Unknown Clinical Significance Research Articles

Sequence variants identification at the KCNQ1OT1:TSS differentially Methylated region in isolated omphalocele cases

BackgroundOmphalocele is a congenital midline ventral body wall defect that can exist as isolated malformation or as part of a syndrome. It can be considered one of the major and most frequent clinical manifestation of Beckwith-Wiedemann Syndrome (BWS) in case of loss of methylation at KCNQ1OT1: Transcription Star Site-Differentially Methylated Region (TSS-DMR) or in presence of CDKN1C mutations. The isolated form of the omphalocele accounts approximately for about the 14% of the total cases and its molecular etiology has never been fully elucidated.MethodsGiven the tight relationship with BWS, we hypothesized that the isolated form of the omphalocele could belong to the heterogeneous spectrum of the BWS associated features, representing an endophenotype with a clear genetic connection. We therefore investigated genetic and epigenetic changes affecting BWS imprinted locus at 11p15.5 imprinted region, focusing in particular on the KCNQ1OT1:TSS DMR.ResultsWe studied 21 cases of isolated omphalocele detected during pregnancy or at birth and identified the following rare maternally inherited variants: i) the non-coding variant G > A at nucleotide 687 (NR_002728.3) at KCNQ1OT1:TSS-DMR, which alters the methylation pattern of the imprinted allele, in one patient; ii) the deletion c.624-629delGGCCCC at exon 1 of CDKN1C, with unknown clinical significance, in two unrelated cases.ConclusionsTaken together, these findings suggest that KCNQ1OT1:TSS-DMR could be a susceptibility locus for the isolated omphalocele.

Application of array comparative genomic hybridization analysis for fetuses with growth anomalies

To explore the genetic etiology for fetuses featuring intrauterine growth anomalies using array-based comparative genomic hybridization (aCGH). Forty-nine fetuses were enrolled in this study. Genomic DNA of the abortive tissues was analyzed with aCGH. Fourteen (28.6%) samples were found with chromosomal aberrations, which included 8 chromosomal aneuploidies and 6 micro-aberrations (4 with known clinical pathogenecity and 2 with unknown clinical significance). Numerical and structural chromosomal aberrations underlie a significant proportion of fetal growth anomalies. aCGH has provided an effective method for delineating their genetic cause.

Identification of Novel Congenital Heart Disease Candidate Genes Using Chromosome Microarray.

While the majority of patients have isolated heart disease, congenital heart disease (CHD) may be associated with other congenital anomalies or syndromes. Our institution utilizes chromosomal microarray (CMA) to identify chromosomal abnormalities, specifically copy number variations (CNVs). While CNVs have been associated with CHD, their direct impact on cardiac development remains unclear. This study sought to identify potential novel CHD candidate genes by comparing CNVs present in our institution's CHD population with those already recognized in the literature. A list of candidate genes was compiled from recent medical literature that utilized CMA. Records from neonatal cases at our institution over 10years were reviewed. Genes identified from CMAs were compared with those reported in the literature and cross-referenced with the Online Mendelian Inheritance in Man catalog. We identified 375 CNVs reported in patients with CHD. At our institution between 2005 and 2015, 307 neonates with CHD had CMA. Of these, 77 patients (25%) had CNVs containing 832 unique candidate genes. 49 patients (16%) had isolated CHD with 353 candidate genes expressed within the CNVs, many of which were previously reported. However, there were 16 unique candidate genes identified that have been expressed with heart structure of the mouse knock-out models. Our findings demonstrate a high incidence of abnormal genes identified by CMA in CHD patients, including many CNVs of "unknown clinical significance". We conclude that a portion of these CNVs (including 16 genes expressed in the heart of the mouse knock-out models) could be candidate genes involved in CHD pathogenesis.

Genetic Testing: Challenges and Changes in Testing for Hereditary Cancer Syndromes

The practice of genetic testing for hereditary cancer syndromes has changed dramatically in recent years, and patients often approach oncology nurses requesting information about genetic testing. . This article aims to explore changes in cancer genetics, the role of genetics professionals in providing comprehensive genetic care, and the implications of these new developments in genetics for oncology nurses. . A literature review was conducted and focused on articles about the updating of genetic tests with panel testing, insurance changes, alternative genetic counseling strategies, and direct-to-consumer genetic testing. . Oncology nurses play an important role in identifying and referring patients, including those who have tested negative for hereditary susceptibility genes, to genetics professionals. Genetics professionals can assist with insurance issues, interpretation of test results, clarification when a variant of unknown clinical significance is detected, and recommendations for care based on personal and family history and testing results. Oncology nurses can assist families with understanding the limitations of direct-to-consumer genetic testing.

Multiplex PCR and NGS-based identification of mRNA splicing variants: Analysis of BRCA1 splicing pattern as a model

Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals.To identify ASVs in a gene of interest, we have proposed an approach based on multiplex PCR (mPCR) amplification of all theoretically possible exon-exon junctions and subsequent characterization of size-selected and pooled mPCR products by next-generation sequencing (NGS). The efficiency of this method is illustrated by a comprehensive analysis of BRCA1 ASVs in human leukocytes, normal mammary, and adipose tissues and stable cell lines.We revealed 94 BRCA1 ASVs, including 29 variants present in all tested samples. While differences in the qualitative expression of BRCA1 ASVs among the analyzed human tissues were minor, larger differences were detected between tissue and cell line samples.Compared with other ASV analysis methods, this approach represents a highly sensitive and rapid alternative for the identification of ASVs in any gene of interest.

A Novel Missense GLA Mutation (p.G35V) Detected in Hemodialysis Screening Leads to Severe Systemic Manifestations of Fabry Disease in Men and Women

Background/Aims: Fabry disease (FD), an X-linked lysosomal storage disorder, leads to accumulation of globotriaosylceramide. Screening in dialysis patients may identify genetic variants of unknown clinical significance. We aimed to characterize the pathogenicity of a novel GLA gene mutation identified during hemodialysis screening and the histologic findings of early Fabry nephropathy. Methods: One out of 108 male hemodialysis patients screened for FD presented low α-galactosidase A activity. A novel missense mutation (p.G35V) in the GLA gene was detected. Family screening identified 11 additional cases (8 women). Clinical investigation was conducted in 10 patients (index case and 9 relatives). Pathogenicity of the new mutation was investigated by clinical and laboratory tests, cardiac and cranial magnetic resonance imaging, and kidney biopsy. Results: Cardiac manifestations were detected in most patient from both genders, such as left ventricular hypertrophy and short PR interval. White matter lesion was present in 3 women. Pulvinar lesion of the thalamus and ischemic stroke were detected in male patients. Abnormal glomerular filtration rate (GFR) and/or albuminuria were present in 5 patients (3 women). Renal biopsies (n = 7) revealed globotriaosylceramide deposits in different cell types and foot processes effacement in all patients, including women with normal albuminuria. Despite a normal GFR, tubulointerstitial fibrosis ranging from 5 to 20% was present in young women and men with normal or high albuminuria, respectively. Conclusion: The novel missense mutation p.G35V leads to severe systemic manifestations of FD in men and women. Kidney histological changes, including tubulointerstitial fibrosis, may predate albuminuria and GFR changes in adult women. Novel non-invasive markers are required for early detection of Fabry nephropathy.

BRCA1/2 missense mutations and the value of in-silico analyses

IntroductionThe clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants. MethodsWe conducted mutation analysis of BRCA1/2 in 523 index patients with suspected hereditary breast and ovarian cancer (HBOC). Classification of the genetic variants was performed according to the German Consortium (GC)-HBOC database. Additionally, all missense variants were classified by the following three in-silico prediction tools: SIFT, Mutation Taster (MT2) and PolyPhen2 (PPH2). ResultsOverall 201 different variants, 68 of which constituted missense variants were ranked as pathogenic, neutral, or unknown. The classification of missense variants by in-silico tools resulted in a higher amount of pathogenic mutations (25% vs. 13.2%) compared to the GC-HBOC-classification. Altogether, more than fifty percent (38/68, 55.9%) of missense variants were ranked differently. Sensitivity of in-silico-tools for mutation prediction was 88.9% (PPH2), 100% (SIFT) and 100% (MT2). ConclusionWe found a relevant discrepancy in variant classification by using in-silico prediction tools, resulting in potential overestimation and/or underestimation of cancer risk. More reliable, notably gene-specific, prediction tools and functional tests are needed to improve clinical counseling.

Factors affecting articular cartilage repair after open-wedge high tibial osteotomy

BackgroundTo evaluate the factors that affect articular cartilage repair after open-wedge high tibial osteotomy (OWHTO) and the relationship between regeneration of articular cartilage repair and clinical outcomes. MethodsAmong the cases of OWHTO that were performed from March 2005 to February 2012, the patients who followed up for >2years and received a second-look arthroscopy were retrospectively reviewed. For clinical evaluation, the Knee Society scores and Western Ontario and McMaster Universities Osteoarthritis Index score were measured. For radiologic evaluation, the Kellgren–Lawrence scale, mechanical femorotibial angle, and joint line obliquity were used. In the initial and second-look arthroscopy, the status of the articular cartilage of the medial compartment was evaluated. ResultsA total of 62 knees (61 patients) were included in this study. Articular cartilage repair was observed in 18 knees (29.0%). In multiple logistic regression analysis, patients with Kellgren–Lawrence Grade 4 (OR 0.076; 95% CI 0.007–0.822; P=0.034), the existence of a bipolar lesion (OR 0.108; 95% CI 0.016–0.724; P=0.022), or joint line obliquity >5° (OR 0.109; 95% CI 0.013–0.936; P=0.043) had significantly lower odds of articular cartilage repair compared to the corresponding counter group. In a comparison of clinical outcomes between a group that had articular cartilage repair and a group without repair, no significant difference was observed (P>0.05). ConclusionsSevere arthrosis, existence of a bipolar lesion, and marked postoperative joint line obliquity had a negative impact on articular cartilage repair after OWHTO. However, articular cartilage repair showed unknown clinical significance.

Sporadic Fundic Gland Polyps and Gastric Acid Suppression Level

BackgroundFundic gland polyps (FGPs) are a common endoscopic finding and are known to be associated with proton pump inhibitors (PPIs) use. It is not known if their prevalence is affected by gastric acidity levels. This study aimed to assess whether there is a correlation between FGPs and gastric acidity levels as identified on 24-hour ambulatory impedance-pH studies in patients on PPI therapy. MethodsWe performed a review of 402 consecutive patients who take at least once daily PPI and underwent esophagogastroduodenoscopy with combined impedance-pH studies in the same setting (time and place) between January 2010 and December 2014. Patients were classified into 2 groups based on the presence or absence of biopsy-confirmed FGPs during endoscopy. ResultsOf the 402 patients, 30 (7%) had FGPs. One of these polyps was found with low-grade dysplasia. There was no significant difference of the distributions of the [H+] in the FGPs versus the nonpolyp groups (P = 0.741). There was no significant difference between the 2 groups regarding PPI dose frequency regimens (once and twice) (P = 0.074). However, we found weak ordinal association with PPI duration (P = 0.01) (Spearman = 0.1). ConclusionsFGPs are common endoscopic lesions. Incidence of dysplasia in FGPs is not only rare, but also of unknown clinical significance. Although they seem to be associated with PPIs, the mechanism remains unclear, as we found no correlation between the presence of FGPs and gastric acid control or PPI dose. Future studies would be useful to elucidate an alternate mechanism.

Abstract 4275: Pathogenic germline variants in Mexican patients with hereditary breast and ovarian cancer syndrome

Abstract Hereditary breast and ovarian cancer syndrome (HBOC) is an autosomal dominant disease that represents approximately 5-10% of all patients with breast cancer. This syndrome is mainly associated to high risk pathogenic alleles in BRCA1/2 genes, but only for 25% of HBOC cases. More than 25 genes have been associated with familial breast and/or ovarian cancer and still more are expected to emerge. In the Mexican population there have been some efforts to analyze this syndrome, but they are limited to BRCA genes. This work aims to find new pathogenic alleles in exonic and splice sites in a panel of 143 cancer-predisposing genes in 309 Mexican cancer patients with suspicion of HBOC and 27 non-cancer patients with a severe family history of cancer, using massive parallel sequencing technology. In the group of cancer patients 14.6% (45/309) had pathogenic variants, 23.9% (74/309) harbored variants with unknown clinical significance (VUS) and 61.5% (109/309) were negative. The genes most frequently affected with pathogenic variants were BRCA2 24.4% (11/45), BRCA1 8.9% (4/45), MSR1 4.4% (2/45), ATM 4.4% (2/45), PDE11A 4.4% (2/45) and FANCI 4.4% (2/45). The non-cancer group had a 18.5% (5/27) of patients with pathogenic variants and 81.5% (22/27) were negative. In this group pathogenic variants were found in BRCA2, FANCF, PDE11A, POLH and WRN. Private or ultra-rare variants defined as VUS (ClinVar, deleterious in SIFT/Polyphen2, less than 0.001% in ExAC/1KG/ESP6500) were found in 53 genes. This study demonstrates that there is a higher contribution of pathogenic alleles in other susceptibility cancer genes (66.7%) than BRCA1/2 (33.3%), confirming that clinical sequencing of expanded gene panels will identify new, rare and private, variants and eventually will translate in better molecular diagnosis and personalized risk assessment in carriers. Clinical impact of the VUS identified here must be further evaluated. This work was supported by the National Autonomous University of Mexico, PAPIIT (IA204215). Citation Format: Felipe Vaca-Paniagua, Rosalía Quezada-Urban, Clara Díaz-Velásquez, Rina Gitler, Gabriela Torres-Mejia, Maria Patricia Rojo-Castillo, Max Sirota-Toporek, Andrea Figueroa-Morales, Oscar Moreno-García, Ivan Delgado-Enciso, Victor Hugo Garzón-Barrientos, Nayeli Lizbeth García-Esquivel, Ernesto Arturo Rojas-Jiménez, Héctor Gregorio-Martínez, Luis Ignacio Terrazas. Pathogenic germline variants in Mexican patients with hereditary breast and ovarian cancer syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4275. doi:10.1158/1538-7445.AM2017-4275

Next-generation sequencing for patients with non-obstructive azoospermia: implications for significant roles of monogenic/oligogenic mutations.

Azoospermia affects up to 1% of adult men. Non-obstructive azoospermia is a multifactorial disorder whose molecular basis remains largely unknown. To date, mutations in several genes and multiple submicroscopic copy-number variations (CNVs) have been identified in patients with non-obstructive azoospermia. The aim of this study was to clarify the contribution of nucleotide substitutions in known causative genes and submicroscopic CNVs in the genome to the development of non-obstructive azoospermia. To this end, we conducted sequence analysis of 25 known disease-associated genes using next-generation sequencing and genome-wide copy-number analysis using array-based comparative genomic hybridization. We studied 40 Japanese patients with idiopathic non-obstructive azoospermia. Functional significance of molecular alterations was assessed by in silico analyses. As a result, we identified four putative pathogenic mutations, four rare polymorphisms possibly associated with disease risk, and four probable neutral variants in 10 patients. These sequence alterations included a heterozygous splice site mutation in SOHLH1 and a hemizygous missense substitution in TEX11, which have been reported as causes of non-obstructive azoospermia. Copy-number analysis detected five X chromosomal or autosomal CNVs of unknown clinical significance, in addition to one known pathogenic Y chromosomal microduplication. Five patients carried multiple molecular alterations. The results indicate that monogenic and oligogenic mutations, including those in SOHLH1 and TEX11, account for more than 10% of cases of idiopathic non-obstructive azoospermia. Furthermore, this study suggests possible contributions of substitutions in various genes as well as submicroscopic CNVs on the X chromosome and autosomes to non-obstructive azoospermia, which require further validation.

Benign, Pathogenic and Copy Number Variations of Unknown Clinical Significance in Patients with Congenital Malformations and Developmental Delay.

The high frequency (3.0-5.0%) of congenital anomalies (CA) and intellectual disabilities (IDs), make them a serious problem, responsible for a high percentage (33.0%) of neonatal mortality. The genetic cause remains unclear in 40.0% of cases. Recently, molecular karyotyping has become the most powerful method for detection of pathogenic imbalances in patients with multiple CAs and IDs. This method is with high resolution and gives us the opportunity to investigate and identify candidate genes that could explain the genotype-phenotype correlations. This article describes the results from analysis of 81 patients with congenital malformations (CMs), developmental delay (DD) and ID, in which we utilized the CytoChip ISCA oligo microarray, 4 × 44 k, covering the whole genome with a resolution of 70 kb. In the selected group of patients with CAs, 280 copy number variations (CNVs) have been proven, 41 were pathogenic, 118 benign and 121 of unknown clinical significance (average number of variations 3.5). In six patients with established pathogenic variations, our data revealed eight pathogenic aberrations associated with the corresponding phenotype. The interpretation of the other CNVs was made on the basis of their frequency in the investigated group, the size of the variation, content of genes in the region and the type of the CNVs (deletion or duplication).

Testing for Noonan syndrome after increased nuchal translucency.

The aim of this study was to report the prevalence of Noonan syndrome (NS) in a cohort of fetuses that presented with increased nuchal translucency (NT) thickness in the first trimester of pregnancy. This is a retrospective chart review. (1) first trimester NT measurement ≥3mm, (2) normal karyotype by either a CVS or an amniocentesis procedure, and (3) prenatal molecular genetic testing for NS completed. Results with known pathogenic variants were considered positive, while those with variants of unknown clinical significance, or with no variants, were considered negative. A total of 804 fetuses had an NT measurement of ≥3mm, with a median NT thickness of 3.6mm. Of these, 302 had karyotyping by CVS or amniocentesis, 200 (66.23%) with normal results. Of fetuses with a normal karyotype, 39 with a median NT thickness of 4.0mm had a NS gene sequencing panel done, and 161 fetuses with a mean NT thickness of 4.3mm were not tested for NS (p=0.05). Of the 39 fetuses who were tested for NS, four (10.3%) had variants consistent with this diagnosis. In euploid fetuses, increased NT is associated with a 10% risk of NS. © 2017 John Wiley & Sons, Ltd.

Application of SNP-array technology in the genetic analysis of pediatric patients with growth retardation

To explore the value of single nucleotide polymorphism array (SNP-array) for the analysis of pediatric patients with growth retardation. One hundred eighty one children with growth retardation were enrolled. DNA was extracted from peripheral samples from the patients, and whole genome copy number variations (CNVs) were detected using Illumina Human Cyto SNP-12. All identified CNVs were further analyzed with reference to databases including ClinGen, ClinVar, DECIPHER, OMIM and DGV as well as comprehensive review of literature from PubMed to determine their pathogenicity. Forty seven patients (26%) with abnormal CNVs were detected, which included 12 known microdeletions/microduplications syndrome (26%), 10 pathogenic non-syndromic CNVs (21%), 3 numerical chromosome aberrations (6%), 3 unbalanced translocations (6%), 4 pathogenic mosaicisms (9%) and 15 cases with unknown clinical significance (32%). After excluding obvious numerical and/or structural chromosomal abnormalities, this study has detected 15 pathogenic microdeletions/microduplications sized 5 Mb or less, which may be missed by routine chromosomal karyotyping. In addition, there were 3 cases with loss of heterozygoisty (LOH) containing known or predicted imprinting genes as well as 2 cases with suspected parental consanguinity. SNP-array technology is a powerful tool for the genetic diagnosis of children with growth disorders with advantages of high resolution and improved accuracy.

Compound heterozygous KCNQ1 mutations (A300T/P535T) in a child with sudden unexplained death: Insights into possible molecular mechanisms based on protein modeling

Sudden death in a child is a devastating event with important medical implications for surviving relatives. Because it may be the first manifestation of unknown inherited cardiac disease, molecular autopsy can be helpful to determine the cause of death and identify at risk family members. The aim of the study was to perform a molecular autopsy in a seven year-old girl with sudden unexplained death, to find evidence supporting the possible pathogenicity of mutations identified in inherited cardiac disease genes, and to clinically and genetically assess first-degree relatives. DNA from the index case was extracted from umbilical cord cells stored at birth, and DNA of first-degree relatives from blood samples. Targeted sequencing was performed using a Haloplex design including 81 cardiogenes. Possible functional consequences of the mutations were analyzed using protein modeling and structural mobility analyses. The child was compound heterozygous for KCNQ1 variants p.Ala300Thr and p.Pro535Thr. Ala300Thr is known to cause long QT syndrome in the homozygous state, while Pro535Thr is novel and of unknown clinical significance. The father and sibling were Ala300Thr heterozygous, and had normal QTc intervals at rest and during exercise. The asymptomatic mother was heterozygous for Pro535Thr, and showed borderline QTc at rest, but prolonged QTc during exercise. Protein modeling predicted that Ala300Thr alters the mobility profile of the Kv7.1 tetramer and Thr535 disrupts a calmodulin-binding site, probably causing co-assembly or trafficking defects of the mutant monomer. Altogether, the evidence strongly suggests that this child was affected with a recessive form of Romano Ward syndrome.

Chromosome copy number variants in fetuses with syndromic malformations.

Chromosome copy number variants (CNVs; gains and losses of DNA sequences >1 kb) are wide-spread throughout the genome of healthy individuals. Laboratory studies show that a subset of CNVs are pathogenic, and not only can be responsible for the pathogenesis of major birth defects and cancer, but are also associated with neurodevelopmental disorders at birth. The characteristics of the pathogenic microdeletions and microduplications are important for both clinical implications and genetic counselling regarding test selection for prenatal screening and diagnosis. Unfortunately, our knowledge of the phenotypic effects of most CNV is still minimal, leading to the classification of many CNVs as "genomic imbalances of unknown clinical significance". Microdeletions and microduplications can occur in all pregnancies and the spectrum of pathogenic CNVs in fetuses with syndromic malformations is not well studied. This review summarizes our current understanding of CNVs, the common detection methods, and the characteristics of pathogenic CNVs identified in fetuses with syndromic malformations. Birth Defects Research 109:725-733, 2017. © 2017 Wiley Periodicals, Inc.

Chromosomal microarray in clinical diagnosis: a study of 337 patients with congenital anomalies and developmental delays or intellectual disability.

AimTo determine the diagnostic yield and criteria that could help to classify and interpret the copy number variations (CNVs) detected by chromosomal microarray (CMA) technique in patients with congenital and developmental abnormalities including dysmorphia, developmental delay (DD) or intellectual disability (ID), autism spectrum disorders (ASD) and congenital anomalies (CA).MethodCMA analysis was performed in 337 patients with DD/ID with or without dysmorphism, ASD, and/or CA. In 30 of 337 patients, chromosomal imbalances had previously been detected by classical cytogenetic and molecular cytogenetic methods.ResultsIn 73 of 337 patients, clinically relevant variants were detected and better characterized. Most of them were >1 Mb. Variants of unknown clinical significance (VOUS) were discovered in 35 patients. The most common VOUS size category was <300 kb (40.5%). Deletions and de novo imbalances were more frequent in pathogenic CNV than in VOUS category. CMA had a high diagnostic yield of 43/307, excluding patients previously detected by other methods.ConclusionCMA was valuable in establishing the diagnosis in a high proportion of patients. Criteria for classification and interpretation of CNVs include CNV size and type, mode of inheritance, and genotype-phenotype correlation. Agilent ISCA v2 Human Genome 8x60 K oligonucleotide microarray format proved to be reasonable resolution for clinical use, particularly in the regions that are recommended by the International Standard Cytogenomic Array (ISCA) Consortium and associated with well-established syndromes.

Copy number variation analysis of patients with intellectual disability from North-West Spain

Intellectual disability (ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In the last decade, microarray-based copy number variation (CNV) analysis has been proved as a strategy particularly useful in the discovery of loci and candidate genes associated with these phenotypes and is widely used in the clinics with a diagnostic purpose. In this study, we evaluated the usefulness of two genome-wide high density SNP microarrays -Cytogenetics Whole-Genome 2.7M SNP array (n=126 patients; Group 1) and CytoScan High-Density SNP array (n=447 patients; Group 2)- in the detection of clinically relevant CNVs in a cohort of ID patients from Galicia (NW Spain). In 159 (27.7%) patients, we detected 186 rare exonic chromosomal imbalances, that were grouped into the following classes: Clinically relevant (67/186; 36.0%), of unknown clinical significance (93/186; 50.0%) and benign (26/186; 14.0%). The 67 pathogenic CNVs were identified in 64 patients, which means an overall diagnostic yield of 11.2%. Overall, we confirmed that ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide high density SNP microarrays in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants.

Data safe havens to combine health and genomic data: benefits and challenges

ABSTRACTObjectivesData safe havens can bring together and combine a rich array of anonymised person-based data for research and policy evaluation within a secure setting. To date, the majority of available datasets have been structured micro-data derived from routine health-related records. Possibilities are opening up for the greater reuse of genomic data such as Genome Wide Association studies (GWAS) and Whole Exome/Genome Sequencing (WES or WGS). However, there are considerable challenges to be addressed if the benefits of using these data in combination with health-related data are to be realized safely.&#x0D; ApproachWe explore the benefits and challenges of using genomic datasets with health-related data, and using the Secure Anonymised Information Linkage (SAIL) system as a case study, the implications and way forward for Data Safe Havens in seeking to incorporate genomic data for use with health-related data.&#x0D; ResultsThe benefits of using GWAS, WES and WGS data in conjunction with health-related data include the potential to explore genetics at a population level and open up novel research areas. These include the ability to increasingly stratify and personalize how medical indications are detected and treated through precision medicine by understanding rare conditions and adding socioeconomic and environmental context to genomic data. Among the challenges are: data availability, computing capacity, technical solutions, legal and regulatory frameworks, public perceptions, individual privacy and organizational risk. Many of the challenges within these areas are common to person-based data in general, and often Data Safe Havens have been designed to address these. But there are also aspects of these challenges, and other challenges, specific to genomic data. These include issues due to the unknown clinical significance of genomic information now or in the future, with corresponding risks for privacy and impact on individuals.&#x0D; ConclusionGenomic data sets contain vast amounts of valuable information, some of which is currently undefined, but which may have direct bearing on individual health at some point. The use of these data in combination with health-related data has the potential to bring great benefits, better clinical trial stratification, epidemiology project design and clinical improvements. It is, therefore, essential that such data are surrounded by a properly-designed, robust governance framework including technical and procedural access controls that enable the data to be used safely.

Preliminary Screening Results of Fabry Disease in Kidney Transplantation Patients: A Single-Center Study

Fabry disease (FD) is a rare X-linked lysosomal storage disorder caused by the deficiency of alfa-galactosidase A (AGALA) and leads to progressive impairment of renal function in almost all male patients and in a significant proportion of female patients. FD is underdiagnosed or even misdiagnosed in patients undergoing kidney transplantation. We initiated a selective screening study for FD among kidney transplant patients in our center. In this study, 1095 male and female patients were included. Dried blood samples on Guthrie papers were used to analyze galactosidase A enzyme for male patients. Genetic analyses were performed in all female and male patients with low enzyme activity. In total, 648 female and 447 male patients with functioning grafts were evaluated. Among 1095 patients, 5 male patients had AGALA activity below threshold and 3 female patients had galactosidase alpha gene DNA variations. One male patient had a disease-causing mutation. The other 4 patients had polymorphisms causing low enzyme activity. All the 3 female patients had mutations that were associated with FD according to Human Gene Mutation Database (ID: CM025441). In contrast, these mutations were reported as unknown clinical significance in Clinvar (rs149391489). The patients with clinical findings suggesting FD were planned to be analyzed for Lyso Gb3. In our selective screening study, 8 variations were found among 1095 kidney transplantation patients, which needs further investigation to determine causes of FD. Clinical findings, physical examination, and family history are also necessary to evaluate the genetic changes as a mutation in this selected population.