Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature

DNA methylation; Episignature; Intellectual disabilityMetilació de l'ADN; Episignatura; Discapacitat intel·lectualMetilación del ADN; Epifirma; Discapacidad intelectualJARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22–p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22–p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22–p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost.Funding for this study is provided in part by the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-188)

Common Variable Immunodeficiency and Neurodevelopmental Delay Due to a 13Mb Deletion on Chromosome 4 Including the NFKB1 Gene: A Case Report

Chromosomal rearrangements; Primary immunodeficiencies; Syndromic immunodeficienciesReordenacions cromosòmiques; Immunodeficiències primàries; Immunodeficiències sindròmiquesReordenamientos cromosómicos; Inmunodeficiencias primarias; Inmunodeficiencias sindrómicasSyndromic immunodeficiencies are a heterogeneous group of inborn errors of immunity that can affect the development of non-immune organs and systems. The genetic basis of these immunodeficiencies is highly diverse, ranging from monogenic defects to large chromosomal aberrations. Antibody deficiency is the most prevalent immunological abnormality in patients with syndromic immunodeficiencies caused by chromosomal rearrangements, and usually manifests as a common variable immunodeficiency (CVID)-like phenotype. Here we describe a patient with a complex phenotype, including neurodevelopmental delay, dysmorphic features, malformations, and CVID (hypogammaglobulinemia, reduced pre-switch and switch memory B cells, and impaired vaccine response). Microarray-based comparative genomic hybridization (aCGH) revealed a 13-Mb deletion on chromosome 4q22.2-q24 involving 53 genes, some of which were related to the developmental manifestations in our patient. Although initially none of the affected genes could be linked to his CVID phenotype, subsequent reanalysis identified NFKB1 haploinsufficiency as the cause. This study underscores the value of periodic reanalysis of unsolved genetic studies performed with high-throughput technologies (eg, next-generation sequencing and aCGH). This is important because of the ongoing incorporation of new data establishing the relationship between genes and diseases. In the present case, NFKB1 had not been associated with human disease at the time aCGH was performed. Eight years later, reanalysis of the genes included in the chromosome 4 deletion enabled us to identify NFKB1 haploinsufficiency as the genetic cause of our patient’s CVID. In the future, other genes included in the deletion may be linked to human disease, allowing us to better define the molecular basis of our patient’s complex clinical phenotype.This study was funded by Instituto de Salud Carlos III, grants PI17/00660 and PI20/00761, cofinanced by the European Regional Development Fund (ERDF). This study was also funded by the Jeffrey Modell Foundation. This work is supported by the European Reference Network for Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases Network (ERN-RITA)

Identification of 22q11.2 deletion syndrome via newborn screening for severe combined immunodeficiency: two years’ experience in Catalonia (Spain)

22q11.2 deletion; Newborn screening; Severe combined immunodeficiencyeDeleción 22q11.2; Examen de recién nacidos; Inmunodeficiencia combinada graveSupressió 22q11.2; Cribratge de nounats; Immunodeficiència combinada greuBackground: The current scenario of newborn screening is changing as DNA studies are being included in the programs of several countries. Severe combined immunodeficiency (SCID) disorders can be detected using quantitative PCR assays to measure T-cell receptor excision circles (TRECs), a byproduct of correct T-cell development. However, in addition to SCID, other T-cell-deficient phenotypes such as 22q11.2 deletion syndrome 22q11.2 duplication syndrome, CHARGE syndrome, and trisomy 21 are detected. Methods: We present our experience with the detection of 22q11.2 deletion syndrome and 22q11.2 duplication syndrome in a series of 103,903 newborns included in the newborn screening program of Catalonia (Spain). Results: Thirty newborns tested were positive (low TREC levels) and five were found to have copy number variations at the 22q11 region (4 deletions and 1 duplication) when investigated with array comparative genomic hybridization technology and MLPA. Conclusion: Newborn screening for SCID enables detection of several conditions, such as 22q syndromes, which should be managed by prompt, proactive approaches with adequate counseling for families by a multidisciplinary team

A Novel Intragenic Duplication in the HDAC8 Gene Underlying a Case of Cornelia de Lange Syndrome

Cornelia de Lange syndrome; Genetic disorder; Intragenic duplicationSíndrome de Cornelia de Lange; Trastorno genético; Duplicación intragénicaSíndrome de Cornelia de Lange; Trastorn genètic; Duplicació intragènicaCornelia de Lange syndrome (CdLS) is a multisystemic genetic disorder characterized by distinctive facial features, growth retardation, and intellectual disability, as well as various systemic conditions. It is caused by genetic variants in genes related to the cohesin complex. Single-nucleotide variations are the best-known genetic cause of CdLS; however, copy number variants (CNVs) clearly underlie a substantial proportion of cases of the syndrome. The NIPBL gene was thought to be the locus within which clinically relevant CNVs contributed to CdLS. However, in the last few years, pathogenic CNVs have been identified in other genes such as HDAC8, RAD21, and SMC1A. Here, we studied an affected girl presenting with a classic CdLS phenotype heterozygous for a de novo ~32 kbp intragenic duplication affecting exon 10 of HDAC8. Molecular analyses revealed an alteration in the physiological splicing that included a 96 bp insertion between exons 9 and 10 of the main transcript of HDAC8. The aberrant transcript was predicted to generate a truncated protein whose accessibility to the active center was restricted, showing reduced ease of substrate entry into the mutated enzyme. Lastly, we conclude that the duplication is responsible for the patient’s phenotype, highlighting the contribution of CNVs as a molecular cause underlying CdLS.This work was supported by the Spanish Ministry of Health-ISCIII Fondo de Investigación Sanitaria (FIS) (Ref. PI19/01860, to F.J.R. and J.P.) and Diputación General de Aragón-FEDER: European Social Fund (Grupo de Referencia B32_17R/B32_20R, to J.P.). A.L.-P. is supported by a “Juan de la Cierva-Incorporación” postdoctoral grant from MICIU (Spanish Ministry of Science and Universities), M.G.-S. is supported by a Predoctoral Fellowship from the Diputación General de Aragón, and C.L.-C. is supported by a Predoctoral Fellowship from the MH-ISCIII. This work was also supported by Spanish government grants RTI2018-094434-B-I00 (MCIU/AEI/FEDER, UE) and DTS20-00024 (ISCIII) to P.G.-P., as well as funds from the European JPIAMR network “EPIC-Alliance” to P.G.-P. The computational support of the “Centro de Computación Científica CCC-UAM” is gratefully recognized. This work was also partially supported by Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias co-funded with ERDF funds, Grant No. FIS PI20/01767) to A.P. and by Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias co-funded with ERDF funds, Grant No. FIS PI18/000687 to E.F.T

Array CGH com a primera opció per al diagnòstic genètic postnatal

La citogenètica convencional detecta un 3-5% dels pacients amb retard global del desenvolupament / discapacitat intel·lectual (RGD / DI) i / o malformacions congènites (MC). L'amplificació de sondes múltiples dependents de lligació (MLPA) permet incrementar la taxa diagnòstica entre 2,4-5,8%. Actualment els arrays d'hibridació genòmica comparada (aCGH) constitueixen l'eina diagnòstica amb major rendiment en pacients amb RGD / DI, MC i trastorns de l'espectre autista (TEA). L'objectiu del present treball ha estat avaluar l'eficiència de l'ús dels aCGH com a tècnica de primera opció diagnòstica en aquestes i altres indicacions (epilèpsia, talla baixa). Per assolir aquest objectiu, s'han estudiat 1.000 pacients afectats de les patologies abans esmentades mitjançant la tècnica de aCGH, utilitzant una estratègia d'hibridació pacient versus pacient i afegint el suport de la tècnica de MLPA en el 50% dels pacients estudiats. En primer lloc es va validar la tècnica i es va escollir la plataforma d’oligoarrays. Per tal de minimitzar costos i incrementar la eficiència, es va utilitzar l’estratègia d’hibridació de pacient versus pacient amb MLPA confirmatòria i es van establir criteris de diagnòstic per optimitzar la detecció de desequilibris patogènics. Per facilitar la interpretació dels resultats es va dissenyar un programa informàtic EasyArray. Es van detectar desequilibris d'efecte patogènic en un 14% dels pacients (140 / 1.000). En funció del fenotip es van diagnosticar un 18,9% dels pacients afectats de RGD / DI; un 13,7% de les MC; un 9,75% de les patologies psiquiàtriques, 1 7,01% dels casos amb epilèpsia i un 13,3% dels pacients amb talla baixa. Dins de les MC destaquen les del sistema nerviós central amb un 14,9% i les cardiopaties congènites amb un 10,6% de diagnòstics. Dins de les patologies psiquiàtriques, destaquen els pacients amb TEA amb un 8.9% de diagnòstics. Podem concloure que la tècnica d’arrayCGH té un rendiment diagnòstic molt superior al del cariotip amb bandes G. La seva utilització com a eina diagnòstica de primera opció juntament amb el disseny d’estratègies d’hibridació no estàndards, suposa una reducció considerable de costos. Els nostres resultats demostren l'efectivitat i eficiència de la utilització de l’arrayCGH com a primera opció en el diagnòstic genètic dels pacients amb sospita de desequilibris genòmics. Tot això avala la seva inclusió dins del Sistema Nacional de Salut.Conventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay / intellectual disability (DD / ID) and / or multiple congenital Anomalies (MCA). Multiplex ligation probes Amplification (MLPA) increases diagnostic rate between 2.4 to 5.8%. Currently the array comparative genomic Hybridization (CGH) is the highest performing diagnostic tool in patients with DD / ID, MC and autism spectrum disorders. Our aim was to evaluate the efficiency of the use of aCGH as first-line test replacing the karyotype and MLPA in these and other pathological indications (epilepsy, short stature). A total of 1000 patients referred by one or more of the above mentioned disorders were analysed by aCGH using a methodology / strategy hybrid alternative patient versus patients adding support MLPA technique in 50% of patients studied. Following a validation period, an oligoarray platform was chosen. In order to minimize costs and increase efficiency, a patient versus patient hybridization strategy plus MLPA confirmation was used, and analysis criteria were set to optimise detection of pathogenic imbalances. In order to facilitate interpretation of results, a database application named Easy Array was designed. Pathogenic genomic imbalances were detected in 14% of the cases (140/1000), with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with DD / ID, 13.7% of MCAS, 9.75% of Psychiatric pathologies, 7.01% of patients with Epilepsy and 13.3% of patients with short Stature. Within the MCA, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnosis respectively. Among the Psychiatric disorders, patients with ASD accounted for 8.9% of diagnosis. We can conclude that Array-CGH provides a substantially higher diagnostic yield tan G-banded chromosomes analysis. Its use as first line test and the development of non-standard hybridization strategies reduces consumable costs considerably. Our results demonstrate the effectiveness and efficiency of the use of arrayCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System

Array CGH com a primera opció per al diagnòstic genètic postnatal

La citogenètica convencional detecta un 3-5% dels pacients amb retard global del desenvolupament / discapacitat intel·lectual (RGD / DI) i / o malformacions congènites (MC). L'amplificació de sondes múltiples dependents de lligació (MLPA) permet incrementar la taxa diagnòstica entre 2,4-5,8%. Actualment els arrays d'hibridació genòmica comparada (aCGH) constitueixen l'eina diagnòstica amb major rendiment en pacients amb RGD / DI, MC i trastorns de l'espectre autista (TEA). L'objectiu del present treball ha estat avaluar l'eficiència de l'ús dels aCGH com a tècnica de primera opció diagnòstica en aquestes i altres indicacions (epilèpsia, talla baixa). Per assolir aquest objectiu, s'han estudiat 1.000 pacients afectats de les patologies abans esmentades mitjançant la tècnica de aCGH, utilitzant una estratègia d'hibridació pacient versus pacient i afegint el suport de la tècnica de MLPA en el 50% dels pacients estudiats. En primer lloc es va validar la tècnica i es va escollir la plataforma d'oligoarrays. Per tal de minimitzar costos i incrementar la eficiència, es va utilitzar l'estratègia d'hibridació de pacient versus pacient amb MLPA confirmatòria i es van establir criteris de diagnòstic per optimitzar la detecció de desequilibris patogènics. Per facilitar la interpretació dels resultats es va dissenyar un programa informàtic EasyArray. Es van detectar desequilibris d'efecte patogènic en un 14% dels pacients (140 / 1.000). En funció del fenotip es van diagnosticar un 18,9% dels pacients afectats de RGD / DI; un 13,7% de les MC; un 9,75% de les patologies psiquiàtriques, 1 7,01% dels casos amb epilèpsia i un 13,3% dels pacients amb talla baixa. Dins de les MC destaquen les del sistema nerviós central amb un 14,9% i les cardiopaties congènites amb un 10,6% de diagnòstics. Dins de les patologies psiquiàtriques, destaquen els pacients amb TEA amb un 8.9% de diagnòstics. Podem concloure que la tècnica d'arrayCGH té un rendiment diagnòstic molt superior al del cariotip amb bandes G. La seva utilització com a eina diagnòstica de primera opció juntament amb el disseny d'estratègies d'hibridació no estàndards, suposa una reducció considerable de costos. Els nostres resultats demostren l'efectivitat i eficiència de la utilització de l'arrayCGH com a primera opció en el diagnòstic genètic dels pacients amb sospita de desequilibris genòmics. Tot això avala la seva inclusió dins del Sistema Nacional de SalutConventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay / intellectual disability (DD / ID) and / or multiple congenital Anomalies (MCA). Multiplex ligation probes Amplification (MLPA) increases diagnostic rate between 2.4 to 5.8%. Currently the array comparative genomic Hybridization (CGH) is the highest performing diagnostic tool in patients with DD / ID, MC and autism spectrum disorders. Our aim was to evaluate the efficiency of the use of aCGH as first-line test replacing the karyotype and MLPA in these and other pathological indications (epilepsy, short stature). A total of 1000 patients referred by one or more of the above mentioned disorders were analysed by aCGH using a methodology / strategy hybrid alternative patient versus patients adding support MLPA technique in 50% of patients studied. Following a validation period, an oligoarray platform was chosen. In order to minimize costs and increase efficiency, a patient versus patient hybridization strategy plus MLPA confirmation was used, and analysis criteria were set to optimise detection of pathogenic imbalances. In order to facilitate interpretation of results, a database application named Easy Array was designed. Pathogenic genomic imbalances were detected in 14% of the cases (140/1000), with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with DD / ID, 13.7% of MCAS, 9.75% of Psychiatric pathologies, 7.01% of patients with Epilepsy and 13.3% of patients with short Stature. Within the MCA, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnosis respectively. Among the Psychiatric disorders, patients with ASD accounted for 8.9% of diagnosis. We can conclude that Array-CGH provides a substantially higher diagnostic yield tan G-banded chromosomes analysis. Its use as first line test and the development of non-standard hybridization strategies reduces consumable costs considerably. Our results demonstrate the effectiveness and efficiency of the use of arrayCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System