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Purpose: A clinically meaningful attribute of some immune-oncology (IO) regimens is potential durable clinical benefit during a treatment-free interval. We characterize treatment-free survival (TFS) with and without ongoing toxicity in trials of frontline IO-VEGF tyrosine kinase inhibitor (TKI) combinations in patients with advanced renal cell carcinoma (aRCC)., Experimental Design: Individual patient data were pooled by treatment arm from randomized trials submitted to the FDA evaluating IO-TKI combination in treatment-naïve aRCC with at least 30 months of median follow-up. OS, TFS, TFS with and without toxicity, and time to all protocol therapy cessation were assessed. TFS was estimated by 30-month restricted mean times, defined as area between Kaplan-Meier curves for two time-to-event endpoints originating at randomization: time to all protocol therapy cessation and time to subsequent systemic therapy initiation or death., Results: Three trials met criteria for analysis; 1,183 patients received IO-TKI versus 1,184 on control arms receiving TKI alone (sunitinib, SUN). IO-TKI and SUN groups spent 9% {2.7 months [95% confidence interval (CI), 1.8-3.5]} and 10% [2.9 months (95% CI, 2.1-3.8)] of the 30-month period alive and treatment-free, respectively. Mean TFS without grade ≥3 toxicity was 1.7 and 2.3 months in IO-TKI and SUN groups, respectively., Conclusions: In this post hoc partitioned survival analysis, TFS and TFS without toxicity appeared similar in the IO-TKI group compared with the SUN group. These findings may reflect contin-uation of TKI until progression per protocol design in all trials and discontinuation of IO after 2 years in two trials. See related commentary by Stadler and Karrison, p. 3098., (©2024 American Association for Cancer Research.)

Summary: While the current approach to precursor hematologic conditions is to "watch and wait," this may change with the development of therapies that are safe and extend survival or delay the onset of symptomatic disease. The goal of future therapies in precursor hematologic conditions is to improve survival and prevent or delay the development of symptomatic disease while maximizing safety. Clinical trial considerations in this field include identifying an appropriate at-risk population, safety assessments, dose selection, primary and secondary trial endpoints including surrogate endpoints, control arms, and quality-of-life metrics, all of which may enable more precise benefit-risk assessment., (©2024 American Association for Cancer Research.)

The narrow eligibility criteria may contribute to the underrepresentation of racial and ethnic subgroups in cancer clinical trials. We conducted a retrospective pooled analysis of multicenter global clinical trials submitted to the US Food and Drug Administration between 2006 and 2019 to support the approval of the use of multiple myeloma (MM) therapies that analyze the rates and reasons for trial ineligibility based on race and ethnicity in MM clinical trials. Race and ethnicity were coded per Office of Management and Budget standards. Patients flagged as having screen failures were identified as ineligible. Ineligibility rates were calculated as the percentage of patients who were ineligible compared with the screened population within the respective racial and ethnic subgroups. Trial eligibility criteria were grouped into specific categories to analyze the reasons for trial ineligibility. Black patients (24%) and other (23%) race subgroups had higher ineligibility rates than White patients (17%). The Asian race had the lowest ineligibility rate (12%) among all racial subgroups. Failure to meet the hematologic laboratory criteria (19%) and treatment-related criteria (17%) were the most common reasons for ineligibility among Black patients and were more common in Black patients than in other races. Failure to meet disease-related criteria was the most common reason for ineligibility among White (28%) and Asian (29%) participants. Our analysis indicates that specific eligibility criteria may contribute to enrollment disparities for racial and ethnic subgroups in MM clinical trials. However, the small number of screened patients in the underrepresented racial and ethnic subgroups limits definitive conclusions.

Background: Patients of certain racial and ethnic groups have been underrepresented in clinical trials for treatment of malignancy. One potential barrier to participation is entry requirements that lead to patients in various racial and ethnic groups not meeting eligibility criteria for studies (ie, "screen failure"). The objective of this study was to analyze the rates and reasons for trial ineligibility by race and ethnicity in trials of acute myeloid leukemia (AML) submitted to the U.S. Food and Drug Administration (FDA) between 2016 and 2019., Materials and Methods: Multicenter, global clinical trials submitted to the FDA to support AML drugs and biologics. We examined the rate of ineligibility among participants screened for studies of AML therapies submitted to the FDA from 2016 to 2019. Data were extracted from 13 trials used in approval evaluations, including race, screen status, and reason for ineligibility., Results: Overall, patients in historically underrepresented racial and ethnic groups were less likely to meet entry criteria for studies compared to White patients, with 26.7% of White patients, 29.4% of Black patients, and 35.9% of Asian patients not meeting entry criteria. Lack of relevant disease mutation was the reason for ineligibility more frequently among Black and Asian patients. The findings were limited by the small number of underrepresented patients screened for participation., Conclusion: Our results suggest that entry requirements for studies may put underrepresented patients at a disadvantage, leading to less eligible patients and thus lower participation in clinical trials., (Published by Elsevier Inc.)

Importance: Single-arm trials have allowed for transformative therapies to be made available to patients expeditiously. However, using single-arm trials to support drug approval presents several challenges that must be carefully considered., Observations: Between January 1, 2002, and December 31, 2021, the US Food and Drug Administration granted 176 new malignant hematology and oncology indications based on single-arm trials, including 116 accelerated approvals (AAs) and 60 traditional approvals. Overall, 87 approvals (49%) were for new molecular entities or original biologics and 89 (51%) were supplemental indications. Response rate (RR) was the most common end point used to support approval in these single-arm trials (173 of 176 [98%]). Of the 116 AAs based on single-arm trials, 45 (38%) fulfilled their postmarketing requirement to verify clinical benefit, 61 (52%) are pending verification of benefit, and 10 (9%) were withdrawn from the market as of December 31, 2021. Most (56 of 61 [92%]) AAs based on single-arm trials pending verification of benefit occurred during the previous 5 years and have ongoing confirmatory trials as of December 2021., Conclusions and Relevance: Single-arm trials have been a common development strategy to support regulatory approval as early-stage expansion cohorts with promising durable RRs have become more prevalent. In the appropriate context, single-arm trials using durable RRs can allow patients expedited access to novel therapies and will continue to serve a role in advancing drug development in oncology. However, single-arm trials have a smaller noncomparative safety data set, inability to use time-to-event end points, and other limitations that require careful consideration within the context of the disease and available therapies. The randomized clinical trial remains the preferred approach in clinical investigation.

In January 2021, the U.S. Food and Drug Administration (FDA) approved crizotinib for pediatric patients 1 year and older and young adults with relapsed or refractory systemic anaplastic large cell lymphoma (sALCL). This is the first approval for pediatric sALCL. Approval was based on a single-arm trial of crizotinib monotherapy that included 26 patients, aged 1-20 years, with previously treated sALCL. Efficacy was based on centrally assessed objective response rate (88%) and duration of response. Herein, we highlight unique aspects of the regulatory review, including extension of the indication to young adults, postmarketing safety, and dose optimization strategies., (Published 2022. This article is a U.S. Government work and is in the public domain in the USA.)

As cancer immunotherapies continue to expand across all areas of oncology, it is imperative to establish a standardized approach for defining and capturing clinically important toxicities, such as cytokine release syndrome (CRS). In this paper, we provide considerations for categorizing the variety of adverse events that may accompany CRS and for recognizing that presentations of CRS may differ among various immunotherapies (e.g., monoclonal antibodies, CAR T cell therapies and T cell engagers, which can include bispecific antibodies and other constructs). The goals of this paper are to ensure accurate and consistent identification of CRS in patients receiving immunotherapies in clinical studies to aid in reporting; enable more precise evaluation of the therapeutic risk-benefit profile and cross-study analyses; support evidence-based monitoring and management of important toxicities related to cancer immunotherapies; and improve patient care and outcomes. These efforts will become more important as the number and variety of molecular targets for immunotherapies broaden and as therapies with novel mechanisms continue to be developed., (Copyright © 2022. Published by Elsevier Inc.)

Remarkable improvements in outcomes for many haematological malignancies have been driven primarily by a proliferation of novel therapeutics over the past two decades. Targeted agents, immune and cellular therapies, and combination regimens have adverse event profiles distinct from conventional finite cytotoxic chemotherapies. In 2018, a Commission comprising patient advocates, clinicians, clinical investigators, regulators, biostatisticians, and pharmacists representing a broad range of academic and clinical cancer expertise examined issues of adverse event evaluation in the context of both newer and existing therapies for haematological cancers. The Commission proposed immediate actions and long-term solutions in the current processes in adverse event assessment, patient-reported outcomes in haematological malignancies, toxicities in cellular therapies, long-term toxicity and survivorship in haematological malignancies, issues in regulatory approval from an international perspective, and toxicity reporting in haematological malignancies and the real-world setting. In this follow-up report, the Commission describes progress that has been made in these areas since the initial report., Competing Interests: Declaration of interests CAJ reports personal fees from Kite/Gilead, Novartis, BMS/Celgene, Precision Biosciences, Nkarta, AbbVie, Bluebird Bio, Epizyme, Lonza, and Ipsen, outside the submitted work. DV reports personal fees from AbbVie, AstraZeneca, Kite/Gilead, Kyowa Kirin, Sandoz Canada, Nanostring, Immunovaccine, Roche, Celgene, Seattle Genetics, and Lundbeck/Teva; and research funding (to his institution) from AstraZeneca and Roche, outside the submitted work. GV reports personal fees from Roche, Eisai, Novartis, and Seattle Genetics; and grants from Breast Cancer Now, EORTC, Yorkshire Cancer Research, Pfizer, and IQVIA, outside the submitted work. JaG reports grants from Novartis, Pfizer, Bristol-Myers Squibb, Incyte, Takeda, Servier, UCB, Amgen, Roche, Alnylam, Boehringer-Ingelheim, Biomarin, Daiichi Sankyo, Janssen, Sobi, Gilead, and Bayer, outside the submitted work. JFS reports grants, personal fees, non-financial support, and speakers bureau participation for AbbVie and Roche; personal fees and non-financial support from BMS; personal fees from Genentech, Mei Pharma, Morphosys, Sunesis, and Takeda; and grants and personal fees from Janssen, outside the submitted work. JRW reports personal fees from Merck, Celgene, Cidara, ReViral, Shire, Ansun, Janssen, and Behring, outside the submitted work. KM reports grants from Pfizer, outside the submitted work. LN reports honoraria from ADC Therapeutics, Bayer, and Morphosys; grants and honoraria from BMS/Celgene, Epizyme, Genentech, Gilead/Kite, Novartis, Pfizer, Takeda, and TG Therapeutics; and grants from Caribou Biosciences and IGM Biosciences, outside the submitted work. M-VM reports personal fees from Janssen, BMS-Celgene, Takeda, Amgen, Sanofi, Oncopeptides, Adaptive, GSK, AbbVie, Roche, Seattle Genetics, Pfizer, and Regeneron, outside the submitted work. MH reports grants from U24 CA076518 National Cancer Institute and grants from U24 HL138660 National Heart, Lung and Blood Institute, during the conduct of the study; grants from Amgen, Vor BioPharma, Gamida Cell, Medac, Magenta Therapeutics, Astellas, OncoImmune, and Genentech; and consulting fees from AlloVir, outside the submitted work. MJM reports personal fees from Genentech, Roche, GlaxoSmithKline, Bayer, Pharmacyclics, Janssen, Seattle Genetics, Immunovaccine Technology, and Takeda; consulting advisory roles for Merck, Juno Therapeutics, Teva, and Daiichi Sankyo; research funding from IGM Biosciences; and a consulting advisory role and research funding from Rocket Medical, outside the submitted work. PM reports personal fees from Janssen, Celgene, BMS, AbbVie, Sanofi, and Amgen, outside the submitted work. PS reports research support from Celgene, Amgen, Janssen, and Takeda; and honoraria and serving on advisory boards for Celgene, Janssen, Amgen, Takeda, BMS, and SkylineDx, outside the submitted work. SS reports grants and consulting fees from BMS, Janssen, and Magenta; grants from Allogene; and consulting fees from Oncopeptides, outside the submitted work. TCE-G reports previous employment at Roche and personal fees from AbbVie, outside the submitted work. All other authors declare no competing interests., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Competing Interests: We declare no competing interests.

African Americans (AAs) have a higher incidence of multiple myeloma (MM) than White patients. Mortality is also higher in AAs compared with White patients. AAs more commonly have immunoglobulin H translocations t(11;14) and t(14;16) compared with White patients. We sought to characterize the demographic representation in MM clinical trials and evaluate outcomes based on race and ethnicity. We conducted a pooled analysis of all trials submitted to the US Food and Drug Administration (FDA) to support approval of a MM therapeutic between 2006 and 2019. Demographic characteristics were analyzed descriptively. An age-adjusted stratified Cox regression model was used to evaluate the relationship between time-to-event outcomes and race and ethnicity. Nineteen global trials comprising 10 157 patients were pooled. White, Asian, and Black patients comprised 84%, 7%, and 4% of the dataset, respectively; Hispanic patients comprised 4%. The age-adjusted overall survival hazard ratio (HR) for Black compared with White patients was 0.89 (95% confidence interval [CI], 0.75-1.05). The age-adjusted HR for US Black vs US White patients was 0.82 (95% CI, 0.66-1.02). For rest-of-world (RoW) Black vs RoW White patients, the HR was 1.31 (95% CI, 0.97-1.77). Black and Hispanic patients were underrepresented in the trials supporting FDA approval of MM drugs. Black patients were primarily enrolled in the United States. Outcomes in US patients were more favorable compared with those in patients in the RoW. Given the higher incidence of MM in AAs and the different disease characteristics, efforts should be made to improve representation of AAs in MM clinical trials.

Background: To review and summarize all U.S. Food and Drug Administration (FDA) approvals of programmed death (PD)-1 and PD-ligand 1 blocking antibodies (collectively referred to as PD-[L]1 inhibitors) over a 6-year period and corresponding companion/complementary diagnostic assays., Materials and Methods: To determine the indications and pivotal trials eligible for inclusion, approval letters and package inserts available on Drugs@FDA were evaluated for approved PD-[L]1 inhibitors to identify all new indications granted from the first approval of a PD-[L]1 inhibitor on September 4, 2014, through September 3, 2020. The corresponding FDA drug and device reviews from the marketing applications for the approved indications were identified through FDA internal records. Two reviewers independently extracted information for the endpoints, efficacy data, basis for approval, type of regulatory approval, and corresponding in vitro diagnostic device test. The results were organized by organ system and tumor type., Results: Of 70 Biologic Licensing Application or supplement approvals that resulted in new indications, 32 (46%) were granted based on response rate (ORR) and durability of response, 26 (37%) on overall survival, 9 (13%) on progression-free survival, 2 (3%) on recurrence-free survival, and 1 (1%) on complete response rate. Most ORR-based approvals were granted under the accelerated approval provisions and were supported with prolonged duration of response. Overall, 21% of approvals were granted with a companion diagnostic. Efficacy results according to tumor type are discussed., Conclusion: PD-[L]1 inhibitors are an effective anticancer therapy in a subset of patients. This class of drugs has provided new treatment options for patients with unmet need across a wide variety of cancer types. Yet, the modest response rates in several tumor types signal a lack of understanding of the biology of these diseases. Further preclinical and clinical investigation may be required to identify a more appropriate patient population, particularly as drug development continues and additional treatment alternatives become available., Implications for Practice: The number of PD-[L]1 inhibitors in drug development and the associated companion and complementary diagnostics have led to regulatory challenges and questions regarding generalizability of trial results. The interchangeability of PD-L1 immunohistochemical assays between PD-1/PD-L1 drugs is unclear. Furthermore, robust responses in some patients with low levels of PD-L1 expression have limited the use of PD-L1 as a predictive biomarker across all cancers, particularly in the setting of diseases with few alternative treatment options. This review summarizes the biomarker thresholds and assays approved as complementary and companion diagnostics and provides regulatory perspective on the role of biomarkers in oncology drug development., (Published 2021. This article is a U.S. Government work and is in the public domain in the USA. The Oncologist published by Wiley Periodicals LLC on behalf of AlphaMed Press.)

The fifth annual Blood and Marrow Transplant Clinical Trials Network Myeloma Intergroup Workshop on Immune Profiling and Minimal Residual Disease Testing in Multiple Myeloma was conducted as one of the American Society of Hematology Annual Meeting Scientific Workshops on Thursday December 3, 2020. This workshop focused on four main topics: (1) integrating minimal residual disease into clinical trial design and practice; (2) the molecular and immunobiology of disease evolution and progression in myeloma; (3) adaptation of next-generation sequencing, next-generation flow cytometry, and cytometry by time of flight techniques; and (4) chimeric antigen receptor T-cell and other cellular therapies for myeloma. In this report, we provide a summary of the workshop presentations and discuss future directions in the field., (Copyright © 2021 The American Society for Transplantation and Cellular Therapy. All rights reserved.)

African Americans are at higher risk of multiple myeloma (MM) yet underrepresented in clinical trials and reap less benefits from novel therapies of the disease. To improve representation of African Americans in MM clinical trials, researchers, providers, patients, industry partners and regulators at the FDA-AACR workshop developed recommendations to all stakeholders. The outlined principles offer a roadmap to addressing disparities broadly in clinical trials.

The Blood and Marrow Transplant Clinical Trials Network (BMT CTN) Myeloma Intergroup has organized an annual workshop focused on minimal residual disease (MRD) testing and immune profiling (IP) in multiple myeloma since 2016. In 2019, the workshop took place as an American Society of Hematology (ASH) Friday Scientific Workshop titled "Immune Profiling and Minimal Residual Disease Testing in Multiple Myeloma." This workshop focused on 4 main topics: the molecular and immunologic evolution of plasma cell disorders, development of new laboratory- and imaging-based MRD assessment approaches, chimeric antigen receptor T cell therapy research, and statistical and regulatory issues associated with novel clinical endpoints. In this report, we provide a summary of the workshop and discuss future directions., (Copyright © 2020 American Society for Transplantation and Cellular Therapy. All rights reserved.)

Background: The rates of people being overweight and obese are recognised as global public health concerns. Negative attitudes towards obese and overweight people are prevalent among health care professionals. Nurses and nursing students have a significant role in health promotion of people who are obese or overweight and can assist people in achieving healthy lifestyles. However, evidence suggests that nurses and nursing students fail to engage in healthy lifestyles themselves and display negative attitudes towards obese and overweight people. Such negative behaviours put nurses and nursing students in a precarious position when advising overweight and obese people to adopt healthy lifestyles., Objectives: This study aimed to ascertain nursing students' obesity risk knowledge, their attitudes towards obese and overweight people, and their own health promoting lifestyle behaviours., Design: A descriptive correlational study was used., Setting: One university in the United Kingdom., Participants: A total of 210 nursing students enrolled on a university degree course in Adult or Mental Health Nursing in years 1, 2 and 3., Methods: Data were collected using three valid and reliable questionnaires: Obesity Risk Knowledge Scale, Attitudes Towards Obese Persons Scale and the Health Promoting Lifestyle Profile. Dependent variables were correlated with independent variables on field of study, year of study, and gender., Results: Results showed that nursing students engage in unhealthy lifestyle behaviours and fail to meet government recommended levels for physical activity. Nursing students had poor knowledge on obesity risk and displayed neutral attitudes towards overweight and obese people., Conclusions: Educational providers of nursing courses should embrace the need for nursing students to interrogate and enhance their own healthy lifestyle behaviours as an integral component of the pre-registration education course. This may strengthen the credibility and suitability of nursing students as future nurses in health promoting activities of patients who are overweight and obese., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Background: Transitional care programs (TCPs) coordinate care to improve safety and efficiency surrounding hospital discharge. While TCPs have the potential to reduce hospital length of stay and readmissions, their financial implications are less well understood., Objective: To perform a cost-benefit analysis of a previously published neurosurgical TCP implemented at an urban academic hospital from 2013 to 2015., Methods: Patients received intensive preoperative education and framing of expectations for hospitalization, in-hospital discharge planning and medication reconciliation with a nurse educator, and a follow-up phone call postdischarge. The cost-benefit analysis involved program costs (nurse educator salary) and total direct hospital costs within the 30-d perioperative window including readmission costs., Results: The average cost of the TCP was $435 per patient. The TCP was associated with an average total cost reduction of 17.2% (95% confidence interval [CI]: 7.3%-26.7%, P = .001). This decrease was driven by a 14.3% reduction in the average initial admission cost (95% CI: 6.2%-23.7%, P = .001), largely attributable to the 16.3% decrease in length of stay (95% CI: 9.93%-23.49%, P < .001). Thirty-day readmissions were significantly decreased in the TCP group, with a 5.5% readmission rate for controls and 2.4% for TCP enrollees (P = .04). The average cost of readmission was decreased by 71.3% (95% CI: 58.7%-74.7%, P < .01)., Conclusion: This neurosurgical TCP was associated with decreased costs of initial admissions, 30-d readmissions, and total costs of hospitalization alongside previously published decreased length of stay and reduced 30-d readmission rates. These results underscore the clinical and financial feasibility and impact of transitional care in a surgical setting., (Copyright © 2018 by the Congress of Neurological Surgeons.)

The second annual Blood and Marrow Transplant Clinical Trials Network (BMT CTN) Myeloma Intergroup Workshop on Minimal Residual Disease and Immune Profiling was convened on December 7, 2017, at the American Society of Hematology (ASH) meeting. During this workshop, investigators from around the world presented their latest research involving assessment of minimal residual disease (MRD) and immune profiling (IP) in myeloma. This document summarizes the workshop presentations as well as relevant ASH abstracts and focuses on the regulatory issues involved in the integration of MRD and IP assessment in clinical trial design and practice., (Copyright © 2018 American Society for Blood and Marrow Transplantation. All rights reserved.)

Haplotype-resolved genome sequencing promises to unlock a wealth of information in population and medical genetics. However, for the vast majority of genomes sequenced to date, haplotypes have not been determined because of cumbersome haplotyping workflows that require fractions of the genome to be sequenced in a large number of compartments. Here we demonstrate barcode partitioning of long DNA molecules in a single compartment using "on-bead" barcoded tagmentation. The key to the method that we call "contiguity preserving transposition" sequencing on beads (CPTv2-seq) is transposon-mediated transfer of homogenous populations of barcodes from beads to individual long DNA molecules that get fragmented at the same time (tagmentation). These are then processed to sequencing libraries wherein all sequencing reads originating from each long DNA molecule share a common barcode. Single-tube, bulk processing of long DNA molecules with ∼150,000 different barcoded bead types provides a barcode-linked read structure that reveals long-range molecular contiguity. This technology provides a simple, rapid, plate-scalable and automatable route to accurate, haplotype-resolved sequencing, and phasing of structural variants of the genome.

Background: Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transposase-based Nextera method was invented. Nextera combines DNA fragmentation and barcoding in a single tube reaction and therefore enables a very fast workflow to sequencing-ready DNA libraries within a couple of hours. When compared to the traditional ligation-based methods, transposed-based Nextera has a slight insertion bias., Results: Here we present the discovery of a mutant transposase (Tn5-059) with a lowered GC insertion bias through protein engineering. We demonstrate Tn5-059 reduces AT dropout and increases uniformity of genome coverage in both bacterial genomes and human genome. We also observe higher library diversity generated by Tn5-059 when compared to Nextera v2 for human exomes, which leads to less sequencing and lower cost per genome. In addition, when used for human exomes, Tn5-059 delivers consistent library insert size over a range of input DNA, allowing up to a tenfold variance from the 50 ng input recommendation., Conclusions: Enhanced DNA input tolerance of Tn5-059 can translate to flexibility and robustness of workflow. DNA input tolerance together with superior uniformity of coverage and lower AT dropouts extend the applications of transposase based library preps. We discuss possible mechanisms of improvements in Tn5-059, and potential advantages of using the new mutant in varieties of applications including microbiome sequencing and chromatin profiling.

Human T-lymphotropic virus type 1 (HTLV-1) and type 2 (HTLV-2) both cause lifelong persistent infections, but differ in their clinical outcomes. HTLV-1 infection causes a chronic or acute T-lymphocytic malignancy in up to 5% of infected individuals whereas HTLV-2 has not been unequivocally linked to a T-cell malignancy. Virus-driven clonal proliferation of infected cells both in vitro and in vivo has been demonstrated in HTLV-1 infection. However, T-cell clonality in HTLV-2 infection has not been rigorously characterized. In this study we used a high-throughput approach in conjunction with flow cytometric sorting to identify and quantify HTLV-2-infected T-cell clones in 28 individuals with natural infection. We show that while genome-wide integration site preferences in vivo were similar to those found in HTLV-1 infection, expansion of HTLV-2-infected clones did not demonstrate the same significant association with the genomic environment of the integrated provirus. The proviral load in HTLV-2 is almost confined to CD8+ T-cells and is composed of a small number of often highly expanded clones. The HTLV-2 load correlated significantly with the degree of dispersion of the clone frequency distribution, which was highly stable over ∼8 years. These results suggest that there are significant differences in the selection forces that control the clonal expansion of virus-infected cells in HTLV-1 and HTLV-2 infection. In addition, our data demonstrate that strong virus-driven proliferation per se does not predispose to malignant transformation in oncoretroviral infections.

Both early- and late-onset noninfectious pulmonary injury are important contributors to the nonrelapse mortality seen after allogeneic stem cell transplantation (allo-SCT), particularly in subjects conditioned with high-dose total body irradiation (TBI). To characterize the kinetics of recovery from pulmonary injury in long-term survivors, we collected data on 138 subjects who survived > 3 years (median survival, 10.2 years) after predominantly TBI-based allo-SCT from their HLA-matched siblings. Baseline pulmonary function tests served as the reference for subsequent measurements at 3, 5, 10, and 15 years for each survivor. The only parameter showing a clinically and statistically significant decline post-transplant was adjusted diffusion capacity of lung for carbon monoxide (DLCO), which reached a nadir at 5 years but surprisingly normalized at the 10-year mark. Multivariable modeling identified chronic graft-versus-host disease (P < .02) and abnormal baseline-adjusted DLCO (P < .03) as the only significant factors associated with the decline in adjusted DLCO at 5 years but excluded smoking, conditioning intensity, baseline C-reactive protein level, TBI dose to the lungs, disease, and demographic variables. In conclusion, pulmonary injury as monitored by the adjusted DLCO continues to deteriorate in the first 5 years after allo-SCT but recovers at 10 years., (Published by Elsevier Inc.)

DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

Motivation: The relative abundance of retroviral insertions in a host genome is important in understanding the persistence and pathogenesis of both natural retroviral infections and retroviral gene therapy vectors. It could be estimated from a sample of cells if only the host genomic sites of retroviral insertions could be directly counted. When host genomic DNA is randomly broken via sonication and then amplified, amplicons of varying lengths are produced. The number of unique lengths of amplicons of an insertion site tends to increase according to its abundance, providing a basis for estimating relative abundance. However, as abundance increases amplicons of the same length arise by chance leading to a non-linear relation between the number of unique lengths and relative abundance. The difficulty in calibrating this relation is compounded by sample-specific variations in the relative frequencies of clones of each length., Results: A likelihood function is proposed for the discrete lengths observed in each of a collection of insertion sites and is maximized with a hybrid expectation-maximization algorithm. Patient data illustrate the method and simulations show that relative abundance can be estimated with little bias, but that variation in highly abundant sites can be large. In replicated patient samples, variation exceeds what the model implies-requiring adjustment as in Efron (2004) or using jackknife standard errors. Consequently, it is advantageous to collect replicate samples to strengthen inferences about relative abundance.

The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Human T-lymphotropic virus type 1 (HTLV-1) persists by driving clonal proliferation of infected T lymphocytes. A high proviral load predisposes to HTLV-1-associated diseases. Yet the reasons for the variation within and between persons in the abundance of HTLV-1-infected clones remain unknown. We devised a high-throughput protocol to map the genomic location and quantify the abundance of > 91,000 unique insertion sites of the provirus from 61 HTLV-1(+) persons and > 2100 sites from in vitro infection. We show that a typical HTLV-1-infected host carries between 500 and 5000 unique insertion sites. We demonstrate that negative selection dominates during chronic infection, favoring establishment of proviruses integrated in transcriptionally silenced DNA: this selection is significantly stronger in asymptomatic carriers. We define a parameter, the oligoclonality index, to quantify clonality. The high proviral load characteristic of HTLV-1-associated inflammatory disease results from a larger number of unique insertion sites than in asymptomatic carriers and not, as previously thought, from a difference in clonality. The abundance of established HTLV-1 clones is determined by genomic features of the host DNA flanking the provirus. HTLV-1 clonal expansion in vivo is favored by orientation of the provirus in the same sense as the nearest host gene.

Intracellular labels such as dextran coated superparamagnetic iron oxide nanoparticles (SPION), bromodeoxyuridine (BrdU) or green fluorescent protein (GFP) are frequently used to study the fate of transplanted cells by in vivo magnetic resonance imaging or fluorescent microscopy. Bystander uptake of labeled cells by resident tissue macrophages (TM) can confound the interpretation of the presence of intracellular labels especially during direct implantation of cells, which can result in more than 70% cell death. In this study we determined the percentages of TM that took up SPION, BrdU or GFP from labeled bone marrow stromal cells (BMSCs) that were placed into areas of angiogenesis and inflammation in a mouse model known as Matrigel plaque perfusion assay. Cells recovered from digested plaques at various time points were analyzed by fluorescence microscopy and flow cytometry. The analysis of harvested plaques revealed 5% of BrdU(+), 5-10% of GFP(+) and 5-15% of dextran(+) macrophages. The transfer of the label was not dependent on cell dose or viability. Collectively, this study suggests that care should be taken to validate donor origin of cells using an independent marker by histology and to assess transplanted cells for TM markers prior to drawing conclusions about the in vivo behavior of transplanted cells.

Background: Many studies have sought to determine the predictors of institutionalization of patients with dementia. Such studies, performed in developed western societies, have come to various conclusions which may not be supported in an East Asian culture such as that found in Korea., Objectives: This study aimed to determine the factors that predict institutionalization of patients in Korea diagnosed with dementia., Methods: Seventy-nine cases (37 institutionalized, 42 community-dwelling) in the Kwangju area were evaluated for patient characteristics, severity of dementia symptoms, caregiver characteristics, burden and distress. Logistic regression was performed to determine predictors of actual institutionalization., Results: Six predictors of institutionalization were identified. Of these, three were patient-related factors: higher score on the Clinical Dementia Rating, higher score on the Brief Psychiatric Rating Scale, and shorter duration of dementia. The other three were caregiver-related factors: younger age, higher education (formal schooling), and higher cost of home care., Conclusions: As seen in previous western studies, institutionalization of dementia sufferers was influenced by both patient and caregiver factors. But, the specific predictors and their relative influences might be explained best by the particular social, cultural and economic situation in Korea. This study was the first of its kind in Korea and, as such, could serve as a reference for future intra-cultural and cross-cultural comparisons., (Copyright 2002 John Wiley & Sons, Ltd.)