Stacey Pereira

Personalized genomic disease risk of volunteers

Significance Replacing traditional methods for genetic testing of inheritable disorders with next-generation sequencing (NGS) will reduce the cost of genetic testing and increase the information available for the patients. NGS will become an invaluable resource for the patient and physicians, especially if the sequencing information is stored properly and reanalyzed as bioinformatics tools and annotations improve. NGS is still at the early stages of development, and it is full of false-positive and -negative results and requires infrastructure and specialized personnel to properly analyze the results. This paper will explain our experience with an adult population, our bioinformatics analysis, and our clinical decisions to assure that our genetic diagnostics were accurate to detect carrier status and serious medical conditions in our volunteers. Next-generation sequencing (NGS) is commonly used for researching the causes of genetic disorders. However, its usefulness in clinical practice for medical diagnosis is in early development. In this report, we demonstrate the value of NGS for genetic risk assessment and evaluate the limitations and barriers for the adoption of this technology into medical practice. We performed whole exome sequencing (WES) on 81 volunteers, and for each volunteer, we requested personal medical histories, constructed a three-generation pedigree, and required their participation in a comprehensive educational program. We limited our clinical reporting to disease risks based on only rare damaging mutations and known pathogenic variations in genes previously reported to be associated with human disorders. We identified 271 recessive risk alleles (214 genes), 126 dominant risk alleles (101 genes), and 3 X-recessive risk alleles (3 genes). We linked personal disease histories with causative disease genes in 18 volunteers. Furthermore, by incorporating family histories into our genetic analyses, we identified an additional five heritable diseases. Traditional genetic counseling and disease education were provided in verbal and written reports to all volunteers. Our report demonstrates that when genome results are carefully interpreted and integrated with an individual’s medical records and pedigree data, NGS is a valuable diagnostic tool for genetic disease risk.

Newborn Sequencing in Genomic Medicine and Public Health.

The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening.

Potential Psychosocial Risks of Sequencing Newborns

Various stakeholders have issued recommendations regarding the use of genomics in pediatrics. These guidelines are driven in part by concerns about psychosocial risks of disclosing predictive genomic information during childhood. As genomic sequencing becomes more commonly used in pediatric settings, it is important to systematically study the psychosocial impact of genomic sequencing of newborns, including the impact on family dynamics. Through review of the psychological and genetic counseling literature, we identify the following 3 domains of family dynamics that have potential to be impacted by the return of genomic results during the newborn period: perceived child vulnerability, parent-child bonding, and self and partner blame. In this article, we outline the complexity of studying these psychosocial outcomes and our plan to examine them in the BabySeq Project, a randomized controlled trial in both healthy and sick infants, in which the return of genomic information will be compared with standard of care.

Adult Genetic Risk Screening

Recent advances in genetic analysis especially DNA sequencing technology open a new strategy for adult disease prevention by genetic screening. Physicians presently treat disease pathology with less emphasis on disease risk prevention/reduction. Genetic screening has reduced the incidence of untreatable childhood genetic diseases and improved the care of newborns. The opportunity exists to expand screening programs and reduce the incidence of adult onset diseases via genetic risk identification and disease intervention. This article outlines the approach, challenges, and benefits of such screening for adult genetic disease risks.

Open Access Data Sharing in Genomic Research

The current emphasis on broad sharing of human genomic data generated in research in order to maximize utility and public benefit is a significant legacy of the Human Genome Project. Concerns about privacy and discrimination have led to policy responses that restrict access to genomic data as the means for protecting research participants. Our research and experience show, however, that a considerable number of research participants agree to open access sharing of their genomic data when given the choice. General policies that limit access to all genomic data fail to respect the autonomy of these participants and, at the same time, unnecessarily limit the utility of the data. We advocate instead a more balanced approach that allows for individual choice and encourages informed decision making, while protecting against the misuse of genomic data through enhanced legislation.

Should you profit from your genome

VOLUME 35 NUMBER 1 JANUARY 2017 NATURE BIOTECHNOLOGY the EGFP expression plasmid (pEGFP-N1) driven by a cytomegalovirus (CMV) promoter. As the expression of NgAgo modified at its N terminus with a nuclear localization signal (NLS; NLS-NgAgo) is also driven by a CMV promoter, the Ekker lab used EGFP expression as a surrogate marker of NgAgo in these cells. At 4, 12, and 24 h after lipofection, HeLa cells and HEK293 cells were fixed with paraformaldehyde and the coverslips mounted on slides. Strong red fluorescence corresponding to Alexa Fluor 594 was observed inside the cells by 4 h and persisted for at least 24 h (Supplementary Fig. 2b). The distribution of red fluorescence was diffuse within cells at 4 h, but later became more punctated. As expected, some EGFP fluorescence was observed by 4 h, with a much stronger signal detected at 12 and 24 h after transfection. Delivery of NgAgo plasmid was also confirmed by PCR assays (Supplementary Fig. 2c). To confirm expression of NgAgo in transfected cells, the extent of RNA or protein expression was determined either by qualitative reverse transcription PCR (RT-PCR; Supplementary Fig. 1e), immunoblot analysis of hemagglutinin (HA)-tagged versions of NgAgo (Supplementary Figs. 1f and 3n), or flow cytometry of a DsRed-tagged version of NgAgo (Supplementary Fig. 1f). Taken together, these data suggest that plasmid DNA and gDNA are efficiently delivered to the human cell lines used here and that all the tested cells are capable of expressing NgAgo. On the basis of the above data, we conclude that in conditions designed to replicate those in Gao et al.3, co-delivery of plasmid DNA encoding NgAgo and a 5ʹ-phosphorylated single-strand gDNA alone is insufficient to induce gene editing at the indel frequencies in cultured human cells reported in the original study.

An open access pilot freely sharing cancer genomic data from participants in Texas

Genomic data sharing in cancer has been restricted to aggregate or controlled-access initiatives to protect the privacy of research participants. By limiting access to these data, it has been argued that the autonomy of individuals who decide to participate in data sharing efforts has been superseded and the utility of the data as research and educational tools reduced. In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank, many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from 7 human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants (http://txcrb.org/open.html).

Return of individual genomic research results: what do consent forms tell participants?

Advances in genomic technology make possible the large-scale collection of genomic data for research purposes. Many international initiatives seek to collect genomic data on large populations, often relying on existing collections to populate their databases. As these efforts progress, the debate over whether or not to return individual genetic research results to study participants remains an area of much contention. Some recommend returning results to participants only if the issue was addressed in the original study consent form. Much of the data being used in current studies, however, may have been derived from biospecimens collected years ago with consent documents that did not anticipate the possibility of returning individual level genomic results. We conducted an analysis of informed consent documents from published genome-wide association studies (GWAS) (n=40) to explore whether future research use of biospecimens or data is anticipated, and if return of results is addressed and how it is described to better understand participants’ expectations for future disclosure. The majority (70%) of the GWAS consent documents we analyzed either stated explicitly that individual genomic results would not be returned or were silent on the issue. This has implications for how researchers and members of Research Ethics Committees manage the return of results from sequencing studies using legacy samples and data.

Motivations and barriers to sharing biological samples: a case study.

One of the most significant impediments to the current goals of genomic research is the limited availability of high quality biological samples. Despite efforts to increase both the quality and quantity of samples collected, access to such samples remains limited. This may be due, at least in part, to a general reluctance of biobanking professionals, clinicians, and researchers to share biological specimens with others. Ethnographic methods were used in a biobank setting to explore professionals’ perspectives toward and practices of sharing samples. Several motivations and barriers to sharing that may influence research practice were identified. Contrary to existing literature that suggests that professionals are unlikely to share samples with one another, the participants of this study were open to and supportive of sharing samples for research. However, clear communication and effective infrastructure are needed to support the distribution of biobank materials.

Do privacy and security regulations need a status update? Perspectives from an intergenerational survey

Background The importance of health privacy protections in the era of the “Facebook Generation” has been called into question. The ease with which younger people share personal information about themselves has led to the assumption that they are less concerned than older generations about the privacy of their information, including health information. We explored whether survey respondents’ views toward health privacy suggest that efforts to strengthen privacy protections as health information is moved online are unnecessary. Methods Using Amazon’s Mechanical Turk (MTurk), which is well-known for recruitment for survey research, we distributed a 45-item survey to individuals in the U.S. to assess their perspectives toward privacy and security of online and health information, social media behaviors, use of health and fitness devices, and demographic information. Results 1310 participants (mean age: 36 years, 50% female, 78% non-Hispanic white, 54% college graduates or higher) were categorized by generations: Millennials, Generation X, and Baby Boomers. In multivariate regression models, we found that generational cohort was an independent predictor of level of concern about privacy and security of both online and health information. Younger generations were significantly less likely to be concerned than older generations (all P < 0.05). Time spent online and social media use were not predictors of level of concern about privacy or security of online or health information (all P > 0.05). Limitations This study is limited by the non-representativeness of our sample. Conclusions Though Millennials reported lower levels of concern about privacy and security, this was not related to internet or social media behaviors, and majorities within all generations reported concern about both the privacy and security of their health information. Thus, there is no intergenerational imperative to relax privacy and security standards, and it would be advisable to take privacy and security of health information more seriously.