Genomic databases access agreements: legal validity and possible sanctions

Large-scale, public genomic databases have greatly improved the capacity of researchers to do genomic research. In order to ensure that the scientific community uses data from these public resources properly, data access agreements have been developed to complement already existing legal and ethical norms. Sanctions to address cases of data misuse constitute an essential part of this compliance framework meant to protect stakeholders in genomic research. Yet very little research and community debate has been done on this most important topic. This paper presents a review of different sanctions that could be invoked in cases of non-compliance from data users. They have been identified through comprehensive research and analysis of over 450 documents (journal articles, policy, guidelines, access policies, etc.) related to this topic. Given the considerable impact on users of even the milder sanctions considered in our paper, it is essential that stakeholders strive to achieve the highest degree of standardization and transparency when designing controlled-access agreements. It is only fair, after all, that users be able to expect that the border between acceptable and unacceptable conduct is clearly delineated and predictable in controlled-access policies. This suggests the importance for researchers to undertake additional empirical studies on the clarity and accessibility of existing database access agreements and related policies in the near future.     

Molecular Cytogenetics and Cytogenomics of Brain Diseases

Molecular cytogenetics is a promising field of biomedical research that has recently revolutionized our thinking on genome structure and behavior. This is in part due to discoveries of human genomic variations and their contribution to biodiversity and disease. Since these studies were primarily targeted at variation of the genome structure, it appears apposite to cover them by molecular cytogenomics. Human brain diseases, which encompass pathogenic conditions from severe neurodegenerative diseases and major psychiatric disorders to brain tumors, are a heavy burden for the patients and their relatives. It has been suggested that most of them, if not all, are of genetic nature and several recent studies have supported the hypothesis assuming them to be associated with genomic instabilities (i.e. single-gene mutations, gross and subtle chromosome imbalances, aneuploidy). The present review is focused on the intriguing relationship between genomic instability and human brain diseases. Looking through the data, we were able to conclude that both interindividual and intercellular genomic variations could be pathogenic representing, therefore, a possible mechanism for human brain malfunctioning. Nevertheless, there are still numerous gaps in our knowledge concerning the link between genomic variations and brain diseases, which, hopefully, will be filled by forthcoming studies. In this light, the present review considers perspectives of this dynamically developing field of neurogenetics and genomics.     

Measuring the performance of international genomics research projects in fostering genomic capacity in the developing world

Therapeutic applications of genomic medicine are slowly finding their way into the healthcare framework of developing countries. The establishment of equitable innovation policies is a determining factor in how genomic-based therapeutic applications will evolve in these countries. In the biomedical field, the commercialization of research results has established itself as the dominant paradigm in the innovation system. However, many recent studies have demonstrated that this emphasis on commercialization and the protection of intellectual property has led to disappointing results. A growing number of stakeholders in this debate argue that it is now necessary to go beyond the commercialization of research and implement policies based on the research valorization paradigm, which supports the achievement of social as well as economic objectives. We thus propose a new set of more inclusive research performance indicators to help policymakers measure the impact of international genomics projects on developing countries.     

Mutation, replicative infidelity of DNA and aneuploidy sequentially in the formation of malignant pleomorphic tumors

Mutations are thought to be involved in tumor formation because (i) tumor cells transmit their abnormalities to their descendants; and (ii) many carcinogens are mutagens. Aneuploidy is thought to be involved in tumor formation because (i) it is a common phenomenon, especially among malignant neoplasms; (ii) certain particular types of tumors are associated with specific karyotypic changes; and (iii) many immortal tumor cell lines are hyperploid. In recent years, acquired somatic cell replicative infidelity of DNA ("mutator phenotype") has been suggested as a mechanism of tumor formation, because more somatic genomic events occur in malignant tumor cells than could be caused by repeated exogenous mutagenic insults. Previously, theories of the genomic pathogenesis of tumors have involved these mechanisms individually. Here it is suggested that all three mechanisms may play roles in the formation of certain tumor types. For example, a sequence could occur such that first, a mutation affects genomic elements for control of growth, and for replicative fidelity of DNA, leading to "mutator phenotype". Second, when replicative infidelity of DNA results in mutation of genomic elements for mitotic-and-chromosomal stability, aneuploidy develops. Third, an asymmetric mitosis (in the course of the aneuploid stage) could produce occasional cells in which the "bad copy" is lost (or an extra "good copy" is gained) of the original genomic element which had supported replicative fidelity of DNA. These resulting cells would regain fidelity of replication of DNA, and hence could give rise to populations which are relatively genomically stable, hyperploid and immortal.     

Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs

Microsatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross‐amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross‐species utility. As EST‐SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross‐species amplification. However, EST‐SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST‐SSRs in studies of within‐species genetic diversity, we compared the relative performance of EST‐ and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST‐ and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST‐ and genomic SSRs is influenced by levels of differentiation. EST‐ and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST‐SSRs when differentiation is moderate. However and interestingly, EST‐SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST‐SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.     

Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10–20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.     

Uncoupling of genomic and epigenetic signals in the maintenance and inheritance of heterochromatin domains in fission yeast

Many essential aspects of genome function, including gene expression and chromosome segregation, are mediated throughout development and differentiation by changes in the chromatin state. Along with genomic signals encoded in the DNA, epigenetic processes regulate heritable gene expression patterns. Genomic signals such as enhancers, silencers, and repetitive DNA, while required for the establishment of alternative chromatin states, have an unclear role in epigenetic processes that underlie the persistence of chromatin states throughout development. Here, we demonstrate in fission yeast that the maintenance and inheritance of ectopic heterochromatin domains are independent of the genomic sequences necessary for their de novo establishment. We find that both structural heterochromatin and gene silencing can be stably maintained over an ~10-kb domain for up to hundreds of cell divisions in the absence of genomic sequences required for heterochromatin establishment, demonstrating the long-term persistence and stability of this chromatin state. The de novo heterochromatin, despite the absence of nucleation sequences, is also stably inherited through meiosis. Together, these studies provide evidence for chromatin-dependent, epigenetic control of gene silencing that is heritable, stable, and self-sustaining, even in the absence of the originating genomic signals.     

Genomics, environmental genomics and the issue of microbial species

A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.     

Scientific Independence and Credibility in Sociopolitical Processes

Abstract: Absence of scientific independence can be associated with a lack of impartiality and therefore with a lack of credibility. Yet scientific credibility is essential for effective participation in sociopolitical processes—processes that necessarily involve politics and often result in decisions about land management, conservation, and public policy. All scientists are aware of these processes, many wish to participate, and some wish to advocate for their personal policy preferences. However, scientists who lack impartiality often create the perception of bias, and they can suffer a concomitant loss of credibility. Some policy-makers also have personal preferences for certain policies, and the term normative policies can be used here even though all policies can be viewed as normative in the sense that they involve multiple inputs. Hence, the idea that scientists must provide unbiased information for unbiased application by policy-makers is sometimes wrong. For scientists to be effective participants in sociopolitical processes that lead to conservation policies or related actions, they should inform the public about issues while avoiding direct involvement in policy development and the political considerations this necessarily entails. Scientists should only participate in the decision-making process with impartial information and in their proper role as objective scientists.     

Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle

Background

In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required.

Methods

We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components.

Results

After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04.

Conclusions

Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals.     

NGC: lossless and lossy compression of aligned high-throughput sequencing data

A major challenge of current high-throughput sequencing experiments is not only the generation of the sequencing data itself but also their processing, storage and transmission. The enormous size of these data motivates the development of data compression algorithms usable for the implementation of the various storage policies that are applied to the produced intermediate and final result files. In this article, we present NGC, a tool for the compression of mapped short read data stored in the wide-spread SAM format. NGC enables lossless and lossy compression and introduces the following two novel ideas: first, we present a way to reduce the number of required code words by exploiting common features of reads mapped to the same genomic positions; second, we present a highly configurable way for the quantization of per-base quality values, which takes their influence on downstream analyses into account. NGC, evaluated with several real-world data sets, saves 33–66% of disc space using lossless and up to 98% disc space using lossy compression. By applying two popular variant and genotype prediction tools to the decompressed data, we could show that the lossy compression modes preserve >99% of all called variants while outperforming comparable methods in some configurations.     

Using the therapy and enhancement distinction in law and policy

In a first major study, the UK’s Royal Society found that 76% of people in the UK are in favour of therapeutic germline genomic editing to correct genetic diseases in human embryos, but found there was little appetite for germline genomic editing for non-therapeutic purposes. Assuming the UK and other governments acted on these findings, can lawmakers and policymakers coherently regulate the use of biomedical innovations by permitting their use for therapeutic purposes but prohibiting their use for enhancement purposes? This paper examines the very common claim in the enhancement literature that the therapy v enhancement distinction does little meaningful work in helping us think through the ethical issues, a claim that has significant implications for these lawmakers and policymakers who may wish to regulate genomic editing techniques to reflect the findings of this important study. The focus of this paper is on germline genomic editing as one of the main themes in this special issue.     

G2 and spindle assembly checkpoint adaptation, and tetraploidy arrest: implications for intrinsic and chemically induced genomic instability

While checkpoints that act in S-phase are essential to the maintenance of genomic stability, these checkpoints do not act alone. Additionally, G2 DNA damage checkpoints, the spindle assembly checkpoint, and a post-mitotic G1 tetraploidy checkpoint act subsequent to DNA replication to ensure genetic fidelity in cell division. In this review, we will examine how these checkpoints cooperate in the maintenance of genomic stability in response to either DNA damage or cytoskeletal disruption. Since the G2 and spindle assembly checkpoints are subject to adaptation, we will discuss how the G1 tetraploidy checkpoint acts in concert with these checkpoints to mediate stable arrest. We will also probe the relationship of these checkpoints by exploring common features of their regulation. Finally, the consequences of malfunction of these checkpoints for both intrinsic and chemically induced genomic instability will be examined. Among these consequences are aneuploidization, extranumerary centrosomes, and micronucleation.     

On the matching and proportional laws of cybernetic models

The Matching and Proportional Laws are heuristic control policies that have found widespread use in cybernetic models of biological systems. Within this context, the laws serve as optimization surrogates for predicting the response of metabolic control circuits that modulate enzyme levels and activities. The key result of the current contribution is to demonstrate clearly the optimality properties of these laws and the assumptions that underlie their development. In doing so, we arrive at generalized versions of the Matching and Proportional Laws that are shown to collapse to the forms originally derived by Kompala et al. (Biotechnol. Bioeng. 1986, 28, 1044-1055) when certain simplifications are applied. As a further line of investigation, we show how Kompala et al.'s cybernetic laws compare with alternative control policies in their ability to describe diauxic growth behavior of microbial cultures. We find that Kompala et al.'s model describes the experimental observations more accurately than other limiting-case models that are either too aggressive or too passive in capturing the mixed-substrate growth rates and intermediate lag periods. Monte Carlo analysis of computational growth experiments in which strains obeying different regulatory policies directly compete for available nutrients reveals that the Matching and Proportional Law policy does not maximize the average growth rate of the culture. However, it allocates metabolic resources more frugally than other policies that outperform it and may be more realistic in reflecting the cell's true fitness-to-cost tradeoff as judged by its agreement with experimental growth data.     

Prediction of genomic islands in seven human pathogens using the Z-Island method

We adopted the method of Zhang and Zhang (the Z-Island method) to identify genomic islands in seven human pathogens, analyzing their chromosomal DNA sequences. The Z-Island method is a theoretical method for predicting genomic islands in bacterial genomes; it consists of determination of the cumulative GC profile and computation of codon usage bias. Thirty-one genomic islands were found in seven pathogens using this method. Further analysis demonstrated that most have the known conserved features; this increases the probability that they are real genomic islands. Eleven genomic islands were found to code for products involved in causing disease (virulence factors) or in resistance to antibiotics (resistance factors). This finding could be useful for research on the pathogenicity of these bacteria and helpful in the treatment of the diseases that they cause. In a comparison of the distribution of mobility elements in genomic islands predicted by different methods, the Z-Island method gave lower false-positive rates. The Z-Island method was found to detect more known genomic islands than the two methods that we compared it with, SIGI-HMM and IslandPick. Furthermore, it maintained a better balance between specificity and sensitivity. The only inconvenience is that the steps for finding genomic islands by the Z-Island method are semi-automatic.     

On the Structural Differences Between Markers and Genomic AC Microsatellites

AC microsatellites have proved particularly useful as genetic markers. For some purposes, such as in population biology, the inferences drawn depend on the quantitative values of their mutation rates. This, together with intrinsic biological interest, has led to widespread study of microsatellite mutational mechanisms. Now, however, inconsistencies are appearing in the results of marker-based versus non-marker-based studies of mutational mechanisms. The reasons for this have not been investigated, but one possibility, pursued here, is that the differences result from structural differences between markers and genomic microsatellites. Here we report a comparison between the CEPH AC marker microsatellites and the global population of AC microsatellites in the human genome. AC marker microsatellites are longer than the global average. Controlling for length, marker microsatellites contain on average fewer interruptions, and have longer segments, than their genomic counterparts. Related to this, marker microsatellites show a greater tendency to concentrate the majority of their repeats into one segment. These differences plausibly result from scientists selecting markers for their high polymorphism. In addition to the structural differences, there are differences in the base composition of flanking sequences, marker flanking regions being richer in C and G and poorer in A and T. Our results indicate that there are profound differences between marker and genomic microsatellites that almost certainly affect their mutation rates. There is a need for a unified model of mutational mechanisms that accounts for both marker-derived and genomic observations. A suggestion is made as to how this might be done.Reviewing Editor: Dr. Magnto Nordborg