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Background To identify genes associated with congenital diaphragmatic hernia (CDH) to help understand the etiology and inform prognosis. Methods We performed exome sequencing on fetuses with CDH and their parents to identify rare genetic variants likely to mediate risk. We reviewed prenatal characteristics and neonatal outcomes. Results Data were generated for 22 parent-offspring trios. Six Likely Damaging (LD) variants were identified in five families (23 %). Three LD variants were in genes that contain variants in other CDH cohorts (NR2F2, PTPN11, WT1), while three were in genes that do not (CTR9, HDAC6, TP53). Integrating these data bolsters the evidence of association of NR2F2, PTPN11, and WT1 with CDH in humans. Of the five fetuses with a genetic diagnosis, one was terminated, two underwent perinatal demise, while two survived until repair. Conclusions Exome sequencing expands the diagnostic yield of genetic testing in CDH. Correlating CDH patients’ exomes with clinical outcomes may enable personalized counseling and therapies.

Human is the host of the Epstein-Barr virus (EBV) especially in childhood and adolescence. Most of them are asymptomatic infection and self-limiting. However, for those patients who suffer from immune dysfunction, EBV infection will be life-threatening. Epstein-Barr virus-associated hemophagocytic lymphohistocytosis (EBV-HLH) is one of the severe effects. The diagnosis and differential diagnosis of EBV-HLH and other EBV infectious diseases are mentioned in this paper. The molecular biology mechanism and complications of EBV-HLH are equally briefly presented. It also provides a practical method for the genetic diagnosis of such diseases and the differential diagnosis with other human immunodeficiency diseases for medical scientists in routine clinical practice.

Chorionic villus sampling (CVS) is a procedure in which biopsies of placental tissue are obtained for prenatal genetic diagnosis. Risk of infection after CVS is low and only sporadic cases of postprocedural sepsis have been reported. Clostridium perfrigens and Escherichia coli are the most commonly described pathogens in cases of sepsis after prenatal invasive diagnostic procedures. However, this report describes a case of sepsis with fetal loss after CVS caused by Atopobium vaginae.

The major advances in genetic neuromuscular disorders in the last 30 years have been: (a) identification of the genetic basis for hundreds of these disorders, (b) through knowing the genes, understanding their pathobiology and (c) subsequent implementation of evidence-based treatments for some of the disorders. New genomic technologies are providing precision diagnosis, mode of inheritance and likely prognosis for more patients than ever before. Parents of children with a genetic diagnosis can then use preimplantation or prenatal diagnosis to avoid having further affected children if they wish. But is this the best we can do for genetic neuromuscular disorders? Since the 1980s, it has been argued it would be better to identify Duchenne muscular dystrophy carrier mothers, rather than diagnose their affected sons. Carrier screening for recessive disorders can identify couples with a high chance of having affected children. It allows couples reproductive choice and can prevent infant morbidity and mortality and significant distress for families. Professional bodies in many countries now recommend prospective parents should be informed about carrier screening. Implementing and funding expensive therapies increases the cost-effectiveness of carrier screening, increasing its attractiveness to governments. Best practice for genetic neuromuscular disorders should include equitable access to carrier screening.

Monogenic diabetes mellitus, which is diabetes caused by a defect in a single gene that is associated with β cell function or insulin action, accounts for 1% to 6% of all pediatric diabetes cases. Accurate diagnosis is important, as the effective treatment differs according to genetic etiology in some types of monogenic diabetes: high-dose sulfonylurea treatment in neonatal diabetes caused by activating mutations in KCNJ11 or ABCC8; low-dose sulfonylurea treatment in HNF1A/HNF4A-diabetes; and no treatment in GCK diabetes. Monogenic diabetes should be suspected by clinicians for certain combinations of clinical features and laboratory results, and approximately 80% of monogenic diabetes cases are misdiagnosed as type 1 diabetes or type 2 diabetes. Here, we outline the types of monogenic diabetes and the clinical implications of genetic diagnosis.

The paper presents the characteristics of clinical periods of 6q24-TNDM development: neonatal hyperglycemia, remission and type 2 diabetes mellitus. We present the clinical features of 6q24-TNDM depending on genetic disorders. The article indicated the clinical and laboratory criteria for 6q24-TNDM diagnosis. The methods of modern molecular and genetic diagnosis and the limitations of prenatal diagnosis were described in detail.

У лекції наведені сучасні міжнародні рекомендації з діагностики гіпопітуїтаризму у дітей, зокрема правила проведення стимуляційних тестів для діагностики гіпосоматотропізму, вторинного гіпогонадизму й гіпокортицизму. Обґрунтовано використання антимюллерова гормона та інгібіну В у діагностиці різних форм гіпогонадизму. Рекомендовано впровадження генетичних методів дослідження з метою встановлення коректного діагнозу, призначення відповідного лікування й проведення медико-генетичної консультації членів сім’ї.

Background As an autosomal dominant disorder, familial hypercholesterolemia (FH) is mainly attributed to disease-causing variants in the low-density lipoprotein receptor (LDLR) gene. The aim of this study was to explore the molecular mechanism of LDLR c.501C>A variant in FH and assess the efficacy of proprotein convertase subtilisin kexin type 9 (PCSK9) inhibitor treatment for FH patients. Methods The whole-exome sequencing was performed on two families to identify disease-causing variants, which were verified by Sanger sequencing. The function of LDLR variant was further explored in HEK293 cells by Western Blot and confocal microscopy. Besides, the therapeutic effects of PCSK9 inhibitor treatment for two probands were assessed for 3 months. Results All members of the two families with the LDLR c.501C>A variant showed high levels of LDLC. The relationship between the clinical phenotype and LDLR variants was confirmed in the current study. Both in silico and in vitro analyses showed that LDLR c.501C>A variant decreased LDLR expression and LDL uptake. PCSK9 inhibitor treatment lowered the lipid level in proband 1 by 24.91%. However, the treatment was ineffective for proband 2. A follow-up study revealed that the PCSK9 inhibitor treatment had low ability of lipid-lowering effect in the patients. Conclusions LDLR c.501C>A variant might be pathogenic for FH. The PCSK9 inhibitor therapy is not a highly effective option for treatment of FH patients with LDLR c.501C>A variant.

Patients with inborn errors of immunity (IEI) present with a heterogeneous clinical and immunological phenotype, therefore a correct molecular diagnosis is crucial for the classification and subsequent therapeutic management. On the other hand, IEI are a group of rare congenital diseases with highly diverse features and, in most cases, an as yet unknown genetic etiology. Next generation sequencing has facilitated genetic examinations of rare inherited disorders during the recent years, thus allowing a suitable molecular diagnosis in the IEI patients. This review aimed to investigate the current findings about these techniques in the field of IEI, suggesting an efficient stepwise approach to molecular diagnosis of inborn errors of immunity.

Background: At least 10% of adults and most of the children who receive renal replacement therapy have inherited kidney diseases. These disorders substantially decrease their life quality and have a large effect on the health-care system. Multisystem complications, with typical challenges for rare disorders, including variable phenotypes and fragmented clinical and biological data, make genetic diagnosis of inherited kidney disorders difficult. In current clinical practice, genetic diagnosis is important for clinical management, estimating disease development, and applying personal treatment for patients. Summary: Inherited kidney diseases comprise hundreds of different disorders. Here, we have summarized various monogenic kidney disorders. These disorders are caused by mutations in genes coding for a wide range of proteins including receptors, channels/transporters, enzymes, transcription factors, and structural components that might also have a role in extrarenal organs (bone, eyes, brain, skin, ear, etc.). With the development of next-generation sequencing technologies, genetic testing and analysis become more accessible, promoting our understanding of the pathophysiologic mechanisms of inherited kidney diseases. However, challenges exist in interpreting the significance of genetic variants and translating them to guide clinical managements. Alport syndrome is chosen as an example to introduce the practical application of genetic testing and diagnosis on inherited kidney diseases, considering its clinical features, genetic backgrounds, and genetic testing for making a genetic diagnosis. Key Messages: Recent advances in genomics have highlighted the complexity of Mendelian disorders, which is due to allelic heterogeneity (distinct mutations in the same gene produce distinct phenotypes), locus heterogeneity (mutations in distinct genes result in similar phenotypes), reduced penetrance, variable expressivity, modifier genes, and/or environmental factors. Implementation of precision medicine in clinical nephrology can improve the clinical diagnostic rate and treatment efficiency of kidney diseases, which requires a good understanding of genetics for nephrologists.

Cascade genetic testing is the identification of individuals at risk for a hereditary condition by genetic testing in relatives of people known to possess particular genetic variants. Cascade testing has health system implications, however cascade costs and health effects are not considered in health technology assessments (HTAs) that focus on costs and health consequences in individual patients. Cascade health service use must be better understood to be incorporated in HTA of emerging genetic tests for children. The purpose of this review was to characterise published research related to patterns and costs of cascade health service use by relatives of children with any condition diagnosed through genetic testing. To this end, a scoping literature review was conducted. Citation databases were searched for English-language papers reporting uptake, costs, downstream health service use, or cost-effectiveness of cascade investigations of relatives of children who receive a genetic diagnosis. Included publications were critically appraised, and findings were synthesised. Twenty publications were included. Sixteen had a paediatric proband population; four had a combined paediatric and adult proband population. Uptake of cascade testing varied across diseases, from 37% for cystic fibrosis, 39% to 65% for hypertrophic cardiomyopathy, and 90% for rare monogenic conditions. Two studies evaluated costs. It was concluded that cascade testing in the child-to-parent direction has been reported in a variety of diseases, and that understanding the scope of cascade testing will aid in the design and conduct of HTA of emerging genetic technologies to better inform funding and policy decisions.

Objectives The development of female or male sex characteristics occurs during fetal life, when the genetic, gonadal, and internal and external genital sex is determined (female or male). Any discordance among sex determination and differentiation stages results in differences/disorders of sex development (DSD), which are classified based on the sex chromosomes found on the karyotype. Content This chapter addresses the physiological mechanisms that determine the development of female or male sex characteristics during fetal life, provides a general classification of DSD, and offers guidance for clinical, biochemical, and genetic diagnosis, which must be established by a multidisciplinary team. Biochemical studies should include general biochemistry, steroid and peptide hormone testing either at baseline or by stimulation testing. The genetic study should start with the determination of the karyotype, followed by a molecular study of the 46,XX or 46,XY karyotypes for the identification of candidate genes. Summary 46,XX DSD include an abnormal gonadal development (dysgenesis, ovotestes, or testes), an androgen excess (the most frequent) of fetal, fetoplacental, or maternal origin and an abnormal development of the internal genitalia. Biochemical and genetic markers are specific for each group. Outlook Diagnosis of DSD requires the involvement of a multidisciplinary team coordinated by a clinician, including a service of biochemistry, clinical, and molecular genetic testing, radiology and imaging, and a service of pathological anatomy.

Diagnosing acutely unwell infants with a potential genetic diagnosis can be challenging for healthcare professionals. Evidence suggests that up to 13% of critically unwell infants on the neonatal intensive care unit (NICU) have an underlying molecular diagnosis and when identified directly affects treatment decisions in 83%. On 1st October 2019, the National Health Service England (NHSE) launched a nationally commissioned service so that rapid whole-exome sequencing can be offered to critically unwell babies and children with a likely monogenic disorder who are admitted to NICU and paediatric intensive care unit (PICU). We present 7 cases from two neonatal units in the West Midlands (UK), where rapid exome sequencing has revealed a genetic diagnosis. Early genetic diagnosis in this cohort has influenced management in all (100%) cases, and in 57% (4 in 7 cases), it has helped in the decision to reorientate care. In some cases, early diagnosis has reduced the need for invasive and unnecessary investigations and avoided the need for post-mortem investigations. The genetic diagnosis has helped in counselling the families regarding the recurrence risk for future pregnancies. In some cases, this has provided parents with the reassurance of a low recurrence. In others, it has resulted in the offer of prenatal diagnosis or assisted conception technologies. What is Known: • Rapid whole-exome sequencing was commissioned in the UK in October 2019. • It is available for critically unwell babies with a likely monogenic aetiology. What is New: • It helps management planning for rare genetic disorders and future pregnancies counselling. • It can reduce the need for invasive investigations and overall intensive care costs.

Pre-Implantation genetic diagnosis is available to couples at risk of conceiving a pregnancy affected with a known genetic disorder. Assisted reproductive techniques are used in combination with micromolecular diagnostic technologies to recognise at-risk embryos with pathogenic genetic variants at the pre-implantation stage using polar body, blastomere or trophectoderm biopsy. This review will discuss the varying genetic disorders diagnosed by Pre-Implantation Genetic Diagnosis, as well as the ethical, legal and safety implications of the process. Pioneering advances in molecular biology and cytogenomics have been utilised to expand the spectrum of genetic disorders detected.

Background Primary adrenal insufficiency (PAI) is life-threatening, and a definitive aetiological diagnosis is essential for management and prognostication. We conducted this study to investigate the genetic aetiologies of PAI in South China and explore their clinical features. Methods Seventy children were enrolled in this cross-sectional study. Clinical information was collected, and combined genetic tests were performed according to the children’s manifestations. Statistical analysis was performed among the different groups. In silico or in vitro experiments were applied to determine the pathogenicity of novel variants. Results Among the 70 children, 84.3% (59/70) were diagnosed with congenital adrenal hyperplasia (CAH), and 21-hydroxylase deficiency (21-OHD) was genetically confirmed in 91.5% of these cases. Salt wasting (SW), simple virilization (SV), and non-classic (NC) CAH accounted for 66.1% (39/59), 30.5% (18/59), and 3.4% (2/59) of the cases, respectively. The 17-hydroxyprogesterone (17-OHP) and testosterone (TES) levels were significantly higher in children with SW than with SV. The 17-OHP and cortisol levels in female SW patients were significantly higher than those in males. The 17-OHP, cortisol, dehydroepiandrosterone (DHEAS) and TES levels in female SW patients were significantly higher than those in female SV patients. Additionally, 72.7% (8/11) of uncharacterized PAI patients had positive genetic findings. Among all the patients, two novel variants in the CYP21A2 gene (c.833dupT and c.651 + 2T > G) were found. A microdeletion (Xp21.2–21.3) and five novel variants, including 2 in the NR0B1 gene (c.323–324CG > GA and c.1231_1234delCTCA), 2 in the AAAS gene (c.399 + 1G > A and c.250delT) and 1 in the NNT gene (c.2274delT), were detected. The novel variant c.399 + 1G > A in the AAAS gene was further confirmed to lead to exon 4 skipping during mRNA transcription and produce a truncated ALADIN protein. Conclusions We found ethnicity-based differences in the CYP21A2 gene variant spectrum among different study populations. Female 21-OHD patients tended to have higher 17-OHP and TES levels, which warrants caution in relation to the effects of virilization. Novel gene variants detected in the CYP21A2, NR0B1, AAAS and NNT genes expanded the genetic spectrum of PAI, however, further improvement of genetic testing tools beyond our protocol are still needed to uncover the complete aetiology of PAI in children.

Purpose of review This review aims to summarise the present cerebellar ataxia, neuropathy, vestibular ataxia syndrome (CANVAS) literature, providing both clinical and genetic insights that might facilitate the timely clinical and genetic diagnosis of this disease. Recent findings Recent advancements in the range of the clinical features of CANVAS have aided the development of a broader, more well-defined clinical diagnostic criteria. Additionally, the identification of a biallelic repeat expansion in RFC1 as the cause of CANVAS and a common cause of late-onset ataxia has opened the door to the potential discovery of a pathogenic mechanism, which in turn, may lead to therapeutic advancements and improved patient care. Summary The developments in the clinical and genetic understanding of CANVAS will aid the correct and timely diagnosis of CANVAS, which continues to prove challenging within the clinic. The insights detailed within this review will raise the awareness of the phenotypic spectrum and currently known genetics. We also speculate on the future directions of research into CANVAS.

Introduction Inherited retinal degenerations (IRD) are rare genetic disorders with > 300 known genetic loci, manifesting variably progressive visual dysfunction. IRDs were historically underserved due to lack of effective interventions. Many novel therapies will require accurate diagnosis (phenotype and genotype), thus an efficient and effective pathway for assessment and management is required. Methods Using surveys of existing practice patterns and advice from international experts, an all-Ireland IRD service (Target 5000) was designed. Detailed phenotyping was followed by next generation genetic sequencing in both a research and accredited laboratory. Unresolved pedigrees underwent further studies (whole gene/whole exome/whole genome sequencing). Novel variants were interrogated for pathogenicity (cascade screening, in silico analysis, functional studies). A multidisciplinary team (MDT; ophthalmologists, physicians, geneticists, genetic counsellors) reconciled phenotype with genotype. A bespoke care plan was created for each patient comprising supports, existing interventions, and novel therapies/clinical trials. Results and discussion Prior to Target 5000, a significant cohort of patients were not engaged with healthcare/support services due to lack of effective interventions. Pathogenic or likely pathogenic variants in IRD-associated genes were detected in 62.3%, with 11.6% having variants of unknown significance. The genotyping arm of Target 5000 allowed a 42.73% cost saving over independent testing, plus the value of MDT expertise/processing. Partial funding has transferred from charitable sources to government resources. Conclusion Target 5000 demonstrates efficacious and efficient clinical/genetic diagnosis, while discovering novel IRD-implicated genes/variants and investigating mechanisms of disease and avenues of intervention. This model could be used to develop similar IRD programmes in small/medium-sized nations.

Purpose of Review Whole exome sequencing (WES) and whole-genome sequencing (WGS) are frontline approaches for the genetic diagnosis of rare diseases. However, WES/WGS fails in up to 75% of cases. Transcriptomics via RNA-sequencing (RNA-Seq) is a novel approach that aims to increase the diagnostic yield in rare diseases. Recent Findings Recent publications focus on the success of RNA-Seq for increasing diagnosis rates in WES/WGS-negative patients in up to 36% of cases, across a range of different diseases, sample sizes, and tissue types. Summary RNA-Seq is beneficial for aiding prioritisation of causative variants currently not detected or often overlooked by WES/WGS alone. An improvement in diagnostic yields has been demonstrated using multiple source tissues, with muscle and fibroblasts being the most representative, but the more accessible blood still demonstrating diagnostic success, particularly in neuromuscular disorders. The introduction of RNA-Seq to the genetic diagnosis toolbox promises to be a useful complementary tool to WES/WGS for improving genetic diagnosis in patients with rare disease.

The search for the new hereditary mutations and a precise molecular genetic diagnosis that determines the causative mutation in each specific case of hereditary breast cancer (BC) is a clinically important task since it helps to define the personal therapeutic approach and increase the effectiveness of preventive measures. Using whole-exome sequencing (WES) we analyzed the full spectrum of hereditary variations in 49 Russian patients with clinical signs of a hereditary disease which allowed us to compile a list of 229 candidate probably pathogenic germ-line variants. Then, the selected candidate mutations were validated by Sanger sequencing and molecular-epidemiological studies, the predisposing roles of three oncologically relevant mutations (USP39 c.*208G>C, SLIT3 p.Arg154Cys, and CREB3 p.Lys157Glu) were confirmed. Our candidate genes are first mentioned in connection with the hereditary risk of BC. The final proofs of the causative roles of these variants could be obtained through functional tests as well as via the analysis of the mutations segregation in BC families.

Purpose Genetic testing is routine practice for individuals with unexplained developmental disabilities and multiple congenital anomalies. However, current testing pathways can be costly and time consuming, and the diagnostic yield low. Genome-wide sequencing, including exome sequencing (ES) and genome sequencing (GS), can improve diagnosis, but at a higher cost. This study aimed to assess the cost-effectiveness of genome-wide sequencing in Ontario, Canada. Methods A cost-effectiveness analysis was conducted using a discrete event simulation from a public payer perspective. Six strategies involving ES or GS were compared. Outcomes reported were direct medical costs, number of molecular diagnoses, number of positive findings, and number of active treatment changes. Results If ES was used as a second-tier test (after the current first-tier, chromosomal microarray, fails to provide a diagnosis), it would be less costly and more effective than standard testing (CAN$6357 [95% CI: 6179-6520] vs. CAN$8783 per patient [95% CI: 2309-31,123]). If ES was used after standard testing, it would cost an additional CAN$15,228 to identify the genetic diagnosis for one additional patient compared with standard testing. The results remained robust when parameters and assumptions were varied. Conclusion ES would likely be cost-saving if used earlier in the diagnostic pathway.

Introduction Primary ciliary dyskinesia (PCD) is characterized by an alteration in the ciliary structure causing difficulty in the clearance of respiratory secretions. Diagnosis is complex and based on a combination of techniques. The objective of this study was to design a gene panel including all known causative genes, and to corroborate their diagnostic utility in a cohort of Spanish patients. Methods This was a multicenter cross-sectional study of patients with a high suspicion of PCD according to European Respiratory Society criteria. We designed a gene panel for massive sequencing using SeqCap EZ capture technology that included 44 genes associated with PCD. Results We included 79 patients, 53 of whom had a diagnosis of confirmed or highly probable PCD. The sensitivity of the gene panel was 81.1%, with a specificity of 100%. Candidate variants were found in some of the genes of the panel in 43 patients with PCD, 51.2% (22/43) of whom were homozygotes and 48.8% (21/43) compound heterozygotes. The most common causative genes were DNAH5 and CCDC39. We found 52 different variants, 36 of which were not previously described in the literature. Conclusions The design and implementation of a tailored gene panel produces a high yield in the genetic diagnosis of PCD. This panel provides a better understanding of the causative factors involved in these patients and lays down the groundwork for future therapeutic approaches.

Rosa M Coco-Martin,1,2 Miguel Diego-Alonso,1,3 W Andres Orduz-Montaña,1 M Rosa Sanabria,1,4 Hortensia Sanchez-Tocino1,3 1Instituto Universitario de Oftalmobiología Aplicada (IOBA), University of Valladolid, Valladolid, Spain; 2Red Temática de Investigación Cooperativa en Salud de Oftalmologia (Oftared), Instituto de Salud Carlos III, Madrid, Spain; 3Department of Ophthalmology, Hospital Universitario Río Hortega, Valladolid, Spain; 4Department of Ophthalmology, Complejo Hospitalario De Palencia, Palencia, SpainCorrespondence: Rosa M Coco-MartinInstituto de Oftalmobiologia Aplicada (IOBA), University of Valladolid, Campus Miguel Delibes, Pº de Belén Nº 17, Valladolid, 47011, SpainTel +34 983423559, ext. 4738Fax +34 983423274Email rosa@ioba.med.uva.esPurpose: To analyze the distribution of inherited retinal diseases (IRDs), describe the clinical characteristics of patients, and determine the percentages of patients with genetic diagnosis in the Castilla y Leon region of Spain.Methods: All patients with an IRD seen in the two major referral units of Castilla y Leon during a 20-year period were included. The ages at symptom onset, diagnosis, and the last visit; sex; family history; history of consanguinity; type of inheritance; status of the fundus and electroretinogram findings; lens and macular status, visual acuity; and visual field data were recorded. Patients were divided into those with retinitis pigmentosa (RP) and all others. Gene mutations were gathered when available.Results: Four hundred eighty-eight patients with IRDs were studied: 216 (44.26%) with RP of which 34 (15.74%) had syndromic diseases, and 272 had other conditions being 161 (59,19%) macular dystrophies. The mean delay in diagnosis was 6– 16.2 years respectively. For the RP group the mean age at the last visit was 47.96± 17,26; mean age of cataract surgery was 48.30 ± 12.01 years; and the foveal area was preserved in 74 (35.07%) patients, atrophic in 101 (47.87%), and edematous in 36 (17.06%). A genetic study had been performed in 58 (26.85%) of patients with RP and 71 (26,1%) of the rest, being indeterminate in 17 (29.31%) out of RP group and 20 (28.16%) out of the others.Conclusion: Clinical characteristics are comparable to other published series. There is a significant delay in diagnosis. The number of patients with IRDs and available genetic diagnosis, thus being possible candidates for undergoing personalized treatments including gene therapy in our region is low and must be improved.Keywords: inherited retinal dystrophies, retinitis pigmentosa, genetic diagnosis, visual acuity, visual field

GABA transaminase deficiency should be considered in the differential diagnosis of early onset epileptic encephalopathies. This case was diagnosed post‐mortem, but increased vigilance to this will allow for earlier diagnoses in other infants and families. This is a case study which involved diagnosis of a rare neurometabolic disorder in one of the babies in the family and eventual genetic counselling of the family. The family has been offered pre‐implantation genetic diagnosis for future pregnancies. This case reporting has been approved by the hospital research and ethical committee.

SUMMARY: Adenosine deaminase 2 deficiency (OMIM #615688) is an autosomal recessive disorder characterized by a wide clinical spectrum, including small- and medium-sized vessel vasculopathies, but data focusing on the associated neuroimaging features are still scarce in the literature. Here, we describe the clinical neuroimaging features of 12 patients with genetically proven adenosine deaminase 2 deficiency (6 males; median age at disease onset, 1.3 years; median age at genetic diagnosis, 15.5 years). Our findings expand the neuroimaging phenotype of this condition demonstrating, in addition to multiple, recurrent brain lacunar ischemic and/or hemorrhagic strokes, spinal infarcts, and intracranial aneurysms, also cerebral microbleeds and a peculiar, likely inflammatory, perivascular tissue in the basal and peripontine cisterns. Together with early clinical onset, positive family history, inflammatory flares and systemic abnormalities, these findings should raise the suspicion of adenosine deaminase 2 deficiency, thus prompting genetic evaluation and institution of tumor necrosis factor inhibitors, with a potential great impact on neurologic outcome.

This paper reviews important aspects in the management of individuals with familial adenomatous polyposis (FAP). Newly discovered germline pathogenic variants (PVs) beyond APC are a rare cause of adenomatous polyposis. The decreasing cost of multi-gene panel testing (MGPT) has broadened the use of commercial panels to enhance the genetic diagnosis of adenomatous polyposis in families where the causative germline PV in APC is not known. We elucidate emerging risks of cancer in FAP particularly gastric cancer and provide best practices to surveillance and cancer prevention in FAP, including dual therapy chemoprevention and trials utilizing novel mechanisms. Genetic testing is indicated in individuals with ≥ 10 lifetime adenomas. FAP and MutYH-associated polyposis (MAP) will be the most common germline causes of colorectal adenomatous polyposis. In FAP, upper endoscopy is indicated for surveillance of gastric polyposis and gastric cancer in addition to duodenal polyposis. Novel agents for chemoprevention have been shown to be effective and considered for selective use in patients with FAP.

PURPOSE OF REVIEW The current review seeks to provide a comprehensive update on the revolutionary technology of whole exome sequencing (WES) which has been used to interrogate abnormal foetal phenotypes since the last few years, and is changing the paradigms of prenatal diagnosis, facilitating accurate genetic diagnosis and optimal management of pregnancies affected with foetal abnormalities, as well enabling delineation of novel Mendelian disorders. RECENT FINDINGS WES has contributed to identification of more than 1000 Mendelian genes and made rapid strides into clinical diagnostics in recent years. Diagnostic yield of WES in postnatal cohorts has ranged from 25 to 50%, and this test is now a first tier investigation for various clinical presentations. Various abnormal perinatal phenotypes have also been investigated using WES since 2014, with diagnostic yields ranging from 8.5 to 80%. Studies in foetal phenotypes have been challenging and guidelines in this cohort are still evolving. SUMMARY WES has proven to be a disrupting technology, enabling genetic diagnosis for pregnancies complicated by previously unexplained foetal abnormalities, and revealing a significant contribution of single gene disorders in these, thereby changing clinical diagnostic paradigms. The application of this technology in perinatal cohorts is also providing interesting insights into single gene defects presenting as previously unknown genetic syndromes, hence contributing to expansion of Mendelian genetics to encompass various foetal phenotypes.

Background: Primary Immune Deficiencies (PID) are rare, under-determined diseases particularly in sub-Saharan Africa. The diagnosis is often suspected with uncommon clinical signs. Infections are the main diagnostic circumstances in infants. Confirmation is often difficult because some additional examinations are unavailable in many of our countries. Aim: Our aim was to share the challenge of diagnosis and treatment in PID. Case Presentation: It is about two infants, a boy and a girl, with early several infections. Both of them presented a hypo-gammaglobulinemia and to the boy, the immuno-phenotyping lymphocyte showed a decreased level of lymphocytes CD19. We are looking for genetic confirmation but it is not easy. The treatment of these infants requires a substitution for life of immunoglobulin which is unavailable in our countries. Conclusion: PID are suspected with atypical clinical signs. Confirmation genetic diagnosis is difficult in low income countries. To improve the follow up, we need to strengthen clinical-biological collaboration.

Introduction: Familial hypercholesterolemia (FH) is a highly prevalent condition, predisposing individuals to premature cardiovascular disease and with a genetic basis more complex than initially thought. Advances in molecular technologies have provided novel insights into the role of next-generation-sequencing, the assessment and classification of newly found variants, the complex genotype-phenotype correlation, and the position of FH in the context of other dyslipidaemias. Areas covered: Understanding the scope of genetic determinants of FH has expanded substantially. This article reviews the current literature on the complexity that comes with this incremental knowledge and highlights the added value of genetic testing as an addition to phenotypic diagnosis of FH. Moreover, we discuss the broad genetic basis of FH, with a focus on the three main FH genes, but we also pay attention to polygenic hypercholesterolemia as well as minor and modulator genes involved in FH. Expert opinion: Both the availability and the need for genetic analysis of FH are on the rise as costs of sequencing continue to drop and new therapies require a genetic diagnosis for reimbursement. However, greater use of genetic testing requires more education of healthcare professionals, since molecular technologies will allow for rapid and accurate evaluation of large numbers of detected variants.

Introduction: The objective was to evaluate: (i) the proportion of prenatally diagnosed congenital heart disease (CHD) associated with an abnormal quantitative fluorescence-PCR (QF-PCR), chromosome microarray (CMA), and exome sequencing (ES) result; and (ii) the diagnostic yield of these technologies based on CHD category and presence of extra-cardiac anomalies (ECAs). Methods: This prospective cohort study was set across 12 UK foetal medicine centres. All cases underwent QF-PCR, CMA, and ES, and the diagnostic yield in n = 147 cases of prenatally diagnosed CHD was assessed. Results: In 34.7% (n = 51/147), a genetic diagnosis was obtained. Using a stepwise testing strategy, the diagnostic yield for QF-PCR, CMA, and ES was 15.6% (n = 23/147), 13.7% (n = 17/124), and 10.2% (n = 11/107), respectively. Abnormal QF-PCR/shunt (septal) defects 31.4% (n = 11/35), p = 0.046, and abnormal CMA/conotruncal anomalies 22.7% (n = 10/44), p = 0.04, had significant associations. Monogenic variants were commonest in complex CHD 36.4% (n = 4/11). Multisystem CHD had a greater diagnostic yield overall compared to isolated OR 2.41 (95% CI, 1.1–5.1), particularly in association with brain and gastrointestinal tract anomalies. The proportion of variants of uncertain significance was 4.7% (n = 5/107) with ES, with none in the CMA group. Conclusion: In the era of prenatal ES, there remains an important role for QF-PCR and CMA. Identification of monogenic pathologic variants further allows delineation of prognosis in CHD.

Objective: To understand the distribution of thalassemia in all districts under the jurisdiction of Chongzuo City. Methods: Collect blood routine indicators from May 2014 to 31 December 2020 in the districts of this city to screen out suspected Mediterranean patients for genetic diagnosis; GGAP-PCR and PCR-reverse dot hybridization were used to analyze the thalassemia gene in the specimens of suspected patients; compare the prevalence of thalassemia in the counties and cities within the jurisdiction of this city, and provide corresponding medical advice to the health authorities. Results: 21,535 venous blood specimens from patients with suspected thalassemia were collected in the city. There were 14,215 positive cases of thalassemia, accounting for 66.01% of the total number of patients, among which 9455 cases (43.91%) were pure α gene positive. 3464 patients (16.09%) were positive for simple β gene. 1296 patients (6.02%) were positive for αβ double gene. The proportions of thalassemia gene testing for α-thalassaemia gene, β-thalassaemia gene, and α-β double gene in various counties and districts were different. According to the multiple rate or the chi-square test of the constituent ratio, the comparison of the distribution of the thalassaemia gene test results in each area, χ2 = 472.6917, P = 0.0000, the difference is statistically significant. Conclusion: Severe thalassemia is a tragedy for a family. It not only needs to spend a lot of money to prolong life, but it also cannot change the situation of losing life and financial emptiness in the end. It is suggested that timely screening, timely diagnosis and medical consultation should be carried out in married and unborn families and early pregnancy, so as to reduce the birth of children with severe thalassemia and avoid the occurrence of tragedies.

The COL4A1 gene (COL4A1) plays an important role in vascular basement membrane function and pathogenic mutations have been reported in mice and humans. The gene is expressed mainly in the human brain, eyes and kidneys. Pathogenic mutations result in a vast array of manifestations that can present throughout life including the foetal period. We present a case of an 11-year-old girl with right hemiparesis, congenital cataracts, epilepsy and magnetic resonance imaging (MRI) brain findings with a pathogenic COL4A1 mutation. Many of her clinical features are similar to those of a non-genetic cause of cerebral palsy highlighting the difficulties and delays in making this genetic diagnosis.

Genetic diagnosis is becoming increasingly sophisticated, with the ability to identify even fine differences in patients with a wide variety of congenital heart lesions. Although we have an incomplete understanding of the clinical consequences of most genetic findings, some categories of mutations can have important implications for disease recurrence and prognosis. Consideration of the biology underlying a genetic deficiency, when known, can be useful in the clinical management of some patients.

Objective of the Review: To discuss the current peculiarities of 21-hydroxylase insufficiency diagnostics. Key Points. Congenital adrenal hyperplasia (CAH) is a group of autosomal-recessive pathologies, associated with a defective enzyme or transport protein participating in cortisol biosynthesis. Currently, there is information on CAH genetics including information on 21-hydroxylase insufficiency. Neonatal screening, antenatal and postnatal methods to diagnose 21-hydroxylase deficit have been developed. Timely diagnosis and correct therapy have been found to facilitate normal physical and mental development of patients. Molecular genetic testing for CAH associated with 21-hydroxylase deficit is widely used both in Russia and globally and is of importance for differential diagnosis, identification of pathogenic CYP21A2 gene carriers and adequate genetic counselling. The best strategy to diagnose 21-hydroxylase insufficiency is 2-stage CYP21A2 gene analysis. The test should include both gene sequence analysis and identification of point replacements, minor deletions and duplication (e.g., dideoxynucleotide chain-termination method or Next Generation Sequencing), and identification of extended deletions and duplication (multiplex ligation dependent probe amplification, real-time polymerase chain reaction). Such a comprehensive approach can help finding a majority of types of possible changes. Conclusion. Correct genetic testing methods ensure detection of pathogen variants in CYP21A2 gene; evaluation of the possible rate of clinical manifestations of the disease, both during antenatal testing and if an unknown clinical CAH form is encountered; prescribing an adequate therapy; and ensuring genetic counselling in order to develop a management strategy, including when planning for pregnancy in a woman with confirmed CAH. Keywords: congenital adrenal hyperplasia, CYP21A2 gene, genetic counselling, 21-hydroxylase

Amac: Kalitsal metabolik hastaliklar, cok genis bir hastalik grubu olarak klinik ve genetik heterojenitenin en sik goruldugu hastaliklardandir. Tek baslarina nadir olmakla birlikte cok sayida olmalari nedeniyle toplamda toplum sikligi yuksektir. Bu arastirmada Cukurova Universitesi Tip Fakultesi Tibbi Genetik Anabilim Dali verilerinin siniflandirilarak hastalarin tani dagilimlarinin saptanmasi amaclanmistir. Hastalar ve Yontem: Cukurova Universitesi Tip Fakultesi Tibbi Genetik Anabilim Dali Klinik Genetik Poliklinigi’ne dogrudan ve Cocuk Metabolizma Beslenme Bilim Dali ile Kadin Hastaliklari ve Dogum Anabilim Dali’ndan yonlendirilerek basvuruda bulunan hastalarin kayitlari geriye donuk olarak Klinik Genetik Poliklinigi’nin acildigi Nisan 2013 ile Nisan 2016 tarihleri arasi incelenmistir. Bulgular: Toplamda 1819 hastaya laboratuvar hizmeti sunulmus olup, 577 aileye genetik danismanlik hizmeti verilmistir. Genetik tani konma oraninin hasta olarak % 31,5 tasiyici olarak ise % 20,15 oldugu gorulmustur. Tum olgular goz onune alindiginda en sik saptanan ilk 3 klinik taninin sirasiyla biotidinaz eksikligi, fenilketonuri ve glikojen depo hastaliklari oldugu, basvuran hastalar icinde en yuksek tani konma oraninin da sirasiyla fenilketonuri, biotinidaz eksikligi ve mukopolisakkaridozlar oldugu gorulmustur. Tablo 1’de on tani ve genetik tani konma yuzdeleri belirtilmistir. Ayrica toplam 21 vakada da endikasyona yonelik prenatal genetik tani testleri yapilmistir. Sonuc: Kompleks klinige sahip ve genetik olarak heterojen olan kalitsal metabolik hastaliklar ulkemizin en ciddi toplum sagligi problemlerindendir. Bu nedenle sik saptanan tanilarin bilinmesi, ozellikle ulkemizde akraba evliliginin sik goruldugu ve genis bir habitata hizmet veren hastanemiz verileri isiginda belirlenmesi ulke genelinde genetik tani hizmetlerinin iyilestirilmesine ve hatta yenidogan tarama programlarinin gelistirilmesine katkida bulunacaktir.

BACKGROUND It is not easy to identify the cause of various iron overload diseases because the phenotypes overlap. Therefore, it is important to perform genetic testing to determine the genetic background of patients. AIM To investigate the genetic background of a patient with hemochromatosis complicated by psoriasis on both lower extremities. METHODS Ten years ago, a 61-year-old male presented with iron overload, jaundice, hemolytic anemia and microcytic hypochromic anemia. Computed tomography of the left knee joint showed enlargement of the tibial medullary cavity and thinned bone cortices. Magnetic resonance imaging showed hepatic hemochromatosis, extensive abnormal signals from bone marrow cavities and nodular lesions in the lateral medullary cavity of the upper left lateral tibia. Single photon emission computed tomography showed radial dots of abnormal concentration in the upper end of the left tibia and radial symmetry of abnormal concentrations in joints of the extremities. The patient showed several hot spot mutations of the HFE and G6PD genes detected by next-generation sequencing, but no responsible gene mutation was found. The thalassemia gene was detected by gap-PCR. RESULTS The patient was found to carry the -α4.2 and --SEA deletion mutations of the globin gene. These two mutations are common causes of Southeast Asian α-thalassemia, but rarely cause severe widespread non-transfusion secondary hemochromatosis osteoarthropathy. The simultaneous presence of an auxiliary superposition effect of a rare missense mutation of the PIEZO1 gene (NM_001142864, c.C4748T, p.A1583V) was considered. Moreover, several rare mutations of the IFIH1, KRT8, POFUT1, FLG, KRT2, and TGM5 genes may be involved in the pathogenesis of psoriasis. CONCLUSION The selection of genetic detection methods for hemochromatosis still needs to be based on an in-depth study of the clinical manifestations of the disease.

Understanding the genetic causes of kidney disease is essential for accurate diagnosis and could lead to improved therapeutic strategies and prognosis. To accurately and promptly identify the genetic background of kidney diseases, we applied a targeted next‐generation sequencing gene panel including 203 genes associated with kidney disease, as well as diseases originating in other organs with mimicking symptoms of kidney disease, to analyze 51 patients with nonspecific nephrogenic symptoms, followed by validation of its efficacy as a diagnostic tool. We simultaneously screened for copy number variants (CNVs) in each patient to obtain a higher diagnostic yield (molecular diagnostic rate: 39.2%). Notably, one patient suspected of having Bartter syndrome presented with chloride‐secreting diarrhea attributable to homozygous SLC26A3 variants. Additionally, in eight patients, NGS confirmed the genetic causes of undefined kidney diseases (8/20, 40%), and initial clinical impression and molecular diagnosis were matched in 11 patients (11/20, 55%). Moreover, we found seven novel pathogenic/likely pathogenic variants in PKD1, PKHD1, COL4A3, and SLC12A1 genes, with a possible pathogenic variant in COL4A3 (c.1229G>A) identified in two unrelated patients. These results suggest that targeted NGS‐panel testing performed with CNV analysis might be advantageous for noninvasive and comprehensive diagnosis of suspected genetic kidney diseases.

As a rare congenital disease, microspherophakia is characterized by small and spherically shaped crystalline lenses. The common complications of microspherophakia include secondary glaucoma and crystalline lens dislocation or subluxation. Microspherophakia patients often show high lenticular myopia. The special morphological characteristics and complex complications bring challenges to the treatment of microspherophakia patients. While there are some studies on microspherophakia, most are case reports. In this article, the morphological characteristics, complications, genetic diagnosis and treatment of MSP were systematically reviewed, providing valuable insight into the clinical diagnosis and treatment of this disease.

BACKGROUND Our genetic code is now readable, writable and hackable. The recent escalation of genome-wide sequencing (GS) applications in population diagnostics will not only enable the assessment of risks of transmitting well-defined monogenic disorders at preconceptional stages (i.e. carrier screening), but also facilitate identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting reproductive fitness. Through GS, the acquisition and curation of reproductive-related findings will warrant the expansion of genetic assessment to new areas of genomic prediction of reproductive phenotypes, pharmacogenomics and molecular embryology, further boosting our knowledge and therapeutic tools for treating infertility and improving women’s health. OBJECTIVE AND RATIONALE In this article, we review current knowledge and potential development of preconception genome analysis aimed at detecting reproductive and individual health risks (recessive genetic disease and medically actionable secondary findings) as well as anticipating specific reproductive outcomes, particularly in the context of IVF. The extension of reproductive genetic risk assessment to the general population and IVF couples will lead to the identification of couples who carry recessive mutations, as well as sub-lethal conditions prior to conception. This approach will provide increased reproductive autonomy to couples, particularly in those cases where preimplantation genetic testing is an available option to avoid the transmission of undesirable conditions. In addition, GS on prospective infertility patients will enable genome-wide association studies specific for infertility phenotypes such as predisposition to premature ovarian failure, increased risk of aneuploidies, complete oocyte immaturity or blastocyst development failure, thus empowering the development of true reproductive precision medicine. SEARCH METHODS Searches of the literature on PubMed Central included combinations of the following MeSH terms: human, genetics, genomics, variants, male, female, fertility, next generation sequencing, genome exome sequencing, expanded carrier screening, secondary findings, pharmacogenomics, controlled ovarian stimulation, preconception, genetics, genome-wide association studies, GWAS. OUTCOMES Through PubMed Central queries, we identified a total of 1409 articles. The full list of articles was assessed for date of publication, limiting the search to studies published within the last 15 years (2004 onwards due to escalating research output of next-generation sequencing studies from that date). The remaining articles’ titles were assessed for pertinence to the topic, leaving a total of 644 articles. The use of preconception GS has the potential to identify inheritable genetic conditions concealed in the genome of around 4% of couples looking to conceive. Genomic information during reproductive age will also be useful to anticipate late-onset medically actionable conditions with strong genetic background in around 2–4% of all individuals. Genetic variants correlated with differential response to pharmaceutical treatment in IVF, and clear genotype–phenotype associations are found for aberrant sperm types, oocyte maturation, fertilization or pre- and post-implantation embryonic development. All currently known capabilities of GS at the preconception stage are reviewed along with persisting and forthcoming barriers for the implementation of precise reproductive medicine. WIDER IMPLICATIONS The expansion of sequencing analysis to additional monogenic and polygenic traits may enable the development of cost-effective preconception tests capable of identifying underlying genetic causes of infertility, which have been defined as ‘unexplained’ until now, thus leading to the development of a true personalized genomic medicine framework in reproductive health.

Progress in medical genetics has changed the practice of medicine in general and child neurology in particular. A genetic diagnosis has become critically important in determining optimal management of many neurodevelopmental disorders, making genetic testing a routine consideration of patient care in outpatient and inpatient settings. Today's child neurologists should be familiar with various genetic testing modalities and their appropriate use. Molecular genetic testing of children with unexplained developmental delays and/or congenital anomalies has a 20% to 30% chance of identifying a causative etiology. Newer methods have made genetic testing more widely available and sensitive but also more likely to produce ambiguous results.

Hypertrophic cardiomyopathy (HCM) is the most common genetic heart disease, with a prevalence of approximately 1 in 500 among the adult cohort. It is a common etiological factor of sudden cardiac death in the young and a common cause of morbidity and mortality in all age groups. HCM is characterized by a complex pathophysiology, which is manifested by a heterogeneous clinical picture. The mechanism of development of this variant of hypertrophy is not fully understood. Currently, only a part of the genetic mutations that correlate with the development of this pathology has been identified. In this regard, the issue of genetic diagnosis of HCM is very relevant, as it will allow us to conduct advanced screening. A very important task is to develop a personalized approach in the conservative and surgical treatment of people suffering from this variant of cardiopathy.

The precise genetic diagnosis of dystrophinopathies can be challenging, largely due to rare deep intronic variants and more complex structural variants (SVs). We report on the genetic characterization of a dystrophinopathy patient. He remained without a genetic diagnosis after routine genetic testing, dystrophin protein and mRNA analysis, and short‐ and long‐read whole DMD gene sequencing. We finally identified a novel complex SV in DMD via long‐read whole‐genome sequencing. The variant consists of a large‐scale (~1Mb) inversion/deletion‐insertion rearrangement mediated by LINE‐1s. Our study shows that long‐read whole‐genome sequencing can serve as a clinical diagnostic tool for genetically unsolved dystrophinopathies.

Spondylo-ocular syndrome (SOS) is a rare autosomal recessive disorder and affects primarily ocular and spinal tissues. This case report presented an Omani child with a novel homozygous variant, c.2070 G > A (p.Trp690Ter) in XYLT2 associated with SOS for the first time. Oman and other Middle East countries have a high consanguine marriage rate. Our case report will increase knowledge of SOS syndrome to be able to provide genetic diagnosis and counseling for other family members and families as well as prenatal diagnostics for the future pregnancies.

Purpose: Glaucoma, the most prevalent cause of irreversible blindness across the world, is progressive optic nerve degeneration and affection (neuropathy) caused by a mixture of both genetic and environmental factors [1]. The extracellular matrix (ECM) structure of the trabecular Meshwork TM has a major role in intraocular pressure IOP control. Transforming growth factor beta (TGF-β) is a growth factor that plays major roles in cellular functions, including encouraging extracellular matrix synthesis and vascular angiogenesis. TGFβ2 treatment of TM cells alters ECM components [8] and induces ECM bonds. Aim of the Study: To study the relationship between family history and glaucoma according to genotype and genetic polymorphism. Methods: Blood collection and DNA extraction Genotyping: TGFB2 Rs99196 genotyping was done using TaqMan SNP genotyping Assay (ID C___8853564_10). StepOne real time PCR system (Applied Biosystem, Ca, USA) was used for amplifiction. Statistical Analysis: The sample size of the study group was calculated using a program at (www.openepi.com/SampleSize/ SSCC.htm). Results: Important genotype differences frequencies were detected between the positive family history and negative family history groups for the codominant, dominant, recessive and overdominant inheritance models. Conclusion: This study recommends that other polymorphisms of genes associated with glaucoma and the analysis of these gene products and their relationship with disease risk factors should be more studied.

Café au lait spots are common birthmarks seen sporadically and in association with several genetic syndromes. Dermatologists are often asked to evaluate these birthmarks both by other physicians and by parents. In some cases, it is challenging to know when and how to pursue further evaluation. Diagnostic challenges may come in the form of the appearance of the individual lesions, areas and patterns of cutaneous involvement, and associated features (or lack thereof). In this review, we aim to clarify when and how to evaluate the child with multiple or patterned café au lait spots and to explain some emerging concepts in our understanding of the genetics of these lesions.