Ethics. DNA returned to tribe, raising questions about consent

From the reference human genome to human pangenome: Premise, promise and challenge

The Reference Human Genome remains the single most important resource for mapping genetic variations and assessing their impact. However, it is monophasic, incomplete and not representative of the variation that exists in the population. Given the extent of ethno-geographic diversity and the consequent diversity in clinical manifestations of these variations, population specific references were developed overtime. The dramatically plummeting cost of sequencing whole genomes and the advent of third generation long range sequencers allowing accurate, error free, telomere-to-telomere assemblies of human genomes present us with a unique and unprecedented opportunity to develop a more composite standard reference consisting of a collection of multiple genomes that capture the maximal variation existing in the population, with the deepest annotation possible, enabling a realistic, reliable and actionable estimation of clinical significance of specific variations. The Human Pangenome Project thus is a logical next step promising a more accurate and global representation of genomic variations. The pangenome effort must be reciprocally complemented with precise variant discovery tools and exhaustive annotation to ensure unambiguous clinical assessment of the variant in ethno-geographical context. Here we discuss a broad roadmap, the challenges and way forward in developing a universal pangenome reference including data visualization techniques and integration of prior knowledge base in the new graph based architecture and tools to submit, compare, query, annotate and retrieve relevant information from the pangenomes. The biggest challenge, however, will be the ethical, legal and social implications and the training of human resource to the new reference paradigm.

The Human Pangenome Project: a global resource to map genomic diversity

The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.

The Need for a Human Pangenome Reference Sequence

The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome.

Place of Strength: Indigenous Artists and Indigenous Knowledge is Prevention Science

The Place of Strength (PoS) project represents an effort to Indigenize program evaluation with Indigenous communities by melding art with prevention science. We propose that Native artists as evaluators: (a) opens avenues of communication for Indigenous perspectives; (b) provides opportunities to capture spiritual, relational, and emotional impacts of prevention programming; and (c) maintains Indigenous processes, language, and values at the center of knowledge production. The New Mexico Tribal Prevention Project (NMTPP) funded seven Southwestern tribes to develop substance abuse prevention programs. In response to their expressed negative experiences with evaluation of prevention strategies, NMTPP piloted PoS. PoS shifted systematic knowledge paradigms to Tribal thought, values, and perspectives embodied in art. Art exists in Native communities as a way of documenting lifeways and historical experiences through various cultural forms. We share the process of collaborating with Native artists to document the impact of substance abuse prevention initiatives through their art within a community context. We offer concepts derived from this project as a community psychology model for re-conceptualizing evaluation utilizing Indigenous knowledge.

Perspectives on communication and engagement with regard to collecting biospecimens and family health histories for cancer research in a rural Alaska Native community

Precision medicine initiatives, such as Cancer Breakthrough 2020, promise to improve cancer outcomes by tailoring treatment to an individual's genes, environment, and lifestyle. This promise will fall short unless researchers successfully engage diverse communities, including those with histories of medical and research abuse. We examined a rural Alaska Native community's viewpoints about biospecimen collection and storage; interest and recall in reporting family health history; and interest and engagement in biospecimen collection for conducting a genetic test for cancer. In 2014, four focus groups were held with 28 adult Alaska Native rural community members. Thematic analysis was performed after establishing a coding scheme by team consensus. Study participants shared interest in engaging in genetic cancer research and suggested ways to improve community engagement in research. These included transparency and continuous communication with researchers at all stages of the research, clear communication about the intent of the research, and that research and results take into consideration the community's needs. These suggestions may be beneficial for future efforts to expand precision medicine research in Alaska Native communities and similar, diverse populations.

Pharmacogenomics in diverse practice settings: implementation beyond major metropolitan areas

AIM

The limited formal study of the clinical feasibility of implementing pharmacogenomic tests has thus far focused on providers at large medical centers in urban areas. Our research focuses on small metropolitan, rural and tribal practice settings.

MATERIALS & METHODS

We interviewed 17 healthcare providers in western Montana regarding pharmacogenomic testing.

RESULTS

Participants were optimistic about the potential of pharmacogenomic tests, but noted unique barriers in small and rural settings including cost, adherence, patient acceptability and testing timeframe. Participants in tribal settings identified heightened sensitivity to genetics and need for community leadership approval as additional considerations.

CONCLUSION

Implementation differences in small metropolitan, rural and tribal communities may affect pharmacogenomic test adoption and utilization, potentially impacting many patients. Original submitted 3 September 2014; Revision submitted 3 December 2014.

Informed consent for biobanking: consensus-based guidelines for adequate comprehension

Purpose

Federal regulations and best practice guidelines identify categories of information that should be communicated to prospective biobank participants during the informed consent process. However, uncertainty remains about which of this information participants must understand to provide valid consent.

Methods

We conducted a Delphi process to define “adequate comprehension” in the context of biobanking consent. The process involved an iterative series of 3 online surveys of a diverse panel of 51 experts, including genome scientists, biobank managers, ethics and policy experts, and community and participant representatives. We sought consensus (greater than 70% agreement) concerning what specific details participants should know about 16 biobank consent topics.

Results

Consensus was achieved for 15 of the 16 consent topics. The exception was the comprehension needed regarding the Genetic Information Nondiscrimination Act.

Conclusions

Our Delphi process was successful in identifying a concise set of key points that prospective participants must grasp to provide valid consent for biobanking. Specifying the level of knowledge sufficient for individuals to make an informed choice provides a basis for improving consent forms and processes, as well as an absolute metric for assessing the effectiveness of other interventions to improve comprehension.

Seeking consent to genetic and genomic research in a rural Ghanaian setting: a qualitative study of the MalariaGEN experience

Background

Seeking consent for genetic and genomic research can be challenging, particularly in populations with low literacy levels, and in emergency situations. All of these factors were relevant to the MalariaGEN study of genetic factors influencing immune responses to malaria in northern rural Ghana. This study sought to identify issues arising in practice during the enrolment of paediatric cases with severe malaria and matched healthy controls into the MalariaGEN study.

Methods

The study used a rapid assessment incorporating multiple qualitative methods including in depth interviews, focus group discussions and observations of consent processes. Differences between verbal information provided during community engagement processes, and consent processes during the enrolment of cases and controls were identified, as well as the factors influencing the tailoring of such information.

Results

MalariaGEN participants and field staff seeking consent were generally satisfied with their understanding of the project and were familiar with aspects of the study relating to malaria. Some genetic aspects of the study were also well understood. Participants and staff seeking consent were less aware of the methodologies employed during genomic research and their implications, such as the breadth of data generated and the potential for future secondary research.

Moreover, trust in and previous experience with the Navrongo Health Research Centre which was conducting the research influenced beliefs about the benefits of participating in the MalariaGEN study and subsequent decision-making about research participation.

Conclusions

It is important to recognise that some aspects of complex genomic research may be of less interest to and less well understood by research participants and that such gaps in understanding may not be entirely addressed by best practice in the design and conduct of consent processes. In such circumstances consideration needs to be given to additional protections for participants that may need to be implemented in such research, and how best to provide such protections.

Capacity building for research ethics committees with limited familiarity with genetic and genomic research, and appropriate engagement with communities to elicit opinions of the ethical issues arising and acceptability of downstream uses of genome wide association data are likely to be important.

Bayesian method to predict individual SNP genotypes from gene expression data

RNA profiling can be used to capture the expression patterns of many genes that are associated with expression quantitative trait loci (eQTLs). Employing published putative cis eQTLs, we developed a Bayesian approach to predict SNP genotypes that is based only on RNA expression data. We show that predicted genotypes can accurately and uniquely identify individuals in large populations. When inferring genotypes from an expression data set using eQTLs of the same tissue type (but from an independent cohort), we were able to resolve 99% of the identities of individuals in the cohort at P(adjusted) ≤ 1 × 10(-5). When eQTLs derived from one tissue were used to predict genotypes using expression data from a different tissue, the identities of 90% of the study subjects could be resolved at P(adjusted) ≤ 1 × 10(-5). We discuss the implications of deriving genotypic information from RNA data deposited in the public domain.

Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations

HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics’ analyses) recommends avoiding outdated racial classifications and population names (e.g. ‘Caucasian’) and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. ‘pan-European’). A standard ‘HLA-NET POPULATION DATA QUESTIONNAIRE’ has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in ‘HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS’. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable of dealing with ambiguous data, such as the ‘gene[rate]’ computer tools to estimate frequencies, test for Hardy–Weinberg equilibrium and selective neutrality on data containing any number and kind of ambiguities. WG4 (Ethical issues) proposes to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. All HLA-NET guidelines and tools are available through its website http://hla-net.eu.

Editorial: genetic and genomic research-changing patterns of accountability

Debates about genomic science have raised questions about the implications for ethics and accountability. Accountability has external and internal aspects. Whereas ethical review, including attention to appropriate consent procedures, has been central to 'giving an account' externally, there are also issues internal to the practice of science itself. The pursuit of truth is central to the scientific endeavour, but truths can sometimes be 'inconvenient', leading to complex questions of accountability that go beyond the issues of consent. This is illustrated by the case of the Havasupai.

Charting a course for genomic medicine from base pairs to bedside

There has been much progress in genomics in the ten years since a draft sequence of the human genome was published. Opportunities for understanding health and disease are now unprecedented, as advances in genomics are harnessed to obtain robust foundational knowledge about the structure and function of the human genome and about the genetic contributions to human health and disease. Here we articulate a 2011 vision for the future of genomics research and describe the path towards an era of genomic medicine.

Research ethics. Research practice and participant preferences: the growing gulf

Reframing research practice to align with participant interests is important for ensuring long-term success of genomic investigation.