Applied & translational genomics最新文献

{"title":"Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease","authors":"Nicola Mulder ,&nbsp;Victoria Nembaware ,&nbsp;Adekunle Adekile ,&nbsp;Kofi A. Anie ,&nbsp;Baba Inusa ,&nbsp;Biobele Brown ,&nbsp;Andrew Campbell ,&nbsp;Furahini Chinenere ,&nbsp;Catherine Chunda-Liyoka ,&nbsp;Vimal K. Derebail ,&nbsp;Amy Geard ,&nbsp;Kais Ghedira ,&nbsp;Carol M. Hamilton ,&nbsp;Neil A. Hanchard ,&nbsp;Melissa Haendel ,&nbsp;Wayne Huggins ,&nbsp;Muntaser Ibrahim ,&nbsp;Simon Jupp ,&nbsp;Karen Kengne Kamga ,&nbsp;Jennifer Knight-Madden ,&nbsp;Ambroise Wonkam","doi":"10.1016/j.atg.2016.03.005","DOIUrl":"10.1016/j.atg.2016.03.005","url":null,"abstract":"<div><p>Sickle cell disease (SCD) is a debilitating single gene disorder caused by a single point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% of SCD in newborns world-wide occurs in sub-Saharan Africa, where neonatal and childhood mortality from sickle cell related complications is high. While SCD research across the globe is tackling the disease on multiple fronts, advances have yet to significantly impact on the health and quality of life of SCD patients, due to lack of coordination of these disparate efforts. Ensuring data across studies is directly comparable through standardization is a necessary step towards realizing this goal. Such a standardization requires the development and implementation of a disease-specific ontology for SCD that is applicable globally. Ontology development is best achieved by bringing together experts in the domain to contribute their knowledge.</p><p>The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"9 ","pages":"Pages 23-29"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.03.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34619083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SeeHaBITaT: A server on bioinformatics applications for Tospoviruses and other species","authors":"Seethalakshmi Sakthivel,&nbsp;S.K.M. Habeeb","doi":"10.1016/j.atg.2016.03.002","DOIUrl":"10.1016/j.atg.2016.03.002","url":null,"abstract":"<div><p>Plant viruses are important limiting factors in agricultural productivity. Tospovirus is one of the severe plant pathogens, causing damage to economically important food and ornamental crops worldwide through thrips as vectors. Database application resources exclusively on this virus would help to design better control measures, which aren't available. SeeHaBITaT is a unique and exclusive web based server providing work bench to perform computational research on tospoviruses and its species. SeeHaBITaT hosts Tospoviruses specific database Togribase, MOLBIT, SRMBIT and SS with PDB. These applications would be of immense help to the Tospovirus scientific community. The server could be accessed at <span>http://bit.srmuniv.ac.in/</span><svg><path></path></svg>.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"9 ","pages":"Pages 30-32"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.03.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34619082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Addressing ethical challenges in the Genetics Substudy of the National Eye Survey of Trinidad and Tobago (GSNESTT)","authors":"Allana N. Roach ,&nbsp;Tasanee Braithwaite ,&nbsp;Christine Carrington ,&nbsp;Elysse Marcellin ,&nbsp;Subash Sharma ,&nbsp;Aroon Hingorani ,&nbsp;Juan P. Casas ,&nbsp;Michael A. Hauser ,&nbsp;R. Rand Allingham ,&nbsp;Samuel S. Ramsewak ,&nbsp;Rupert Bourne","doi":"10.1016/j.atg.2016.05.001","DOIUrl":"10.1016/j.atg.2016.05.001","url":null,"abstract":"<div><h3>Background</h3><p>The conduct of international collaborative genomics research raises distinct ethical challenges that require special consideration, especially if conducted in settings that are research-naïve or resource-limited. Although there is considerable literature on these issues, there is a dearth of literature chronicling approaches taken to address these issues in the field. Additionally no previous ethical guidelines have been developed to support similar research in Trinidad and Tobago.</p></div><div><h3>Methods</h3><p>A literature review was undertaken to identify strategies used to address common ethical issues relevant to human genetics and genomics research in research-naïve or resource-limited settings. Strategies identified were combined with novel approaches to develop a culturally appropriate, multifaceted strategy to address potential challenges in the Genetics Substudy of the National Eye Survey of Trinidad and Tobago (GSNESTT).</p></div><div><h3>Results</h3><p>Regarding the protection of study participants, we report a decision to exclude children as participants; the use of a Community Engagement and Sensitization Strategy to increase the genetic literacy of the target population; the involvement of local expertise to ensure cultural sensitivity and to address potential comprehension barriers in informed consent; and an audit of the informed consent process to ensure valid consent. Concerning the regulation of the research, we report on ethics approvals from relevant authorities; a Materials Transfer Agreement to guide sample ownership and export; and a Sample Governance Committee to oversee data use and data access. Finally regarding the protection of the interests of scientists from the host country, we report on capacity building efforts to ensure that local scientists have access to data collected through the project and appropriate recognition of their contributions in future publications.</p></div><div><h3>Conclusion</h3><p>This paper outlines an ethical framework for the conduct of population-based genetics and genomics research in Trinidad and Tobago; highlights common issues arising in the field and strategies to address these.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"9 ","pages":"Pages 6-14"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34332044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementation of genomic medicine in Sri Lanka: Initial experience and challenges","authors":"Nirmala D. Sirisena,&nbsp;Nilaksha Neththikumara,&nbsp;Kalum Wetthasinghe,&nbsp;Vajira H.W. Dissanayake","doi":"10.1016/j.atg.2016.05.003","DOIUrl":"10.1016/j.atg.2016.05.003","url":null,"abstract":"<div><p>The recent advances in next generation sequencing technologies have made it possible to implement genomic medicine in developing countries such as Sri Lanka where capacity for utilization is limited. This paper aims to describe our initial experience and challenges faced in integrating genomic medicine into routine clinical practice. Using the Illumina MiSeq Next generation sequencing (NGS) platform and an in-house developed bioinformatics pipeline/workflow, we successfully implemented clinical exome sequencing for rare disorders, complex disorders with unusual coexisting phenotypes, and multigene cancer panel testing for inherited cancer syndromes. The advantages of implementing these tests, the challenges for bioinformatics analysis and reporting, the ethical, legal, and social implications of moving from genetic to genomic counseling, and special policy issues related to implementing these tests are further discussed. The implementation of genomic medicine into our routine clinical practice has facilitated improved care for our patients, attesting to the ability of resource limited countries to improve care using advanced genomic technology.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"9 ","pages":"Pages 33-36"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.05.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34620340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unsung heroes: Genomic successes in the developing world","authors":"Vajira H.W. Dissanayake,&nbsp;Carol Isaacson Barash","doi":"10.1016/j.atg.2016.05.002","DOIUrl":"10.1016/j.atg.2016.05.002","url":null,"abstract":"","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"9 ","pages":"Pages 1-2"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.05.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34619077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Life as a numerator: Putting the person in personal genomics","authors":"Sharon F. Terry","doi":"10.1016/j.atg.2016.01.007","DOIUrl":"10.1016/j.atg.2016.01.007","url":null,"abstract":"","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"8 ","pages":"Pages 40-41"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.01.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85680800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotype with a side of genotype, please: Patients, parents and priorities in rare genetic disease","authors":"Christy Collins","doi":"10.1016/j.atg.2016.01.002","DOIUrl":"10.1016/j.atg.2016.01.002","url":null,"abstract":"<div><p>As the parent and caregiver of a child with an ultra-rare disease and advocate for others with the same condition, I discuss the importance of phenotyping in rare disease research. I emphasize the need for more clinical geneticists, deeper and more intentional integration of clinical genetics in complex patient care, and a greater appreciation of patients and families as an informational resource.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"8 ","pages":"Pages 42-44"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.01.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81477570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An old problem in a new age: Revisiting the clinical dilemma of misattributed paternity","authors":"Laura Hercher ,&nbsp;Leila Jamal","doi":"10.1016/j.atg.2016.01.004","DOIUrl":"10.1016/j.atg.2016.01.004","url":null,"abstract":"<div><p>Clinical genetics has wrestled with the problem of misattributed paternity for decades. While there are no clear directives on policy, surveys suggest that genetics professionals are inclined to avoid disclosure when possible. Changes associated with the increased use of genomic testing will alter the context and may limit the benefits of non-disclosure. Multi-site testing will preclude the uncertainty often associated with single-gene testing. Increased use of genetic testing in clinical and non-clinical settings will create new opportunities for the subsequent unmasking of misattributed relationships, as will the presence of test results in the electronic medical record. Family health history information will become more valuable as it is used more often and to better effect in risk assessment, diagnosis, treatment and reproductive decision-making. These changes associated with genomic testing increase the risks and decrease the benefits associated with the nondisclosure of misattributed paternity. For ethical and practical reasons, genetics professionals, and those who advise them, should consider a greater emphasis on the value of carefully planned disclosure.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"8 ","pages":"Pages 36-39"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.01.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84407639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Attitudes towards personal genomics among older Swiss adults: An exploratory study","authors":"Laura Mählmann ,&nbsp;Christina Röcke ,&nbsp;Angela Brand ,&nbsp;Ernst Hafen ,&nbsp;Effy Vayena","doi":"10.1016/j.atg.2016.01.009","DOIUrl":"10.1016/j.atg.2016.01.009","url":null,"abstract":"<div><h3>Objectives</h3><p>To explore attitudes of Swiss older adults towards personal genomics (PG).</p></div><div><h3>Methods</h3><p>Using an anonymized voluntary paper-and-pencil survey, data were collected from 151 men and women aged 60–89<!--> <!-->years attending the Seniorenuniversität Zurich, Switzerland (Seniors' University). Analyses were conducted using descriptive and inferential statistics.</p></div><div><h3>Results</h3><p>One third of the respondents were aware of PG, and more than half indicated interest in undergoing PG testing. The primary motivation provided was respondents' interest in finding out about their own disease risk, followed by willingness to contribute to scientific research. Forty-four percent were not interested in undergoing testing because results might be worrisome, or due to concerns about the validity of the results. Only a minority of respondents mentioned privacy-related concerns. Further, 66% were interested in undergoing clinic-based PG motivated by the opportunity to contribute to scientific research (78%) and 75% of all study participants indicated strong preferences to donate genomic data to public research institutions.</p></div><div><h3>Conclusion</h3><p>This study indicates a relatively positive overall attitude towards personal genomic testing among older Swiss adults, a group not typically represented in surveys about personal genomics. Genomic data of older adults can be highly relevant to late life health and maintenance of quality of life. In addition they can be an invaluable source for better understanding of longevity, health and disease. Understanding the attitudes of this population towards genomic analyses, although important, remains under-examined.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"8 ","pages":"Pages 9-15"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.01.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72459584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How Geisinger made the case for an institutional duty to return genomic results to biobank participants","authors":"W. Andrew Faucett,&nbsp;F. Daniel Davis","doi":"10.1016/j.atg.2016.01.003","DOIUrl":"10.1016/j.atg.2016.01.003","url":null,"abstract":"","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"8 ","pages":"Pages 33-35"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.01.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73596540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}