days.

Methods

Retrospective data was collected on consecutive patients who had a large polyp resection (size &gt;2cm as documented per endoscopy report) from January 1st, 2014 to January 1st, 2016. Information was collected on patients from UAH as well as seven surrounding hospitals within the Edmonton geographic zone. Data was extracted from electronic health records.

Results

Of 258 patients identified patients, 250 had complete data. Of these 250 patients, 151 (60.4 %) were male and median age was 67 (IQR 60 - 72). Eighty-two cases (32.8%) were performed at UAH, with 168 cases (67.2%) at other hospitals. Polyps were removed by gastroenterologists (n=215, 86.0%), surgeons (n=26, 10.4%), and others (n=9, 3.6%).

Fifty-two patients (20.8%) had no formal follow up on electronic health records, while 198 patients (79.2%) had a repeat colonoscopy. 57 patients (29.1 %) had a repeat colonoscopy within 180 days. The median follow-up time was 224 days (IQR 172–365).

Of the 82 cases performed at UAH, 74 (90.2%) had follow up. Out of the 168 cases at the other hospitals, 124 (73.8%) had follow up (p&lt;0.01). Sixteen (21.9%) and 41 (33.3%) cases were followed up within 180days at UAH and other hospitals, respectively (p=0.09).

Of the 74 cases with follow up at UAH, 12 (15.7%) had residual tissue confirmed by pathology. Of the 124 cases at other hospitals, 26 (21.0%) had follow up (p=0.41). Median polyp size was 2.5cm (IQR 2.0cm - 3.5cm)

Conclusions

Only 29.1% of patients with large sessile polyp removal in the Edmonton zone had a repeat colonoscopy within 180 days. Patients with large polypectomy performed at the academic hospital were more likely to be followed up compared to non-academic hospitals. Further validation studies with larger data sets are needed. These findings highlight the need for standardized pathways to appropriately manage and survey large polyps post-EMR.

Funding Agencies

None

A27 INCREASING INCIDENCE OF COLORECTAL CANCER IN ADULTS UNDER AGE OF 50 IN ALBERTA

Background

Overall colorectal cancer (CRC) incidence has been decreasing in Canada since the early 2000s, most likely due to increased use of colorectal cancer screening for adults over the age of 50. However, the incidence of CRC may be rising in adults younger than age 50 both in Canada and the USA. The American Cancer Society in 2018 issued a qualified recommendation that people with an average risk of CRC should start screening at age 45. The burden of CRC in adults under the age of 50 is not well-characterized in Alberta.

Aims

The aim of this study is to determine the incidence trends in colorectal cancer in adults under the age of 50 compared to those over the age of 50 in Alberta.

Methods

This cohort study determined the incidence of colorectal cancer in patients under the age of 50 compared to those over the age of 50 reported to the Alberta Cancer Registry (ACR) from 2010 to 2017. Annualized percentage changes (APCs) in incidence rate were estimated using the Joinpoint Regression Program 4.7.0.0 (Nation Cancer Institute). APCs in relative risk of CRC in different age groups compared to the 50–74 age group were also estimated in the same methodology.

Results

From 2010 to 2017 there were 17167 incident cases of colorectal cancer. Of these, 92% were in adults over the age of 50 while 8% were in those under the age of 50. For adults under the age of 50, incidence of CRC increased from 6 to 7.2 per 100,000 with a mean annual percentage change of 2.58% between 2010 and 2017. This is in contrast to adults over the age of 50, where the incidence of CRC decreased from 170 to 128 per 100,000 with a mean annual percentage change of -1.64% from 2010 to 2015 and -9.42% from 2015 to 2017. Compared to the 50–74 age group, the average relative risk of CRC in the 46–49 age group is 0.26 with an annual increase of 0.55%; while in the 40–45 age group the average relative risk of CRC is 0.15 with an annual increase of 2.61%.

Conclusions

Similar to national incidence trends, the incidence of CRC in adults under the age of 50 is increasing in Alberta. Although the overall incidence in this population is relatively low, suspicion of CRC in adults under age 50 can help prevent delays in diagnosis.

Funding Agencies

None

[Tumor derived IgG suppress the proliferation of T cells in cord blood]

OBJECTIVE

To explore the function of tumor derived IgG (tIgG) and whether the tIgG can inhibit T cells activity.

METHODS

The tIgG was purified from ovarian cancer tissue. The cord blood monocyte cells (CBMC) and cord blood lymphocyte (CBL) were isolate from human umbilical cord blood. The CBMC and CBL were stimulated with phytohaemagg lutinin (PHA) in order to let the CBMC and CBL in the state of proliferation. Carboxyfluorescein succinimidyl amino ester (CFSE) was cultured with CBMC and CBL. CFSE had no cell toxicity, which could penetrate through the cell membrane and combine the intracellular protein. The fluorescence intensity decreased with the proliferation of cells step by step, so the proliferation of these cells could be detected in flow ctytometry. The tIgG which was purified from ovarian cancer tissue was divided into three groups, 1 mg/L group, 10 mg/L group, and 100 mg/L group, and the intravenous immunoglobulin (IVIG) was also divided into three groups too. The CBMC and CBL were treated by tIgG with 1 mg/L, 10 mg/L, and 100 mg/L in order to observe the proliferation of T cells. The cells were treated with IVIG as a positive control group, and the cells were treated with phosphate buffer saline (PBS) as a negative control. The proliferation of CD4⁺ or CD8⁺ T cells were detected in CBMC and CBL. The proliferation of the T cells in CBMC and CBL after 64 h and 86 h were detected.

RESULTS

In the system of CBMC, the tIgG could suppress the proliferation of CD4⁺ or CD8⁺ T cells. The results could also be found in the system of CBL. The CD4⁺ or CD8⁺ T cells in the group which were treated with PBS were more active than those in the group which were treated with tIgG and IVIG. The suppression in the group which were treated with tIgG, was stronger than that in the group treated with IVIG. In addition, the suppression of T cells in the group which were stimulated with tIgG as 100 mg/L was more effective than that in the group which were stimulated with tIgG as 10 mg/L. This could prove that tIgG had the function of immunomodulation.

CONCLUSION

The tIgG can be involved in immune escape of cancer.

A SNP panel and online tool for checking genotype concordance through comparing QR codes

In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (forQR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

Expressed sequence tag analysis of functional genes associated with adventitious rooting in Liriodendron hybrids

Liriodendron hybrids (Liriodendron chinense x L. tulipifera) are important landscaping and afforestation hardwood trees. To date, little genomic research on adventitious rooting has been reported in these hybrids, as well as in the genus Liriodendron. In the present study, we used adventitious roots to construct the first cDNA library for Liriodendron hybrids. A total of 5176 expressed sequence tags (ESTs) were generated and clustered into 2921 unigenes. Among these unigenes, 2547 had significant homology to the non-redundant protein database representing a wide variety of putative functions. Homologs of these genes regulated many aspects of adventitious rooting, including those for auxin signal transduction and root hair development. Results of quantitative real-time polymerase chain reaction showed that AUX1, IRE, and FB1 were highly expressed in adventitious roots and the expression of AUX1, ARF1, NAC1, RHD1, and IRE increased during the development of adventitious roots. Additionally, 181 simple sequence repeats were identified from 166 ESTs and more than 91.16% of these were dinucleotide and trinucleotide repeats. To the best of our knowledge, the present study reports the identification of the genes associated with adventitious rooting in the genus Liriodendron for the first time and provides a valuable resource for future genomic studies. Expression analysis of selected genes could allow us to identify regulatory genes that may be essential for adventitious rooting.

Up-and-down shift in residence depth of slickheads (Alepocephalidae) revealed by otolith stable oxygen isotopic composition

Otolith δ(18)O profiles for four slickhead species (Alepocephalidae) suggested that Alepocephalus umbriceps, Talismania okinawensis and Rouleina watasei migrated hundreds of metres to shallower depths during the juvenile to young stages before returning to their original depth or even deeper waters. Xenodermichthys nodulosus gradually shifted residence depth from shallow to deeper water during their life. These migratory patterns indicated that the slickheads examined had allopatric residence depths at different life stages, which might enhance the pelagic survival and growth rates of the juvenile and young fishes.

Vertical habitat shift of viviparous and oviparous deep-sea cusk eels revealed by otolith microstructure and stable-isotope composition

Otolith stable-oxygen-isotope composition and microstructure were analysed in order to investigate the vertical habitat shift of deep-sea cusk eels (Ophidiiformes). Otolith δ¹⁸ O profiles suggested that both viviparous blind cusk eels and oviparous cusk eels experienced a pelagic larval stage and then settled to the deep-sea floor over a vertical distance that ranged among individuals from 200 to >1000 m. This result shows that the larvae of viviparous Barathronus maculatus undertake an ontogenetic vertical migration after a period of larval drift that may facilitate their wide distribution on the sea floor.

High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline

Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient Collaborative Cross to investigate the roles of sex and genetic background in mammalian recombination. Our results confirm the observation that map length is longer when measured through female meiosis than through male meiosis, but we find that this difference is modified by genotype at loci on both the X chromosome and the autosomes. In addition, we report a striking concentration of crossovers in the distal ends of autosomes in male meiosis that is absent in female meiosis. The presence of this pattern in both single- and double-recombinant chromosomes, combined with the absence of a corresponding asymmetry in the distribution of double-strand breaks, indicates a regulated sequence of events specific to male meiosis that is anchored by chromosome ends. This pattern is consistent with the timing of chromosome pairing and evolutionary constraints on male recombination. Finally, we identify large regions of reduced crossover frequency that together encompass 5% of the genome. Many of these "cold regions" are enriched for segmental duplications, suggesting an inverse local correlation between recombination rate and mutation rate for large copy number variants.

Imputation of coding variants in African Americans: better performance using data from the exome sequencing project

SUMMARY

Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3-11.4% for coding variants with minor allele frequency <1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2's two-panel combination.

CONTACT

yunli@med.unc.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A comprehensive SNP and indel imputability database

MOTIVATION

Genotype imputation has become an indispensible step in genome-wide association studies (GWAS). Imputation accuracy, directly influencing downstream analysis, has shown to be improved using re-sequencing-based reference panels; however, this comes at the cost of high computational burden due to the huge number of potentially imputable markers (tens of millions) discovered through sequencing a large number of individuals. Therefore, there is an increasing need for access to imputation quality information without actually conducting imputation. To facilitate this process, we have established a publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major populations and covering multiple GWAS genotyping platforms.

RESULTS

SNP and indel imputability information can be retrieved through a user-friendly interface by providing the ID(s) of the desired variant(s) or by specifying the desired genomic region. The query results can be refined by selecting relevant GWAS genotyping platform(s). This is the first database providing variant imputability information specific to each continental group and to each genotyping platform. In Filipino individuals from the Cebu Longitudinal Health and Nutrition Survey, our database can achieve an area under the receiver-operating characteristic curve of 0.97, 0.91, 0.88 and 0.79 for markers with minor allele frequency >5%, 3-5%, 1-3% and 0.5-1%, respectively. Specifically, by filtering out 48.6% of markers (corresponding to a reduction of up to 48.6% in computational costs for actual imputation) based on the imputability information in our database, we can remove 77%, 58%, 51% and 42% of the poorly imputed markers at the cost of only 0.3%, 0.8%, 1.5% and 4.6% of the well-imputed markers with minor allele frequency >5%, 3-5%, 1-3% and 0.5-1%, respectively.

AVAILABILITY

http://www.unc.edu/∼yunmli/imputability.html

MaCH-admix: genotype imputation for admixed populations

Imputation in admixed populations is an important problem but challenging due to the complex linkage disequilibrium (LD) pattern. The emergence of large reference panels such as that from the 1,000 Genomes Project enables more accurate imputation in general, and in particular for admixed populations and for uncommon variants. To efficiently benefit from these large reference panels, one key issue to consider in modern genotype imputation framework is the selection of effective reference panels. In this work, we consider a number of methods for effective reference panel construction inside a hidden Markov model and specific to each target individual. These methods fall into two categories: identity-by-state (IBS) based and ancestry-weighted approach. We evaluated the performance on individuals from recently admixed populations. Our target samples include 8,421 African Americans and 3,587 Hispanic Americans from the Women' Health Initiative, which allow assessment of imputation quality for uncommon variants. Our experiments include both large and small reference panels; large, medium, and small target samples; and in genome regions of varying levels of LD. We also include BEAGLE and IMPUTE2 for comparison. Experiment results with large reference panel suggest that our novel piecewise IBS method yields consistently higher imputation quality than other methods/software. The advantage is particularly noteworthy among uncommon variants where we observe up to 5.1% information gain with the difference being highly significant (Wilcoxon signed rank test P-value < 0.0001). Our work is the first that considers various sensible approaches for imputation in admixed populations and presents a comprehensive comparison.

Genotype imputation of Metabochip SNPs using a study-specific reference panel of ~4,000 haplotypes in African Americans from the Women's Health Initiative

Genetic imputation has become standard practice in modern genetic studies. However, several important issues have not been adequately addressed including the utility of study-specific reference, performance in admixed populations, and quality for less common (minor allele frequency [MAF] 0.005-0.05) and rare (MAF < 0.005) variants. These issues only recently became addressable with genome-wide association studies (GWAS) follow-up studies using dense genotyping or sequencing in large samples of non-European individuals. In this work, we constructed a study-specific reference panel of 3,924 haplotypes using African Americans in the Women's Health Initiative (WHI) genotyped on both the Metabochip and the Affymetrix 6.0 GWAS platform. We used this reference panel to impute into 6,459 WHI SNP Health Association Resource (SHARe) study subjects with only GWAS genotypes. Our analysis confirmed the imputation quality metric Rsq (estimated r(2) , specific to each SNP) as an effective post-imputation filter. We recommend different Rsq thresholds for different MAF categories such that the average (across SNPs) Rsq is above the desired dosage r(2) (squared Pearson correlation between imputed and experimental genotypes). With a desired dosage r(2) of 80%, 99.9% (97.5%, 83.6%, 52.0%, 20.5%) of SNPs with MAF > 0.05 (0.03-0.05, 0.01-0.03, 0.005-0.01, and 0.001-0.005) passed the post-imputation filter. The average dosage r(2) for these SNPs is 94.7%, 92.1%, 89.0%, 83.1%, and 79.7%, respectively. These results suggest that for African Americans imputation of Metabochip SNPs from GWAS data, including low frequency SNPs with MAF 0.005-0.05, is feasible and worthwhile for power increase in downstream association analysis provided a sizable reference panel is available.

The relationship between aortic stiffness and changes in retinal microvessels among Asian ischemic stroke patients

Large-artery stiffness is a risk factor for stroke, including cerebral small-vessel disease. Retinal microvascular changes are thought to mirror those in cerebral microvessels. We investigated the relationship between aortic stiffness and retinal microvascular changes in Asian ischemic stroke patients. We studied 145 acute ischemic stroke patients in Singapore who had aortic stiffness measurements using carotid-femoral pulse wave velocity (cPWV). Retinal photographs were assessed for retinal microvessel caliber and qualitative signs of focal arteriolar narrowing, arteriovenous nicking and enhanced arteriolar light reflex. Aortic stiffening was associated with retinal arteriolar changes. Retinal arteriolar caliber decreased with increasing cPWV (r=-0.207, P=0.014). After adjusting for age, gender, hypertension, diabetes, mean arterial pressure and small-vessel stroke subtype, patients within the highest cPWV quartile were more likely to have generalized retinal arteriolar narrowing defined as lowest caliber tertile (odds ratio (OR) 6.84, 95% confidence interval (CI) 1.45-32.30), focal arteriolar narrowing (OR 13.85, CI 1.82-105.67), arteriovenous nicking (OR 5.08, CI 1.12-23.00) and enhanced arteriolar light reflex (OR 3.83, CI 0.89-16.48), compared with those within the lowest quartile. In ischemic stroke patients, aortic stiffening is associated with retinal arteriolar luminal narrowing as well as features of retinal arteriolosclerosis.

Genetic analysis of complex traits in the emerging Collaborative Cross

The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites-all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits.

Efficient genome ancestry inference in complex pedigrees with inbreeding

Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation.

Results: We present an accurate and efficient method that can accept complex pedigrees with inbreeding in inferring genome ancestry. Inbreeding is a commonly used process in generating genetically diverse and reproducible animals. It is often carried out for many generations and can account for most of the computational complexity in real-world model animal pedigrees. Our method builds a hidden Markov model that derives the ancestry probabilities through inbreeding process without explicit modeling in every generation. The ancestry inference is accurate and fast, independent of the number of generations, for model animal resources such as the Collaborative Cross (CC). Experiments on both simulated and real CC data demonstrate that our method offers comparable accuracy to those methods that build an explicit model of the entire pedigree, but much better scalability with respect to the pedigree size.

Contact:weiwang@cs.unc.edu

Semi-nested PCR detection of Babesia orientalis in its natural hosts Rhipicephalus haemaphysaloides and buffalo

Babesiosis has recently been recognized as an emerging infectious disease of buffalo in China. In order to investigate the epidemiology and enzootic potential of this parasite in Hubei province, we sought to develop a semi-nested PCR to detect Babesia orientalis in buffalo and the potential tick vector-Rhipicephalus haemaphysaloides by amplifying a specific 257bp fragment of B. orientalis 18S rRNA gene. The practical limit of detection showed that it had high sensitivity and an approximate parasitemia of 0.00000012% was detected by the PCR system. The blood samples of 121 asymptomatic buffaloes collected from four babesia endemic counties and that of 71 asymptomatic buffaloes collected from three babesia free counties in Hubei province of China were examined for the presence of B. orientalis using both Wright-Giemsa stained blood smear and semi-nested PCR. Microscopic examination revealed that 5/121 animals were positive, whereas 24/121 animals were positive by the semi-nested PCR assay. Of 378 ticks (R. haemaphysaloides) collected from buffaloes and examined by the semi-nested PCR, 35 were positive. The results showed that the semi-nested PCR was a useful method to investigate the epidemiology of buffalo babesiosis (B. orientalis), which is widely distributed in Hubei province, China.

Study on some molecular characterization of Babesia orientalis

The study on buffalo babesiosis indicated that its pathogen was different from other Babesia on many aspects such as morphology, transmission and pathogenicity. Therefore, it was named as a new species-Babesia orientalis. In order to prove the validity of this taxon, molecular taxonomic study on the pathogen was done in this experiment. The complete 18S rRNA gene sequence of B. orientalis was determined by PCR. It was sequenced and blasted. The results indicated that the classification of the parasite belonged to the genus Babesia. The 1700 bp complete sequence was compared with 15 other Babesia sp. available in GenBank. The data were analyzed and a phylogenetic tree was established. The results indicated that the hereditary distance of the parasite was close to that of Babesia sp. from South Africa and Babesia ovis, and the hereditary distance was far from Babesia bigemina and B. bovis.

Analysis of factors affecting the epidemiology of tuberculosis in China

SETTING

The tuberculosis (TB) epidemic situation is both a public health problem and a socio-economic issue in China.

OBJECTIVE

To examine the effects of socio-economic development and of the TB control strategy on the TB epidemic in China.

METHODS

Based on the four National Epidemiological Surveys of TB and the indices of socio-economic development in China, correlation co-efficiency was used to analyse the relationship between changes in the TB epidemic situation, the socio-economic level and the Health V TB control Project.

RESULTS

The prevalence of smear-positive TB had significant medium correlation with the per capita net income of the rural population, the consumption level of the urban population, the per capita GDP, the population density, and the proportion of rural to total population, among which the correlation with the first four was negative and with the last was positive. The decline in prevalence in the project areas was much greater than in the non-project areas (44.4% vs. 12.3%), while their GDP increases were similar.

CONCLUSION

With socio-economic development, correlation between the socio-economic indices and the TB epidemic becomes more significant. The TB control project is vital to reduce the prevalence of TB in China.

A 13-year study of antimicrobial susceptibility of common gram-negative bacteria isolated from the bloodstream in a teaching hospital

The choice of antimicrobial therapy for the treatment of bacteremia is often empirical and based on the knowledge of susceptibility profiles of the most common bacteria. We analyzed blood culture isolates from a teaching hospital for 13 years prospectively. This study examined the susceptibility profiles of 6,616 gram-negative bacteria. Escherichia coli ranked among the commonest bacteria, representing 43.6% (2,890) of all gram-negative isolates. Klebsiella sp. ranked second, 17.7% (1,171) and 16.7% were resistant to ceftazidime in 1997. There was a trend towards an increase in resistance to fluoroquinolones in the common gram-negative bacteria. Imipenem was the most active agent against gram-negative bacteria. The results of the susceptibility of gram-negative bacteria causing bacteremia provide valuable information for implementing the appropriate chemotherapy for bacteremia.

In vitro activity of trovafloxacin (CP 99,219), a new fluoroquinolone against hospital isolates

The susceptibility of 492 Enterobacteriaceae, 227 other gram-negative bacteria, 448 gram-positive bacteria and 108 anaerobic organisms was determined by the agar dilution method against trovafloxacin and other antibiotics. Trovafloxacin was highly active against most of the Enterobacteriaceae including Enterobacter spp. and Citrobacter spp. [minimum inhibitory concentration (MIC)90 <1 mg/l], Acinetobacter spp. and Pseudomonas aeruginosa (MIC90 = 0.25 and 2 mg/l, respectively). The antimicrobial activity was extended to the gram-positive bacteria including streptococci, Streptococcus pneumoniae, coagulase-negative staphylococci and methicillin-sensitive Staphylococcus aureus with MIC90 <1 mg/l. Enterococci and methicillin-resistant S. aureus were inhibited (MIC90 = 2 mg/l; sparfloxacin and ciprofloxacin were 16 and 64 mg/l, respectively). Almost all anaerobic organisms were inhibited by trovafloxacin (MIC90 = 1 mg/l).

Effects of blood transfusion and cyclosporin on rabbit corneal graft survival

Blood transfusion prolongs renal, cardiac, and skin allograft survival, but promotes rejection of bone marrow allografts. At present, it is unclear whether transfusion induces allograft tolerance or sensitization in corneal transplants. We performed eccentric penetrating keratoplasty on New Zealand albino rabbits, using Dutch rabbits as donors. Twenty-four recipient rabbits were randomly allocated into four groups. The control group received no pretreatment. The other three groups received a donor-specific whole-blood transfusion and/or cyclosporin seven days before the corneal transplants. A single blood transfusion accelerated allograft rejection by an average of 8.8 days (p = 0.0005). In contrast, a single cyclosporin pretreatment prolonged graft survival by an average of 5.3 days (p = 0.02). There was no evidence of interaction effects between transfusion and cyclosporin (p = NS). Therefore, unlike renal, cardiac, and skin allografts and similar to bone marrow allografts, prior blood transfusion accelerates corneal allograft rejection in our rabbit model. Although our data can not be extrapolated to human corneal transplants, our results raise the question whether blood transfusion can sensitize humans to corneal allografts.