The hidden harm behind the return of results from personal genome services: a need for rigorous and responsible evaluation

AbstractThe complexities of the informed consent process for participating in research in genomic medicine are well-documented. Inspired by the potential for Dynamic Consent to increase participant choice and autonomy in decision-making, as well as the opportunities for ongoing participant engagement it affords, we wanted to trial Dynamic Consent and to do so developed our own web-based application (web app) called CTRL (control). This paper documents the design and development of CTRL, for use in the Australian Genomics study: a health services research project building evidence to inform the integration of genomic medicine into mainstream healthcare. Australian Genomics brought together a multi-disciplinary team to develop CTRL. The design and development process considered user experience; security and privacy; the application of international standards in data sharing; IT, operational and ethical issues. The CTRL tool is now being offered to participants in the study, who can use CTRL to keep personal and contact details up to date; make consent choices (including indicate preferences for return of results and future research use of biological samples, genomic and health data); follow their progress through the study; complete surveys, contact the researchers and access study news and information. While there are remaining challenges to implementing Dynamic Consent in genomic research, this study demonstrates the feasibility of building such a tool, and its ongoing use will provide evidence about the value of Dynamic Consent in large-scale genomic research programs.

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Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation

BMJ ◽

10.1136/bmj.n214 ◽

2021 ◽

pp. n214

Author(s):

Weedon MN ◽

Jackson L ◽

Harrison JW ◽

Ruth KS ◽

Tyrrell J ◽

...

Keyword(s):

Positive Predictive Value ◽

Predictive Value ◽

Population Based ◽

Genome Project ◽

Personal Genome ◽

Uk Biobank ◽

Sequencing Data ◽

Snp Chip ◽

Pathogenic Variants ◽

The Uk

Abstract Objective To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population. Design Retrospective, population based diagnostic evaluation. Participants 49 908 people recruited to the UK Biobank with SNP chip and next generation sequencing data, and an additional 21 people who purchased consumer genetic tests and shared their data online via the Personal Genome Project. Main outcome measures Genotyping (that is, identification of the correct DNA base at a specific genomic location) using SNP chips versus sequencing, with results split by frequency of that genotype in the population. Rare pathogenic variants in the BRCA1 and BRCA2 genes were selected as an exemplar for detailed analysis of clinically actionable variants in the UK Biobank, and BRCA related cancers (breast, ovarian, prostate, and pancreatic) were assessed in participants through use of cancer registry data. Results Overall, genotyping using SNP chips performed well compared with sequencing; sensitivity, specificity, positive predictive value, and negative predictive value were all above 99% for 108 574 common variants directly genotyped on the SNP chips and sequenced in the UK Biobank. However, the likelihood of a true positive result decreased dramatically with decreasing variant frequency; for variants that are very rare in the population, with a frequency below 0.001% in UK Biobank, the positive predictive value was very low and only 16% of 4757 heterozygous genotypes from the SNP chips were confirmed with sequencing data. Results were similar for SNP chip data from the Personal Genome Project, and 20/21 individuals analysed had at least one false positive rare pathogenic variant that had been incorrectly genotyped. For pathogenic variants in the BRCA1 and BRCA2 genes, which are individually very rare, the overall performance metrics for the SNP chips versus sequencing in the UK Biobank were: sensitivity 34.6%, specificity 98.3%, positive predictive value 4.2%, and negative predictive value 99.9%. Rates of BRCA related cancers in UK Biobank participants with a positive SNP chip result were similar to those for age matched controls (odds ratio 1.31, 95% confidence interval 0.99 to 1.71) because the vast majority of variants were false positives, whereas sequence positive participants had a significantly increased risk (odds ratio 4.05, 2.72 to 6.03). Conclusions SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.

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Solutions for Unexpected Challenges Encountered when Integrating Research Genomics Results into the EHR

ACI Open ◽

10.1055/s-0040-1719059 ◽

2020 ◽

Vol 04 (02) ◽

pp. e132-e135

Author(s):

Luke V. Rasmussen ◽

Christin Hoell ◽

Maureen E. Smith ◽

Rex Chisholm ◽

Justin Starren ◽

...

Keyword(s):

Genetic Research ◽

Lessons Learned ◽

Return Of Results ◽

Patient Portal ◽

Test Results ◽

Research Results ◽

Genetic Test Results ◽

Future Return ◽

New Research ◽

Genetic Results

Abstract Background While there have been published reports detailing technical challenges of incorporating genetic test results into the electronic health record (EHR) with proposed solutions, less has been published about unanticipated sociotechnological or practical communication challenges involved in this process. Objectives This study was aimed to describe unanticipated issues that arose returning genetic research results through the EHR as part of the National Human Genome Research Institute (NHGRI)-funded electronic Medical Records and Genomics (eMERGE) 3 consortium, and provide lessons learned for future implementations Methods We sequenced 3,000 participants on a 109-gene panel and returned genetic results initially in person and/or by letter, with a later release directly into the EHR and patient portal. Results When results were returned through the EHR, multiple participants expressed confusion and contacted the health system, resulting in our institution temporarily freezing our return of research results. Discussion We determined the likely causes of this issue to be (1) the delay between enrollment and results return, (2) inability to personalize mass e-mail messages announcing new research test results in the EHR, (3) limited space for description of test results in the EHR, and (4) the requirement to list an ordering physician for research results in the EHR. For future return of results, we propose sending preparatory e-mails to participants, including screenshots of how they can expect to see their results presented in the EHR portal. Conclusion We hope our lessons learned can provide helpful guidance to other sites implementing research genetic results into the EHR and can encourage EHR developers to incorporate greater flexibility in the future.

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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00586-y ◽

2021 ◽

Author(s):

Seyoung Mun ◽

Songmi Kim ◽

Wooseok Lee ◽

Keunsoo Kang ◽

Thomas J. Meyer ◽

...

Keyword(s):

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Personal Genome ◽

Human Populations ◽

Whole Genome ◽

Structural Variations ◽

Insert Size ◽

Human Genomes ◽

Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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The Oral Bacterial Community in Melanophryniscus admirabilis (Admirable Red-Belly Toads): Implications for Conservation

Microorganisms ◽

10.3390/microorganisms9020220 ◽

2021 ◽

Vol 9 (2) ◽

pp. 220

Author(s):

Michele Bertoni Mann ◽

Janira Prichula ◽

Ícaro Maia Santos de Castro ◽

Juliana Mello Severo ◽

Michelle Abadie ◽

...

Keyword(s):

Endangered Species ◽

Bacterial Community ◽

High Throughput Sequencing ◽

Dietary Diversity ◽

Natural Habitat ◽

Critically Endangered ◽

Personal Genome ◽

Oral Microbiota ◽

Critically Endangered Species ◽

Anthropogenic Environment

Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad’s adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species.

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Pediatric Cancer Genetics Research and an Evolving Preventive Ethics Approach for Return of Results after Death of the Subject

The Journal of Law Medicine & Ethics ◽

10.1111/jlme.12295 ◽

2015 ◽

Vol 43 (3) ◽

pp. 529-537

Author(s):

Sarah Scollon ◽

Katie Bergstrom ◽

Laurence B. McCullough ◽

Amy L. McGuire ◽

Stephanie Gutierrez ◽

...

Keyword(s):

Cancer Genetics ◽

Recurrence Risk ◽

Genomic Research ◽

Return Of Results ◽

Genetics Research ◽

Personal Significance ◽

Pediatric Diseases ◽

Increased Risk ◽

Preventive Ethics ◽

Risk Of Cancer

In the pediatric clinical setting, the parent/guardian will almost always be the authorized representative and designated recipient of clinical and research results, making the issue of to whom results should be returned in the pediatric setting less complex than in adult settings. It is also clear that, in genomic research related to pediatric diseases such as cancer, results may be of considerable clinical, ethical, and personal significance for parents in a number of ways, including a genomic explanation of the origin of their child’s cancer, implications for the genetic testing and medical care of other siblings and of the parents themselves, and reproductive planning with regard to the recurrence risk for future children to have an increased risk of cancer. However, what remains unclear is which results should be disclosed, and under what circumstances, to parents of deceased children.

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