Gene and Genome

Consent and Autonomy in the Genomics Era Abstract Purpose of Review Genomic tests offer increased opportunity for diagnosis, but their outputs are often uncertain and complex; results may need to be revised and/or may not be relevant until some future time. We discuss the challenges that this presents for consent and autonomy. Recent Findings Popular discourse around genomic testing tends to be strongly deterministic and optimistic, yet many findings from genomic tests are uncertain or unclear. Clinical conversations need to anticipate and potentially challenge unrealistic expectations of what a genomic test can deliver in order to enhance autonomy and ensure that consent to genomic testing is valid. Summary We conclude that 'fully informed' consent is often not possible in the context of genomic testing, but that an open-ended approach is appropriate. We consider that such broad consent can only work if located within systems or organisations that are trustworthy and that have measures in place to ensure that such open-ended agreements are not abused. We suggest that a relational concept of autonomy has benefits in encouraging focus on the networks and relationships that allow decision making to flourish.

Management and Screening in Neurofibromatosis Types 1 and 2 Abstract Purpose of Review Neurofibromatosis types 1 and 2 (NF1 & NF2) are complex genetic diseases that provide challenges in diagnosis, monitoring, clinical management and genetic counselling. This review highlights these challenges and provides insight into the general and specialist management considerations. Recent Findings Multidisciplinary care with a focus on evidence based interventions and quality of life outcomes has benefited patients. Anti-VEGF therapy has recently altered the management paradigm for NF2. Other novel molecularly targeted therapies are being trialled in both NF1 and NF2. Improved understanding of associated risks and natural history has informed screening regimes. Summary Both diseases have significant associated morbidity and mortality, with the prognosis for some patients with NF2 particularly poor. A holistic and multidisciplinary approach provides the best model of care.

The Changing Role of the Genetic Counsellor in the Genomics Era Abstract Purpose of Review Rapid advances in the scope, affordability and clinical utility of genetic testing have driven significant change and expansion of the genetic counselling profession. Increasing volume, complexity and diversity of patients and their genomic data present a challenge. To manage this, examination of how genetic counsellors can adapt and thrive in the genomics era is warranted. Recent Findings Digital applications, web-based educational platforms and artificial intelligence are being harnessed to support and enhance genetic counselling delivery for patients and consumers. Genetic counsellors are also ideally placed to educate and support other healthcare professionals delivering genomic medicine. Concurrently, core genetic counselling skills in managing psychosocial, familial and ethical issues have continued relevance, and further investment in evidence-based research is needed to guide practice. A focus on improving diversity and equity of access to genetic counselling is also necessary. Summary Working in a changing and uncertain environment is not unfamiliar ground for genetic counsellors. Their specialist knowledge and core skills will continue to be highly valued in the genomics era. Genomic medicine has the potential to positively transform public health, and the genetic counselling profession has the opportunity to play a pivotal role.

GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations Abstract Purpose of Review Neurodegenerative diseases, neuropsychiatric disorders, and related traits have highly complex etiologies but are also highly heritable; identifying the causal genes and biological pathways underlying these traits may advance the development of treatments and preventive strategies. While many genome-wide association studies (GWAS) have successfully identified variants contributing to polygenic neurodegenerative and neuropsychiatric phenotypes including Alzheimer's disease (AD), schizophrenia (SCZ), and bipolar disorder (BPD) among others, interpreting the biological roles of significantly associated variants in the genetic architecture of these traits remains a significant challenge. Here, we review several 'omics' approaches which attempt to bridge the gap from associated genetic variants to phenotype by helping define the functional roles of GWAS loci in the development of neuropsychiatric disorders and traits. Recent Findings Several common 'omics' approaches have been applied to examine neuropsychiatric traits, such as nearest-gene mapping, trans-ethnic fine mapping, annotation enrichment analysis, transcriptomic analysis, and pathway analysis, and each of these approaches has strengths and limitations in providing insight into biological mechanisms. One popular emerging method is the examination of tissue-specific genetically regulated gene expression (GReX), which aggregates the genetic variants' effects at the gene level. Furthermore, proteomic, metabolomic, and microbiomic studies and phenome-wide association studies will further enhance our understanding of neuropsychiatric traits. Summary GWAS has been applied to neuropsychiatric traits for a decade, but our understanding about the biological function of identified variants remains limited. Today, technological advancements have created analytical approaches for integrating transcriptomics, metabolomics, proteomics, pharmacology, and toxicology as tools for understanding the functional roles of genetic variants. These data, as well as the broader clinical information provided by electronic health records, can provide additional insight and complement genomic analyses.

Benefits and Challenges of Rare Genetic Variation in Alzheimer's Disease Abstract Purpose of Review It is well established that sporadic Alzheimer's disease (AD) is polygenic with common and rare genetic variation alongside environmental factors contributing to disease. Here, we review our current understanding of the genetic architecture of disease, paying specific attention to rare susceptibility variants, and explore some of the limitations in rare variant detection and analysis. Recent Findings Rare variation has been shown to robustly associate with disease. These include potentially damaging and loss of function mutations that are easily modelled in silico, in vitro and in vivo, and represent potentially druggable targets. A number of risk genes, including TREM2, SORL1 and ABCA7 show multiple independent associations suggesting that they may influence disease via multiple mechanisms. With transcriptional regulation, inflammatory response and modification of protein production suggested to be of primary importance. Summary We are at the beginning of our journey of rare variant detection in AD. Whole exome sequencing has been the predominant technology of choice. While fruitful, this has introduced a number of challenges with regard to data integration. Ultimately the future of disease-associated rare variant identification lies in whole genome sequencing projects that will allow the testing of the full range of genomic variation.

Sex Differences in the Genetic Architecture of Alzheimer's Disease Abstract Purpose of Review Summarize sex-specific contributors to the genetic architecture of Alzheimer's disease (AD). Recent Findings There are sex differences in the effects of apolipoprotein E (APOE), genes along the APOE pathway, and genes along the neurotrophic signaling pathway in predicting AD. Reported sex differences are largely driven by stronger associations among females. Evidence also suggests that genetic predictors of amyloidosis are largely shared across sexes, while sex-specific genetic effects emerge downstream of amyloidosis and drive the clinical manifestation of AD. Summary There is a lack of comprehensive assessments of sex differences in genome-wide analyses of AD and a need for more systematic reporting of sex-stratified genetic effects. The emerging emphasis on sex as a biological variable provides an opportunity for transdisciplinary collaborations aimed at addressing major analytical challenges that have hampered advancements in the field. Ultimately, sex-specific genetic association studies represent a logical first step towards precision medicine.

Polygenic Risk Scores in Neurodegenerative Diseases: a Review Abstract Purpose of the Review This review summarizes the current state of the art of polygenic risk scores (PRSs) in the assessment of risk for neurodegenerative diseases. Recent Findings Polygenic risk scores have been used to identify the shared genetic architecture between comorbid complex traits, disease presentations, and disease endophenotypes. Summary The pathological and symptomatologic overlap between neurodegenerative diseases is strikingly high. In some cases, the diagnostic decision is arbitrary depending on the first appearance of symptomatology. Genetic studies have demonstrated that the genetic architecture of each of these diseases is different, but has a high degree of overlap. The creation of polygenic risk scores has allowed a more accurate calculation of this overlap. However, the power of the PRS is dependent on the power of the genome-wide association studies (GWAS) used to describe the genetic architecture. Even though not all neurodegenerative disease GWAS have the same sample size, and thus the same power, the use of polygenic risk scores has been successful in demonstrating the genetic overlap that has been observed phenotypically.

Recent Advances in the Genetics of Frontotemporal Dementia Abstract Purpose of Review In this review, we highlight recent advances in the human genetics of frontotemporal dementia (FTD). In addition to providing a broad survey of genes implicated in FTD in the last several years, we also discuss variation in genes implicated in both hereditary leukodystrophies and risk for FTD (e.g., TREM2, TMEM106B, CSF1R, AARS2, NOTCH3). Recent Findings Over the past 5 years, genetic variation in approximately 50 genes has been confirmed or suggested to cause or influence risk for FTD and FTD-spectrum disorders. We first give background and discuss recent findings related to C9ORF72, GRN, and MAPT, the genes most commonly implicated in FTD. We then provide a broad overview of other FTD-associated genes and go on to discuss new findings in FTD genetics in East Asian populations, including pathogenic variation in CHCHD10, which may represent a frequent cause of disease in Chinese populations. Finally, we consider recent insights gleaned from genome-wide association and genetic pleiotropy studies. Summary Recent genetic discoveries highlight cellular pathways involving autophagy, the endolysosomal system, and neuroinflammation and reveal an intriguing overlap between genes that confer risk for leukodystrophy and FTD.

Protective Variants in Alzheimer's Disease Abstract Purpose of Review Over the last decade, over 40 loci have been associated with risk of Alzheimer's disease (AD). However, most studies have either focused on identifying risk loci or performing unbiased screens without a focus on protective variation in AD. Here, we provide a review of known protective variants in AD and their putative mechanisms of action. Additionally, we recommend strategies for finding new protective variants. Recent Findings Recent Genome-Wide Association Studies have identified both common and rare protective variants associated with AD. These include variants in or near APP, APOE, PLCG2, MS4A, MAPT-KANSL1, RAB10, ABCA1, CCL11, SORL1, NOCT, SCL24A4-RIN3, CASS4, EPHA1, SPPL2A, and NFIC. Summary There are very few protective variants with functional evidence and a derived allele with a frequency below 20%. Additional fine mapping and multi-omic studies are needed to further validate and characterize known variants as well as specialized genome-wide scans to identify novel variants.

Fragile Sites as Drivers of Gene and Genome Evolution Abstract Purpose of Review Although the detailed composition of the human genome is known base by base for its major part, the orchestration of and which elements exactly facilitate organization and flexibility of higher order gene and genome architecture, are poorly understood and scarcely studied. Recent Findings This review focuses on fragile sites (FSs). They are considered as regions of chromosome breakage with overlapping signatures for breakpoints observed repeatedly in tumor and constitutional rearrangements, and also in evolutionary conserved breakpoints. Thus, FSs are promising targets to study and get deeper insights into chromosome, gene, and genome evolution. Summary Here, we summarize the current knowledge on FSs and their correlation with aforementioned breakpoint categories. Based on that, we introduce a new model for FSs driven gene and genome evolution, which also can explain the recently observed spreading of (pseudo-)gene family members among the human genome. FSs therefore may provide an "infrastructure" to distribute gene copies onto different sites of the genome and may be the underlying cause for formation of gene families.

Alexandros Sfakianakis
Anapafseos 5 . Agios Nikolaos
Crete.Greece.72100
2841026182

6948891480

alsfakia@gmail.com