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1.  Climate change and soil salinity: The case of coastal Bangladesh 
Ambio  2015;44(8):815-826.
This paper estimates location-specific soil salinity in coastal Bangladesh for 2050. The analysis was conducted in two stages: First, changes in soil salinity for the period 2001–2009 were assessed using information recorded at 41 soil monitoring stations by the Soil Research Development Institute. Using these data, a spatial econometric model was estimated linking soil salinity with the salinity of nearby rivers, land elevation, temperature, and rainfall. Second, future soil salinity for 69 coastal sub-districts was projected from climate-induced changes in river salinity and projections of rainfall and temperature based on time trends for 20 Bangladesh Meteorological Department weather stations in the coastal region. The findings indicate that climate change poses a major soil salinization risk in coastal Bangladesh. Across 41 monitoring stations, the annual median projected change in soil salinity is 39 % by 2050. Above the median, 25 % of all stations have projected changes of 51 % or higher.
PMCID: PMC4646857  PMID: 26152508
Climate change; Coastal areas; Soil salinity; Bangladesh
2.  A new approach for investigating venom function applied to venom calreticulin in a parasitoid wasp 
A new method is developed to investigate functions of venom components, using venom gene RNA interference knockdown in the venomous animal coupled with RNA sequencing in the envenomated host animal. The vRNAi/eRNA-Seq approach is applied to the venom calreticulin component (v-crc) of the parasitoid wasp Nasonia vitripennis. Parasitoids are common, venomous animals that inject venom proteins into host insects, where they modulate physiology and metabolism to produce a better food resource for the parasitoid larvae. vRNAi/eRNA-Seq indicates that v-crc acts to suppress expression of innate immune cell response, enhance expression of clotting genes in the host, and up-regulate cuticle genes. V-crc KD also results in an increased melanization reaction immediately following envenomation. We propose that v-crc inhibits innate immune response to parasitoid venom and reduces host bleeding during adult and larval parasitoid feeding. Experiments do not support the hypothesis that v-crc is required for the developmental arrest phenotype observed in envenomated hosts. We propose that an important role for some venom components is to reduce (modulate) the exaggerated effects of other venom components on target host gene expression, physiology, and survival, and term this venom mitigation. A model is developed that uses vRNAi/eRNA-Seq to quantify the contribution of individual venom components to total venom phenotypes, and to define different categories of mitigation by individual venoms on host gene expression. Mitigating functions likely contribute to the diversity of venom proteins in parasitoids and other venomous organisms.
PMCID: PMC4674333  PMID: 26359852
Nasonia; Calreticulin; Clotting factor; vRNAi/eRNA-seq
Parasitoid wasps inject insect hosts with a cocktail of venoms to manipulate the physiology, development, and immunity of the hosts and to promote development of the parasitoid offspring. The jewel wasp Nasonia vitripennis is a model parasitoid with at least 79 venom proteins. We conducted a high-throughput analysis of Nasonia venom effects on temporal changes of 249 metabolites in pupae of the flesh fly host (Sarcophaga bullata), over a five-day time course. Our results show that venom does not simply arrest the metabolism of the fly host. Rather, it targets specific metabolic processes while keeping hosts alive for at least five days post venom injection by the wasp. We found that venom: (a) Activates the sorbitol biosynthetic pathway while maintaining stable glucose levels, (b) Causes a shift in intermediary metabolism by switching to anaerobic metabolism and blocking the tricarboxylic acid cycle, (c) Arrests chitin biosynthesis that likely reflects developmental arrest of adult fly structures, (d) Elevates the majority of free amino acids, and (e) May be increasing phospholipid degradation. Despite sharing some metabolic effects with cold treatment, diapause, and hypoxia, the venom response is distinct from these conditions. Because Nasonia venom dramatically increases sorbitol levels without changing glucose levels, it could be a useful model for studying the regulation of the sorbitol pathway, which is relevant to diabetes research. Our findings generally support the view that parasitoid venoms are a rich source of bioactive molecules with potential biomedical applications.
PMCID: PMC5113827  PMID: 27867325
Venom; Nasonia; Sorbitol; Anaerobic respiration; Chitin; Amino acids
4.  Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease 
The Journal of Clinical Investigation  null;126(8):2881-2892.
The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood.
PMCID: PMC4966312  PMID: 27427983
5.  The VITAH Trial—Vitamin D Supplementation and Cardiac Autonomic Tone in Patients with End-Stage Kidney Disease on Hemodialysis: A Blinded, Randomized Controlled Trial 
Nutrients  2016;8(10):608.
End-stage kidney disease (ESKD) patients are at increased cardiovascular risk. Vitamin D deficiency is associated with depressed heart rate variability (HRV), a risk factor depicting poor cardiac autonomic tone and risk of cardiovascular death. Vitamin D deficiency and depressed HRV are highly prevalent in the ESKD population. We aimed to determine the effects of oral vitamin D supplementation on HRV ((low frequency (LF) to high frequency (HF) spectral ratio (LF:HF)) in ESKD patients on hemodialysis. Fifty-six subjects with ESKD requiring hemodialysis were recruited from January 2013–March 2015 and randomized 1:1 to either conventional (0.25 mcg alfacalcidol plus placebo 3×/week) or intensive (0.25 mcg alfacalcidol 3×/week plus 50,000 international units (IU) ergocalciferol 1×/week) vitamin D for six weeks. The primary outcome was the change in LF:HF. There was no difference in LF:HF from baseline to six weeks for either vitamin D treatment (conventional: p = 0.9 vs. baseline; intensive: p = 0.07 vs. baseline). However, participants who remained vitamin D-deficient (25-hydroxyvitamin D < 20 ng/mL) after treatment demonstrated an increase in LF:HF (conventional: n = 13, ∆LF:HF: 0.20 ± 0.06, p < 0.001 vs. insufficient and sufficient vitamin D groups; intensive: n = 8: ∆LF:HF: 0.15 ± 0.06, p < 0.001 vs. sufficient vitamin D group). Overall, six weeks of conventional or intensive vitamin D only augmented LF:HF in ESKD subjects who remained vitamin D-deficient after treatment. Our findings potentially suggest that while activated vitamin D, with or without additional nutritional vitamin D, does not appear to improve cardiac autonomic tone in hemodialysis patients with insufficient or sufficient baseline vitamin D levels, supplementation in patients with severe vitamin D deficiency may improve cardiac autonomic tone in this higher risk sub-population of ESKD. Trial Registration:, NCT01774812.
PMCID: PMC5083996  PMID: 27690095
autonomic nervous system; chronic kidney disease; heart rate variability; hemodialysis; vitamin D
6.  Propensity score matching and persistence correction to reduce bias in comparative effectiveness: the effect of cinacalcet use on all‐cause mortality†  
The generalisability of randomised controlled trials (RCTs) may be limited by restrictive entry criteria or by their experimental nature. Observational research can provide complementary findings but is prone to bias. Employing propensity score matching, to reduce such bias, we compared the real‐life effect of cinacalcet use on all‐cause mortality (ACM) with findings from the Evaluation of Cinacalcet Therapy to Lower Cardiovascular Events (EVOLVE) RCT in chronic haemodialysis patients.
Incident adult haemodialysis patients receiving cinacalcet, recruited in a prospective observational cohort from 2007–2009 (AROii; n = 10,488), were matched to non‐exposed patients regardless of future exposure status. The effect of treatment crossover was investigated with inverse probability of censoring weighted and lag‐censored analyses. EVOLVE ACM data were analysed largely as described for the primary composite endpoint.
AROii patients receiving cinacalcet (n = 532) were matched to 1790 non‐exposed patients. The treatment effect of cinacalcet on ACM in the main AROii analysis (hazard ratio 1.03 [95% confidence interval (CI) 0.78–1.35]) was closer to the null than for the Intention to Treat (ITT) analysis of EVOLVE (0.94 [95%CI 0.85–1.04]). Adjusting for non‐persistence by 0‐ and 6‐month lag‐censoring and by inverse probability of censoring weight, the hazard ratios in AROii (0.76 [95%CI 0.51–1.15], 0.84 [95%CI 0.60–1.18] and 0.79 [95%CI 0.56–1.11], respectively) were comparable with those of EVOLVE (0.82 [95%CI 0.67–1.01], 0.83 [95%CI 0.73–0.96] and 0.87 [95%CI 0.71–1.06], respectively).
Correcting for treatment crossover, we observed results in the ‘real‐life’ setting of the AROii observational cohort that closely mirrored the results of the EVOLVE RCT. Persistence‐corrected analyses revealed a trend towards reduced ACM in haemodialysis patients receiving cinacalcet therapy. © 2015 The Authors. Pharmacoepidemiology and Drug Safety Published by John Wiley & Sons Ltd.
PMCID: PMC5033013  PMID: 26011775
cinacalcet; haemodialysis; mortality; persistence; bias; pharmacoepidemiology
7.  Smoking and Adverse Outcomes in Patients With CKD: The Study of Heart and Renal Protection (SHARP) 
The absolute and relative importance of smoking to vascular and nonvascular outcomes in people with chronic kidney disease (CKD), as well its relevance to kidney disease progression, is uncertain.
Study Design
Observational study.
Setting & Participants
9,270 participants with CKD enrolled in SHARP.
Baseline smoking status (current, former, and never).
Vascular events, site-specific cancer, ESRD, rate of change in estimated glomerular filtration rate (eGFR), and cause-specific mortality.
At baseline, 1,243 (13%) participants were current smokers (median consumption, 10 cigarettes/day); 3,272 (35%), former smokers; and 4,755 (51%), never smokers. Median follow-up was 4.9 years. Vascular event rates were 36% higher for current than never smokers (2,317 events; relative risk [RR], 1.36; 95% CI, 1.19-1.55), reflecting increases in both atherosclerotic (RR, 1.49; 95% CI, 1.26-1.76) and nonatherosclerotic (RR, 1.25; 95% CI, 1.05-1.50) events. Cancer was 37% higher among current smokers (632 events; RR, 1.37; 95% CI, 1.07-1.76), with the biggest RRs for lung (RR, 9.31; 95% CI, 4.37-19.83) and upper aerodigestive tract (RR, 4.87; 95% CI, 2.10-11.32) cancers. For 6,245 patients not receiving dialysis at baseline, ESRD incidence did not differ significantly between current and never smokers (2,141 events; RR, 1.02; 95% CI, 0.89-1.17), nor did estimated rate of change in eGFR (current smokers, −1.77 ± 0.14 [SE]; never smokers, −1.70 ± 0.07 mL/min/1.73 m2 per year). All-cause mortality was 48% higher among current smokers (2,257 events; RR, 1.48; 95% CI, 1.30-1.70), with significant increases in vascular (RR, 1.35; 95% CI, 1.07-1.69) and nonvascular (RR, 1.60; 95% CI, 1.34-1.91) causes of death, especially cancer (RR, 2.32; 95% CI, 1.58-3.40) and respiratory (RR, 2.25; 95% CI, 1.51-3.35) mortality.
Smoking status not assessed during follow-up.
In this study of patients with CKD, smoking significantly increased the risks for vascular and nonvascular morbidity and mortality, but was not associated with kidney disease progression. The associations with vascular and neoplastic disease are in keeping with those observed in the general population and are likely modifiable by cessation.
PMCID: PMC4996629  PMID: 27118687
Cigarette smoking; tobacco; chronic kidney disease (CKD); vascular morbidity; end-stage renal disease (ESRD); risk factor; cause-specific mortality; vascular events; cancer; estimated glomerular filtration rate (eGFR); disease progression; Study of Heart and Renal Protection (SHARP)
8.  Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle 
The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individual's cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p.N546K) and PIK3CA (p.H1047R) and a germline pathogenic variant in PTPN11 (p.N308S) diagnostic for Noonan syndrome. The molecular landscape of RGNT is not well-described, but these data are consistent with prior observations regarding the importance of the interconnected MAPK and PI3K/AKT/mTOR signaling pathways in this rare tumor. The co-occurrence of FGFR1, PIK3CA, and PTPN11 alterations provides further evidence for consideration of RGNT as a distinct molecular entity from pediatric low-grade gliomas and suggests potential therapeutic strategies for this patient in the event of tumor recurrence as novel agents targeting these pathways enter pediatric clinical trials. Although RGNT has not been definitively linked with cancer predisposition syndromes, two prior cases have been reported in patients with RASopathies (Noonan syndrome and neurofibromatosis type 1 [NF1]), providing an additional link between these tumors and the mitogen-activated protein kinase (MAPK) signaling pathway. In summary, this case provides an example of the potential for genome-scale sequencing technologies to provide insight into the biology of rare tumors and yield both tumor and germline results of potential relevance to patient care.
PMCID: PMC5002928  PMID: 27626068
neoplasm of the central nervous system
9.  Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates 
Nature Communications  2016;7:12601.
Cutaneous squamous cell carcinoma (cuSCC) comprises 15–20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible.
Cutaneous squamous cell of the skin is a common neoplasm that frequently arises from precancerous actinic keratoses. Here, the authors carry out genomic analysis on matched sets of human lesions and compare with those in ultraviolet treated mice and identify conserved drivers of tumour development.
PMCID: PMC5013636  PMID: 27574101
10.  MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data 
Genome Biology  2016;17(1):178.
Subclonal mutations reveal important features of the genetic architecture of tumors. However, accurate detection of mutations in genetically heterogeneous tumor cell populations using next-generation sequencing remains challenging. We develop MuSE (, Mutation calling using a Markov Substitution model for Evolution, a novel approach for modeling the evolution of the allelic composition of the tumor and normal tissue at each reference base. MuSE adopts a sample-specific error model that reflects the underlying tumor heterogeneity to greatly improve the overall accuracy. We demonstrate the accuracy of MuSE in calling subclonal mutations in the context of large-scale tumor sequencing projects using whole exome and whole genome sequencing.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-016-1029-6) contains supplementary material, which is available to authorized users.
PMCID: PMC4995747  PMID: 27557938
Somatic mutation calling; Sensitivity and specificity; Bayesian inference; Model-based cutoff finding; Next-generation sequencing
11.  Ampullary cancers harbor ELF3 tumor suppressor gene mutations and exhibit frequent WNT dysregulation 
Cell reports  2016;14(4):907-919.
The ampulla of Vater is a complex cellular environment from which adenocarcinomas arise to form a group of histopathologically heterogenous tumors. To evaluate the molecular features of these tumors, 98 ampullary adenocarcinomas, were evaluated and compared to 44 distal bile duct and 18 duodenal adenocarcinomas. Genomic analyses revealed mutations in the WNT signaling pathway among half of the patients and in all three adenocarcinomas irrespective of their origin and histological morphology. These tumors were characterized by a high frequency of inactivating mutations of ELF3, a high rate of microsatellite instability, and common focal deletions and amplifications, suggesting common attributes in the molecular pathogenesis are at play in these tumors. The high frequency of WNT pathway activating mutation, coupled with small molecule inhibitors of beta catenin in clinical trials, suggests future treatment decisions for these patients may be guided by genomic analysis.
PMCID: PMC4982376  PMID: 26804919
12.  Standardised Outcomes in Nephrology—Children and Adolescents (SONG-Kids): a protocol for establishing a core outcome set for children with chronic kidney disease 
Trials  2016;17:401.
Children with chronic kidney disease (CKD), requiring dialysis or kidney transplantation, have a mortality rate of up to 30-fold higher than the general aged-matched population, and severely impaired quality of life. Symptoms such as fatigue and pain are prevalent and debilitating. Children with CKD are at risk of cognitive impairment, and poorer educational, vocational, and psychosocial outcomes compared with their well peers, which have consequences through to adulthood. Treatment regimens for children with CKD are long-term, complex, and highly intrusive. While many trials have been conducted to improve outcomes in children with CKD, the outcomes measured and reported are often not relevant to patients and clinicians, and are highly variable. These problems can diminish the value of trials as a means to improve the lives of children with CKD. The Standardised Outcomes in Nephrology—Children and Adolescents (SONG-Kids) study aims to develop a core outcome set for trials in children and adolescents with any stage of CKD that is based on the shared priorities of all stakeholders.
SONG-Kids involves five phases: a systematic review to identify outcomes (both domains and measures) that have been reported in randomised controlled trials involving children aged up to 21 years with CKD; focus groups (using nominal group technique) with adolescent patients and caregivers of paediatric patients (all ages) to identify outcomes that are relevant and important to patients and their family and the reasons for their choices; semistructured key informant interviews with health professionals involved in the care of children with CKD to ascertain their views on establishing core outcomes in paediatric nephrology; an international three-round online Delphi survey with patients, caregivers, clinicians, researchers, policy-makers, and members from industry to develop consensus on important outcome domains; and a stakeholder workshop to review and finalise the set of core outcome domains for trials in children with CKD (including nondialysis-dependent, dialysis, and kidney transplantation).
Establishing a core outcome set to be reported in all trials conducted in children with any stage of CKD will enhance the relevance, transparency, and impact of research to improve the lives of children and adolescents with CKD.
PMCID: PMC4982996  PMID: 27519274
Core outcome set; Outcomes research; Patient-centred outcomes; Clinical trials; Dialysis; Haemodialysis; Chronic kidney disease; Paediatrics
13.  The venom gland transcriptome of the parasitoid wasp Nasonia vitripennis highlights the importance of novel genes in venom function 
BMC Genomics  2016;17:571.
Prior to egg laying the parasitoid wasp Nasonia vitripennis envenomates its pupal host with a complex mixture of venom peptides. This venom induces several dramatic changes in the host, including developmental arrest, immunosuppression, and altered metabolism. The diverse and potent bioactivity of N. vitripennis venom provides opportunities for the development of novel acting pharmaceuticals based on these molecules. However, currently very little is known about the specific functions of individual venom peptides or what mechanisms underlie the hosts response to envenomation. Many of the venom peptides also lack bioinformatically derived annotations because no homologs can be identified in the sequences databases. The RNA interference system of N. vitripennis provides a method for functional characterisation of venom protein encoding genes, however working with the current list of 79 candidates represents a daunting task. For this reason we were interested in determining the expression levels of venom encoding genes in the venom gland, as this information could be used to rank candidates for further study. To do this we carried out deep transcriptome sequencing of the venom gland and ovary tissue and used RNA-seq to rank the venom protein encoding genes by expression level. The generation of a specific venom gland transcriptome dataset also provides further opportunities to investigate novel features of this specialised organ.
RNA-seq revealed that the highest expressed venom encoding gene in the venom gland was ‘Venom protein Y’. The highest expressed annotated gene in this tissue was serine protease Nasvi2EG007167, which has previously been implicated in the apoptotic activity of N. vitripennis venom. As expected the RNA-seq confirmed that venom encoding genes are almost exclusively expressed in the venom gland relative to the neighbouring ovary tissue. Novel genes appear to perform key roles in N. vitripennis venom function, with over half of the 15 highest expressed venom encoding loci lacking bioinformatic annotations. The high throughput sequencing data also provided evidence for the existence of an additional 472 previously undescribed transcribed regions in the N. vitripennis genome. Finally, metatranscriptomic analysis of the venom gland transcriptome finds little evidence for the role of Wolbachia in the venom system.
The expression level information provided here for the N. vitripennis venom protein encoding genes represents a valuable dataset that can be used by the research community to rank candidates for further functional characterisation. These candidates represent bioactive peptides valuable in the development of new pharmaceuticals.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-2924-7) contains supplementary material, which is available to authorized users.
PMCID: PMC4977848  PMID: 27503142
Ovary; RNA-seq; Transcriptomics; Serine protease; Drug development; Venom gene
14.  Unique features of a global human ectoparasite identified through sequencing of the bed bug genome 
Benoit, Joshua B. | Adelman, Zach N. | Reinhardt, Klaus | Dolan, Amanda | Poelchau, Monica | Jennings, Emily C. | Szuter, Elise M. | Hagan, Richard W. | Gujar, Hemant | Shukla, Jayendra Nath | Zhu, Fang | Mohan, M. | Nelson, David R. | Rosendale, Andrew J. | Derst, Christian | Resnik, Valentina | Wernig, Sebastian | Menegazzi, Pamela | Wegener, Christian | Peschel, Nicolai | Hendershot, Jacob M. | Blenau, Wolfgang | Predel, Reinhard | Johnston, Paul R. | Ioannidis, Panagiotis | Waterhouse, Robert M. | Nauen, Ralf | Schorn, Corinna | Ott, Mark-Christoph | Maiwald, Frank | Johnston, J. Spencer | Gondhalekar, Ameya D. | Scharf, Michael E. | Peterson, Brittany F. | Raje, Kapil R. | Hottel, Benjamin A. | Armisén, David | Johan Crumière, Antonin Jean | Refki, Peter Nagui | Santos, Maria Emilia | Sghaier, Essia | Viala, Sèverine | Khila, Abderrahman | Ahn, Seung-Joon | Childers, Christopher | Lee, Chien-Yueh | Lin, Han | Hughes, Daniel S. T. | Duncan, Elizabeth J. | Murali, Shwetha C. | Qu, Jiaxin | Dugan, Shannon | Lee, Sandra L. | Chao, Hsu | Dinh, Huyen | Han, Yi | Doddapaneni, Harshavardhan | Worley, Kim C. | Muzny, Donna M. | Wheeler, David | Panfilio, Kristen A. | Vargas Jentzsch, Iris M. | Vargo, Edward L. | Booth, Warren | Friedrich, Markus | Weirauch, Matthew T. | Anderson, Michelle A. E. | Jones, Jeffery W. | Mittapalli, Omprakash | Zhao, Chaoyang | Zhou, Jing-Jiang | Evans, Jay D. | Attardo, Geoffrey M. | Robertson, Hugh M. | Zdobnov, Evgeny M. | Ribeiro, Jose M. C. | Gibbs, Richard A. | Werren, John H. | Palli, Subba R. | Schal, Coby | Richards, Stephen
Nature communications  2016;7:10165.
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the last two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
PMCID: PMC4740739  PMID: 26836814
15.  Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma 
Linehan, W. Marston | Spellman, Paul T. | Ricketts, Christopher J. | Creighton, Chad J. | Fei, Suzanne S. | Davis, Caleb | Wheeler, David A. | Murray, Bradley A. | Schmidt, Laura | Vocke, Cathy D. | Peto, Myron | Al Mamun, Abu Amar M. | Shinbrot, Eve | Sethi, Anurag | Brooks, Samira | Rathmell, W. Kimryn | Brooks, Angela N. | Hoadley, Katherine A. | Robertson, A. Gordon | Brooks, Denise | Bowlby, Reanne | Sadeghi, Sara | Shen, Hui | Weisenberger, Daniel J. | Bootwalla, Moiz | Baylin, Stephen B. | Laird, Peter W. | Cherniack, Andrew D. | Saksena, Gordon | Haake, Scott | Li, Jun | Liang, Han | Lu, Yiling | Mills, Gordon B. | Akbani, Rehan | Leiserson, Mark D.M. | Raphael, Benjamin J. | Anur, Pavana | Bottaro, Donald | Albiges, Laurence | Barnabas, Nandita | Choueiri, Toni K. | Czerniak, Bogdan | Godwin, Andrew K. | Hakimi, A. Ari | Ho, Thai | Hsieh, James | Ittmann, Michael | Kim, William Y. | Krishnan, Bhavani | Merino, Maria J. | Mills Shaw, Kenna R. | Reuter, Victor E. | Reznik, Ed | Shelley, Carl Simon | Shuch, Brian | Signoretti, Sabina | Srinivasan, Ramaprasad | Tamboli, Pheroze | Thomas, George | Tickoo, Satish | Burnett, Kenneth | Crain, Daniel | Gardner, Johanna | Lau, Kevin | Mallery, David | Morris, Scott | Paulauskis, Joseph D. | Penny, Robert J. | Shelton, Candace | Shelton, W. Troy | Sherman, Mark | Thompson, Eric | Yena, Peggy | Avedon, Melissa T. | Bowen, Jay | Gastier-Foster, Julie M. | Gerken, Mark | Leraas, Kristen M. | Lichtenberg, Tara M. | Ramirez, Nilsa C. | Santos, Tracie | Wise, Lisa | Zmuda, Erik | Demchok, John A. | Felau, Ina | Hutter, Carolyn M. | Sheth, Margi | Sofia, Heidi J. | Tarnuzzer, Roy | Wang, Zhining | Yang, Liming | Zenklusen, Jean C. | Zhang, Jiashan (Julia) | Ayala, Brenda | Baboud, Julien | Chudamani, Sudha | Liu, Jia | Lolla, Laxmi | Naresh, Rashi | Pihl, Todd | Sun, Qiang | Wan, Yunhu | Wu, Ye | Ally, Adrian | Balasundaram, Miruna | Balu, Saianand | Beroukhim, Rameen | Bodenheimer, Tom | Buhay, Christian | Butterfield, Yaron S.N. | Carlsen, Rebecca | Carter, Scott L. | Chao, Hsu | Chuah, Eric | Clarke, Amanda | Covington, Kyle R. | Dahdouli, Mahmoud | Dewal, Ninad | Dhalla, Noreen | Doddapaneni, HarshaVardhan | Drummond, Jennifer | Gabriel, Stacey B. | Gibbs, Richard A. | Guin, Ranabir | Hale, Walker | Hawes, Alicia | Hayes, D. Neil | Holt, Robert A. | Hoyle, Alan P. | Jefferys, Stuart R. | Jones, Steven J.M. | Jones, Corbin D. | Kalra, Divya | Kovar, Christie | Lewis, Lora | Li, Jie | Ma, Yussanne | Marra, Marco A. | Mayo, Michael | Meng, Shaowu | Meyerson, Matthew | Mieczkowski, Piotr A. | Moore, Richard A. | Morton, Donna | Mose, Lisle E. | Mungall, Andrew J. | Muzny, Donna | Parker, Joel S. | Perou, Charles M. | Roach, Jeffrey | Schein, Jacqueline E. | Schumacher, Steven E. | Shi, Yan | Simons, Janae V. | Sipahimalani, Payal | Skelly, Tara | Soloway, Matthew G. | Sougnez, Carrie | Tam, Angela | Tan, Donghui | Thiessen, Nina | Veluvolu, Umadevi | Wang, Min | Wilkerson, Matthew D. | Wong, Tina | Wu, Junyuan | Xi, Liu | Zhou, Jane | Bedford, Jason | Chen, Fengju | Fu, Yao | Gerstein, Mark | Haussler, David | Kasaian, Katayoon | Lai, Phillip | Ling, Shiyun | Radenbaugh, Amie | Van Den Berg, David | Weinstein, John N. | Zhu, Jingchun | Albert, Monique | Alexopoulou, Iakovina | Andersen, Jeremiah J | Auman, J. Todd | Bartlett, John | Bastacky, Sheldon | Bergsten, Julie | Blute, Michael L. | Boice, Lori | Bollag, Roni J. | Boyd, Jeff | Castle, Erik | Chen, Ying-Bei | Cheville, John C. | Curley, Erin | Davies, Benjamin | DeVolk, April | Dhir, Rajiv | Dike, Laura | Eckman, John | Engel, Jay | Harr, Jodi | Hrebinko, Ronald | Huang, Mei | Huelsenbeck-Dill, Lori | Iacocca, Mary | Jacobs, Bruce | Lobis, Michael | Maranchie, Jodi K. | McMeekin, Scott | Myers, Jerome | Nelson, Joel | Parfitt, Jeremy | Parwani, Anil | Petrelli, Nicholas | Rabeno, Brenda | Roy, Somak | Salner, Andrew L. | Slaton, Joel | Stanton, Melissa | Thompson, R. Houston | Thorne, Leigh | Tucker, Kelinda | Weinberger, Paul M. | Winemiller, Cythnia | Zach, Leigh Anne | Zuna, Rosemary
The New England journal of medicine  2015;374(2):135-145.
Papillary renal cell carcinoma, accounting for 15% of renal cell carcinoma, is a heterogeneous disease consisting of different types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal cell carcinoma; no effective forms of therapy for advanced disease exist.
We performed comprehensive molecular characterization utilizing whole-exome sequencing, copy number, mRNA, microRNA, methylation and proteomic analyses of 161 primary papillary renal cell carcinomas.
Type 1 and Type 2 papillary renal cell carcinomas were found to be different types of renal cancer characterized by specific genetic alterations, with Type 2 further classified into three individual subgroups based on molecular differences that influenced patient survival. MET alterations were associated with Type 1 tumors, whereas Type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-ARE pathway. A CpG island methylator phenotype (CIMP) was found in a distinct subset of Type 2 papillary renal cell carcinoma characterized by poor survival and mutation of the fumarate hydratase (FH) gene.
Type 1 and Type 2 papillary renal cell carcinomas are clinically and biologically distinct. Alterations in the MET pathway are associated with Type 1 and activation of the NRF2-ARE pathway with Type 2; CDKN2A loss and CIMP in Type 2 convey a poor prognosis. Furthermore, Type 2 papillary renal cell carcinoma consists of at least 3 subtypes based upon molecular and phenotypic features.
PMCID: PMC4775252  PMID: 26536169
16.  Autosomal Dominant Polycystic Kidney Disease (ADPKD): Executive Summary from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference 
Kidney international  2015;88(1):17-27.
Autosomal Dominant Polycystic Kidney Disease (ADPKD) affects up to 12 million individuals and is the 4th most common cause for renal replacement therapy worldwide. There have been many recent advances in the understanding of its molecular genetics and biology, and in the diagnosis and management of its manifestations. Yet, diagnosis, evaluation, prevention and treatment vary widely and there are no broadly accepted practice guidelines. Barriers to translation of basic science breakthroughs to clinical care exist, with considerable heterogeneity across countries. The KDIGO Controversies Conference on ADPKD brought together a panel of multi-disciplinary clinical expertise and engaged patients to identify areas of consensus, gaps in knowledge, and research and health care priorities related to diagnosis, monitoring of kidney disease progression, management of hypertension, renal function decline and complications, end-stage renal disease, extrarenal complications, and practical integrated patient support. These are summarized in this report.
PMCID: PMC4913350  PMID: 25786098
ADPKD; diagnosis; end-stage renal disease; management; patient support; polycystic kidney disease
17.  SV-STAT accurately detects structural variation via alignment to reference-based assemblies 
Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich source of information in which to detect breakpoints of structural variations at base-pair resolution. However, accurate prediction of SVs remains challenging, and existing informatics tools predict rearrangements with significant rates of false positives or negatives.
To address this challenge, we developed ‘Structural Variation detection by STAck and Tail’ (SV-STAT) which implements a novel scoring metric. The software uses this statistic to quantify evidence for structural variation in genomic regions suspected of harboring rearrangements. To demonstrate SV-STAT, we used targeted and genome-wide approaches. First, we applied a custom capture array followed by Roche/454 and SV-STAT to three pediatric B-lineage acute lymphoblastic leukemias, identifying five structural variations joining known and novel breakpoint regions. Next, we detected SVs genome-wide in paired-end Illumina data collected from additional tumor samples. SV-STAT showed predictive accuracy as high as or higher than leading alternatives. The software is freely available under the terms of the GNU General Public License version 3 at
SV-STAT works across multiple sequencing chemistries, paired and single-end technologies, targeted or whole-genome strategies, and it complements existing SV-detection software. The method is a significant advance towards accurate detection and genotyping of genomic rearrangements from DNA sequencing data.
Electronic supplementary material
The online version of this article (doi:10.1186/s13029-016-0051-0) contains supplementary material, which is available to authorized users.
PMCID: PMC4913042  PMID: 27330550
Algorithm; Genome; Sequencing; Structural variation; Genotype; Translocation; Cancer
19.  Genomic profiling of Sézary Syndrome identifies alterations of key T-cell signaling and differentiation genes 
Nature genetics  2015;47(12):1426-1434.
Sézary Syndrome is a rare leukemic form of cutaneous T-cell lymphoma defined as erythroderma, adenopathy, and circulating atypical T-lymphocytes. It is rarely curable with poor prognosis. Here we present a multi-platform genomic analysis of 37 Sézary Syndrome patients that implicates dysregulation of the cell cycle checkpoint and T-cell signaling. Frequent somatic alterations were identified in TP53, CARD11, CCR4, PLCG1, CDKN2A, ARID1A, RPS6KA1, and ZEB1. Activating CCR4 and CARD11 mutations were detected in nearly a third of patients. ZEB1, a transcription repressor essential for T-cell differentiation, was deleted in over half of patients. IL32 and IL2RG were over-expressed in nearly all cases. Analysis of T-cell receptor Vβ and Vα expression revealed ongoing rearrangement of the receptors after the expansion of a malignant clone in one third of subjects. Our results demonstrate profound disruption of key signaling pathways in Sézary Syndrome and suggest potential targets for novel therapies.
PMCID: PMC4829974  PMID: 26551670
20.  Standardized Outcomes in Nephrology-Transplantation: A Global Initiative to Develop a Core Outcome Set for Trials in Kidney Transplantation 
Transplantation Direct  2016;2(6):e79.
Although advances in treatment have dramatically improved short-term graft survival and acute rejection in kidney transplant recipients, long-term graft outcomes have not substantially improved. Transplant recipients also have a considerably increased risk of cancer, cardiovascular disease, diabetes, and infection, which all contribute to appreciable morbidity and premature mortality. Many trials in kidney transplantation are short-term, frequently use unvalidated surrogate endpoints, outcomes of uncertain relevance to patients and clinicians, and do not consistently measure and report key outcomes like death, graft loss, graft function, and adverse effects of therapy. This diminishes the value of trials in supporting treatment decisions that require individual-level multiple tradeoffs between graft survival and the risk of side effects, adverse events, and mortality. The Standardized Outcomes in Nephrology-Transplantation initiative aims to develop a core outcome set for trials in kidney transplantation that is based on the shared priorities of all stakeholders.
This will include a systematic review to identify outcomes reported in randomized trials, a Delphi survey with an international multistakeholder panel (patients, caregivers, clinicians, researchers, policy makers, members from industry) to develop a consensus-based prioritized list of outcome domains and a consensus workshop to review and finalize the core outcome set for trials in kidney transplantation.
Developing and implementing a core outcome set to be reported, at a minimum, in all kidney transplantation trials will improve the transparency, quality, and relevance of research; to enable kidney transplant recipients and their clinicians to make better-informed treatment decisions for improved patient outcomes.
PMCID: PMC4946524  PMID: 27500269
21.  Using Hierarchical Cluster Models to Systematically Identify Groups of Jobs With Similar Occupational Questionnaire Response Patterns to Assist Rule-Based Expert Exposure Assessment in Population-Based Studies 
Annals of Occupational Hygiene  2014;59(4):455-466.
Rule-based expert exposure assessment based on questionnaire response patterns in population-based studies improves the transparency of the decisions. The number of unique response patterns, however, can be nearly equal to the number of jobs. An expert may reduce the number of patterns that need assessment using expert opinion, but each expert may identify different patterns of responses that identify an exposure scenario. Here, hierarchical clustering methods are proposed as a systematic data reduction step to reproducibly identify similar questionnaire response patterns prior to obtaining expert estimates. As a proof-of-concept, we used hierarchical clustering methods to identify groups of jobs (clusters) with similar responses to diesel exhaust-related questions and then evaluated whether the jobs within a cluster had similar (previously assessed) estimates of occupational diesel exhaust exposure.
Using the New England Bladder Cancer Study as a case study, we applied hierarchical cluster models to the diesel-related variables extracted from the occupational history and job- and industry-specific questionnaires (modules). Cluster models were separately developed for two subsets: (i) 5395 jobs with ≥1 variable extracted from the occupational history indicating a potential diesel exposure scenario, but without a module with diesel-related questions; and (ii) 5929 jobs with both occupational history and module responses to diesel-relevant questions. For each subset, we varied the numbers of clusters extracted from the cluster tree developed for each model from 100 to 1000 groups of jobs. Using previously made estimates of the probability (ordinal), intensity (µg m−3 respirable elemental carbon), and frequency (hours per week) of occupational exposure to diesel exhaust, we examined the similarity of the exposure estimates for jobs within the same cluster in two ways. First, the clusters’ homogeneity (defined as >75% with the same estimate) was examined compared to a dichotomized probability estimate (<5 versus ≥5%; <50 versus ≥50%). Second, for the ordinal probability metric and continuous intensity and frequency metrics, we calculated the intraclass correlation coefficients (ICCs) between each job’s estimate and the mean estimate for all jobs within the cluster.
Within-cluster homogeneity increased when more clusters were used. For example, ≥80% of the clusters were homogeneous when 500 clusters were used. Similarly, ICCs were generally above 0.7 when ≥200 clusters were used, indicating minimal within-cluster variability. The most within-cluster variability was observed for the frequency metric (ICCs from 0.4 to 0.8). We estimated that using an expert to assign exposure at the cluster-level assignment and then to review each job in non-homogeneous clusters would require ~2000 decisions per expert, in contrast to evaluating 4255 unique questionnaire patterns or 14983 individual jobs.
This proof-of-concept shows that using cluster models as a data reduction step to identify jobs with similar response patterns prior to obtaining expert ratings has the potential to aid rule-based assessment by systematically reducing the number of exposure decisions needed. While promising, additional research is needed to quantify the actual reduction in exposure decisions and the resulting homogeneity of exposure estimates within clusters for an exposure assessment effort that obtains cluster-level expert assessments as part of the assessment process.
PMCID: PMC4385262  PMID: 25477475
case–control studies; diesel exhaust; hierarchical clusters; occupational exposures
22.  ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data 
BMC Bioinformatics  2016;17:188.
Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. There is a critical need to develop efficient methods to recover these important mutational events.
In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all unmapped and partially mapped reads from whole exome NGS data using a De Bruijn graphs approach to select reads that harbor cycles of appropriate length, followed by assembly using overlap-layout-consensus. We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a truth set. ITD Assembler identified the highest percentage of reported FLT3-ITDs when compared to other ITD detection algorithms, and discovered additional ITDs in FLT3, KIT, CEBPA, WT1 and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data.
ITD Assembler is a very sensitive tool which can detect partial, large and complex tandem duplications. This study highlights the need to more effectively look for ITD’s in other cancers and Mendelian diseases.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-016-1031-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4847212  PMID: 27121965
Tandem duplication; De Bruijn graphs; Assembly; FLT3; Data mining; Cancer genetics; AML; Clustering; Somatic mutations
23.  Comparison of Ordinal and Nominal Classification Trees to Predict Ordinal Expert-Based Occupational Exposure Estimates in a Case–Control Study 
Annals of Occupational Hygiene  2014;59(3):324-335.
To evaluate occupational exposures in case–control studies, exposure assessors typically review each job individually to assign exposure estimates. This process lacks transparency and does not provide a mechanism for recreating the decision rules in other studies. In our previous work, nominal (unordered categorical) classification trees (CTs) generally successfully predicted expert-assessed ordinal exposure estimates (i.e. none, low, medium, high) derived from occupational questionnaire responses, but room for improvement remained. Our objective was to determine if using recently developed ordinal CTs would improve the performance of nominal trees in predicting ordinal occupational diesel exhaust exposure estimates in a case–control study.
We used one nominal and four ordinal CT methods to predict expert-assessed probability, intensity, and frequency estimates of occupational diesel exhaust exposure (each categorized as none, low, medium, or high) derived from questionnaire responses for the 14983 jobs in the New England Bladder Cancer Study. To replicate the common use of a single tree, we applied each method to a single sample of 70% of the jobs, using 15% to test and 15% to validate each method. To characterize variability in performance, we conducted a resampling analysis that repeated the sample draws 100 times. We evaluated agreement between the tree predictions and expert estimates using Somers’ d, which measures differences in terms of ordinal association between predicted and observed scores and can be interpreted similarly to a correlation coefficient.
From the resampling analysis, compared with the nominal tree, an ordinal CT method that used a quadratic misclassification function and controlled tree size based on total misclassification cost had a slightly better predictive performance that was statistically significant for the frequency metric (Somers’ d: nominal tree = 0.61; ordinal tree = 0.63) and similar performance for the probability (nominal = 0.65; ordinal = 0.66) and intensity (nominal = 0.65; ordinal = 0.65) metrics. The best ordinal CT predicted fewer cases of large disagreement with the expert assessments (i.e. no exposure predicted for a job with high exposure and vice versa) compared with the nominal tree across all of the exposure metrics. For example, the percent of jobs with expert-assigned high intensity of exposure that the model predicted as no exposure was 29% for the nominal tree and 22% for the best ordinal tree.
The overall agreements were similar across CT models; however, the use of ordinal models reduced the magnitude of the discrepancy when disagreements occurred. As the best performing model can vary by situation, researchers should consider evaluating multiple CT methods to maximize the predictive performance within their data.
PMCID: PMC4365762  PMID: 25433003
classification; diesel exhaust; occupational exposure; ordinal data; statistical learning
24.  Identifying Gene Disruptions in Novel Balanced de novo Constitutional Translocations in Childhood Cancer Patients by Whole Genome Sequencing 
We applied whole genome sequencing to children diagnosed with neoplasms and found to carry apparently balanced constitutional translocations, to discover novel genic disruptions.
We applied SV calling programs CREST, Break Dancer, SV-STAT and CGAP-CNV, and developed an annotative filtering strategy to achieve nucleotide resolution at the translocations.
We identified the breakpoints for t(6;12) (p21.1;q24.31) disrupting HNF1A in a patient diagnosed with hepatic adenomas and Maturity Onset Diabetes of the Young (MODY). Translocation as the disruptive event of HNF1A, a gene known to be involved in MODY3, has not been previously reported. In a subject with Hodgkin’s lymphoma and subsequent low-grade glioma, we identified t(5;18) (q35.1;q21.2), disrupting both SLIT3 and DCC, genes previously implicated in both glioma and lymphoma.
These examples suggest that implementing clinical whole genome sequencing in the diagnostic work-up of patients with novel but apparently balanced translocations may reveal unanticipated disruption of disease-associated genes and aid in prediction of the clinical phenotype.
PMCID: PMC4496310  PMID: 25569436
Whole-Genome Sequencing; Structural Variation; Translocation; Cancer; Next-Generation Cytogenetics
25.  Recurrent DGCR8, DROSHA, and SIX Homeodomain Mutations in Favorable Histology Wilms Tumors 
Cancer cell  2015;27(2):286-297.
We report the most common single nucleotide substitution/deletion mutations in Favorable Histology Wilms Tumors (FHWT) to occur within SIX1/2 (7% of 534 tumors) and microRNA processing genes (miRNAPG) DGCR8 and DROSHA (15% of 534 tumors). Comprehensive analysis of 77 FHWTs indicates that tumors with SIX1/2 and/or miRNAPG mutations show a pre-induction metanephric mesenchyme gene expression pattern and are significantly associated with both perilobar nephrogenic rests and 11p15 imprinting aberrations. Significantly decreased expression of mature Let-7a and the miR-200 family (responsible for mesenchymal-to-epithelial transition) in miRNAPG-mutant tumors is associated with an undifferentiated blastemal histology. The combination of SIX and miRNAPG mutations in the same tumor is associated with evidence of RAS activation and a higher rate of relapse and death.
PMCID: PMC4800737  PMID: 25670082

Results 1-25 (171)