Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high-risk disease.

Genomic events associated with poor outcome in chronic myeloid leukemia (CML) are poorly understood. We performed whole-exome sequencing, copy-number variation, and/or RNA sequencing for 65 patients to discover mutations at diagnosis and blast crisis (BC). Forty-six patients with chronic-phase disease with the extremes of outcome were studied at diagnosis. Cancer gene variants were detected in 15 (56%) of 27 patients with subsequent BC or poor outcome and in 3 (16%) of 19 optimal responders (P = .007). Frequently mutated genes at diagnosis were ASXL1, IKZF1, and RUNX1 The methyltransferase SETD1B was a novel recurrently mutated gene. A novel class of variant associated with the Philadelphia (Ph) translocation was detected at diagnosis in 11 (24%) of 46 patients comprising fusions and/or rearrangement of genes on the translocated chromosomes, with evidence of fragmentation, inversion, and imperfect sequence reassembly. These were more frequent at diagnosis in patients with poor outcome: 9 (33%) of 27 vs 2 (11%) of 19 optimal responders (P = .07). Thirty-nine patients were tested at BC, and all had cancer gene variants, including ABL1 kinase domain mutations in 58%. However, ABL1 mutations cooccurred with other mutated cancer genes in 89% of cases, and these predated ABL1 mutations in 62% of evaluable patients. Gene fusions not associated with the Ph translocation occurred in 42% of patients at BC and commonly involved fusion partners that were known cancer genes (78%). Genomic analysis revealed numerous relevant variants at diagnosis in patients with poor outcome and all patients at BC. Future refined biomarker testing of specific variants will likely provide prognostic information to facilitate a risk-adapted therapeutic approach.

Medication management in dialysis: Barriers and strategies.

People with end-stage kidney disease (ESKD) who require chronic dialysis are often reliant on complicated medication regimens to manage their health conditions. Due to the complexities of the advanced kidney disease, underlying comorbidities, and special instructions, medication regimens for patients on dialysis put patients at high risk for medication therapy problems related to safety, effectiveness, appropriateness, and adherence. This article explores the factors that affect optimal medication use for people on dialysis, including the broader drug use system, and offers recommendations around medication reconciliation, medication review, deprescribing, and considering social determinants of health to improve medication management among patients with ESKD.

Assessment of literacy and numeracy skills related to medication labels in patients on chronic in-center hemodialysis.

OBJECTIVES: Patients on hemodialysis have complicated medication regimens requiring the ability to accurately interpret medication information. Literacy and numeracy skills have been shown to differ by the types of materials provided to patients. The aims of this study were to determine prescription and over-the-counter medication label understanding and to assess the prevalence of low health literacy regarding medication labeling among in-center hemodialysis patients. DESIGN, SETTING AND PARTICIPANTS: The Medication Literacy and Numeracy in Dialysis (MedLitD) tool is an assessment of a person's ability to read and understand medication labels. A comparison with the Rapid Estimate of Adult Literacy in Medicine Short Form (REALM-SF), an established literacy tool, was conducted to determine if there were differences in the literacy results from the 2 tools that could be leveraged to target education initiatives for this specialized population. RESULTS: A total of 110 patients receiving hemodialysis from 3 dialysis facilities in the Capital Region of upstate New York were enrolled in the study. Most patients (77%) achieved a maximum REALM-SF score, indicating a high level of literacy proficiency; however, their MedLitD scores varied. Patients who were 65 years and older had lower scores on the MedLitD tool compared with younger patients. Gender, education, and the number of medications did not influence the MedLitD scores. Only 16% of all participants correctly answered the question asking for an indication of the phosphate binder (PB), although the most patients were currently taking PBs. CONCLUSION: A continuum of medication literacy levels exists among patients on hemodialysis. Appropriate evaluation of medication literacy should be done to better inform individualized education and counseling.

De novo UBE2A mutations are recurrently acquired during chronic myeloid leukemia progression and interfere with myeloid differentiation pathways.

Despite the advent of tyrosine kinase inhibitors, a proportion of chronic myeloid leukemia patients in chronic phase fail to respond to imatinib or to second-generation inhibitors and progress to blast crisis. Until now, improvements in the understanding of the molecular mechanisms responsible for chronic myeloid leukemia transformation from chronic phase to the aggressive blast crisis remain limited. Here we present a large parallel sequencing analysis of 10 blast crisis samples and of the corresponding autologous chronic phase controls that reveals, for the first time, recurrent mutations affecting the ubiquitin-conjugating enzyme E2A gene (UBE2A, formerly RAD6A). Additional analyses on a cohort of 24 blast crisis, 41 chronic phase as well as 40 acute myeloid leukemia and 38 atypical chronic myeloid leukemia patients at onset confirmed that UBE2A mutations are specifically acquired during chronic myeloid leukemia progression, with a frequency of 16.7% in advanced phases. In vitro studies show that the mutations here described cause a decrease in UBE2A activity, leading to an impairment of myeloid differentiation in chronic myeloid leukemia cells.

The impact of multiple low-level BCR-ABL1 mutations on response to ponatinib.

The third-generation tyrosine kinase inhibitor (TKI) ponatinib shows activity against all common BCR-ABL1 single mutants, including the highly resistant BCR-ABL1-T315I mutant, improving outcome for patients with refractory chronic myeloid leukemia (CML). However, responses are variable, and causal baseline factors have not been well-studied. The type and number of low-level BCR-ABL1 mutations present after imatinib resistance has prognostic significance for subsequent treatment with nilotinib or dasatinib as second-line therapy. We therefore investigated the impact of low-level mutations detected by sensitive mass-spectrometry before ponatinib initiation (baseline) on treatment response in 363 TKI-resistant patients enrolled in the PONATINIB for Chronic Myeloid Leukemia Evaluation and Ph(+)Acute Lymphoblastic Leukemia trial, including 231 patients in chronic phase (CP-CML). Low-level mutations were detected in 53 patients (15%, including low-level T315I in 14 patients); most, however, did not undergo clonal expansion during ponatinib treatment and, moreover, no specific individual mutations were associated with inferior outcome. We demonstrate however, that the number of mutations detectable by mass spectrometry after TKI resistance is associated with response to ponatinib treatment and could be used to refine the therapeutic approach. Although CP-CML patients with T315I (63/231, 27%) had superior responses overall, those with multiple mutations detectable by mass spectrometry (20, 32%) had substantially inferior responses compared with those with T315I as the sole mutation detected (43, 68%). In contrast, for CP-CML patients without T315I, the inferior responses previously observed with nilotinib/dasatinib therapy for imatinib-resistant patients with multiple mutations were not seen with ponatinib treatment, suggesting that ponatinib may prove to be particularly advantageous for patients with multiple mutations detectable by mass spectrometry after TKI resistance.

Compound mutations in BCR-ABL1 are not major drivers of primary or secondary resistance to ponatinib in CP-CML patients.

BCR-ABL1 kinase domain mutations can confer resistance to first- and second-generation tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML). In preclinical studies, clinically achievable concentrations of the third-generation BCR-ABL1 TKI ponatinib inhibit T315I and all other single BCR-ABL1 mutants except T315M, which generates a single amino acid exchange, but requires 2 sequential nucleotide exchanges. In addition, certain compound mutants (containing ≥2 mutations in cis) confer resistance. Initial analyses based largely on conventional Sanger sequencing (SS) have suggested that the preclinical relationship between BCR-ABL1 mutation status and ponatinib efficacy is generally recapitulated in patients receiving therapy. Thus far, however, such analyses have been limited by the inability of SS to definitively identify compound mutations or mutations representing less than ~20% of total alleles (referred to as "low-level mutations"), as well as limited patient follow-up. Here we used next-generation sequencing (NGS) to define the baseline BCR-ABL1 mutation status of 267 heavily pretreated chronic phase (CP)-CML patients from the PACE trial, and used SS to identify clonally dominant mutants that may have developed on ponatinib therapy (30.1 months median follow-up). Durable cytogenetic and molecular responses were observed irrespective of baseline mutation status and included patients with compound mutations. No single or compound mutation was identified that consistently conferred primary and/or secondary resistance to ponatinib in CP-CML patients. Ponatinib is effective in CP-CML irrespective of baseline mutation status.

BAM-matcher: a tool for rapid NGS sample matching.

UNLABELLED: The standard method used by high-throughput genome sequencing facilities for detecting mislabelled samples is to use independently generated high-density SNP data to determine sample identity. However, as it has now become commonplace to have multiple samples sequenced from the same source, such as for analysis of somatic variants using matched tumour and normal samples, we can directly use the genotype information inherent in the sequence data to match samples and thus bypass the need for additional laboratory testing. Here we present BAM-matcher, a tool that can rapidly determine whether two BAM files represent samples from the same biological source by comparing their genotypes. BAM-matcher is designed to be simple to use, provides easily interpretable results, and is suitable for deployment at early stages of data processing pipelines. AVAILABILITY AND IMPLEMENTATION: BAM-matcher is licensed under the Creative Commons by Attribution license, and is available from: https://bitbucket.org/sacgf/bam-matcher SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: paul.wang@sa.gov.au.

Prognosis for patients with CML and >10% BCR-ABL1 after 3 months of imatinib depends on the rate of BCR-ABL1 decline.

In chronic myeloid leukemia (CML) patients, a breakpoint cluster region-Abelson (BCR-ABL1) value >10% at 3 months of therapy is statistically associated with poorer outcome, yet many of these patients still achieve satisfactory outcomes. We investigated 528 first-line imatinib-treated patients to determine whether patients with the poorest outcome can be better discriminated at 3 months. All outcomes were significantly superior for the 410 patients with BCR-ABL1 ≤10% at 3 months (P < .001). However, the poorest outcomes among the 95 evaluable patients with BCR-ABL1 >10% at 3 months were identified by the rate of BCR-ABL1 decline from baseline, assessed by estimating the number of days over which BCR-ABL1 halved. Patients with BCR-ABL1 halving time <76 days (n = 74) had significantly superior outcomes compared with patients whose BCR-ABL1 values did not halve by 76 days (n = 21; 4-year overall survival, 95% vs 58%, P = .0002; progression-free survival, 92% vs 63%, P = .008; failure-free survival, 59% vs 6%, P < .0001; and major molecular response, 54% vs 5%, P = .008). By multivariate analysis, the halving time was an independent predictor of outcome in this poor risk group. Our study highlighted that the rate of BCR-ABL1 decline may be a critical prognostic discriminator of the patients with very poor outcome among those >10% at 3 months. The International Randomized IFN vs STI571 (IRIS) trial was registered at http://www.clinicaltrials.gov as #NCT00006343. The Tyrosine Kinase Inhibitor Optimization and Selectivity (TOPS) trial was registered at http://www.clinicaltrials.gov as #NCT00124748. The Therapeutic Intensification in DE-novo Leukaemia (TIDEL) I trial was registered at http://www.ANZCTR.org.au as #ACTRN12607000614493. The TIDEL II trial was registered at http://www.ANZCTR.org.au as #ACTRN12607000325404.

Management of Zygomatic Fractures: A National Survey.

INTRODUCTION: Repair of zygomatic fractures can be classified into the early closed reduction or the more recent open reduction and rigid internal fixation (ORIF) methods. Surgical training and literature advocate ORIF, but the actual frequency of the different techniques in clinical practice is unknown. The purpose of this study was to determine the current trends in the management of zygomatic fractures among US surgeons and elucidate their influences. METHODS: A 10-question survey was developed and distributed to over 16,000 practicing US facial trauma surgeons, including plastic surgeons (PS), oral and maxillofacial surgeons (OMFS), and otorhinolaryngologists (ENT). The survey queried training background, zygoma fracture treatment preferences, and rationale. Responses were tabulated and both univariate and bivariate statistical analyses completed. RESULTS: One thousand six hundred eleven (10%) total responses were received. Zygomatic fractures are treated most commonly by OMFS (61%), then PS (20%) and ENT (19%), with 71% of repairs being performed in private practice. Open reduction and rigid internal fixation is the most common treatment modality (81%), with most surgeons using 2 to 3 sites for exposure, reduction, and fixation with titanium miniplates (70%). Thirty-five percent of surgeons perform routine orbital floor exploration. Forty-three percent quoted training and 32% reported accuracy of repair as the primary reason for choosing ORIF. CONCLUSIONS: This is the largest reported survey on the repair of zygoma fractures. The response rate suggests dominance of OMFS in zygoma fracture care, an area pioneered by PS. Evolution of technique is also evident by predominance of ORIF with emphasis of multiple points of exposure, reduction, and fixation with rigid hardware.

False precision, surprise and improved uncertainty assessment.

An uncertainty report describes the extent of an agent's uncertainty about some matter. We identify two basic requirements for uncertainty reports, which we call faithfulness and completeness. We then discuss two pitfalls of uncertainty assessment that often result in reports that fail to meet these requirements. The first involves adopting a one-size-fits-all approach to the representation of uncertainty, while the second involves failing to take account of the risk of surprises. In connection with the latter, we respond to the objection that it is impossible to account for the risk of genuine surprises. After outlining some steps that both scientists and the bodies who commission uncertainty assessments can take to help avoid these pitfalls, we explain why striving for faithfulness and completeness is important.

Scheduling the Stork: Media Portrayals of Women's and Physicians' Reasons for Elective Cesarean Delivery.

BACKGROUND: Media interest in cesarean delivery has grown in recent years driven both by rising cesarean delivery rates and the decision by the American College of Obstetrics and Gynecology (ACOG) to permit elective cesarean (EC) delivery. METHODS: A content analysis of United States newspaper and magazine articles from 2000 to 2013 (n = 131 articles) was completed to understand how the news media portrays ECs. RESULTS: The majority of articles (71.8%) emphasized reasons to support women having an EC, while 38.2 percent of the articles exhibited themes of physician support for ECs. Relatively few articles mentioned reasons against ECs either from the women's perspective (11.5%) or the practitioners' (3.8%). The most common themes given for women choosing ECs were convenience/scheduling (48.9%), avoidance of pain or fear of labor (29.8%), and physical harm to women from vaginal birth (17.6%). Doctors' perspectives were less prevalent in the media than women's perspectives, but when mentioned they were almost exclusively in support of ECs for reasons including avoiding malpractice (28.2%), avoiding physical harm to the woman or baby (16.8%), and timing/scheduling (14.5%). DISCUSSION: Media coverage suggests ECs are widely accepted by both women and doctors, with women choosing an EC mainly for convenience/scheduling and fear. However, 43 percent of doctors surveyed by ACOG said they were not willing to perform the procedure, and surveys report that mothers rarely request an EC.

Multidisciplinary views toward pharmacist-delivered medication therapy management services in dialysis facilities.

OBJECTIVE: To determine views of staff of dialysis centers toward pharmacist-delivered medication therapy management (MTM) services. DESIGN: Focus group study. SETTING: Three private, nonprofit, outpatient dialysis facilities. PARTICIPANTS: Multidisciplinary dialysis staff. INTERVENTION: Two focus group sessions were conducted using a semistructured interview guide. MAIN OUTCOME MEASURES: Views of staff toward MTM services at a dialysis center. RESULTS: A total of 13 staff members of dialysis centers participated in the study. Participants included nurses, patient care technicians, a social worker, dietitian, and administrative personnel. Key themes included: the need for access to MTM services in dialysis facilities exists; services should include medication reconciliation and patient education; services should be proactive, consistent, individualized, and covered by insurance; and that pharmacists are uniquely suited to provide MTM services. CONCLUSION: Dialysis staff support the integration of MTM services in facilities. Further research is needed to identify barriers and opportunities in the implementation process, including patient perspectives.

A comparative analysis of algorithms for somatic SNV detection in cancer.

MOTIVATION: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer-normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer-normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm. RESULTS: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates. AVAILABILITY: Data accession number SRA081939, code at http://code.google.com/p/snv-caller-review/ CONTACT: david.adelson@adelaide.edu.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Poor response to second-line kinase inhibitors in chronic myeloid leukemia patients with multiple low-level mutations, irrespective of their resistance profile.

Specific imatinib-resistant BCR-ABL1 mutations (Y253H, E255K/V, T315I, F317L, and F359V/C) predict failure of second-line nilotinib or dasatinib therapy in patients with chronic myeloid leukemia; however, such therapy also fails in approximately 40% of patients in the chronic phase of this disease who do not have these resistant mutations. We investigated whether sensitive mutation analysis could identify other poor-risk subgroups. Analysis was performed by direct sequencing and sensitive mass spectrometry on 220 imatinib-resistant patients before they began nilotinib or dasatinib therapy. Patients with resistant mutations by either method (n = 45) were excluded because inferior response was known. Of the remaining 175 patients, 19% had multiple mutations by mass spectrometry versus 9% by sequencing. Compared with 0 or 1 mutation, the presence of multiple mutations was associated with lower rates of complete cytogenetic response (50% vs 21%, P = .003) and major molecular response (31% vs 6%, P = .005) and a higher rate of new resistant mutations (25% vs 56%, P = .0009). Sensitive mutation analysis identified a poor-risk subgroup (15.5% of all patients) with multiple mutations not identified by standard screening.

Desmoid tumor of the hand: a case report.

SUMMARY: Extra-abdominal desmoid tumors are extremely rare in the hand. These tumors do not metastasize; however, they are potentially locally invasive and have extremely high local recurrence rates after surgical excision with reports of up to 78% recurrence, specifically in the hand. We describe the first case of a desmoid tumor originating from the extensor mechanism of a digit and discuss our treatment approach. In addition, a literature review performed shows a male predominance of desmoid tumors in the hand in the 30- to 50-year-old age group. Current evidence supports aggressive early wide surgical excision and reconstruction to preserve function.

Values and uncertainties in climate prediction, revisited.

Philosophers continue to debate both the actual and the ideal roles of values in science. Recently, Eric Winsberg has offered a novel, model-based challenge to those who argue that the internal workings of science can and should be kept free from the influence of social values. He contends that model-based assignments of probability to hypotheses about future climate change are unavoidably influenced by social values. I raise two objections to Winsberg's argument, neither of which can wholly undermine its conclusion but each of which suggests that his argument exaggerates the influence of social values on estimates of uncertainty in climate prediction. I then show how a more traditional challenge to the value-free ideal seems tailor-made for the climate context.

Novel modes of MPL activation in triple-negative myeloproliferative neoplasms.

The identification of a somatic mutation associated with myeloid malignancy is of diagnostic importance in myeloproliferative neoplasms (MPNs). Individuals with no mutation detected in common screening tests for variants in JAK2, CALR, and MPL are described as 'triple-negative' and pose a diagnostic challenge if there is no other evidence of a clonal disorder. To identify potential drivers that might explain the clinical phenotype, we used an extended sequencing panel to characterise a cohort of 44 previously diagnosed triple-negative MPN patients for canonical mutations in JAK2, MPL and CALR at low variant allele frequency (found in 4/44 patients), less common variants in the JAK-STAT signalling pathway (12 patients), or other variants in recurrently mutated genes from myeloid malignancies (18 patients), including hotspot variants of potential clinical relevance in eight patients. In one patient with thrombocytosis we identified biallelic germline MPL variants. Neither MPL variant was activating in cell proliferation assays, and one of the variants was not expressed on the cell surface, yet co-expression of both variants led to thrombopoietin hypersensitivity. Our results highlight the clinical value of extended sequencing including germline variant analysis and illustrate the need for detailed functional assays to determine whether rare variants in JAK2 or MPL are pathogenic.

Data models, representation and adequacy-for-purpose.

We critically engage two traditional views of scientific data and outline a novel philosophical view that we call the pragmatic-representational (PR) view of data. On the PR view, data are representations that are the product of a process of inquiry, and they should be evaluated in terms of their adequacy or fitness for particular purposes. Some important implications of the PR view for data assessment, related to misrepresentation, context-sensitivity, and complementary use, are highlighted. The PR view provides insight into the common but little-discussed practices of iteratively reusing and repurposing data, which result in many datasets' having a phylogeny-an origin and complex evolutionary history-that is relevant to their evaluation and future use. We relate these insights to the open-data and data-rescue movements, and highlight several future avenues of research that build on the PR view of data.