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In recent decades, some monogenic forms of arterial hypertension have been identified. They were caused by specific pathways due to rare disruptive mutations in individual genes that determined an early and severe hypertension phenotype. At least 37 genes are known, the disruption of which is clearly accompanied by a dysfunction of the blood pressure regulation. This knowledge improves our understanding of both the mechanisms of development and treatment of hypertension. The genetic causes of secondary hypertension are usually due to a single gene disorder. The discovery of genes responsible for monogenic forms of hypertension revealed the role of the kidneys and adrenal glands as important players in the regulation of blood pressure. Most of these syndromes are caused by mutations that lead to increased of the function or its loss, which in turn leads to changes in the content of mineralocorticoids, glucocorticoids or sympathetic pathway activation. Monogenic forms of hypertension often lead to severe forms of hypertension, electrolyte and hormonal disorders, accompanied by drug resistance, and often cause a higher risk of cardiovascular events and premature death. The lecture provides recommendations for genetic testing in hypertension, an algorithm for diagnostic examination of a patient with suspected monogenic form of hypertension, as well as features of the clinical course and treatment of the main known forms of monogenic hypertension.

Congenital bronchopulmonary malformations are relatively common and arise during various periods of morphogenesis. Although some are isolated or sporadic occurrences, others may result from single gene mutations or cytogenetic imbalances. Single gene mutations have been identified, which are etiologically related to primary pulmonary hypoplasia, lung segmentation defects as well as pulmonary vascular and lymphatic lesions. Functional defects in cystic fibrosis, primary ciliary dyskinesias, alpha-1-antitrypsin deficiency, and surfactant proteins caused by gene mutations may result in progressive pulmonary disease. This article provides an overview of pediatric pulmonary disease from a genetic perspective.

PurposePredictive diagnostics play an increasingly important role in personalized medicine for cancer treatment. Whole genome sequencing (WGS) based treatment selection is expected to rapidly increase worldwide. Detailed and comparative cost analyses of diagnostic techniques are an essential element in decision-making. This study aimed to calculate and compare the total cost of currently used diagnostic techniques and of WGS in treatment of non-small cell lung carcinoma (NSCLC), melanoma, colorectal cancer (CRC) and gastrointestinal stromal tumor (GIST) in the Netherlands.MethodsThe activity-based costing (ABC) method was conducted to calculate the total cost of included diagnostic techniques based on data provided by Dutch pathology laboratories and the Dutch centralized cancer WGS facility. Costs were allocated to four categories: capital costs, maintenance costs, software costs and operational costs. Outcome measures were total cost per cancer patient per included technique, and the total cost per cancer patient per most commonly applied technique (combination) for each cancer type.ResultsThe total cost per cancer patient per technique varied from € 58 (Sanger sequencing, 3 amplicons) to € 4738 (paired tumor-normal WGS). The operational costs accounted for the vast majority over 90 % of the total per cancer patient technique costs. The most important operational cost drivers were consumables followed by personnel (for sample preparation and primary data analysis).ConclusionThis study outlined in detail all costing aspects and cost prices of current and new diagnostic modalities used in treatment of NSCLC, melanoma, CRC and GIST in the Netherlands. Detailed cost differences and value comparisons between these diagnostic techniques enable future economic evaluations to support decision-making on implementation of WGS and other diagnostic modalities in routine clinical practice.

Background Next-generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide targeted therapy; however, little is known about the performance of the Oncomine Dx Target Test compared with conventional single gene tests for detecting EGFR mutations. The objective of this study was to evaluate the performance of the Oncomine Dx Target Test compared with a PNA-LNA PCR clamp test to detect EGFR mutations. Methods We retrospectively reviewed consecutive patients with non-small cell lung cancer (NSCLC) from whom FFPE samples were simultaneously submitted for the Oncomine Dx Target Test, and a PNA-LNA PCR clamp test using the same specimen. We subsequently compared the analysis success rates and detection rates between the two tests. Results A total of 116 samples were identified. The success rates and detection rates of EGFR mutations in the total number of samples were 90% and 28%, respectively for the Oncomine Dx Target Test, and 100% and 35% for the PNA-LNA PCR clamp test. The Oncomine Dx Target Test was unable to analyze three samples (2%) due to the samples not passing the nucleic acid concentration threshold, and nine (8%) samples had invalid results. The exon 19 deletion was not detected by the Oncomine Dx Target Test in four cases (4%). Conclusions The analytical performance of the Oncomine Dx Target Test analysis for EGFR mutations may not be comparable with conventional single gene tests due to both invalid and false-negative results. Key points Significant findings of the study The success rate of the Oncomine Dx Target Test was significantly lower than the PNA-LNA PCR clamp test. Among the samples successfully analyzed, four exon 19 deletions were not detected by the Oncomine Dx Target Test. What this study adds The analytical performance of the Oncomine Dx Target Test may not be comparable with conventional single gene tests. We should revise the sampling procedures, and review the sample quality assessment methods, to improve the analytical performance.

Pseudoxanthoma elasticum (PXE) is a rare genetic disorder characterised by elastic tissue alterations and caused by mutations in a single gene, ABCC6, on chromosome 16p that includes manifestations that are predominantly cutaneous, ocular and cardiovascular. PXE-like lesions in association with β-thalassemia have previously been reported in the literature in patients with β-thalassaemia intermediate and major, being clinically indistinguishable from classic PXE. The case is presented of a 10-year-old boy with β-thalassaemia minor and characteristic lesions of PXE. It is worth noting the benefit of multimodal imaging in the diagnosis and monitoring of the lesions.

Background and Aims: Hemoglobinopathies and thalassemias are the commonest single gene disorders in India. In Terai region of India, Hemoglobinopathies and thalassemias are the most common in the Tharu community. Therefore, in this study, we aim to evaluate the Hb variant analysis of hemoglobinopathies and thalassemias in a Tharu population in Lakhimpur Kheri Districts of Uttar Pradesh, India. Materials and Methods: Total 493 individuals were recruited in this study. The demographic details and blood samples were collected from different location at Kheri district during mega health camp. Hb variant analysis was performed by high performance liquid chromatography (HPLC) system beta thalassemia short program in BIO-RAD VARIANT. Results: Out of 493, 108 (21.9%) individual suffers with abnormal haemoglobinopathies. In which β-thalassemia trait is the commonest haemoglobinopathy (12.98%), followed by HbE trait (7.50%), and compound heterozygous HbS/β-Thalassemia trait (1.42%) in overall population. The HbF was significantly greater in HbS heterozygous (1.45 ± 1.41), whereas mean HbA2 was significantly greater in β-Thalassemia trait (5.17 ± 1.36). Conclusion: The high incidence of hemoglobinopathies and thalassemias were observed in Tharu community in Lakhimpur Kheri districts of Uttar Pradesh, Indian.

There have been significant advancements in precision medicine and approaches to medication selection based on pharmacogenetic results. With the availability of direct-to-consumer genetic testing and growing awareness of genetic interindividual variability, patient demand for more precise, individually tailored drug regimens is increasing. The University of Florida (UF) Health Precision Medicine Program (PMP) was established in 2011 to improve integration of genomic data into clinical practice. In the ensuing years, the UF Health PMP has successfully implemented several single-gene tests to optimize the precision of medication prescribing across a variety of clinical settings. Most recently, the UF Health PMP launched a custom-designed pharmacogenetic panel, including pharmacogenes relevant to supportive care medications commonly prescribed to patients undergoing chemotherapy treatment, referred to as "GatorPGx." This tutorial provides guidance and information to institutions on how to transition from the implementation of single-gene pharmacogenetic testing to a preemptive panel-based testing approach. Here, we demonstrate application of the preemptive panel in the setting of an adult solid tumor oncology clinic. Importantly, the information included herein can be applied to other clinical practice settings.

Prion disease is a rare, fatal, and exceptionally rapid neurodegenerative disease. Although incurable, prion disease follows a clear pathogenic mechanism, in which a single gene gives rise to a single prion protein (PrP) capable of converting into the sole causal disease agent, the misfolded prion. As efforts progress to leverage this mechanistic knowledge toward rational therapies, a principal challenge will be the design of clinical trials. Previous trials in prion disease have been done in symptomatic patients who are often profoundly debilitated at enrolment. About 15% of prion disease cases are genetic, creating an opportunity for early therapeutic intervention to delay or prevent disease. Highly variable age of onset and absence of established prodromal biomarkers might render infeasible existing models for testing drugs before disease onset. Advancement of near-term targeted therapeutics could crucially depend on thoughtful design of rigorous presymptomatic trials.

Preimplantation genetic testing for monogenic conditions (PGT-M) has become a valued reproductive option for couples at risk of having a child with a single gene condition. In line with developments in molecular genetics, there has been an overall trend toward laboratory techniques with higher accuracy in comparison to earlier PGT-M techniques. The recommendation for confirmatory prenatal diagnostic testing has remained a standard component of PGT-M counseling, reflecting the inherent difficulties of testing the limited number of cells obtained from embryo biopsy, as well as recognition of the biological and human factors that may lead to misdiagnosis in a PGT-M cycle. Reported misdiagnosis rates are less than 1 in 200 pregnancies following PGT-M, although updated data regarding newer methods of PGT-M are required. There is limited evidence available regarding clinician and patient behavior in pregnancies resulting from PGT-M cycles. It remains essential that clinicians involved in the care of patients undergoing PGT-M provide appropriate counseling regarding the risks of misdiagnosis and the importance of confirmatory prenatal diagnosis. The nature of PGT-M test design lends itself to cell-free DNA-based noninvasive prenatal testing for monogenic conditions (NIPT-M), which is likely to become a popular method in the near future.

Background: Current prognostic signatures are based on measurements of numerous targets and require specialized equipment and complex calculations. While the overall prognostic capabilities of the tests may be comparable in ER+/HER2- breast cancer, side by side comparisons of different tests have shown that results differ on the individual patient level (Bartlett et al., JNCI, 2016). Here we determined risk scores and classifications in 160 tumors to the following commercial and academic prognostic tests using a custom gene panel for which the publically available algorithms were trained against the actual commercial test scores: Mammaprint®, Oncotype DX®, Prosigna® including PAM50 subtyping; and academic risk scores: IHC4-like, 95-gene score and the Genomic Grade Index. These trained risk classifiers were compared to the results of the MammaTyper® IVD-kit. Methods: RNA was extracted from FFPE tissue sections and analyzed on the Nanostring nCounter® using a probe set containing all targets and reference genes used in the original signatures (N=199). Nanostring measurements and calculations of simulated risk classifiers were carried out as described previously (Bayani et al., npj Breast Cancer, 2017) and retrained against actual commercial test scores (Bartlett et al., in prep.). MammaTyper® RT-qPCR of ERBB2, ESR1, PGR and MKI67 (normalized to CALM2) was carried out on a separate aliquot of the same RNA sample. St. Gallen surrogate subtypes were assigned based on binary mRNA expression according to pre-defined cutoffs. For calculating pairwise agreements between test categorizations, simulated test results with ternary classification were transformed to binary classifications (IHC4-like: low + int vs. high, Oncotype DX-trained: RS≤25 vs. RS>25, Prosigna-trained ROR-P: low vs. int + high). Comparison of MammaTyper® with simulated risk scores was done on the level of surrogate subtypes and on the level of continuous MKI67 and LRP score values. The MammaTyper® LRP score is a previously developed signature to predict RS ≤25 results with high specificity. Results: Marker positivity rate by RT-qPCR was 83% for ESR1, 72% for PGR, 9% for ERBB2 and 58% for MKI67 based on the pre-specified MammaTyper® cutoffs. The highest rate of low risk results was found for binary RS classification with 68.1% of RS ≤25 samples. MammaTyper® Luminal A-like result was found in 30.6% of samples a rate similar to ROR-P, Genomic Grade Index or MammaPrint-trained low risk results (35.0%, 38.1% and 38.8% respectively). The highest agreement between the simulated risk classifications was observed between binary OncotypeDX-trained RS and IHC4-like classifications with 93.1%. Prosigna-trained (ROR-P) and IHC4-like score had the lowest pairwise agreement with only 65.0% agreement. Oncotype DX-trained and the 95 gene score had the highest concordance to MammaTyper® Luminal A-like subtype with 100% and 96% of Luminal A-like samples classified as RS ≤25 and low risk also by these signatures, respectively. ROC analyses of MammaTyper®MKI67 against binary 95-gene score risk classifier resulted in an AUC of 0.949. The lowest AUC for MKI67 was achieved against simulated MammaPrint-trained classification (AUC=0.874). When applying the LRP score to ROC analysis, almost identical AUCs were achieved for IHC4-like and binary Oncotype DX-trained classifications with AUCs of 0.976 and 0.969 respectively. Conclusion: Low cost local RT-qPCR measurements by MammaTyper® show a high agreement with the scores generated by our Oncotype DX-trained scores. The academic and well validated 95-gene signature agrees well with MammaTyper®MKI67 single gene measurement. Therefore, the locally performed MammaTyper® test may serve as cost effective surrogate for complex prognostic signatures or at least enables a pre-screening for molecularly “obviously” low risk samples. Citation Format: Mark Laible, Sebastian Aulmann, Alfred Etzrodt, Marcus Schmidt, Cheryl Crozier, Ralph Wirtz, Jane Bayani, Ugur Sahin, John MS Bartlett. Comparison of MammaTyper® RT-qPCR based subtyping with simulated breast cancer prognostic signatures [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-07-08.

Hemoglobinopathies are the most common single gene disorders (monogenic disorders) in the world population. Due to specific position of Iran and the presence of multi-ethnic groups in the country, there are many varieties in the molecular genetics and clinical features of hemoglobinopathies in Iran. Hemoglobinopathies include structural variants, thalassemias, and hereditary persistence of fetal hemoglobin. In this review, we look at the common structural variants in various parts of the country along with their hematological and clinical characteristics. Also, we discuss about the burden of the thalassemias in the country, different types, complications, molecular defects and therapy.

Helsmoortel Van der Aa syndrome also known as ADNP syndrome is a neurological disorder which is caused by genetic changes in the ADNP gene. These genetic mutations occur impulsively in most patients, showing that there has been no family history of the disorder. These mutations mostly affect the intellectual abilities of the person, delays motor planning, and also may lead to autism or autism spectrum disorder. In 2014 ADNP disorder was discovered, and it is found that ADNP gene was one of the most consistent single gene causes of autism. Although several researchers have discovered a clear view with characteristics of the "core" effects associated with several mutations in the ADNP gene, a lot of things about the disorder is still unknown. Detecting ADNP syndrome in a person can be challenging as it is developed spontaneously without a long development curve. For this research of predicting the ADNP syndrome, a dataset comprising the details of 150 children, where 23 were diagnosed with ADNP syndrome and 127 were typically developing (TD) children was taken. The dataset comprises features such as a person's age, sex, whether he/she has been treated with jaundice, and their family history with ADNP and some other additional features.

Multiplexed detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rather than detection targeting a single gene is crucial to ensure more accurate coronavirus disease 2019 (COVID-19) diagnostics. Here, we develop a monolithic, 3D-printed, lab-on-disc platform for multiplexed molecular detection of SARS-CoV-2. The centrifugal lab-on-disc is fabricated in one step using simple 3D printing technology, circumventing the need for aligning and binding multiple layers. By combining isothermal amplification technology, this lab-on-disc platform is capable of simultaneously detecting the nucleoprotein and envelope genes of SARS-CoV-2 as well as an internal control of the human POP7 gene. Within a 50-minute incubation period, 100 copies SARS-CoV-2 RNA can be detected through visual detection according to color and fluorescence changes in the disc. Further, we clinically validated the lab-on-disc platform by testing 20 nasopharyngeal swab samples and demonstrated a sensitivity of 100% and an accuracy of 95%. Therefore, the monolithic, 3D-printed, lab-on-disc platform provides simple, rapid, disposable, sensitive, reliable, and multiplexed molecular detection of SARS-CoV-2, holding promise for COVID-19 diagnostics at the point of care., Graphical abstract

Background CRMO is a sterile auto inflammatory bone disease that affects the pediatric population. Recently, single gene mutations in LPIN2, DIRA, and IL1RN have been reported in murine models of CRMO. Materials and methods The medical records and histopathological slides of twelve patients were reviewed. Results The diagnosis was determined by multiple lesions, imaging, negative cultures, bone biopsy, and lack of antibiotic response. Biopsy showed early neutrophilic infiltrates, and older lesions showed lymphoplasmacytic infiltrates and fibrosis. Patients were treated with anti-inflammatory medication with some lesions completely resolving. Conclusion Bone biopsy aids the diagnosis of CRMO in correlation with clinical presentation, imaging, and culture findings. Our findings indicate the kinetics of CRMO is not well defined and the fibrosis may be reached after months, in contrast to the previously reported several years. We hope that these genetic mutations can be further studied in human models to describe the genetics behind CRMO.

Primary immunodeficiencies (PIDs) have become a prime target for gene therapy given the morbidity, mortality, and the single gene etiology. Given that outcomes are better the earlier gene therapy is implemented, it is possible that fetal gene therapy may be an important future direction for the treatment of PIDs. In this chapter, the current treatments available for several PIDs will be reviewed, as well as the history and current status of gene therapy for PIDs. The possibility of in utero gene therapy as a possibility will then be discussed.

The term “proteoforms” describes the range of different structures of a protein product of a single gene, including variations in amino acid sequence and post-translational modifications. This diversity in protein structure contributes to the biological complexity observed in living organisms. As the concentration of a particular proteoform may increase or decrease in abnormal physiological states, proteoforms have long been used in medicine as biomarkers of health and disease. Notably, the analytical approaches used to analyze proteoforms have evolved considerably over the years. While ligand binding methods continue to play a large role in proteoform measurement in the clinical laboratory, unanticipated or unknown post-translational modifications and sequence variants can upend even extensively tested and vetted assays that have successfully made it through the medical regulatory process. As an alternate approach, mass spectrometry—with its high molecular selectivity—has become an essential tool in detection, characterization, and quantification of proteoforms in biological fluids and tissues. This review explores the analytical techniques used for proteoform detection and quantification, with an emphasis on mass spectrometry and its various applications in clinical research and patient care including, revealing new biomarker targets, helping improve the design of contemporary ligand binding in vitro diagnostics, and as mass spectrometric laboratory developed tests used in routine patient care.

Motivation Alternative splicing generates multiple isoforms from a single gene, greatly increasing the functional diversity of a genome. Although gene functions have been well studied, little is known about the specific functions of isoforms, making accurate prediction of isoform functions highly desirable. However, the existing approaches to predicting isoform functions are far from satisfactory due to at least two reasons: (i) unlike genes, isoform-level functional annotations are scarce. (ii) The information of isoform functions is concealed in various types of data including isoform sequences, co-expression relationship among isoforms, etc. Results In this study, we present a novel approach, DIFFUSE (Deep learning-based prediction of IsoForm FUnctions from Sequences and Expression), to predict isoform functions. To integrate various types of data, our approach adopts a hybrid framework by first using a deep neural network (DNN) to predict the functions of isoforms from their genomic sequences and then refining the prediction using a conditional random field (CRF) based on co-expression relationship. To overcome the lack of isoform-level ground truth labels, we further propose an iterative semi-supervised learning algorithm to train both the DNN and CRF together. Our extensive computational experiments demonstrate that DIFFUSE could effectively predict the functions of isoforms and genes. It achieves an average area under the receiver operating characteristics curve of 0.840 and area under the precision–recall curve of 0.581 over 4184 GO functional categories, which are significantly higher than the state-of-the-art methods. We further validate the prediction results by analyzing the correlation between functional similarity, sequence similarity, expression similarity and structural similarity, as well as the consistency between the predicted functions and some well-studied functional features of isoform sequences. Availability and implementation https://github.com/haochenucr/DIFFUSE. Supplementary information Supplementary data are available at Bioinformatics online.

Since the discovery of hypoxia-inducible factor (HIF), numerous studies on the hypoxia signaling pathway have been performed. The role of HIF stabilization during hypoxia has been extended from the induction of a single gene erythropoietin to the upregulation of a couple of hundred downstream targets, which demonstrates the complexity and importance of the HIF signaling pathway. Accordingly, HIF and its downstream targets are emerging as novel therapeutic options to treat various organ injuries. In this review, we discuss the current understanding of HIF signaling in four different organ systems, including the heart, lung, liver, and kidney. We also discuss the divergent roles of HIF in acute and chronic disease conditions and their revealed functions. Finally, we introduce some of the efforts that are being performed to translate our current knowledge in hypoxia signaling to clinical medicine., Low oxygen: Protein signalling in human disease A protein family that plays diverse roles in acute and chronic hypoxia (low oxygen) may prove valuable in developing novel therapies for different diseases. Hypoxia, the short- or long-term depletion of oxygen in cells, tissues and organs, is involved in many disease conditions. Holger Eltzschig at the McGovern Medical School in Houston, USA, and co-workers reviewed research into the roles of a key hypoxia regulator, the hypoxia-inducible factor (HIF) protein group, in diseases affecting the heart, lung, liver and kidneys. HIF protein activity is often beneficial in acute conditions such as myocardial ischemia, sending signals to protect cells and increasing tissue tolerance to hypoxia. However, during chronic hypoxia, HIF signaling may contribute to the progression of disease, for example in pulmonary fibrosis. HIF stabilizers and HIF-induced targets as drugs could prove valuable in future treatments.

ObjectiveTo evaluate the clinical and cost savings benefits of adoption of a carrier screen with reflex single-gene non-invasive prenatal test (sgNIPT) in prenatal care.MethodA decision-analytic model was developed to compare carrier screen with reflex sgNIPT (maternal carrier status and fetal risk reported together) as first-line carrier screening to the traditional carrier screening workflow (positive maternal carrier screen followed by paternal screening to evaluate fetal risk). The model compared the clinical outcomes and cost effectiveness between the two screening methods. These results were used to simulate appropriate pricing for reflex sgNIPT.ResultsReflex sgNIPT carrier screening detected 108 of 110 affected pregnancies per 100,000 births (98.5% sensitivity), whereas traditional carrier screening detected 46 of 110 affected pregnancies (41.5% sensitivity). The cost to identify one affected pregnancy was reduced by 62% in the reflex sgNIPT scenario compared to the traditional scenario. Adding together the testing cost savings and the savings from earlier clinical intervention made possible by reflex sgNIPT, the total cost savings was $37.6 million per 100,000 pregnancies. Based on these cost savings, we simulated appropriate reflex sgNIPT pricing range: if the cost to identify one affected pregnancy is the unit cost, carrier screening with reflex sgNIPT can be priced up to $1,859 per test (or $7,233 if sgNIPT is billed separately); if the cost per 100,000 pregnancies is the unit cost, carrier screening with sgNIPT can be priced up to $1,070 per test (or $2,336 if sgNIPT is billed separately).ConclusionUsing the carrier screen with reflex sgNIPT as first-line screening improves the detection of affected fetuses by 2.4-fold and can save costs for the healthcare system. A real-life experience will be needed to assess the clinical utility and exact cost savings of carrier screen with reflex sgNIPT.

1.1SummaryMental illnesses are one of the biggest contributors to the global disease burden. Despite the increased recognition, diagnosis and ongoing research of mental health disorders, the etiology and underlying molecular mechanisms of these disorders are yet to be fully elucidated. Moreover, despite many treatment options available, a large subset of the psychiatric patient population is non-responsive to standard medications and therapies. There has not been a comprehensive study to date examining the burden and impact of treatable genetic disorders (TGDs) that can present with neuropsychiatric features in psychiatric patient populations. In this study, we test the hypothesis that TGDs that present with psychiatric symptoms are more prevalent within psychiatric patient populations compared to the general population by performing targeted next-generation sequencing (NGS) of 129 genes associated with 108 TGDs in a cohort of 2301 psychiatric patients. In total, 72 putative affected and 293 putative carriers for TGDs were identified, with known or likely pathogenic variants in 78 genes. Despite screening for only 108 genetic disorders, this study showed an approximately four-fold (4.13%) enrichment for genetic disorders within the psychiatric population relative to the estimated 1% cumulative prevalence of all single gene disorders globally. This strongly suggests that the prevalence of these, and most likely all, genetic diseases are greatly underestimated in psychiatric populations. Increasing awareness and ensuring accurate diagnosis of TGDs will open new avenues to targeted treatment for a subset of psychiatric patients.

Genome-wide sequencing (exome and whole genome) has transformed our ability to diagnose patients with suspected genetic disorders. Cerebral palsy (CP), although historically thought to be due to birth injury (perinatal hypoxia), represents a clinical spectrum of disorders, many of which have been attributed to a genetic cause. GWS has elucidated the underlying single gene cause for many patients with CP and has important implications for the customization of treatment, management, and genetic counseling. International guidelines recommend genetic counseling for all families considering genome-wide sequencing. Genetic counselors educate and support families and help them to make testing decisions based on their values. They can help families adapt to, and understand the implications of a genomic diagnosis. Here, we review advances in sequencing for CP, clinical features suggestive of a genetic etiology of CP, practice guidelines for GWS, and a practical approach to the genetic counseling of these families. This includes: the content to be addressed in pre-test and post-test genetic counseling sessions, the benefits of a establishing a genetic cause and importantly, the need for ongoing support.

Genodermatoses are inherited, genetic skin conditions which can be classified into these three categories: chromosomal defect, a single gene defect or polygenetic. They may run in families (inherited skin disorders) or may occur as a result of a new mutation. Some are obvious at birth (congenital) while others may only become apparent in childhood or adult life (e.g. tuberous sclerosis). Early diagnosis is important to limit morbidity and mortality. Genetic counselling is vital if the affected person is planning a family.

Cotton fiber quality is a complex trait which is influenced by environmental stresses. Breeding alone is not found up to the mark to get the desired fiber quality. Combination of approaches to bring all fiber quality traits through gene pyramiding can only be attained by genetic modification followed by breeding. Genetic modification is increasingly being used in biotechnology. Improved cotton fiber quality is always preferred by the textile industry. Researchers are working hard to reveal genes involved in controlling various fiber characteristics; resultantly several genes have been identified. Studies determined the effects of variation in expression of fiber-related genes transcription factors, and genes expressing phytohormones can have its impact on altering the fiber quality. Introduction of single gene cannot impart the desired results, but combination of fiber-related genes and transcription factor controlling gene expression can be useful strategy for fiber improvement. This chapter highlights the structure and composition of fiber at various developmental stages and also the impact of transgene in improving fiber traits.

The development of high-throughput technologies has changed the conduct of biological experiments in the last decade. From single gene studies, research has shifted to measuring gene signatures at the transcriptome level. The dramatic decrease in the financial expenses of next generation sequencing techniques has enabled their routine implementation. However, very often, economic constraints restrict the number of samples and sequence quality. Careful planning and design may overcome this limitation, and attain the maximum information from a given experiment.Among the factors that affect the quality and quantity of data resulting from next generation sequencing experiments are sample size and the number of replicates, sequence depth and coverage, randomization, and batches. Here, we discuss the design of high-throughput experiments, while focusing on RNA-sequencing experiments. We suggest critical rules of thumb, from biological, statistical, and bioinformatics points of view, aimed to obtain a successful experiment, beyond the economic constraints.

Since their discovery, relevant efforts have been made to optimize the detection approaches to EGFR mutations as well as the clinical management of EGFR-mutated NSCLC. The recent shift from single gene testing to novel comprehensive detection platforms along with the development of new generation tyrosine kinase inhibitors, targeting both common and uncommon EGFR-mutations, is leading to a progressive increase in the number of patients who may benefit from targeted approaches, with subsequent impact on their long-term survival and quality of life. However, a prompt and adequate implementation of the most recent diagnostic and treatment advances in the routine practice often remains critical to be specifically addressed. In this review we provide a complete and updated overview of the different detection platforms and therapeutic options currently available for the clinical management of advanced EGFR-positive NSCLC, summarizing scientific evidence and describing molecular testing as well as treatment practice in the real-word scenario.

Mucopolysaccharidosis type IIIA (MPS IIIA, Sanfilippo A syndrome) is a single gene (SGSH) childhood onset neurodegenerative disease for which gene therapy is in clinical trial. Theoretically, the transfer of a working gene should enable functional expression of the defective protein and rescue the phenotype when administered before the onset of irreversible disease. Recombinant adeno-associated virus (AAV) is being used as a vehicle for a number of gene therapy applications and the neurotropism of serotype 9 affords utility for monogenetic neurological disorders. To assess the efficacy of restoring the underlying biochemistry in the MPS IIIA brain, tail vein injections of self-complementary AAV9 human N-sulfoglucosamine sulfohydrolase (scAAV9.U1A.hSGSH) at 3 x 10(13) vg/kg were administered to 6- and 16-week-old MPS IIIA mice. Heparan sulfate (HS) and G(M2) and G(M3) gangliosides were cleared from the cortex, hippocampus and subcortex with residual storage remaining in the brain stem and cerebellum. SGSH activity increased in the brain of the MPS IIIA-treated mice, but remained significantly reduced compared with wild-type. Motor activity as assessed in an open-field arena, and gait length, improved in MPS IIIA mice treated at both 6 and 16 weeks of age. However, functional assessment of cognition in the water cross-maze test, as well as gait width, normalized in mice treated at 6 weeks of age only, with mice treated at 16 weeks performing similar to untreated MPS IIIA mice. Astrogliosis was reduced in mice treated at 6 and 16 weeks of age compared to untreated MPS IIIA mice. These results demonstrate that the gene product is actively clearing primary HS and secondary ganglioside accumulation in MPS IIIA mice, but in older mice, neurocognitive impairments remain. This is likely due to secondary downstream consequences of HS affecting neurological functions that are not reversible upon substrate clearance. usc Refereed/Peer-reviewed

Gene and cell therapy products approved over the past decade in Europe and North America have provided new therapeutic options for single gene disorders and for hematologic malignancies. Lessons learned, and limitations identified, are reviewed.

This short article describes the method of digital cytopathology using Z-stack scanning with or without extended focusing. This technology is suitable to observe such thick clusters as adenocarcinoma on cytologic specimens. Artificial intelligence (AI) has been applied to histological images, but its application on cytologic images is still limited. This article describes our attempt to apply AI technology to cytologic digital images. For molecular analysis, cytologic materials, such as smear, LBC, and cell blocks, have been successfully used for targeted single gene detection and multiplex gene analysis with next-generation sequencing. As a future perspective, the system can be connected to full automation by combining digital cytopathology with AI application to detect target cancer cells and to perform molecular analysis. The literature review is updated according to the subjects.

Predicting the phenotypes resulting from molecular perturbations is one of the key challenges in genetics. Both forward and reverse genetic screen are employed to identify the molecular mechanisms underlying phenotypes and disease, and these resulted in a large number of genotype–phenotype association being available for humans and model organisms. Combined with recent advances in machine learning, it may now be possible to predict human phenotypes resulting from particular molecular aberrations. We developed DeepPheno, a neural network based hierarchical multi-class multi-label classification method for predicting the phenotypes resulting from loss-of-function in single genes. DeepPheno uses the functional annotations with gene products to predict the phenotypes resulting from a loss-of-function; additionally, we employ a two-step procedure in which we predict these functions first and then predict phenotypes. Prediction of phenotypes is ontology-based and we propose a novel ontology-based classifier suitable for very large hierarchical classification tasks. These methods allow us to predict phenotypes associated with any known protein-coding gene. We evaluate our approach using evaluation metrics established by the CAFA challenge and compare with top performing CAFA2 methods as well as several state of the art phenotype prediction approaches, demonstrating the improvement of DeepPheno over established methods. Furthermore, we show that predictions generated by DeepPheno are applicable to predicting gene–disease associations based on comparing phenotypes, and that a large number of new predictions made by DeepPheno have recently been added as phenotype databases., Author summary Gene–phenotype associations can help to understand the underlying mechanisms of many genetic diseases. However, experimental identification, often involving animal models, is time consuming and expensive. Computational methods that predict gene–phenotype associations can be used instead. We developed DeepPheno, a novel approach for predicting the phenotypes resulting from a loss of function of a single gene. We use gene functions and gene expression as information to prediction phenotypes. Our method uses a neural network classifier that is able to account for hierarchical dependencies between phenotypes. We extensively evaluate our method and compare it with related approaches, and we show that DeepPheno results in better performance in several evaluations. Furthermore, we found that many of the new predictions made by our method have been added to phenotype association databases released one year later. Overall, DeepPheno simulates some aspects of human physiology and how molecular and physiological alterations lead to abnormal phenotypes.

Patients with a known genetic cause of aortic root dilation usually have a single underlying aetiology, either a single gene defect as in Marfan syndrome or chromosomal anomaly as in Turner syndrome. However, it is possible, although unlikely, for a patient to inherit multiple independent risk factors for aortic root dilation. We describe such a patient, who inherited Marfan syndrome and a very unusual form of mosaic Turner syndrome. Long-term follow-up of this patient may provide insight into the natural history of this unique genetic combination.

What’s already known about this topic?Sequencing-based noninvasive testing can detect large copy number abnormalities and some auto-somal dominant single-gene disordersExome sequencing (ES) on fetal samples provides 20% diagnostic yield for structural abnormalities after normal karyotype & microarrayWhat does this study add?ES on cell-free DNA in three gravid patients with suspected genetic disease in the fetusWe demonstrate broad sequencing approaches are limited by sampling and technical difficulties, concluding broad sequencing is currently inappropriate for noninvasive testing

Objective: To simultaneously detect fetal aneuploidies and single gene diseases using a novel noninvasive prenatal testing (NIPT) method called the Targeted And Genome-wide simultaneous sequencing (TAGs-seq). Design: Comparison of TAGs-seq NIPT results with conventional NIPT and diagnostic results. Setting: Shenzhen People’s Hospital and Chinese PLA General Hospital Population or Sample: 26 normal pregnancies, 7 pregnancies with fetal aneuploidies, 7 pregnancies with fetal achondroplasia (ACH) or thanatophoric dysplasia (TD), 18 pregnancies with ACH/TD-like ultrasound findings, and 10 pregnancies with fetal risk of beta-thalassemia. Methods: Plasma cfDNA was amplified by TAGs-seq to simultaneously obtain the whole-genome sequence of 0.1-3× depth and reads on target genes of >1000× depth. The whole-genome sequence was analyzed for fetal aneuploidy risk using a binary hypothesis T-score, and the reads on target genes were analyzed for single gene diseases by calculating minor allelic frequency of loci on FGFR3 and HBB. Main Outcome Measures: Concordance between the TAGs-seq NIPT, conventional NIPT and diagnostic results. Results: Consistent to conventional NIPT and diagnostic results, all cases of fetal aneuploidies and fetal ACH/TD were correctly identified from 58 pregnancies by TAGs-seq NIPT with high sensitivities and specificities. Two cases of paternal mutations of beta-thalassemia were correctly identified by TAGs-seq NIPT from 10 pregnancies, although one false-negative result was obtained. Conclusions: The TAGs-seq assay demonstrated a good potential to simultaneously detect fetal aneuploidies and single gene diseases as a novel NIPT method.

Kidney parenchyma and collecting system arise from two different embryologic units as a result of a close interaction between them. Therefore, their congenital abnormalities are classified together under the same heading named CAKUT (congenital abnormalities of the kidney and urinary tract). The pathogenesis of CAKUT is thought to be multifactorial. Ureteropelvic junction obstruction (UPJO) is the most common and most investigated form of CAKUT. Despite years of experimental and clinical research, and the information gained on the embryogenesis of the kidney; its etiopathogenesis is still unclear. It involves both genetic and environmental factors. Failure in development of the renal pelvis, failure in the recanalization of ureteropelvic junction, abnormal pyeloureteral innervation, and impaired smooth muscle differentiation are the main proposed mechanisms for the occurrence of UPJO. There are also single gene mutations like AGTR2, BMP4, Id2 proposed in the etiopathogenesis of UPJO.

This chapter introduces hypertension, a disorder which affects more than 1 billion people worldwide, and a major cause of morbidity and mortality. We start by providing a brief overview of the key blood pressure regulation systems and then describe the causes of hypertension—genes and lifestyle factors. Up to 95% of people with hypertension have essential hypertension and 5% of individuals have mutations in a single gene causing their hypertension. Using case studies as exemplars, we describe the clinical features of five single gene (monogenic) causes of hypertension and provide information on causative mutations and genes, pathophysiology of disease, and patient diagnosis and management. We provide a discussion on the overlap of genes causing monogenic and essential hypertension, and progress on finding genes for essential hypertension. We conclude with the clinical implications of genetic studies thus far and some future perspectives for genomic cardiovascular medicine.

Monogenic disorders are remained a common issue in some countries due to poor environmental factors and unnecessary mutations, more specifically in the rural areas, the monogenic disorder ratio is much more higher because of the consanguineous marriages. According to the OMIM database, there are currently more than 8,000 single-gene diseases identified. Although monogenic diseases are rare, the overall incidence is nearly 1/100. Among various birth defects, the proportion of single gene diseases is as high as \(22.2\%\). Among neonatal deaths, \(20\%\) of them are caused by recessive genetic diseases, and \(80\%\) of patients with recessive genetic diseases have no family genetic history. Screening of carriers of single-gene inherited diseases based on specific populations has been proposed since the 1970s, however the cost was very high and it was impossible to be widely used. In the past few years, with the fast development of genetic testing technology and clinical applications, more and more single-gene associated diseases have been discovered, and the cost for screening monogenic disorders has become less and less. In this paper we first introduce the single-gene inherited diseases, then we explain how to identify the single-gene inherited diseases, finally we describe the working mechanism and implementation of the genetic interpretation system for screening monogenic disorders carriers.

Background: We assessed the sensitivity, specificity and positive and negative predictive value (PPV and NPV) of molecular and serological tests for the diagnosis of SARS-CoV-2 infection. Methods: A total of 346 patients were enrolled in the emergency room. We evaluated three Reverse Transcriptase-real time PCRs (RT-PCRs) including six different gene targets, five serologic rapid diagnostic tests (RDT) and one ELISA. The final classification of infected/non-infected patients was performed using Latent Class Analysis combined with clinical re-assessment of incongruous cases. Results: Out of these, 24.6% of patients were classified as infected. The molecular test RQ-SARS-nCoV-2 showed the highest performance with 91.8% sensitivity, 100% specificity, 100.0% PPV and 97.4% NPV respectively. Considering the single gene targets, S and RdRp of RQ-SARS-nCoV-2 had the highest sensitivity (94.1%). The in-house RdRp presented the lowest sensitivity (62.4%). The specificity ranged from 99.2% for in-house RdRp and N2 to 95.0% for E. The PPV ranged from 97.1% of N2 to 85.4% of E and the NPV from 98.1% of S to 89.0% of in-house RdRp. All serological tests had &lt, 50% sensitivity and low PPV and NPV. VivaDiag IgM (RDT) had 98.5% specificity, with 84.0% PPV, but 24.7% sensitivity. Conclusion: Molecular tests for SARS-CoV-2 infection showed excellent specificity, but significant differences in sensitivity. Serological tests have limited utility in a clinical context.

Cleft lip and palate are common craniofacial deformities. The etiology underlying these deformities is complex and multifactorial and they can occur as part of one of many chromosomal syndromes, Mendelian single gene disorders, teratogenic effects, and as yet uncharacterized syndromes. Our paper will provide an overview of the multiple genes and molecular pathways that have been implicated in palatal fusion. We believe that understanding the molecular mechanisms of cleft formation can help clinicians anticipate which patients may have difficulties healing and in the future allow them to make surgical and medical treatment decisions based on genetic information.

The discovery of cell-free fetal DNA (cffDNA) in maternal plasma has enabled a paradigm shift in prenatal testing, allowing for safer, earlier detection of genetic conditions of the fetus. Non-invasive prenatal testing (NIPT) for fetal aneuploidies has provided an alternative, highly efficient approach to first-trimester aneuploidy screening, and since its inception has been rapidly adopted worldwide. Due to the genome-wide nature of some NIPT protocols, the commercial sector has widened the scope of cell-free DNA (cfDNA) screening to include sex chromosome aneuploidies, rare autosomal trisomies and sub-microscopic copy-number variants. These developments may be marketed as ‘expanded NIPT’ or ‘NIPT Plus’ and bring with them a plethora of ethical and practical considerations. Concurrently, cfDNA tests for single-gene disorders, termed non-invasive prenatal diagnosis (NIPD), have been developed for an increasing array of conditions but are less widely available. Despite the fact that all these tests utilise the same biomarker, cfDNA, there is considerable variation in key parameters such as sensitivity, specificity and positive predictive value depending on what the test is for. The distinction between diagnostics and screening has become blurred, and there is a clear need for the education of physicians and patients regarding the technical capabilities and limitations of these different forms of testing. Furthermore, there is a requirement for consistent guidelines that apply across health sectors, both public and commercial, to ensure that tests are validated and robust and that careful and appropriate pre-test and post-test counselling is provided by professionals who understand the tests offered.

As child mortality rates overall are decreasing, non-communicable conditions, such as genetic disorders, constitute an increasing proportion of child mortality, morbidity and disability. To date, policy and public health programmes have focused on common genetic disorders. Rare single gene disorders are an important source of morbidity and premature mortality for affected families. When considered collectively, they account for an important public health burden, which is frequently under-recognised. To document the collective frequency and health burden of rare single gene disorders, it is necessary to aggregate them into large manageable groupings and take account of their family implications, effective interventions and service needs. Here, we present an approach to estimate the burden of these conditions up to 5 years of age in settings without empirical data. This approaches uses population-level demographic data, combined with assumptions based on empirical data from settings with data available, to provide population-level estimates which programmes and policy-makers when planning services can use. Electronic supplementary material The online version of this article (10.1007/s12687-018-0376-2) contains supplementary material, which is available to authorized users.

Background Since April 2013, the UK’s National Health Service Breast Screening Programme (NHSBSP) centers have been obliged to provide services for women at the highest risk of breast cancer, including those carrying highly penetrant single gene mutations (BRCA1, BRCA2, TP53). Since then, such individuals previously undergoing surveillance in the Royal Marsden Hospital were referred to their local NHSBSP centers. We aimed to assess patient experience of surveillance provided by local NHSBSP services at 1 and 3 years after repatriation. Patients and Methods High-risk gene mutation carriers referred to the NHSBSP for breast cancer surveillance were identified from a departmental database in the Cancer Genetics Unit and invited to complete questionnaires about their experience of surveillance under this new pathway, first in 2014 and again in 2016. Results Three hundred forty-six individuals were invited to participate in 2014, of whom 182 responded (53%). A total of 464 patients were invited in 2016, of whom 246 (53%) completed the second questionnaire. Ninety-four percent of patients with residual breast tissue received some screening at the first (n = 161) and second (n = 185) time points. Ninety-one percent of patients (n = 146) received at least recommended surveillance in the year preceding the initial survey, a proportion decreasing slightly by the second time point (n = 164, 87%). Seventeen percent of individuals required additional diagnostic investigations, with cancers detected in 2%. These proportions remained stable between surveys. Conclusion Repatriation of high-risk individuals from Royal Marsden Hospital to NHSBSP centers has been successfully accomplished. Most individuals received appropriate recommended annual surveillance. Further improvements are required to ensure equal and timely provision of recommended surveillance.

OBJECTIVE As diagnostic methodologies evolve, we sought to determine whether invasive testing rates would decline, whether there would be a shift in indications for invasive testing, and whether the diagnostic yield would increase. METHODS We conducted a retrospective, observational study from 2006 through 2015. We quantified the number of invasive procedures per year and examined what percentage of these procedures yielded abnormal results. We also examined the indications for testing and determined the trend of these indications during the study period. RESULTS The number of amniocenteses showed a steady decline (P

Molecular testing for lung cancer has evolved dramatically over the last decade, driven primarily by the rapid development of targeted therapies. Initial testing was intended to make appropriate therapeutic choices with primary single gene testing and has evolved into larger sensitive and specific panels to evaluate multiple genes. The wide array of technologies and an increasing number of targeted therapies have resulted in increasingly complex management algorithms. In this article, we review the current guidelines, briefly discuss individual targets, and introduce some of the complexities associated with genomic testing. We generally recommend next generation sequencing (NGS) panel testing when available and discuss other reasonable alternatives. Circulating tumor assays are commonly utilized, particularly when tissue is unavailable for genomic testing.