Last data update: Jun 11, 2024. (Total: 46992 publications since 2009)
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The Human Phenotype Ontology in 2024: phenotypes around the world
Gargano MA , Matentzoglu N , Coleman B , Addo-Lartey EB , Anagnostopoulos AV , Anderton J , Avillach P , Bagley AM , Bakštein E , Balhoff JP , Baynam G , Bello SM , Berk M , Bertram H , Bishop S , Blau H , Bodenstein DF , Botas P , Boztug K , Čady J , Callahan TJ , Cameron R , Carbon SJ , Castellanos F , Caufield JH , Chan LE , Chute CG , Cruz-Rojo J , Dahan-Oliel N , Davids JR , de Dieuleveult M , de Souza V , de Vries BBA , de Vries E , DePaulo JR , Derfalvi B , Dhombres F , Diaz-Byrd C , Dingemans AJM , Donadille B , Duyzend M , Elfeky R , Essaid S , Fabrizzi C , Fico G , Firth HV , Freudenberg-Hua Y , Fullerton JM , Gabriel DL , Gilmour K , Giordano J , Goes FS , Moses RG , Green I , Griese M , Groza T , Gu W , Guthrie J , Gyori B , Hamosh A , Hanauer M , Hanušová K , He YO , Hegde H , Helbig I , Holasová K , Hoyt CT , Huang S , Hurwitz E , Jacobsen JOB , Jiang X , Joseph L , Keramatian K , King B , Knoflach K , Koolen DA , Kraus ML , Kroll C , Kusters M , Ladewig MS , Lagorce D , Lai MC , Lapunzina P , Laraway B , Lewis-Smith D , Li X , Lucano C , Majd M , Marazita ML , Martinez-Glez V , McHenry TH , McInnis MG , McMurry JA , Mihulová M , Millett CE , Mitchell PB , Moslerová V , Narutomi K , Nematollahi S , Nevado J , Nierenberg AA , Čajbiková NN , Nurnberger JI Jr , Ogishima S , Olson D , Ortiz A , Pachajoa H , Perez de Nanclares G , Peters A , Putman T , Rapp CK , Rath A , Reese J , Rekerle L , Roberts AM , Roy S , Sanders SJ , Schuetz C , Schulte EC , Schulze TG , Schwarz M , Scott K , Seelow D , Seitz B , Shen Y , Similuk MN , Simon ES , Singh B , Smedley D , Smith CL , Smolinsky JT , Sperry S , Stafford E , Stefancsik R , Steinhaus R , Strawbridge R , Sundaramurthi JC , Talapova P , Tenorio Castano JA , Tesner P , Thomas RH , Thurm A , Turnovec M , van Gijn ME , Vasilevsky NA , Vlčková M , Walden A , Wang K , Wapner R , Ware JS , Wiafe AA , Wiafe SA , Wiggins LD , Williams AE , Wu C , Wyrwoll MJ , Xiong H , Yalin N , Yamamoto Y , Yatham LN , Yocum AK , Young AH , Yüksel Z , Zandi PP , Zankl A , Zarante I , Zvolský M , Toro S , Carmody LC , Harris NL , Munoz-Torres MC , Danis D , Mungall CJ , Köhler S , Haendel MA , Robinson PN . Nucleic Acids Res 2023 52 D1333-D1346 The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs. |
Stable high-density and maternally inherited Wolbachia infections in Anopheles moucheti and Anopheles demeilloni mosquitoes.
Walker T , Quek S , Jeffries CL , Bandibabone J , Dhokiya V , Bamou R , Kristan M , Messenger LA , Gidley A , Hornett EA , Anderson ER , Cansado-Utrilla C , Hegde S , Bantuzeko C , Stevenson JC , Lobo NF , Wagstaff SC , Nkondjio CA , Irish SR , Heinz E , Hughes GL . Curr Biol 2021 31 (11) 2310-2320 e5 Wolbachia, a widespread bacterium that can reduce pathogen transmission in mosquitoes, has recently been reported to be present in Anopheles (An.) species. In wild populations of the An. gambiae complex, the primary vectors of Plasmodium malaria in Sub-Saharan Africa, Wolbachia DNA sequences at low density and infection frequencies have been detected. As the majority of studies have used highly sensitive nested PCR as the only method of detection, more robust evidence is required to determine whether Wolbachia strains are established as endosymbionts in Anopheles species. Here, we describe high-density Wolbachia infections in geographically diverse populations of An. moucheti and An. demeilloni. Fluorescent in situ hybridization localized a heavy infection in the ovaries of An.moucheti, and maternal transmission was observed. Genome sequencing of both Wolbachia strains obtained genome depths and coverages comparable to those of other known infections. Notably, homologs of cytoplasmic incompatibility factor (cif) genes were present, indicating that these strains possess the capacity to induce the cytoplasmic incompatibility phenotype, which allows Wolbachia to spread through host populations. These strains should be further investigated as candidates for use in Wolbachia biocontrol strategies in Anopheles aiming to reduce the transmission of malaria. |
A mobile health-facilitated behavioural intervention for community health workers improves exclusive breastfeeding and early infant HIV diagnosis in India: a cluster randomized trial
Suryavanshi N , Kadam A , Gupte N , Hegde A , Kanade S , Sivalenka S , Kumar VS , Gupta A , Bollinger RC , Shankar A , McKenzie-White J , Mave V . J Int AIDS Soc 2020 23 (7) e25555 INTRODUCTION: India's national AIDS Control Organization implemented World Health Organization's option B+ HIV prevention of mother-to-child transmission (PMTCT) guidelines in 2013. However, scalable strategies to improve uptake of new PMTCT guidelines to reduce new infection rates are needed. This study assessed impact of Mobile Health-Facilitated Behavioral Intervention on the uptake of PMTCT services. METHODS: A cluster-randomized trial of a mobile health (mHealth)-supported behavioural training intervention targeting outreach workers (ORWs) was conducted in four districts of Maharashtra, India. Clusters (one Integrated Counselling and Testing Center (ICTC, n = 119), all affiliated ORWs (n = 116) and their assigned HIV-positive pregnant/postpartum clients (n = 1191)) were randomized to standard-of-care (SOC) ORW training vs. the COMmunity home Based INDia (COMBIND) intervention - specialized behavioural training plus a tablet-based mHealth application to support ORW-patient communication and patient engagement in HIV care. Impact on uptake of maternal antiretroviral therapy at delivery, exclusive breastfeeding at six months, infant nevirapine prophylaxis, and early infant diagnosis at six months was assessed using multi-level random-effects logistic regression models. RESULTS: Of 1191 HIV-positive pregnant/postpartum women, 884 were eligible for primary outcome assessment; 487 were randomized to COMBIND. Multivariable analyses identified no statistically significant differences in any primary outcome by study arm. COMBIND was associated with higher uptake of exclusive breastfeeding at two months (adjusted Odds Ratio (aOR), 2.10; 95% CI 1.06 to 4.15) and early infant diagnosis at six weeks (aOR, 2.19; 95% CI 1.05 to 3.98) than SOC. CONCLUSIONS: The COMBIND intervention was easily integrated into India's existing PMTCT programme and improved early uptake of two PMTCT components that require self-motivated health-seeking behaviour, thus providing preliminary evidence to support COMBIND as a potentially scalable PMTCT strategy. Further study would identify modifications needed to optimize other PMTCT outcomes. |
Burden of laboratory-confirmed shigellosis infections in Guatemala 2007-2012: Results from a population-based surveillance system
Hegde S , Benoit SR , Arvelo W , Lindblade K , López B , McCracken JP , Bernart C , Roldan A , Bryan JP . BMC Public Health 2019 19 474 Background: We describe the epidemiology and antimicrobial susceptibility patterns of culture-confirmed Shigella infections in facility-based surveillance sites in Guatemala. Current studies using quantitative molecular diagnostics suggest Shigella may contribute most to the global diarrheal disease burden. Since identification of Shigella requires culturing techniques using stool specimens and few laboratories in Guatemala routinely culture for this pathogen, little is known about the true burden of Shigella in Guatemala or, importantly, the antimicrobial resistance patterns. Methods: Clinical, epidemiological, and laboratory data were collected on 5399 patients with acute diarrhea (≥3 loose stools in 24 h) from June 2007-August 2012. Multidrug resistance (MDR) was defined as resistance to ampicillin and trimethoprim/sulfamethoxazole. Results: Five percent (261) of stool specimens yielded Shigella spp. The annual incidence of laboratory-confirmed infections ranged from 5.0 to 24.1 per 100,000 persons in Santa Rosa and 0.3 to 6.2 per 100,000 in Quetzaltenango; 58% of cases occurred in children < 5 years of age. Thirty patients were hospitalized; one patient died. Oral rehydration or intravenous solution was used to treat 72% of hospitalized and 15% of ambulatory cases. Fifty-nine percent of cases were S. flexneri and 51% of cases were MDR. Conclusions: Shigella is an important cause of bacterial diarrhea in children and prevalence of MDR highlights the importance of appropriate treatment regimens. This study demonstrates that strengthening laboratory capacity in Guatemala can help determine causes which can lead to prevention of diarrheal diseases, particularly in children. Such capacity building is also critical for rapid detection and control of public health threats at their source and therefore for global health security. |
Using healthcare-seeking behaviour to estimate the number of Nipah outbreaks missed by hospital-based surveillance in Bangladesh
Hegde ST , Salje H , Sazzad HMS , Hossain MJ , Rahman M , Daszak P , Klena JD , Nichol ST , Luby SP , Gurley ES . Int J Epidemiol 2019 48 (4) 1219-1227 BACKGROUND: Understanding the true burden of emergent diseases is critical for assessing public-health impact. However, surveillance often relies on hospital systems that only capture a minority of cases. We use the example of Nipah-virus infection in Bangladesh, which has a high case-fatality ratio and frequent person-to-person transmission, to demonstrate how healthcare-seeking data can estimate true burden. METHODS: We fit logistic-regression models to data from a population-based, healthcare-seeking study of encephalitis cases to characterize the impact of distance and mortality on attending one of three surveillance hospital sites. The resulting estimates of detection probabilities, as a function of distance and outcome, are applied to all observed Nipah outbreaks between 2007 and 2014 to estimate the true burden. RESULTS: The probability of attending a surveillance hospital fell from 82% for people with fatal encephalitis living 10 km away from a surveillance hospital to 54% at 50 km away. The odds of attending a surveillance hospital are 3.2 (95% confidence interval: 1.6, 6.6) times greater for patients who eventually died (i.e. who were more severely ill) compared with those who survived. Using these probabilities, we estimated that 119 Nipah outbreaks (95% confidence interval: 103, 140)-an average of 15 outbreaks per Nipah season-occurred during 2007-14; 62 (52%) were detected. CONCLUSIONS: Our findings suggest hospital-based surveillance missed nearly half of all Nipah outbreaks. This analytical method allowed us to estimate the underlying burden of disease, which is important for emerging diseases where healthcare access may be limited. |
Challenges and opportunities for outreach workers in the Prevention of Mother to Child Transmission of HIV (PMTCT) program in India
Suryavanshi N , Mave V , Kadam A , Kanade S , Sivalenka S , Kumar VS , Harvey P , Gupta R , Hegde A , Gupte N , Gupta A , Bollinger RC , Shankar A . PLoS One 2018 13 (9) e0203425 BACKGROUND: The Prevention of Mother-to-Child Transmission of HIV (PMTCT) program in India is one of the largest in the world. It uses outreach workers (ORWs) to facilitate patient uptake of services, however, the challenges faced by the ORWs, and their views about the effectiveness of this program are unknown. METHODS: The COMmunity-Home Based INDia (COMBIND) Prevention of Mother to Child Transmission of HIV study evaluated an integrated mobile health and behavioral intervention to enhance the capacity of ORWs in India. To understand the challenges faced by ORWs, and their perceptions of opportunities for program improvement, four group discussions were conducted among 60 ORW from four districts of Maharashtra, India, as part of the baseline assessment for COMBIND. Data were qualitatively analyzed using a thematic approach. RESULTS: Numerous personal-, social-, and structural-level challenges existed for ORW as they engaged with their patients. Personal-level challenges for ORWs included disclosure of their own HIV status and travelling costs for home visits. Personal-level challenges for patients included financial costs of travelling to ART centers, non-adherence to ART, loss of daily wages, non-affordability of infant formula, lack of awareness of the baby's needs, financial dependence on family, four time points (6weeks, 6 months, 12 months and 18 months) for HIV tests, and need for nevirapine (NVP) prophylaxis. Social-level challenges included lack of motivation by patients and/or health care staff, social stigma, and rude behavior of health care staff and their unwillingness to provide maternity services to women in the PMTCT programme. Structural-level challenges included cultural norms around infant feeding, shortages of HIV testing kits, shortages of antiretroviral drugs and infant NVP prophylaxis, and lack of training/knowledge related to PMTCT infant feeding guidelines by hospital staff. The consensus among ORWs was that there was a critical need for tools and training to improve their capacity to effectively engage with patients, and deliver appropriate care, and for motivation through periodic feedback. CONCLUSIONS: Given the significant challenges in PMTCT programme implementation reported by ORW, novel strategies to address these challenges are urgently needed to improve patient engagement, and access to and retention in care. |
Convergence of humans, bats, trees, and culture in Nipah virus transmission, Bangladesh
Gurley ES , Hegde ST , Hossain K , Sazzad HMS , Hossain MJ , Rahman M , Sharker MAY , Salje H , Islam MS , Epstein JH , Khan SU , Kilpatrick AM , Daszak P , Luby SP . Emerg Infect Dis 2017 23 (9) 1446-1453 Preventing emergence of new zoonotic viruses depends on understanding determinants for human risk. Nipah virus (NiV) is a lethal zoonotic pathogen that has spilled over from bats into human populations, with limited person-to-person transmission. We examined ecologic and human behavioral drivers of geographic variation for risk of NiV infection in Bangladesh. We visited 60 villages during 2011-2013 where cases of infection with NiV were identified and 147 control villages. We compared case villages with control villages for most likely drivers for risk of infection, including number of bats, persons, and date palm sap trees, and human date palm sap consumption behavior. Case villages were similar to control villages in many ways, including number of bats, persons, and date palm sap trees, but had a higher proportion of households in which someone drank sap. Reducing human consumption of sap could reduce virus transmission and risk for emergence of a more highly transmissible NiV strain. |
Investigating rare risk factors for Nipah virus in Bangladesh: 2001-2012
Hegde ST , Sazzad HM , Hossain MJ , Alam MU , Kenah E , Daszak P , Rollin P , Rahman M , Luby SP , Gurley ES . Ecohealth 2016 13 (4) 720-728 Human Nipah encephalitis outbreaks have been identified almost yearly in Bangladesh since 2001. Though raw date palm sap consumption and person-to-person contact are recognized as major transmission pathways, alternative pathways of transmission are plausible and may not have been identified due to limited statistical power in each outbreak. We conducted a risk factor analysis using all 157 cases and 632 controls surveyed in previous investigations during 2004-2012 to identify exposures independently associated with Nipah, since date palm sap was first asked about as an exposure in 2004. To further explore possible rare exposures, we also conducted in-depth interviews with all cases, or proxies, since 2001 that reported no exposure to date palm sap or contact with another case. Cases were 4.9 (95% 3.2-7.7) times more likely to consume raw date palm sap and 7.3 (95% 4.0-13.4) times more likely to have contact with a Nipah case than controls. In-depth interviews revealed that 39/182 (21%) of Nipah cases reporting neither date palm sap consumption nor contact with another case were misclassified. Prevention efforts should be focused on interventions to interrupt transmission through date palm sap consumption and person-to-person contact. Furthermore, pooling outbreak investigation data is a good method for assessing rare exposures. |
Good laboratory practice for clinical next-generation sequencing informatics pipelines.
Gargis AS , Kalman L , Bick DP , da Silva C , Dimmock DP , Funke BH , Gowrisankar S , Hegde MR , Kulkarni S , Mason CE , Nagarajan R , Voelkerding KV , Worthey EA , Aziz N , Barnes J , Bennett SF , Bisht H , Church DM , Dimitrova Z , Gargis SR , Hafez N , Hambuch T , Hyland FC , Luna RA , MacCannell D , Mann T , McCluskey MR , McDaniel TK , Ganova-Raeva LM , Rehm HL , Reid J , Campo DS , Resnick RB , Ridge PG , Salit ML , Skums P , Wong LJ , Zehnbauer BA , Zook JM , Lubin IM . Nat Biotechnol 2015 33 (7) 689-93 We report principles and guidelines (Supplementary Note) that were developed by the Next-Generation Sequencing: Standardization of Clinical Testing II (Nex-StoCT II) informatics workgroup, which was first convened on October 11–12, 2012, in Atlanta, Georgia, by the US Centers for Disease Control and Prevention (CDC; Atlanta, GA). We present here recommendations for the design, optimization and implementation of an informatics pipeline for clinical next-generation sequencing (NGS) to detect germline sequence variants in compliance with existing regulatory and professional quality standards1. The workgroup, which included informatics experts, clinical and research laboratory professionals, physicians with experience in interpreting NGS results, NGS test platform and software developers and participants from US government agencies and professional organizations, also discussed the use of NGS in testing for cancer and infectious disease. A typical NGS analytical process and selected workgroup recommendations are summarized in Table 1, and detailed in the guidelines presented in the Supplementary Note. |
Reporting incidental findings in genomic scale clinical sequencing--a clinical laboratory perspective: a report of the Association for Molecular Pathology.
Hegde M , Bale S , Bayrak-Toydemir P , Gibson J , Bone Jeng LJ , Joseph L , Laser J , Lubin IM , Miller CE , Ross LF , Rothberg PG , Tanner AK , Vitazka P , Mao R . J Mol Diagn 2015 17 (2) 107-17 Advances in sequencing technologies have facilitated concurrent testing for many disorders, and the results generated may provide information about a patient's health that is unrelated to the clinical indication, commonly referred to as incidental findings. This is a paradigm shift from traditional genetic testing in which testing and reporting are tailored to a patient's specific clinical condition. Clinical laboratories and physicians are wrestling with this increased complexity in genomic testing and reporting of the incidental findings to patients. An enormous amount of discussion has taken place since the release of a set of recommendations from the American College of Medical Genetics and Genomics. This discussion has largely focused on the content of the incidental findings, but the laboratory perspective and patient autonomy have been overlooked. This report by the Association of Molecular Pathology workgroup discusses the pros and cons of next-generation sequencing technology, potential benefits, and harms for reporting of incidental findings, including the effect on both the laboratory and the patient, and compares those with other areas of medicine. The importance of genetic counseling to preserve patient autonomy is also reviewed. The discussion and recommendations presented by the workgroup underline the need for continued research and discussion among all stakeholders to improve our understanding of the effect of different policies on patients, providers, and laboratories. |
Development of a genomic DNA reference material panel for myotonic dystrophy type 1 (DM1) genetic testing.
Kalman L , Tarleton J , Hitch M , Hegde M , Hjelm N , Berry-Kravis E , Zhou L , Hilbert JE , Luebbe EA , Moxley RT 3rd , Toji L . J Mol Diagn 2013 15 (4) 518-25 Myotonic dystrophy type 1 (DM1) is caused by expansion of a CTG triplet repeat in the 3' untranslated region of the DMPK gene that encodes a serine-threonine kinase. Patients with larger repeats tend to have a more severe phenotype. Clinical laboratories require reference and quality control materials for DM1 diagnostic and carrier genetic testing. Well-characterized reference materials are not available. To address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the genetic testing community, the National Registry of Myotonic Dystrophy and Facioscapulohumeral Muscular Dystrophy Patients and Family Members, and the Coriell Cell Repositories, has established and characterized cell lines from patients with DM1 to create a reference material panel. The CTG repeats in genomic DNA samples from 10 DM1 cell lines were characterized in three clinical genetic testing laboratories using PCR and Southern blot analysis. DMPK alleles in the samples cover four of five DM1 clinical categories: normal (5 to 34 repeats), mild (50 to 100 repeats), classical (101 to 1000 repeats), and congenital (>1000 repeats). We did not identify or establish Coriell cell lines in the premutation range (35 to 49 repeats). These samples are publicly available for quality control, proficiency testing, test development, and research and should help improve the accuracy of DM1 testing. |
Assuring the quality of next-generation sequencing in clinical laboratory practice.
Gargis AS , Kalman L , Berry MW , Bick DP , Dimmock DP , Hambuch T , Lu F , Lyon E , Voelkerding KV , Zehnbauer BA , Agarwala R , Bennett SF , Chen B , Chin EL , Compton JG , Das S , Farkas DH , Ferber MJ , Funke BH , Furtado MR , Ganova-Raeva LM , Geigenmuller U , Gunselman SJ , Hegde MR , Johnson PL , Kasarskis A , Kulkarni S , Lenk T , Liu CS , Manion M , Manolio TA , Mardis ER , Merker JD , Rajeevan MS , Reese MG , Rehm HL , Simen BB , Yeakley JM , Zook JM , Lubin IM . Nat Biotechnol 2012 30 (11) 1033-6 We direct your readers’ attention to the principles and guidelines (Supplementary Guidelines) developed by the Next-generation Sequencing: Standardization of Clinical Testing (Nex-StoCT) workgroup. These guidelines represent initial steps to ensure that results from tests based on next-generation sequencing (NGS) are reliable and useful for clinical decision making. The US Centers for Disease Control and Prevention (CDC) convened this national workgroup, which collaborated to define platform-independent approaches for establishing technical process elements of a quality management system (QMS) to assure the analytical validity and compliance of NGS tests with existing regulatory and professional quality standards. The workgroup identified and addressed gaps in quality practices that could compromise the quality of both clinical laboratory services and translational efforts needed to advance the implementation and utility of NGS in clinical settings. | The workgroup was composed of experts with knowledge of and experience with NGS and included clinical laboratory directors, clinicians, platform and software developers and informaticians, as well as individuals actively engaged in NGS guideline development from accreditation bodies and professional organizations. Representatives from US government agencies also participated. |
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