Comprehensive Molecular Diagnosis Research Articles

Glioma subtype prediction based on radiomics of tumor and peritumoral edema under automatic segmentation

Comprehensive and non-invasive preoperative molecular diagnosis is important for prognostic and therapy decision-making in adult-type diffuse gliomas. We employed a deep learning method for automatic segmentation of brain gliomas directly from conventional magnetic resonance imaging (MRI) scans of the tumor core and peritumoral edema regions based on available glioma MRI data provided in the BraTS2021. Three-dimensional volumes of interest were segmented from 424 cases of glioma imaging data retrospectively obtained from two medical centers using the segmentation method and radiomic features were extracted. We developed a subtype prediction model based on extracted radiomic features and analyzed significance and correlations between glioma morphological characteristics and pathological features using data from patients with adult-type diffuse glioma. The automated segmentation achieved mean Dice scores of 0.884 and 0.889 for the tumor core and whole tumor, respectively. The area under the receiver operating characteristic curve for the prediction of adult-type diffuse gliomas subtypes was 0.945. “Glioblastoma, IDH-wildtype”, “Astrocytoma, IDH-mutant”, and “Oligodendroglioma, IDH-mutant, 1p/19q-coded” showed AUCs of 0.96, 0.914, and 0.961, respectively, for subtype prediction. Glioma morphological characteristics, molecular and pathological levels, and clinical data showed significant differences and correlations. An automatic segmentation model for gliomas based on 3D U-Nets was developed, and the prediction model for gliomas built using the parameters obtained from the automatic segmentation model showed high overall performance.

NANOPORE-BASED INTRA-OPERATIVE CLASSIfiCATION OF CENTRAL NERVOUS SYSTEM TUMOURS IN THE NHS

Abstract AIMS The 2021 WHO classification of CNS tumours necessitates the use of molecular testing in order to reach a confident diagnosis of many tumour types. At present, this is achieved using array-based technology delivered by a centralised model. This approach has inherent delays that mean it is often several weeks before the treating clinical team is informed of diagnosis, delaying the start of adjuvant therapy and causing significant distress for patients. As such, there is an urgent need to rethink this pathway and improve time to diagnosis. Nanopore longread sequencing technology has the potential to enable a paradigm shift in diagnostic and therapeutic pathways, offering rapid, comprehensive molecular diagnosis that can be performed in the intra-operative setting. We aimed to test the hypothesis that intra-operative methylation-based classification can be performed using nanopore sequencing and thereby expediently inform surgical and oncological decision-making. METHOD Oxford Nanopore Technology (ONT) is a native-strand, long-read sequencing platform that can perform copy- number profiling along with parallel single-gene methylation, structural variant, mutational and methylation analyses. Capital and consumable costs are relatively low, and testing can be performed in the local setting on single samples. We have optimised DNA extraction and library preparation for rapid tissue processing. We have developed a robust bioinformatic pipeline which is able to produce intraoperative classification within minutes of sequencing and full molecular profiling after 24 hours. RESULTS We demonstrate the feasibility of using ONT to deliver intra-operative methylation-based classification of CNS tumours in ‘realtime’ within an NHS hospital setting and will discuss the challenges of implementing this testing and the opportunities to inform neuro-oncological practice. CONCLUSION By giving a summary of our novel protocol of rapid DNA extraction, library preparation and bioinformatic analysis, we will show that this approach can revolutionise the diagnosis of brain tumours and has the potential for rapid adoption by non-expert laboratories.

INTEGRIN BETA2 GENE VARIANT CAUSING LEUKOCYTE ADHESION DEFICIENCY TYPE 1 IN A PAKISTANI FAMILY

Background: Leukocyte adhesion deficiency type 1 (LAD1), an autosomal recessive condition, arises from partial or complete deficiency of CD18 expression. LAD1 patients commonly manifest recurrent skin and respiratory tract infections, delayed umbilical cord separation, and impaired wound healing due to hindered leukocyte migration. This study aims to clinically and molecularly diagnose LAD in a highly consanguineous Pakistani family, investigating a recurrent mutation within the integrin ?2 (ITGB2) gene. Methods: A comprehensive clinical and molecular diagnosis of LAD1 was made in on a patient from a consanguineous Pakistani family. Lymphocyte subset analysis was performed using a flow cytometer, followed by whole exome sequencing and DNA Sanger sequencing to identify the pathogenic mutation within the ITGB2 gene. Further to provide genetic counselling all the healthy siblings were also Sanger sequenced. Results: Flow cytometry indicated CD18 deficiency, while sequencing of the ITGB2 gene unveiled a nonsense mutation, c.186C>A, p. (Cys62*), located in exon four. This mutation segregates in an autosomal recessive pattern within the family. Conclusion: A mutation c.186C>A (Cys62*) in a patient of LAD1 was identified which is potentially pathogenic in nature. Pak J Physiol 2024;20(1):15-8

Molecular Identification of Escherichia coli Pathotypes and their Antimicrobial Resistance Profiles in Stool Samples Isolated from Patients in the West of Iran.

Gastroenteritis refers to an infection in the stomach and small intestine that may be caused by bacteria, viruses, and other pathogenic agents. Most strains of Escherichia coli (E. coli) in the gastrointestinal system have shared a symbiotic relationship with humans, but some serotypes are pathogenic. This study aimed to identify E. coli pathotypes isolated from stool samples and determine the antibiotic resistance profiles of these pathotypes in the west of Iran. The study was conducted on 106 samples of diarrheal feces which were sent to Imam Reza laboratory. First E. coli was detected and then the DNA was extracted. Next, the antibiotic sensitivity test was performed by the disk diffusion method. The E. coli pathotypes were qualitatively detected using the Amplisense Escherichioses-FRT PCR kit after DNA extraction from E. coli isolated in the stool sample. In this study, out of 106 E. coli-positive samples, pathogenic E. coli were detected in 62 samples including 5 samples (8.1%) which only contained the EPEC pathotype, 10 samples (16.1%) contained only the EAEC pathotype, and 12 samples (19.4%) had only the EHEC pathotype. ETEC and EIEC were not isolated from any of the samples. The sensitivity to Meropenem (97%) and Gentamicin (96.2%) showed the highest frequency among the samples. The highest level of resistance was related to Amoxicillin (93.4%) and Ampicillin (78%). The epidemiological results show that the predominant pathotype among all isolates is EHEC and most antibiotic resistances were related to Amoxicillin and Ampicillin. Finally, a comprehensive molecular diagnosis of E. coli pathotypes, investigation of their incidence, and antibiogram profiles will help to determine better diagnostic and therapeutic measures for managing diarrheal diseases.

Whole exome sequencing identifies novel pathogenic variants in TGM1 and ALOX12B in patients with hereditary ichthyosis.

Hereditary ichthyosis is a clinically and genetically heterogeneous disorder associated with more than 50 genes with TGM1, ALOX12B, and ALOXE3 being the most prevalent. Establishing an accurate diagnosis is important for effective genetic counseling and optimal patient management. We studied the diagnostic value of whole exome sequencing (WES) in a small case series with hereditary ichthyosis. During a 1-year period, index cases of 5 unrelated families clinically diagnosed with hereditary ichthyosis went through WES, followed by extensive segregation analysis. Prenatal diagnosis (PND) was conducted where indicated. We identified 4 homozygous variants-2 in TGM1 (c.655A>G and c.797A>G) and 2 in ALOX12B (c.527+2T>G and c.1654G>T)-alongside a heterozygous variant in TGM1 (c.428G>A) in 5 families. The variants were all pathogenic/likely pathogenic according to the ACMG classification and segregation analysis, except for c.797A>G in TGM1 which remained a variant of unknown clinical significance. Four variants were novel. All families were referred either during pregnancy or before reproductive planning; 4 benefited from WES as it identified the mutation in the probands and enabled carrier detection in at-risk relatives; PND was conducted in 2 families. Our findings further support WES is a powerful tool for the comprehensive, accurate, and rapid molecular diagnosis of hereditary ichthyosis and can offer opportunities for reproductive planning, carrier screening and prenatal diagnosis to at-risk families.

Noninvasive detection of microsatellite instability in patients with endometrial cancer.

The analysis of mismatch repair proteins in solid tissue is the standard of care (SoC) for the microsatellite instability (MSI) characterization in endometrial cancer (EC). Uterine aspirates (UAs) or circulating-DNA (cfDNA) samples capture the intratumor heterogeneity and provide a more comprehensive and dynamic molecular diagnosis. Thus, MSI analysis by droplet-digital PCR (ddPCR) in UAs and cfDNA can provide a reliable tool to characterize and follow-up the disease. The UAs, paraffin-embedded tumor tissue (FFPE) and longitudinal plasma samples from a cohort of 90 EC patients were analyzed using ddPCR panel and compared to the SoC. A high concordance (96.67%) was obtained between the analysis of MSI markers in UAs and the SoC. Three discordant cases were validated as unstable by ddPCR on FFPE samples. Besides, a good overall concordance (70.27%) was obtained when comparing the performance of the ddPCR assay on UAs and cfDNA in high-risk tumors. Importantly, our results also evidenced the value of MSI analysis to monitor the disease evolution. MSI evaluation in minimally invasive samples shows great accuracy and sensitivity and provides a valuable tool for the molecular characterization and follow-up of endometrial tumors, opening new opportunities for personalized management of EC.

P042: A next generation sequencing strategy for a comprehensive molecular diagnosis in chronic lymphocytic leukemia: Mexican experience

P042: A next generation sequencing strategy for a comprehensive molecular diagnosis in chronic lymphocytic leukemia: Mexican experience

Missing heritability of Wilson disease: a search for the uncharacterized mutations.

Wilson disease (WD), a copper metabolism disorder caused by mutations in ATP7B, manifests heterogeneous clinical features. Interestingly, in a fraction of clinically diagnosed WD patients, mutations in ATP7B appears to be missing. In this review we discuss the plausible explanations of this missing heritability and propose a workflow that can identify the hidden mutations. Mutation analyses of WD generally includes targeted sequencing of ATP7B exons, exon-intron boundaries, and rarely, the proximal promoter region. We propose that variants in the distal cis-regulatory elements and/or deep intronic variants that impact splicing might well represent the hidden mutations. Heterozygous del/ins that remain refractory to conventional PCR-sequencing method may also represent such mutations. In this review, we also hypothesize that mutations in the key copper metabolism genes, like, ATOX1, COMMD1, and SLC31A1, could possibly lead to a WD-like phenotype. In fact, WD does present overlapping symptoms with other rare genetic disorders; hence, the possibility of a misdiagnosis and thus adding to missing heritability cannot be excluded. In this regard, it seems that whole-genome analysis will provide a comprehensive and rapid molecular diagnosis of WD. However, considering the associated cost for such a strategy, we propose an alternative customized screening schema of WD which include targeted sequencing of ATP7B locus as well as other key copper metabolism genes. Success of such a schema has been tested in a pilot study.

Laser-induced assembly of Au nano-polyhedron clusters as stable 3D superstructures with ultrabroadband plasmonic resonance for promoting multi-band SERS

Multi-band surface-enhanced Raman spectroscopy (SERS) via multiple excitation wavelengths operated on broadband resonant substrate can empower a high-dimensional comprehensive molecular diagnosis of complex analytes. Herein, we demonstrate an extraordinary multi-resonant SERS active substrate that is composed of three-dimensional (3D) hierarchical plasmonic Au superstructures (SS) with both horizontal and vertical close-packed nano-polyhedron clusters on fluorine-doped tin oxide-coated (FTO) support. The stable solid-state Au SS can be simplistically developed by ultraviolet laser irradiation of FTO plate in HAuCl4 solution that facilitates photoexcited reduction of Au ions and then anisotropic nucleation of Au atoms. The 3D Au SS with ultrabroadband plasmonic resonance ranging from visible light to near-infrared region (400∼2000nm) provide remarkable enhanced multi-band SERS performances under 532, 633 and 785 nm excitation wavelengths, in comparison with the reference normal Au nanoparticles (NPs). Especially, the 785 nm NIR excitation of the generated SERS substrate enables the ultra-low detection limit of crystal violet (CV) molecules to be achieved as low as 10−16 M, which is obviously better than many previous works. The ultrahigh multi-band SERS activity is highly related the strong synergetic coupling effects of these interconnected Au nano-polyhedrons with hybridized multiple plasmonic modes. Besides, the ingenious Au configuration also possesses excellent SERS spatial uniformity, long-term stability and reproducibility, having more promising potentials for practical operation. Therefore, the versatile 3D plasmonic SS may grant attractive alternative pathway toward robust multi-band SERS analyses in the near future.

A stepwise haematological screening and whole-exome sequencing reveal multiple mutations from SUPT5H causing an elevation of Hb A2 from a cohort of 47336 individuals.

Though an increase in Hb A2 is one of the most key markers of β-thal carriers, a few independent cases are reported to show elevated Hb A2 levels caused by mutations in other genes beyond β-globin gene. We reviewed the haematological indices of 47336 individuals to analyse the phenotype-genotype correlation and identified 1439 individuals (3.04%) positive in the elevation of Hb A2 . Globin and KLF1 genes analysis was performed, and further whole-exome sequencing was carried to dissect the genetic causes of those positive samples without β-thalassemic or KLF1 mutations. Of these 1439 individuals with elevated Hb A2 , 1381 had a molecular defect in globin genes, and most were β-thalassemic mutation; 10 had a molecular defect in KLF1 gene. Finally, among the 38 individuals without β-thalassemic or KLF1 mutations, 7 were identified to carried a loss-of-function mutation in SUPT5H. This study has provided a mutation spectrum of SUPT5H in a cohort screening leading to the elevation of Hb A2 . According to the previous observations that individuals with a combination of β-thal mutation and a SUPT5H variant might present moderate β-thaelassemia, these findings emphasized the importance of comprehensive molecular diagnosis to prevent birth defects of β-thaelassemia caused by rare mutations from modifier genes.

Comprehensive Molecular Analysis of DMD Gene Increases the Diagnostic Value of Dystrophinopathies: A Pilot Study in a Southern Italy Cohort of Patients.

Duchenne/Becker muscular dystrophy (DMD/BMD) is an X-linked neuromuscular disease due to pathogenic sequence variations in the dystrophin (DMD) gene, one of the largest human genes. More than 70% of DMD gene defects result from genomic rearrangements principally leading to large deletions, while the remaining are small nucleotide variants, including nonsense and missense variants, small insertions/deletions or splicing alterations. Considering the large size of the gene and the wide mutational spectrum, the comprehensive molecular diagnosis of DMD/BMD is complex and may require several laboratory methods, thus increasing the time and costs of the analysis. In an attempt to simplify DMD/BMD molecular diagnosis workflow, we tested an NGS method suitable for the detection of all the different types of genomic variations that may affect the DMD gene. Forty previously analyzed patients were enrolled in this study and re-analyzed using the next generation sequencing (NGS)-based single-step procedure. The NGS results were compared with those from multiplex ligation-dependent probe amplification (MLPA)/multiplex PCR and/or Sanger sequencing. Most of the previously identified deleted/duplicated exons and point mutations were confirmed by NGS and 1 more pathogenic point mutation (a nonsense variant) was identified. Our results show that this NGS-based strategy overcomes limitations of traditionally used methods and is easily transferable to routine diagnostic procedures, thereby increasing the diagnostic power of DMD molecular analysis.

A comprehensive molecular study identified 12 complementation groups with 56 novel FANC gene variants in Indian Fanconi anemia subjects.

Fanconi anemia (FA) is a rare autosomal or X-linked genetic disorder characterized by chromosomal breakages, congenital abnormalities, bone marrow failure (BMF), and cancer. There has been a discovery of 22 FANC genes known to be involved in the FA pathway. This wide number of pathway components makes molecular diagnosis challenging for FA. We present here the most comprehensive molecular diagnosis of FA subjects from India. We observed a high frequency (4.42 ± 1.5 breaks/metaphase) of chromosomal breakages in 181 FA subjects. The major clinical abnormalities observed were skin pigmentation (70.2%), short stature (46.4%), and skeletal abnormalities (43.1%), along with a few minor clinical abnormalities. The combination of Sanger sequencing and Next Generation Sequencing could molecularly characterize 164 (90.6%) FA patients and identified 12 different complementation groups [FANCA (56.10%), FANCG (16.46%), FANCL (12.80%), FANCD2 (4.88%), FANCJ (2.44%), FANCE (1.22%), FANCF (1.22%), FANCI (1.22%), FANCN (1.22%), FANCC (1.22%), FANCD1 (0.61%) and FANCB (0.61%)]. A total of 56 novel variants were identified in our cohort, including a hotspot variant: a deletion of exon 27 in the FANCA gene and a nonsense variant at c.787 C>T in the FANCG gene. Our comprehensive molecular findings can aid in the stratification of molecular investigation in the diagnosis and management of FA patients.

Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus.

Aspergillus fumigatus is a ubiquitous fungus and the main agent of aspergillosis, a common fungal infection in the immunocompromised population. Triazoles such as itraconazole and voriconazole are the common first-line drugs for treating aspergillosis. However, triazole resistance in A. fumigatus has been reported in an increasing number of countries. While most studies of triazole resistance have focused on mutations in the triazole target gene cyp51A, >70% of triazole-resistant strains in certain populations showed no mutations in cyp51A. To identify potential non-cyp51A mutations associated with triazole resistance in A. fumigatus, we analyzed the whole genome sequences and triazole susceptibilities of 195 strains from 12 countries. These strains belonged to three distinct clades. Our genome-wide association study (GWAS) identified a total of six missense mutations significantly associated with itraconazole resistance and 18 missense mutations with voriconazole resistance. In addition, to investigate itraconazole and pan-azole resistance, Fisher’s exact tests revealed 26 additional missense variants tightly linked to the top 20 SNPs obtained by GWAS, of which two were consistently associated with triazole resistance. The large number of novel mutations related to triazole resistance should help further investigations into their molecular mechanisms, their clinical importance, and the development of a comprehensive molecular diagnosis toolbox for triazole resistance in A. fumigatus.

A next-generation sequencing-based strategy combining microsatellite instability and tumor mutation burden for comprehensive molecular diagnosis of advanced colorectal cancer

BackgroundMismatch repair (MMR)/microsatellite instability (MSI) and tumor mutational burden (TMB) are independent biomarkers that complement each other for predicting immune checkpoint inhibitors (ICIs) efficacy. Here we aim to establish a strategy that integrates MSI and TMB determination for colorectal cancer (CRC) in one single assay.MethodsSurgical or biopsy specimens retrospectively collected from CRC patients were subjected to NGS analysis. Immunohistochemistry (IHC) and polymerase chain reaction (PCR) were also used to determine MMR/MSI for those having enough tissues. The NGS-MSI method was validated against IHC and PCR. The MSI-high (MSI-H) or microsatellite stable (MSS) groups were further stratified based on tumor mutational burden, followed by validation using the The Cancer Genome Atlas (TCGA) CRC dataset. Immune microenvironment was evaluated for each subgroup be profiling the expression of immune signatures.ResultsTissues from 430 CRC patients were analyzed using a 381-gene NGS panel. Alterations in KRAS, NRAS, BRAF, and HER2 occurred at a significantly higher incidence among MSI-H tumors than in MSS patients (83.6% vs. 58.4%, p = 0.0003). A subset comprising 98 tumors were tested for MSI/MMR using all three techniques, where NGS proved to be 99.0 and 93.9% concordant with PCR and IHC, respectively. Four of the 7 IHC-PCR discordant cases had low TMB (1.1–8.1 muts/Mb) and were confirmed to have been misdiagnosed by IHC. Intriguingly, 4 of the 66 MSS tumors (as determined by NGS) were defined as TMB-high (TMB-H) using a cut-off of 29 mut/Mb. Likewise, 15 of the 456 MSS tumors in the TCGA CRC cohort were also TMB-H with a cut-off of 9 muts/Mb. Expression of immune signatures across subgroups (MSS-TMB-H, MSI-H-TMB-H, and MSS-TMB-L) confirmed that the microenvironment of the MSS-TMB-H tumors was similar to that of the MSI-H-TMB-H tumors, but significantly more immune-responsive than that of the MSS-TMB-L tumors, indicating that MSI combined with TMB may be more precise than MSI alone for immune microenvironment prediction.ConclusionThis study demonstrated that NGS panel-based method is both robust and tissue-efficient for comprehensive molecular diagnosis of CRC. It also underscores the importance of combining MSI and TMB information for discerning patients with different microenvironment.

Dual diagnosis of osteogenesis imperfecta (OI) and short stature and advanced bone age with or without early-onset osteoarthritis and/or osteochondritis dissecans (SSOAOD) reveals a cumulative effect on stature caused by mutations in COL1A1 and ACAN genes

Short stature is a feature when a person's height is more than 2 SDS below the corresponding mean height for a given age, gender and population. It can be influenced by many factors essential to growth plate. Here we report a three-generation family with 13 patients affected by osteogenesis imperfecta (OI) type I, short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans (SSOAOD) or both. Panel sequencing of the proband revealed mutations in two extracellular matrix related genes: COL1A1 and ACAN. When comparing the quantitative trait, height within the family of different mutation carrier groups, we found an interesting cumulative effect, the ones with both mutations manifest shortest stature. Dual diagnoses of the family also suggest the necessity of a comprehensive molecular diagnosis method, such as panel/exome sequencing, especially encountering patients with novel phenotype or extreme trait.

Six molecular patterns leading to hemophilia A phenotype in 18 females from Poland

IntroductionFemale hemophilia is an intriguing rare disorder and few larger reports on its genetic etiology are available. While historically the diagnosis was satisfactorily reached by factor VIII activity assays, the clinical and potentially therapeutic heterogeneity of female hemophilia calls for comprehensive molecular diagnosis in each case. Currently, the genetic investigations are not a part of routine, state-funded, diagnostics in Poland, and thus molecular epidemiological data are missing. AimWe set out to perform a comprehensive genetic analysis of Polish females with hemophilia A. Patients/methodsEighteen females with hemophilia A (including 2 with severe and 5 with moderate hemophilia phenotype) consented for genetic diagnostics. To establish F8 mutations, we used next-generation sequencing of a panel of genes associated with hematological disorders, standard assays for recurrent intragenic F8 inversions and MLPA when deletions were suspected. When appropriate we also used karyotyping, genomic microarrays and X chromosome inactivation assays. ResultsWhile abnormally skewed X-chromosome inactivation combined with a F8 variant on the active allele was, as expected, the most common genetic etiology, a number of other genetic scenarios were unraveled. This included: misdiagnosis (molecular diagnosis of vWd), Turner syndrome, compound heterozygosity and androgen insensitivity syndrome (a phenotypical 46,XY female with a novel androgen receptor gene mutation). We report 3 novel F8 mutations. ConclusionEvery case of female hemophilia warrants full genomic diagnostics, as this may change the diagnosis or reveal broader morbidity than a coagulation disorder (Turner syndrome, androgen insensitivity, or cardiovascular morbidity that we described previously in a SHAM syndrome carrier).

Usefulness of Two Independent DNA and RNA Tissue-Based Multiplex Assays for the Routine Care of Advanced NSCLC Patients.

Personalized medicine is nowadays a paradigm in lung cancer management, offering important benefits to patients. This study aimed to test the feasibility and utility of embedding two multiplexed genomic platforms as the routine workup of advanced non-squamous non-small cell lung cancer (NSCLC) patients. Two parallel multiplexed approaches were performed based on DNA sequencing and direct digital detection of RNA with nCounter® technology to evaluate gene mutations and fusions. The results were used to guide genotype-directed therapies and patient outcomes were collected. A total of 224 advanced non-squamous NSCLC patients were prospectively included in the study. Overall, 85% of samples were successfully characterized at DNA and RNA levels and oncogenic drivers were found in 68% of patients, with KRAS, EGFR, METΔex14, BRAF, and ALK being the most frequent (31%, 19%, 5%, 4%, and 4%, respectively). Among all patients with complete genotyping results and follow-up data (n = 156), the median overall survival (OS) was 1.90 years (confidence interval (CI) 95% 1.69–2.10) for individuals harbouring an actionable driver treated with a matched therapy, compared with 0.59 years (CI 95% 0.39–0.79) in those not eligible for any targeted therapy and 0.61 years (CI 95% 0.12–1.10) in patients with no drivers identified (p < 0.001). Integrating DNA and RNA multiplexing technologies into the routine molecular testing of advanced NSCLC patients is feasible and useful and highlights the necessity of widespread integrating comprehensive molecular diagnosis into lung cancer care.

The impact of exome sequencing on the diagnostic yield of muscular dystrophies in consanguineous families.

Muscular dystrophies (MDs) are a heterogeneous group of inherited disorders that are characterized by progressive skeletal muscle weakness and dystrophic changes on muscle biopsy. The broad genetic and clinical heterogeneity of MDs make the accurate diagnosis difficult via conventional approaches. This study investigated 23 patients from eight unrelated consanguineous families with MDs. Previous clinical assessments did not accurately clarify the type of their MD and/or misdiagnose them with another disease. Exome sequencing (ES) is an efficient, time-saving, and cost-effective tool, enabling disease-causing variant (DCV) detection in affected individuals. We investigated the use of ES to diagnose MD and discover the underlying genetic etiology. We achieved a remarkable diagnostic success rate of 87.5% (7 out of 8 families) which is the highest rate reported thus far compared to previous studies. We identified two novel pathogenic variants in DYSF gene (c.4179delG, c.1149+3G>C). The latter variant impacts the splicing machinery of DYSF mRNA. Moreover, we further assessed the pathogenicity of four recurrent variants ((DYSF, c.4076T>C), (GMPPB, c.458C>T), (SGCA, c.739G>A) (TTN, c.7331G>A), designated their neurological impact and added new phenotypes in patients with these variants. To our knowledge, this is the first study applying an ES-based comprehensive molecular diagnosis to Jordanian cohort with MDs. Our findings confirmed that ES is a powerful approach for the diagnosis of MD patients. This efficient method of molecular diagnosis is crucial for guiding patient clinical care, genetic counseling, and most importantly, paving the way for gene therapy which is currently in clinical trials.

Novel de novo interstitial deletion in 2q36.1q36.3 causes syndromic hearing loss and further delineation of the 2q36 deletion syndrome

Background: Deletions of the interstitial 2q36 are uncommon and associated with varying phenotypes. However, the list of currently known phenotypes is still far complete for an understanding of the interstitial 2q36 deletion syndrome characteristics.Aims/Objectives: To identify the genetic and clinical characterization of a 6-year-old male patient suffering from a severe form of syndromic hearing loss, with brachydactyly family history.Material and Methods: We performed conventional cytogenetic analysis on the peripheral blood lymphocytes and whole exome sequencing and SNP array analysis on DNA samples from the family.Results: The proband showed signs such as bilateral sensorineural deafness, ocular hypertelorism, flat facial profile and several decayed teeth, slightly ulnar deviation of the hands, single transverse palmar crease, short stature and intellectual disability. Through cytogenetic and molecular genetic analysis, we discovered that the syndromic hearing loss was the result of a de novo 5.175-Mb microdeletion at chromosome 2q36.1q36.3 whose breakpoints had been precisely mapped by us.Conclusions and Significance: Our study warns that auditory assessment should be evaluated even if the patient with 2q36 deletion syndrome is not obviously presenting hearing loss. In addition, a comprehensive molecular genetics diagnosis involving multiple methods is important to support accurate genetic characterization of this syndrome.

SAT-333 Genetic studies of inherited kidney diseases causing chronic kidney disease

The genetic investigation of inherited ciliopathies and cystic kidney disease is crucial as it provides valuable diagnostic information and allows screening of at-risk individuals and genetic counseling to be undertaken. The continuous growing of the number of disease causative genes is making-routine clinical diagnosis through next-generation sequencing technologies is consistent in routine clinical diagnosis. A comprehensive diagnosis panel targeting 49 genes associated with cystic kidney disease and ciliopathy syndromes were designed and validated using Agilent SureDesign tool. The captured and indexed libraries were prepared using HaloPlex HS Target Enrichment System and sequenced as a multiplex of 12 samples on an IlluminaMiSeq sequencer in 250 bp paired-end mode. The panel was efficient and specific at covering the candidate genes and providing rapid and accurate genetic diagnosis. Moreover, it was sensitive at detecting different types of mutations including missense, nonsense, small INDELS and whole gene deletion. A total of 11 unreported pathogenic mutations suspected as the causative genetic aetiology were detected by the NGS in the PKD1, PKHD1, SDCCAG8, WDR19, NPHP1, NPHP3 and NPHP4genes. All suspected pathogenic mutations were validated by Sanger sequence. Overall, using this customized targeted NGS resulted in a comprehensive molecular genetics diagnosis in 34/45 patients (75.6%). Tabled 1Cystic kidney diseases and the associated genes included in the panelDisease GroupDisease NameOMIM No.MOICharacteristic fearturesGene symbol(s)Cystic CiliopathiesADPKD (Type 1 & 2)#601313, #173910ADpolycystic kidneys, liver cysts, brain aneurysms, CKDPKD1, PKD2ARPKD#263200ARpolycystic kidneys, liver fibrosis, CKDPKHD1Nephronophthisis types 1-9#256100ARpolyuria, polydipsia, anemia, CKDNPHP1-NPHP9Medullary cystic kidney disease#174000ADAdult onset CKD, hyperuricemiaUMOD, MUC1Meckel-Gruber syndrome (MKS)#249000 #607361ARPolycystic kidneys, multiple organ dysplasia, perinatal lethalMKS1, MKKS, CC2D2ABardet-Biedl syndrome types 1–12#209900ARRetinitis pigmentosa, polydactyly, MR, hypogenitalism and obesity, rarely cause CKDBBS1-BBS12, ARL6Polycystic liver disease#174050ADMultiple fluid-filled cysts throughout the liver, cysts of biliary epithelial origin, renal cysts, few (in some patients)PRKCSH, SEC63Renal cysts and diabetes syndrome# 137920ADcongenital anomalies of the kidney and urinary tract (CAKUT), chronic renal failure, structural kidney abnormalities, unilateral kidney agenesis, renal cystsHNF1BOther cystic kidney disease#601331,ADRenal dysplasiaBICC1#213300ARJoubert syndromeAHI1, CEP290, TMEM67, TTC21B, RPGRIP1L# 267430ARRenal tubular dysgenesisREN Open table in a new tab Tabled 1Clinical diagnosisMean age (Y/M) (range)M/FTotalGenetic etiologyNo genetic etiologyPercentage of GeneticADPKD40.2 (7 -55 Y)7/61311285%ARPKD9.2 (2M -28Y)6/1016160100%Nephronophthisis (NPHP)6.3 (0- 13Y)2/8116555%Meckel Gruber syndrome5.3 (3-10M)2/131233%Joubert syndrome1/01010%BBS1/01010% Open table in a new tab The high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad NGS-based testing for patients with suspected inherited kidney disease.