Jasper Bovenberg

Whole-genome sequence variation, population structure and demographic history of the Dutch population

Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30–500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies.

Communication of Biobanks' Research Results: What Do (Potential) Participants Want?

The aim of this study was to investigate (potential) research participants (a) information preferences with regard to receiving biobanks genetic research results, and (b) attitudes towards the duties of researchers to communicate research results. A total group of 1,678 was analyzed, consisting of a sample of the general Dutch population (Nu2009=u20091,163) and patients with asthma, rhinitis, and thrombosis (Nu2009=u2009515) who completed a survey including six fictitious genetic research results each presented as aggregate and individual result, varied for treatability and kind of disease. Five questions assessed attitudes towards researchers duties to communicate research results. Additionally, background characteristics were measured. A majority of the respondents wanted to receive aggregate results as well as individual results. A small majority (59%) held the view that researchers should communicate individual results with no health consequences. One third agreed with an information duty only when treatment is available. A preference for individual results and an attitude in favor of communicating results were both associated with belonging to the general Dutch population rather than being a patient, wanting to learn about own health as the reason for biobank‐participation, a monitoring coping style, a general desire for health information, perceived meaningfulness of genetic information and no anticipated anxiousness. A sizable majority of respondents showed a high information preference for individual results, even when it is unclear that treatment is available. Fewer were of the opinion that researchers should make this possible. For their communication policy biobanks should take notice of (potential) participants high information preferences and expectations.

Ethics review for international data-intensive research

Ad hoc approaches mix and match existing components Historically, research ethics committees (RECs) have been guided by ethical principles regarding human experimentation intended to protect participants from physical harms and to provide assurance as to their interests and welfare. But research that analyzes large aggregate data sets, possibly including detailed clinical and genomic information of individuals, may require different assessment. At the same time, growth in international data-sharing collaborations adds stress to a system already under fire for subjecting multisite research to replicate ethics reviews, which can inhibit research without improving the quality of human subjects protections (1, 2). “Top-down” national regulatory approaches exist for ethics review across multiple sites in domestic research projects [e.g., United States (3, 4), Canada (5), United Kingdom, (6), Australia (7)], but their applicability for data-intensive international research has not been considered. Stakeholders around the world have thus been developing “bottom-up” solutions. We scrutinize five such ef orts involving multiple countries around the world, including resource-poor settings (table S1), to identify models that could inform a framework for mutual recognition of international ethics review (i.e., the acceptance by RECs of the outcome of each others review).

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100u2009bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.

Researchers’ opinions towards the communication of results of biobank research: a survey study.

Eighty Dutch investigators (response 41%) involved in biobank research responded to a web-based survey addressing communication of results of biobank research to individual participants. Questions addressed their opinion towards an obligation to communicate results and related issues such as ownership of blood samples, privacy, therapeutic relationship, costs and implications for participants. Most researchers (74%) indicated that participants only have to be informed when results have implications for treatment or prevention. Researchers were generally not inclined to provide more feedback to patients as compared with healthy participants, nor were they inclined to provide feedback in return for participants’ contribution to the biobank. Our results demonstrate major and significant differences in opinion about the feedback of individual results within the community of biobank researchers.

A framework for the detection of de novo mutations in family-based sequencing data

Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants and short insertions and deletions (indels) from sequence data collected in parent-offspring trios. We compute the joint probability of the data given the genotype likelihoods in the individual family members, the known familial relationships and a prior probability for the mutation rate. Candidate de novo mutations (DNMs) are reported along with their posterior probability, providing a systematic way to prioritize them for validation. Our tool is integrated in the Genome Analysis Toolkit and can be used together with the ReadBackedPhasing module to infer the parental origin of DNMs based on phase-informative reads. Using simulated data, we show that PBT outperforms existing tools, especially in low coverage data and on the X chromosome. We further show that PBT displays high validation rates on empirical parent-offspring sequencing data for whole-exome data from 104 trios and X-chromosome data from 249 parent-offspring families. Finally, we demonstrate an association between father’s age at conception and the number of DNMs in female offspring’s X chromosome, consistent with previous literature reports.

Your Biobank, Your Doctor?: The right to full disclosure of population biobank findings

The advent of personal genomics companies offering direct translation of scientific data into personal health information, calls into question traditional policies to refuse disclosure of such scientific data to research participants. This seems especially true for population biobanks, as they collect not only genotype information but also associated phenotype information, and thus may be in a unique position to translate their scientific findings into personal health information for their participants. Disclosure of such information seems mandated by the expectations raised by biobanks (to help bring about the era of personalized medicine) and their participants rights to know health information, to know clinical research results, to life and health and particularly their right to benefit. Refusals to disclose such information can be grounded in the lack of analytical validity and/or clinical utility of most findings, the need to avoid the therapeutic misconception, the complexity and costs involved in translation and disclosure and the disproportionate burden resulting from the obligation to respect participants right not to know before any disclosure can be made. Currently, any demands by participants in population biobanks for full disclosure of all pertinent personal health information potentially resulting from the biobanks scientific findings are unlikely to be granted by a Dutch court under Dutch and international law. As the law stands now, a population biobank is neither a doctor nor a personal genomics company. However, in view of the rapid scientific, medical, technological, commercial and social developments, population biobanks must prepare to take more care of their participants legitimate interest in receiving as much validated personal health information as reasonably possible, in a timely fashion, by developing appropriate translation and disclosure mechanisms. This paper examines whether population biobank participants have the right, under Dutch civil law and international law, to full disclosure, i.e. to all information generated by the biobank that is pertinent to their present and future health. It pioneers the format of a hypothetical court case to elucidate the legal and policy arguments for and against full disclosure.

Streamlining ethical review of data intensive research

Unfounded concerns about local liability should not delay urgent reform

Patients v. Myriad or the GDPR Access Right v. the EU Database Right

In 2016, four US cancer patients legally challenged Myriad by claiming full access to all genomic information produced in the course of Myriad’s testing of their risks for a variety of cancers. Asserting that Myriad’s refusal to provide them with this information violated the HIPAA Privacy Rule, the patients sought a determination of a right to access all their genetic information from testing laboratories. Such access would not only serve their own care, but also enable them to share their genetic data with the scientific community which they alleged Myriad failed to do. A similar case may be brought in Europe under the novel EU GDPR. Specifically, it would put the GDPR right of access to personal data against Myriad’s database right under the EU Database Right Directive. The outcome of this case could impact the fate of personalized medicine, which depends on the one hand on patients’ having control over their genetic data, and on the other hand on incentives for genetic testing companies to generate these data. We first address the issue of whether the GDPR applies to medical records. We then analyse how GDPR rights could play out in the context of clinical genetic testing and conclude that the GDPR access right stops short of granting unconditional access to all dataxa0generated in the process of testing, to the extent that its exercise would result in the violation of medical-professional norms, expose the testing company to potential liability, or compromise normal exploitation of the database of which the personal data form part.