Aim: Whole exome sequencing technology has permitted the discovery of genes that cause Mendelian disorders and was used in clinical laboratories. However, identifying the disease causing variant(s) for a specific disorder from thousands of variants is challenging. In this study, we describe the Cincinnati Clinical Exome Pipeline Analysis Suite (CCEPAS) that utilizes a four-level framework into one analysis procedure that rapidly identify the most likely causative gene variants to establish a clinical diagnosis.

Methods: We developed and validated CCEPAS using 100 clinical exome cases. We applied this pipeline to clinical cases by first translating phenotypic information into candidate gene lists using Pheno2Gene. This list of candidate genes was given to the VarEval algorithm to guide variant filtering and prioritization. Finally, a short list of filtered variants was produced for clinical interpretation.

Results: We demonstrated the development and implementation of CCEPAS to aid in the variant prioritization and filtering to produce a short list of candidate variants for clinical diagnosis. Its unique Pheno2Gene tool utilized an extensive list of resources and provided an accurate, sensitive and specific way to obtain gene lists from clinical feature keywords. In addition, VarEval narrowed down the variants from ~150,000 to the top 20 (trios) and top 50 (singleton) for further variant curation and candidate determination.

Conclusion: Significantly, employment of CCEPAS rapidly provided causative variants in the top 20 and top 50 variants for single and trio cases, respectively, thus, ending the diagnostic odyssey in more than 30% of our clinical exome cases.

The dosage compensation in placental mammals is achieved by silencing of one copy of the X chromosomes in a female cell by a process called X chromosome inactivation (XCI). XCI ensures equal gene dosage for X-linked genes between the two genders. Although the choice of X chromosome to be silenced is random, once the silencing of the X chromosome has been established, this process is highly regulated and maintained throughout subsequent cell divisions. A long non-coding RNA, Xist, and its interacting proteins execute this multistep process, but several of these regulatory proteins remain unidentified. Recent technological advances based on the genetic and proteomics screening have identified several new regulatory factors as well as dissected the molecular details of XCI regulation. Moreover, identification of regulators of XCI offers an opportunity to explore reactivation of the inactive X chromosome (Xi) as a potential therapeutic strategy to treat X-linked diseases, like Rett syndrome. Here, we summarize recent reports that identified new regulatory proteins and RNA species playing a crucial role in Xist localization and spreading, recruitment of silencing machinery to the Xi, Xist interaction with chromatin, and structural organization of the Xi in the nuclei.

Aim: There are many coronary artery disease (CAD) cases in which the explanation for its development cannot be readily explained by traditional risk factors. The purpose of this study was to examine the data whether ADAMTS7 polymorphisms is related to the presence or severity of CAD.

Methods: A systematic review of the literature was conducted to address the relationship between ADAMTS7 polymorphism and atherosclerosis.

Results: Nine studies were evaluated that examined the relationship between ADAMTS7 and coronary atherosclerosis and 3 studies that examined the relationship between ADAMTS7 and coronary calcification. The single nucleotide polymorphs (SNPs) included rs3825807, rs79265682, rs1994016, rs4380028, for coronary atherosclerosis and rs7173743, rs3825807 and rs1994016 for coronary artery calcification. The most consistent evidence for an association with coronary artery stenosis on coronary angiogram was with ADAMTS7 rs3825807 risk allele A vs. control G, followed by rs4380028. ADAMTS7 SNP rs3825807 was consistently association with coronary artery calcification. ADAMTS7 was associated with CAD severity and adverse CAD prognosis.

Conclusion: ADAMTS7 polymorphisms especially SNP rs4380028 allele has been consistently associated with CAD with ADAMTS7 rsrs4380028 being the next most strongly associated. ADAMTS7 warrants further exploration for a role in the pathogenesis of CAD.

Parathyroid carcinoma is a rare but clinically-aggressive tumor. While most cases are sporadic, parathyroid cancer is overrepresented in hyperparathyroidism-jaw tumor syndrome, or rarely other heritable syndromes. Evidence suggests that sporadic parathyroid carcinomas rarely, if ever, evolve through an identifiable benign tumor intermediate. A few genes have been directly implicated in the pathogenesis of sporadic parathyroid cancer; somatic (and less common germline) mutations in the CDC73 tumor suppressor gene are the most frequent finding and the only firmly established molecular drivers of parathyroid cancer. Alterations in other important human cancer genes, including CCND1/cyclin D1, PIK3CA, MTOR and PRUNE2 have also been described in parathyroid cancer, however their abilities to drive malignant parathyroid tumorigenesis remains to be demonstrated experimentally.

Aim: Idiopathic cardiomyopathy is often genetic in origin, typically autosomal dominant, and restrictive cardiomyopathy (RCM) is the rarest form. Clinically, RCM prognosis is poor with most patients requiring heart transplant due to impaired diastolic function leading to heart failure. In some cases, desminopathy is also observed, whereby desmin protein aggregates in the myocardium. Many genes are known to be involved in cardiomyopathy, and we sought to find the pathogenic mutation of a four-generation family with RCM and desminopathy.

Methods: We employed whole exome sequence analysis of four RCM patients from the family, to identify the underlying pathogenic mutation(s).

Results: Analysis of the exome data led to identification of two putative pathogenic variants. One, a nonsense mutation in ADD3, encoding adducin 3, was found in the proband and his affected daughter, but not other family members. The other was a missense mutation (G1546S) in the gene encoding filamin C (FLNC), found in all of the affected individuals. Both of these proteins interact with proteins involved in sarcomere function, and are expressed in both heart and skeletal muscle. FLNC has recently been implicated as a cardiomyopathy gene, but ADD3 has not at this point.

Conclusion: We present bioinformatic analyses that suggest that the FLNC variant is the major pathogenic variant affecting this family, but cannot rule out some contribution of the ADD3 mutation in at least two patients.

There is a general failure of reductionist and mechanistic approaches to rejuvenation biomedical technologies which aim at providing treatments against aging (defined as “time-dependent dysfunction”). Importantly, it is becoming increasingly recognised that genomic research findings in animals may not adequately be translated into effective human anti-aging therapies. There exist translational impediments, which although individually formidable, can theoretically be overcome. However, the combined effects of these obstacles render this reductionist avenue of quest unattainable, at least for the foreseeable future. Some of the clinical problems of physical and genomic-based therapies against aging include side effects, interactions, inter-subject variability, compliance, patient self-reporting of data, motivation, administrative issues, infrastructure, etc. A systematic review spanning over the past 5 years, describes these problems and identifies novel approaches. New and emerging disciplines and concepts such as molecular pathological epidemiology, social genomics and other “systems-thinking” methods provide a more comprehensive view of the entire subject of aging, and study its indivisible bonds with the environment, society and culture. The so-called “fountain of youth” cannot be found in a physical item.

Leukocyte adhesion deficiency type 1 (LAD-I) characterized by immune-deficiency and leukocytosis is rare in infant patients. A 43-day-old boy with severe leukocytosis, recurrent infections, defective wound healing and hepatosplenomegaly associated with an acquired cytomegalovirus infection. To establish the diagnosis definitively, a high-throughput targeted exome sequencing was performed, which yielded the diagnosis of LAD-I. A homozygous mutation in integrin subunit beta 2 (ITGB2), c.817G>A (p.G273R) was identified. Though LAD-I has been thoroughly-studied, with more than 300 detailed cases and 96 mutations in ITGB2, establishing a definitive diagnosis of LAD-I in infancy is challenging because of the lack of typical clinical presentations. Better understanding the molecular characterization of this disease is necessary to increase awareness and identification of infants with LAD-I.

The mitochondrion is a unique organelle that predominantly functions to produce useful cellular energy in the form of adenosine triphosphate (ATP). Unlike other non-nuclear eukaryotic organelles (with the exception of chloroplasts), mitochondria have two lipid membranes that enclose their own mitochondrial DNA (mtDNA) and ribosomes for protein production. Similar to nuclear DNA, mtDNA is equally susceptible to mutations that may be classified as either pathogenic or nonpathogenic. Myoclonic Epilepsy with Ragged Red Fibers (MERRF) and Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episodes (MELAS) are mitochondrial diseases originating from pathogenic point mutations located within mtDNA. Currently, there is no cure and patient care primarily focuses on treating each disease’s associated symptoms. When considering the multiple barriers existing between the extracellular surface of the plasma membrane and the location of the mtDNA within the mitochondrial matrix, developing a pharmacological therapeutic that can both overcome these barriers and correct an mtDNA causing mitochondrial disease remains difficult at best. Interestingly, the field of gene therapy may provide an opportunity for effective therapeutic intervention by introducing a genetic payload (to a particular cellular gene) to induce the correction. This review primarily focuses on understanding the principles of mitochondrial biology leading to the mtDNA diseases, MERRF and MELAS, while providing a landscape perspective of gene therapy research devoted to curing these diseases.

Ewing sarcoma (EWS) is a bone- and soft tissue tumour affecting primarily children and young adults. A quarter of patients present with metastases at the time of diagnosis and have a poor outlook in terms of overall survival. Efforts are made across the field to gain deeper insight in the genetics of this enigmatic neoplasm. EWS is characterized by presence of an oncogenic translocation gene, EWSR1-ETS. In addition, there are a limited number of known recurrent DNA copy number variations and mutations. Subsequent of the above, the epigenetic profile of EWS is subject of interest. In this review, we summarize the current available knowledge on the genetics underpinning EWS, explore the current knowledge of its epigenetic profile, discuss in vitro and in vivo model systems, and explore the unravelling knowledge of potential targets for treatment including recent insights into potential immunotherapy.

Eosinophilic esophagitis (EoE) is a chronic inflammatory disease that is increasingly recognized as the cause of common gastrointestinal symptoms including dysphagia, chest and abdominal pain, heartburn, food impaction, and food refusal in children and adults. Often referred to as “asthma of the esophagus”, eosinophilic esophagitis, like its asthma counterpart, is an allergic disorder on the rise worldwide. Clinically managed by food avoidance, steroid therapy, recurring endoscopic evaluations and dilations as needed, eosinophilic esophagitis is a poorly understood disease process with limited therapies and even fewer diagnostic tools to predict and surveil active inflammation. As a result, there is a critical need to identify noninvasive biomarkers and therapeutic targets for eosinophilic esophagitis. Here we review the known contributions of miRNAs to eosinophilic inflammation of the esophagus and the potential for miRNA biomarkers for EoE in the clinical setting.

Aim: To investigate the potential relationship between the strength of evidence for a gene-disease association and inclusion of the gene on a targeted, indication-based gene panel test for hereditary long QT syndrome (LQTS) and to explore factors that may influence laboratory decisions about the inclusion or exclusion of genes from these clinical tests.

Methods: A comprehensive literature search was performed to quantify existing evidence supporting putative LQTS gene-disease associations. This evidence included the year that the gene was first implicated in LQTS, the total number of published cases of LQTS attributed to the gene, and the presence of published segregation and functional data for the gene. To explore the possible relationship between the published evidence for clinical validity of each gene and availability of clinical genetic testing, semi-structured interviews were conducted with key laboratory stakeholders. Representatives from nine US laboratories offering clinical LQTS gene testing agreed to be interviewed regarding decision-making about when and why genes comprising their clinical LQTS test offerings were added.

Results: Genes associated with LQTS before 2006 generally had more reported cases of LQTS and the greatest amount of supporting segregation and functional data prior to being offered as a clinical test. For genes first linked to LQTS after 2006, these trends are less linear and the timeframe between initial report and inclusion on clinical test menus decreased substantially. Advances in technology, lifting of patents, clinician request, and literature searches were cited as the main factors that influence composition of LQTS gene panel tests. Paradoxically, one lab director noted that it may require more evidence to remove a gene than to add a gene to a clinical test panel.

Conclusion: Our evaluation of the LQTS genes illustrates the nuanced relationship between published evidence supporting a gene-disease association and availability of clinical testing. Expert assessment of clinical validity of gene-disease associations may help laboratories to determine gene panel content. The ultimate impact of such information on the composition of clinical gene tests as well as their utilization by clinicians and coverage by health insurance policies remains to be seen.

Many important medical conditions may be the result of an inherited mutation in one of a number of different genes. Technical advances have reduced the cost of whole genome sequencing and whole exome sequencing to a level where it is now feasible to analyse multiple genes in one test. Every human carries several hundred potentially pathogenic coding variants, so a major challenge is to understand which of these is relevant to the patient’s disease. This requires considerable computing power, the use of international unaffected “normal” population and disease cohort databases, clinical scientist input as well as a medical context provided by accurate phenotyping and understanding of Bayesian probability. The guidelines of the American College of Medical Genetics provide a useful framework for the evaluation and reporting of sequence variants. In England, the 100,000 Genomes Project was established within the National Health Service to introduce these technologies into mainstream healthcare. From January 2019, genomic laboratory hubs will deliver a genomics service. In this paper, we review what has been learnt from the project to date and consider how other health care systems could use similar approaches.

Melanoma represents just 1% of skin cancer but is responsible for the vast majority of skin cancer deaths. Given its implications for therapeutic advancement, the field of melanoma genomics has dramatically expanded in recent years. At one time classified mainly by anatomical location - non-acral cutaneous melanoma (NACM), acral cutaneous melanoma (ACM), mucosal melanoma (MuM), or uveal melanoma (UM) are now further sub-classified based on the mutated genes that drive their initiation, progression, and survival. BRAF gene mutations in NACM are the most frequently occurring and the best-studied, giving rise to the successful use of BRAF inhibitors in clinical practice for the last decade. This development has opened the door for many promising clinical trials and countless investigations into melanoma’s genetic underpinnings. In this review, we offer an overview of melanoma genomics and discuss the most relevant somatic mutations such as BRAF, NRAS, and NF1 in NACM, KIT in ACM and MuM, and GNAQ, GNA11, and BAP1 in UM. Particular emphasis is placed on the biochemical pathways driven by each mutation, their associated clinical manifestations, and their role as current and future therapeutic targets.

Medulloblastoma is a heterogeneous disease comprising four molecular subgroups - wingless (WNT), sonic hedge hog (SHH), group 3, and group 4, with distinct developmental origins, unique transcriptional profiles, diverse phenotypes, and varying clinical outcomes. Magnetic resonance imaging (MRI) is the preferred first-line imaging modality in the diagnosis and staging of suspected brain tumors including medulloblastoma. It is being increasingly recognized that imaging features reflect underlying disease biology that can serve as independent predictive and prognostic biomarkers. Radiogenomics is an emerging field of research that aims to define relationships between non-invasive imaging features (radio-phenotypes) and genomic data/molecular markers (molecular phenotypes). Recent studies have reported encouraging data regarding imaging genomics of medulloblastoma with certain MRI features correlating with specific molecular subgroups. These include lateralized cerebellar location for SHH-subgroup; cerebellopontine angle location for WNT-subgroup; and inferior location with dilation of superior recess of the IVth ventricle for group 4 tumors. Minimal enhancement of primary tumor and ependymal metastases (infundibular/suprasellar) with mismatching pattern is a specific feature of group 4 medulloblastoma. A 5-metabolite signature profile on magnetic resonance spectroscopy reliably differentiates SHH-subgroup from non-WNT/non-SHH medulloblastoma. SHH-specific binary nomogram (location on horizontal and vertical axis, relationship with dorsal brainstem, pattern of contrast-enhancement, and peri-tumoral edema as discriminating imaging features) is associated with excellent predictive accuracy, followed by group 4-specific nomogram, with suboptimal accuracy of WNT and group 3-specific nomograms. The advent of deep machine-learning techniques and convoluted artificial neural networks should provide unique opportunities to further improve the accuracy of such radiogenomic correlation and prediction.

The large number of different syndromes and seizure types together with an interindividual variable response to antiepileptic drugs (AEDs) make the treatment of epilepsy challenging. Fortunately, the last few years have been characterized by a huge interest in epilepsy genetics and two methods, genome-wide analyses and next-generation sequencing, have definitely given the possibility to write a new chapter in the book of treatment of epilepsy, the chapter on precision medicine. Epilepsy offers a good opportunity for the personalization of therapy if we consider that at least one third of epileptic patients do not achieve complete seizure control with the currently available pharmacological treatments, treatment is still often empirical and precise therapy, based on the pathogenesis and the mechanism of each AED is not generally possible because this mechanism often remains incompletely known. In addition, new drugs are often not targeted but developed using in vivo seizure models, to be potentially used by the largest number of patients. This method leads to a therapy aimed at treating the symptoms and the seizures rather than the single pathogenic mechanism of each seizure type or syndrome. In this narrative review, we summarize the established evidence regarding pharmacogenomics in epilepsy and discuss the basis of precision medicine.

Renal cell carcinoma (RCC) represents a heterogeneous group of malignancies derived from the kidney, of which clear cell RCC (ccRCC) accounts for nearly 75% of cases. Despite major advances in effective therapies, metastatic ccRCC is still associated with a 10%-20% 5-year survival and remains quite lethal. Great effort has been placed into understanding the genetics and genomics of ccRCC and their prognostic and therapeutic implications. Large-scale cancer genomics sequencing studies have identified several driver genes beyond VHL, particularly PBRM1 (40%), SETD2 (15%), and BAP1 (10%), drastically changing the concept of single-gene pathology underlying sporadic ccRCC. In this mini-review, we explore the pathways by which the loss of VHL, PBRM1, SETD2, and/or BAP1 induce ccRCC through discussion of gene function, disease models, prognostic indications, and therapeutic advances.

Aim: Asthma is a chronic inflammatory syndrome that is characterized by heterogeneous disease pathogeneses that produce distinct subtypes. There is a great need to develop biomarkers to distinguish these subtypes and help guide specific therapy and better predict outcomes, particularly in severe asthma where a number of targeted therapeutics are now available. We sought to determine whether expression of asthma-specific microRNAs (miRNAs) could distinguish phenotypic differences in a diverse cohort of asthmatic subjects that spanned a range of disease severity.

Methods: RNA was isolated from peripheral blood from human subjects. Expression of 39 miRNAs was then screened. Sample cycle threshold values were normalized. Normally distributed data were analyzed and hierarchical cluster was performed.

Results: Peripheral blood was obtained from 62 adults. We identified four clusters of asthmatics defined by 5 distinct miRNA expression patterns. Cluster 1 was associated with mild asthma, low inhaled corticosteroid use, and low eosinophil levels. Cluster 3 and 4 consisted primarily of severe asthmatics with poor asthma control, and Cluster 3 was specifically associated with high IgE, high blood eosinophil levels, and racial disparity (higher proportion of Black subjects). Cluster 2 was comprised predominantly of mild-moderate asthmatics that had higher blood eosinophils than Cluster 1.

Conclusion: These results indicate the miRNA expression profiling can be useful to identify distinct asthma phenotypes, and have potential to better understand disease pathogenesis and help guide therapy.

Aim: Triple negative breast cancer (TNBC) is the most severe subtype of breast cancer with poor prognosis even when treated at a localized stage. The treatment of metastatic TNBC is still challenging daily clinical practice, mainly because of the lack of targeted therapies. In the last years, a molecular sub-classification of TNBC has opened the way to personalized medicine for this type of severe cancer.

Methods: In this study, we assessed the added value of combining molecular analyses with individual xenografts to personalize the treatment of resort for five women with metastatic TNBC. While a patient was receiving one or two lines of chemotherapy, the corresponding xenograft model was tested with different drugs or drug combinations, mainly based on transcriptomic analyses of the tumor and on theoretical activated canonical pathways.

Results: On the basis of transcriptomic analyses and chemosensitivity data obtained from TNBC individual xenografts, we personalized the resort treatment for the five women in our study. In all cases, despite the fact that this resort treatment was a third-line or a fourth-line treatment, the time to progression was longer than that observed with previous lines of chemotherapy. When we explored the 19 chemotherapy regimens given to these women and their corresponding xenograft models, there was a strong correlation between ΔSUV_max (maximum standard uptake value) on positron emission tomography-computed tomography and the corresponding coefficients of inhibition obtained in mice.

Conclusion: The combination of gene expression profiling and individual xenografts is a promising method and could be proposed as a personalized therapeutic resort for women with metastatic TNBCs.

This article discusses the benefits of personalized genomic medicine, some of the challenges of adoption into the clinic, and provides examples of UK and European projects that are developing the practice of personalized genomic medicine. It highlights the work of the UK Pharmacogenetics and Stratified Medicine Network in providing information, developing multidisciplinary collaborations, and organizing events, to support the advancement of personalized genomic medicine.

Prostate cancer is the second most frequently diagnosed non-skin male malignancy worldwide, with over 1.1 million new diagnoses each year. Population screening based on serum prostate-specific antigen (PSA) has shifted the disease burden toward earlier stage, localized disease. However, clinical outcomes for localized prostate cancer are highly heterogeneous, despite the use of clinical prognostic factors (PSA, Gleason grade, and TNM stage). Recent advances in massively-parallel DNA sequencing and computational biology have permitted detailed genomic analyses of all major human cancer types, including prostate cancer. However, the long natural history of prostate cancer has largely precluded rapid translation of this knowledge into clinical practice. Herein, we provide a “state of the field” overview of prostate cancer genomics, with particular focus on localized, non-indolent disease. We discuss recurrent somatic aberrations, across multiple mutational classes, which characterize this disease state, and suggest strategies through which an improved understanding of these molecular aberrations may be utilized in the curative setting. Finally, we summarize the major outstanding questions in prostate cancer genomics, and discuss hypotheses and potential strategies to begin to address these questions.