Consent Forms in Genomics: The Difference between Law and Practice

2011 ◽  
Vol 18 (5) ◽  
pp. 491-519 ◽  
Author(s):  
Heather Gowans ◽  
Nadja Kanellopoulou ◽  
Naomi Hawkins ◽  
Liam Curren ◽  
Karen Melham ◽  
...  
Keyword(s):  
Informed Consent ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Consent Forms ◽  
Research Participants ◽  
Genome Wide ◽  
The Difference ◽  
Principal Method ◽  
Participant Information ◽  
Selection Of

AbstractConsent forms are the principal method for obtaining informed consent from biomedical research participants. The significance of these forms is increasing as more secondary research is undertaken on existing research samples and information, and samples are deposited in biobanks accessible to many researchers. We reviewed a selection of consent forms used in European Genome-Wide Association Studies (GWAS) and identified four common elements that were found in every consent form. Our analysis showed that only two of the four most commonly found elements in our sample of informed consent forms were required in UK law. This raises questions about what should be put in informed consent forms for research participants. These findings could be beneficial for the formulation of participant information and consent documentation in the future studies.

scholarly journals Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251745
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Caio Cesar Ferrari Barbosa ◽  
Gabriel de Moraes Cunha Gonçalves ◽  
Roberto Fritsche-Neto ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Association Studies ◽  
Colletotrichum Lindemuthianum ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide Association Studies ◽  
Anthracnose Resistance ◽  
Resistant Cultivars ◽  
Genome Wide ◽  
Selection Of

Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.

scholarly journals Gene-Based Testing of Interactions Using XGBoost in Genome-Wide Association Studies

2021 ◽  
Vol 9 ◽  
Author(s):  
Yingjie Guo ◽  
Chenxi Wu ◽  
Zhian Yuan ◽  
Yansu Wang ◽  
Zhen Liang ◽  
...  
Keyword(s):  
Association Studies ◽  
Real Data ◽  
Gene Interaction ◽  
Genome Wide Association ◽  
Superior Performance ◽  
Gene Interactions ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
The Difference

Among the myriad of statistical methods that identify gene–gene interactions in the realm of qualitative genome-wide association studies, gene-based interactions are not only powerful statistically, but also they are interpretable biologically. However, they have limited statistical detection by making assumptions on the association between traits and single nucleotide polymorphisms. Thus, a gene-based method (GGInt-XGBoost) originated from XGBoost is proposed in this article. Assuming that log odds ratio of disease traits satisfies the additive relationship if the pair of genes had no interactions, the difference in error between the XGBoost model with and without additive constraint could indicate gene–gene interaction; we then used a permutation-based statistical test to assess this difference and to provide a statistical p-value to represent the significance of the interaction. Experimental results on both simulation and real data showed that our approach had superior performance than previous experiments to detect gene–gene interactions.

Selection of representative SNP sets for genome-wide association studies: a metaheuristic approach

2011 ◽  
Vol 6 (6) ◽  
pp. 1207-1218 ◽  
Author(s):  
Gürkan Üstünkar ◽  
Süreyya Özöğür-Akyüz ◽  
Gerhard W. Weber ◽  
Christoph M. Friedrich ◽  
Yeşim Aydın Son
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Selection Of

scholarly journals Preparing accessible and understandable clinical research participant information leaflets and consent forms: a set of guidelines from an expert consensus conference

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Eleanor Coleman ◽  
Lydia O’Sullivan ◽  
Rachel Crowley ◽  
Moira Hanbidge ◽  
Seán Driver ◽  
...  
Keyword(s):  
Informed Consent ◽  
Clinical Research ◽  
Research Participant ◽  
Consensus Conference ◽  
Expert Consensus ◽  
Consent Process ◽  
Consent Forms ◽  
Research Participants ◽  
Information Leaflets ◽  
Participant Information

Abstract Background In line with Good Clinical Practice and the Declaration of Helsinki, it is the investigator’s responsibility to ensure that research participants are sufficiently informed, to enable the provision of informed consent. The Participant Information Leaflet/Informed Consent Form is key to facilitating this communication process. Although studies have indicated that clinical research Participant Information Leaflets/Informed Consent Forms are not optimal in terms of accessibility, there is little or no specific guidance available. The aim of this research was to propose and agree a set of guidelines for academic researchers and sponsors for preparing accessible and understandable Participant Information Leaflets/Informed Consent Forms. Methods A literature review identified guidance for the preparation of patient-facing documents. Following critical appraisal, key recommendations were extracted and a set of recommendations which can be applied to clinical research Participant Information Leaflets/Informed Consent Forms were prepared. These recommendations were evaluated and amended by an Expert Consensus Conference consisting of a group of key stakeholders. The stakeholders included members of a Research Ethics Committee (both lay and expert), a patient advocate, experienced clinical researchers, a plain English editor and a Data Protection Officer. Consensus was reached regarding a final set of recommendations. Results 44 recommendations were agreed upon and grouped into five categories: Layout, Formatting, Content, Language and Confirming Readability. These recommendations aimed to maximize accessibility for lay participants, including readers with dyslexia, literacy or numeracy challenges, thereby improving the quality of the consent process. Conclusions More empirical research is needed to further improve the informed consent process for research participants. However, these recommendations are informed by the current literature and have been ratified by expert stakeholders. It is hoped that these recommendations will help investigators and sponsors to consistently and efficiently produce more accessible clinical research Participant Information Leaflets/Informed Consent Forms.

scholarly journals Genome-wide association studies of impulsive personality traits (BIS-11 and UPPSP) and drug Experimentation in up to 22,861 adult research participants

2018 ◽  
Author(s):  
Sandra Sanchez-Roige ◽  
Pierre Fontanillas ◽  
Sarah L. Elson ◽  
Michelle Agee ◽  
Babak Alipanahi ◽  
...  
Keyword(s):  
Personality Traits ◽  
Genetic Variants ◽  
Sensation Seeking ◽  
Association Studies ◽  
Risk Tolerance ◽  
Genome Wide Association ◽  
European Ancestry ◽  
Genome Wide Association Studies ◽  
Research Participants ◽  
Genome Wide

AbstractBackgroundImpulsive personality traits are complex heritable traits that are governed by frontal-subcortical circuits and are associated with numerous neuropsychiatric disorders, particularly drug abuse.MethodsIn collaboration with the genetics company 23andMe, Inc., we performed several genome-wide association studies (GWAS) on measures of impulsive personality traits (the short version of the UPPSP Impulsive Behavior Scale, and the Barratt Impulsiveness Scale [BIS-11]) and drug experimentation (the number of drug classes an individual has tried in their lifetime) in up to 22,861 male and female adult research participants of European ancestry.ResultsImpulsive personality traits and drug experimentation showed SNP-heritabilities that ranged from 5 to 11%. Genetic variants in the CADM2 locus were significantly associated with the UPPSP Sensation Seeking subscale (P = 8.3 × 10-9, rs139528938) and showed a suggestive association with drug experimentation (P = 3.0 × 10-7, rs2163971; r2 = 0.68 with rs139528938); CADM2 has been previously associated with measures of risky behaviors and self-reported risk tolerance, cannabis initiation, alcohol consumption, as well as information speed processing, body mass index (BMI) variation and obesity. Furthermore, genetic variants in the CACNA1I locus were significantly associated with the UPPSP Negative Urgency subscale (P = 3.8 × 10-8, rs199694726). Multiple subscales from both UPPSP and BIS showed strong genetic correlations (>0.5) with drug experimentation and other substance use traits measured in independent cohorts, including smoking initiation, and lifetime cannabis use. Several UPPSP and BIS subscales were genetically correlated with attention-deficit/hyperactivity disorder (rg = 0.30-0.51, p < 8.69 x 10-3), supporting their validity as endophenotypes.ConclusionsOur findings demonstrate a role for common genetic contributions to individual differences in impulsivity. Furthermore, our study is the first to provide a genetic dissection of the relationship between different types of impulsive personality traits and various psychiatric disorders.

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