Chromosome Xp11 Research Articles

Genotype–Phenotype Correlation in a Couple in Which the Wife Is a Carrier of the Beta-Thalassemia Trait and the Husband Is a Carrier of a Mutation in the ALAS2 Gene: Both Gene Defects Are Associated with Non-Iron-Deficiency Microcytic Anemia

Introduction: Generally, microcytic anaemia is caused by sideropenia or a genetic gap. The suspicion that microcytic anaemia is caused by a genetic gap must always be considered in the face of an inadequate response to martial therapy. The aim of this paper is to highlight how biochemical diagnosis alone is sometimes not sufficient to understand the cause of microcytic anaemia. For this reason, for a correct genotype–phenotype correlation, it is essential to identify the defective gene underlying the microcytic anaemia. Detailed Case Description: This case concerns a married couple who both have microcytic anaemia. They came to our attention because the lady, pregnant at 12 weeks, underwent screening for chromosomal abnormalities using combined tests in the first trimester of pregnancy. A biochemical screening performed ten years earlier showed that both spouses were healthy carriers of the beta-thalassemia trait. A careful analysis of the biochemical data and an in-depth molecular diagnosis of the alpha and beta globin genes showed that the woman was a healthy carrier of the beta-thalassemia trait while the husband was a healthy carrier of a mutation in the ALAS2 gene. Analysis of the biochemical data of her husband and family members revealed that she had X-linked microcytic sideroblastic anaemia caused by an alteration in the function of the ALAS2 (5′-Aminolevulinate Synthase 2) gene located on the short arm of the X chromosome (Xp11.21). Discussion and Conclusions: This result is very relevant as, during genetic counselling, we explained to the couple that invasive prenatal diagnosis was not necessary as there is no risk of procreating a transfusion-dependent individual.

Clinical and Genetic Analysis of 8 Children With Ornithine Transcarbamylase Deficiency: Two Novel Mutations.

Cases and studies of neurologic symptoms in children caused by genetic metabolic diseases have been widely reported. Ornithine transcarbamylase deficiency (OTCD) is the most common urea cycle disorder, which is due to mutations in the OTC gene located on chromosome Xp21.1. In this study, we analyzed the clinical and genetic characteristics of 8 Chinese children diagnosed with OTCD. A total of 8 patients (5 male and 3 female) were diagnosed with OTCD by biochemical and molecular analysis between 2015 and 2023. Clinical manifestations, biochemical features, and OTC gene sequencing analysis were reviewed retrospectively. The effect of c.664-1G>C on OTC mRNA synthesis was confirmed by a minigene splicing assay. All children were late-onset patients, with a median onset age of 3.6 years (range 1.8-17 years). Neurologic symptoms caused by hyperammonemia include vomiting, coma, dyssomnia, and seizures. The peak plasma ammonia levels ranged from 149 to 4,490 μmol/L, and alanine transaminase levels ranged from 20 to 1316 U/L. Four of them had received CRRT, and only 1 patient was admitted for liver transplantation. By December 2023, 4 patients had survived and 4 were deceased. Blood amino acids or urinary organic acids were detected in 7 cases. All patients underwent whole-exome sequencing, and 2 novel mutations were revealed (P1, c.617dupT and P2, c.664-1G>C). The alteration (c.664-1G>C) leads to the deletion of a 54-bp sequence in the exon 7 of the OTC gene (NM_000531.6: c.664_717del). Two novel pathogenic variants in the OTC gene were confirmed in 8 Chinese children by biochemical findings and genetic analysis. These findings will provide a better understanding of the diagnosis and treatment of pediatric patients with OTCD.

Unexpected Findings of Duchenne Muscular Dystrophy in Prenatal Screening of Chromosome Abnormality Based on Cell-Free Fetal DNA.

This study aims to assess the feasibility of detecting and diagnosing Duchenne muscular dystrophy (DMD) during prenatal screening for chromosome abnormalities using cell-free fetal DNA extracted from peripheral blood samples of pregnant women. Two pregnant women identified as high risk through noninvasive prenatal testing (NIPT) underwent amniocentesis to obtain fetal cells. Subsequent fetal chromosomal karyotyping was conducted, and genomic DNA from fetal cells was extracted for copy number variation sequencing (CNV-Seq) analysis, complemented by multiplex ligation-dependent probe amplification (MLPA) to detect deletions or duplications within the DMD gene. NIPT results for the two samples indicated potential abnormalities involving chromosomes 21 and 18. However, karyotype analysis of the fetuses revealed no abnormalities. CNV-Seq identified deletions of 0.28 and 0.18 Mb within chromosome Xp21.1, encompassing the DMD gene, in each fetus. In family 1, MLPA results indicated a maternal heterozygous deletion spanning exons 12 to 41 in the DMD gene, while the fetus exhibited deletions in exons 12 to 41. In family 2, MLPA results confirmed normal DMD gene status in the pregnant woman's peripheral blood genomic DNA but revealed a fetal deletion spanning exons 48 to 52. Both fetuses were diagnosed with DMD and subsequently underwent termination. Abnormalities identified through NIPT necessitate further invasive prenatal diagnostic procedures. For cases involving chromosomal microdeletions or microduplications, a combination of karyotyping and CNV-Seq testing is essential for comprehensive diagnosis. NIPT followed by CNV-Seq may offer insights into large exon deletions within the DMD gene in specific instances. · NIPT results can offer valuable insights into the deletion and duplication of DMD gene for the fetus.. · It's crucial to notice unexpected findings in NIPT.. · A combination of karyotyping and CNV-Seq testing is essential for comprehensive diagnosis..

A genetic basis for sex differences in Xp11 translocation renal cell carcinoma

Xp11 translocation renal cell carcinoma (tRCC) is a rare, female-predominant cancer driven by a fusion between the transcription factor binding to IGHM enhancer 3 (TFE3) gene on chromosome Xp11.2 and a partner gene on either chromosome X (chrX) or an autosome. It remains unknown what types of rearrangements underlie TFE3 fusions, whether fusions can arise from both the active (chrXa) and inactive X (chrXi) chromosomes, and whether TFE3 fusions from chrXi translocations account for the female predominance of tRCC. To address these questions, we performed haplotype-specific analyses of chrX rearrangements in tRCC whole genomes. We show that TFE3 fusions universally arise as reciprocal translocations and that oncogenic TFE3 fusions can arise from chrXi:autosomal translocations. Female-specific chrXi:autosomal translocations result in a 2:1 female-to-male ratio of TFE3 fusions involving autosomal partner genes and account for the female predominance of tRCC. Our results highlight how X chromosome genetics constrains somatic chrX alterations and underlies cancer sex differences.

Chromosome Xp22.3 deletion syndrome with X-linked ichthyosis, Kallmann syndrome, short stature, generalized epilepsy, hearing loss, attention deficit hyperactivity disorder, and intellectual disability – A rare report with review of literature

Chromosome Xp22.3 deletion syndrome is a very rare contiguous gene deletion syndrome with variable phenotype due to the deletion of genes from the distal short arm of the X chromosome (Xp), including the short-stature homeobox (SHOX), anosmin-1 (ANOS1), arylsulfatase (ARSL), neuroligin-4 (NLGN4), and steroid sulfatase (STS) genes. We have reviewed the available literature on the chromosome Xp22.3 deletion syndrome. A 10-year-old boy presented with global developmental delay, generalized epilepsy, decreased hearing, and hyperactivity. He had no significant family history. Examination revealed microcephaly, short stature, and dry and scaly skin lesions on the trunk. He had thick arched eyebrows, a depressed nasal bridge, a long philtrum, high arched palate, retrognathia, brachytelephalangy, brachymetatarsia, and mild scoliosis. Brainstem-evoked response audiometry testing revealed moderate hearing loss. Magnetic resonance imaging showed cerebellar tonsillar ectopia. Clinical exome sequencing revealed a likely pathogenic contiguous deletion (~8.10 Mb) spanning genomic location chrX:g.(_630898)_(8732037_)del encompassing ANOS1, ARSL, NLGN4X, SHOX, and STS genes. We have reviewed the available literature for reported associations of Chromosome Xp22.3 deletion syndrome and report a novel association of X-linked ichthyosis, Kallmann syndrome, global developmental delay, short stature, bilateral hearing loss, generalized epilepsy, attention deficit hyperactivity disorder, and intellectual disability.

Abstract B018: KDM6A and MTAP expression loss enable identification of a large fraction of low grade non-invasive urothelial neoplasia of the urinary bladder

Abstract The identification of low-grade urothelial neoplasia in cytologic samples or in biopsies with dysplastic lesions poses a particular problem for pathologists in routine diagnostics. Improved diagnosis of low-grade urothelial neoplasia could help to reduce the number of cystoscopic follow-up examinations. KDM6A, also known as UTX (ubiquitously transcribed X chromosome tetratricopeptide repeat protein) is an epigenetic regulator which is frequently mutated in urothelial carcinoma. Because KDM6A is localized on chromosome Xp11.3, and because of the male predominance in bladder cancer, many KDM6A mutations should result in a complete loss of KDM6A protein expression and become detectable by immunohistochemistry (IHC). Similarly, S-methyl-5′-thioadenosine phosphorylase (MTAP), a critical enzyme for DNA and RNA synthesis, is co-deleted with the CDKN2A tumor suppressor located on chromosome 9p21 in about 25% of bladder cancers, resulting in reduced or lost protein expression. To study the prevalence and diagnostic potential of immunohistochemical loss of KDM6A and MTAP expression, 928 tumors were analyzed by IHC in a tissue microarray format. The cohort included 628 non-invasive papillary tumors (pTa) and 300 tumors from patients who underwent radical cystectomy for muscle-invasive disease (pT2-4). A complete KDM6A expression loss occurred in 35% of 342 pTa G2 low-grade, 23% of 150 pTa G2 high-grade, 17.8% of 90 pTa G3 tumors, and 20.1% of 243 interpretable muscle invasive (pT2-4) cancers (p<0.0001). Within pTa tumors, there was a strong correlation between KDM6A loss and low tumor grade (p=0.0003), whereas no significant difference was found between pT3 G3 and muscle invasive cancers (p=0.8828). Complete absence of MTAP expression occurred in 11% of 297 pTa G2 low-grade, 29.6% of 125 pTa G2 high-grade, 18.4% of 76 pTa G3 tumors, and 26.3% of 217 muscle invasive (pT2-4) cancers (p<0.0001). A combined analysis of 702 cancers with interpretable data for KDM6A and MTAP showed that 6.6% of tumors had expression loss of both KDM6A and MTAP, 20% had KDM6A loss only, and 13% had MTAP loss only. The rate of expression loss of KDM6A and/or MTAP was markedly higher in pTa G2 low (41.2%) and in pTa G2 high (40.3%) than in pTa G3 tumors (29%). In summary, our data demonstrate that about 40% of low-grade non-invasive urothelial neoplasias – which are usually not detected by urine cytology – had a completed expression loss of either KDM6A or MTAP. In patients with these alterations, follow-up could be potentially facilitated by immunohistochemistry. Citation Format: Florian Viehweger, Neele Heckmann, Natalia Gorbokon, Henning Plage, Sebastian Hofbauer, Sarah Weinberger, Florian Roßner, Simon Schallenberg, Sefer Elezkurtaj, Maximilian Lennartz, Tim Mandelkow, Elena Bady, Margit Fisch, Thorsten Ecke, Stefan Koch, Nico Adamini, Ronald Simon, Guido Sauter, Tobias Klatte, Thorsten Schlomm, David Horst, Henrik Zecha, Martina Kluth, Sarah Minner. KDM6A and MTAP expression loss enable identification of a large fraction of low grade non-invasive urothelial neoplasia of the urinary bladder [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B018.

Abstract 6449: KDM6A expression loss is a common feature in low grade non-invasive urothelial carcinomas of the urinary bladder

Abstract KDM6A, also known as UTX (ubiquitously transcribed X chromosome tetratricopeptide repeat protein) is an epigenetic regulator which is frequently mutated in urothelial carcinoma. Because KDM6A loss causes a dependency on EZH2, a potential therapeutic target, KDM6A analysis may have therapeutic importance. Most data on KDM6A mutations are derived from next generation sequencing (NGS). However, because of the combination of a high rate of truncating KDM6A mutations, the localization of KDM6A on chromosome Xp11.3, and the male predominance in bladder cancer, many KDM6A mutations should result in a complete loss of KDM6A protein expression and become detectable by immunohistochemistry (IHC). To study the prevalence and the potential diagnostic and clinical role of KDM6A expression loss, more than 2,100 tumors were analyzed by IHC in a tissue microarray format. The cohort included 1,128 patients who underwent radical cystectomy for muscle-invasive disease (pT2-4). A complete KDM6A expression loss occurred in 36% of 350 pTa G2 low-grade, 23% of 152 pTa G2 high-grade, and 18.5% of 92 pTa G3 tumors (p=0.0002). As compared to pTa G3 tumors, the frequency of KDM6A expression loss did not differ significantly in pT2 (17.2%), pT3 (21.9%), and pT4 (18.2%) cancers. Within pT2-4 carcinomas, KDM6A staining was unrelated to pT, pN, grade, L-status, V-status, overall survival, recurrence-free survival, and cancer-specific survival (p≥0.18 each). A KDM6A loss was more common in male (22.2%) than in female patients (15.4%; p<0,0001), and within male patients, a KDM6A loss was more frequent in tumors with Y-chromosome loss (36.1%) than in cancers without a Y-chromosome loss (16.3%; p<0.0001). KDM6A expression loss was significantly associated with increased p63 expression (p<0.0001) and high uroplakin 1b staining (p=0.0013) but unrelated to CK20, GATA3, UpK1b, and p53 staining. In summary, our data demonstrate that truncating KDM6A mutations occur in a significant subset of urothelial carcinomas which is linked to low-grade non-invasive cancer, male gender and loss of the Y chromosome. The predominance of KDM6A loss in low grade tumors makes KDM6A IHC a promising new tool for identification of low grade dysplasia in biopsies and early bladder cancer detection in cytology. Citation Format: Florian Viehweger, Natalia Gorbokon, Henning Plage, Sebastian Hofbauer, Kira Furlano, Sarah Weinberger, Bernhard Ralla, Antonia Franz, Annika Fendler, Michela de Martino, Florian Roßner, Simon Schallenberg, Sefer Elezkurtaj, Maximilian Lennartz, Tim Mandelkow, Elena Bady, Andreas H. Marx, Henrik Samtleben, Margit Fisch, Michael Rink, Marcin Slojewski, Krystian Kaczmarek, Thorsten Ecke, Stefan Koch, Nico Adamini, Ronald Simon, Guido Sauter, Joachim Weischenfeldt, Tobias Klatte, Thorsten Schlomm, David Horst, Henrik Zecha, Martina Kluth, Sarah Minner. KDM6A expression loss is a common feature in low grade non-invasive urothelial carcinomas of the urinary bladder [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6449.

Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration

Pathogenic variants in WDR45 on chromosome Xp11 cause neurodegenerative disorder beta-propeller protein-associated neurodegeneration (BPAN). Currently, there is no effective therapy for BPAN. Here we report a 17-year-old female patient with BPAN and show that antisense oligonucleotide (ASO) was effective in vitro. The patient had developmental delay and later showed extrapyramidal signs since the age of 15 years. MRI findings showed iron deposition in the globus pallidus and substantia nigra on T2 MRI. Whole genome sequencing and RNA sequencing revealed generation of pseudoexon due to inclusion of intronic sequences triggered by an intronic variant that is remote from the exon–intron junction: WDR45 (OMIM #300526) chrX(GRCh37):g.48935143G > C, (NM_007075.4:c.235 + 159C > G). We recapitulated the exonization of intron sequences by a mini-gene assay and further sought antisense oligonucleotide that induce pseudoexon skipping using our recently developed, a dual fluorescent splicing reporter system that encodes two fluorescent proteins, mCherry, a transfection marker designed to facilitate evaluation of exon skipping and split eGFP, a splicing reaction marker. The results showed that the 24-base ASO was the strongest inducer of pseudoexon skipping. Our data presented here have provided supportive evidence for in vivo preclinical studies.

CDKL5 Deficiency Disorder: Some Lessons Learned 20 Years After the First Description.

Loss of function variants in the Cyclin-dependent kinase-like 5 gene (CDKL5) causes CDKL5 deficiency disorder (CDD). Most cases of CDD are due to a de novo missense or truncating variants. The CDKL5 gene was discovered in 1998 as part of the genomic mapping of the chromosome Xp22 region that led to the discovery of the serine-threonine kinases STK9. Since then, there have been significant advancements in the description of the disease in humans, the understanding of the pathophysiology, and the management of the disease. There have been many lessons learned since the initial description of the condition in humans in 2003. In this article, we will focus on pathophysiology, clinical manifestations, with particular focus on seizures because of its relevance to the medical practitioners and researchers and guidelines for management. We finalize the manuscript with the voice of the parents and caregivers, as discussed with the 2019 meeting with the Food and Drug Administration.

Identification of a novel intronic mutation of MAGED2 gene in a Chinese family with antenatal Bartter syndrome

BackgroundAntenatal Bartter syndrome is a life-threatening disease caused by a mutation in the MAGED2 gene located on chromosome Xp11. It is characterized by severe polyhydramnios and extreme prematurity. While most reported mutations are located in the exon region, variations in the intron region are rarely reported.MethodsIn our study, we employed whole exome sequencing and Sanger sequencing to genotype members of this family. Additionally, a minigene assay was conducted to evaluate the impact of genetic variants on splicing.ResultsOur findings reveal a novel intronic variant (NM_177433.3:c.1271 + 4_1271 + 7delAGTA) in intron 10 of the MAGED2 gene. Further analysis using the minigene assay demonstrated that this variant activated an intronic cryptic splice site, resulting in a 96 bp insertion in mature mRNA.ConclusionsOur results indicate that the novel intronic variant (c.1271 + 4_1271 + 7delAGTA) in intron 10 of the MAGED2 gene is pathogenic. This expands the mutation spectrum of MAGED2 and highlights the significance of intronic sequence analysis.

A Case of X-linked Intellectual Disability with Novel Chromosome 9p12-pter Unbalanced Translocation on Chromosome Xp.

Abnormalities in genes on the X chromosome or large defects in the X chromosome itself cause X-linked intellectual disability. The proband was a 27-year-old man. His medical history included strabismus, cryptorchidism, and severe intellectual disabilities. He also had epilepsy. His mother seemed to have slight intellectual disability. A physical examination revealed malformations. The lateral and fourth ventricles were dilated using computed tomography. CGG repeats in the 5' untranslated region of FMR1 gene were normal. G-banding and spectral karyotyping revealed a novel unbalanced X-autosomal translocation, with a karyotype of 46,Y,der (X) t (X;9) (p22.33;p12); distal trisomy of 9p and distal Xp nullisomy.

Differential alternative splicing analysis links variation in ZRSR2 to a novel type of oral-facial-digital syndrome

PurposeOral-facial-digital (OFD) syndromes are genetically heterogeneous developmental disorders, caused by pathogenic variants in genes involved in primary cilia formation and function. We identified a previously undescribed type of OFD with brain anomalies, ranging from alobar holoprosencephaly to pituitary anomalies, in 6 unrelated families. MethodsExome sequencing of affected probands was supplemented with alternative splicing analysis in patient and control lymphoblastoid and fibroblast cell lines, and primary cilia structure analysis in patient fibroblasts. ResultsIn 1 family with 2 affected males, we identified a germline variant in the last exon of ZRSR2, NM_005089.4:c.1211_1212del NP_005080.1:p.(Gly404GlufsTer23), whereas 7 affected males from 5 unrelated families were hemizygous for the ZRSR2 variant NM_005089.4:c.1207_1208del NP_005080.1:p.(Arg403GlyfsTer24), either occurring de novo or inherited in an X-linked recessive pattern. ZRSR2, located on chromosome Xp22.2, encodes a splicing factor of the minor spliceosome complex, which recognizes minor introns, representing 0.35% of human introns. Patient samples showed significant enrichment of minor intron retention. Among differentially spliced targets are ciliopathy-related genes, such as TMEM107 and CIBAR1. Primary fibroblasts containing the NM_005089.4:c.1207_1208del ZRSR2 variant had abnormally elongated cilia, confirming an association between defective U12-type intron splicing, OFD and abnormal primary cilia formation. ConclusionWe introduce a novel type of OFD associated with elongated cilia and differential splicing of minor intron-containing genes due to germline variation in ZRSR2.

Cutaneous, Cranial, and Skeletal Defects in Children and Adults with Focal Dermal Hypoplasia.

The diagnostic process for children and adults manifesting a constellation of ectodermal abnormalities requires a conscientious and highly structured process. Six girls (aged 6-month-8 years) and two older girls (aged 13 and 16 years) were born with variable skin lesions of varying intensities associated with noticeable cranial and skeletal malformation complexes. Cleft palate, abnormal dentition, and multiple papillomas were evident around the mouth, mostly bilateral but asymmetrical in the upper and lower limbs. Exaggerated frontal bossing (macrocephaly) and in some patients' microcephaly with variable skeletal defects of the craniocervical junction and diverse forms of lower limb deformities of syndactyly, polydactyly, and split-hand/foot (ectrodactyly). All patients manifested the constellation of abnormalities with variable intensities ranging between alopecia, papillomas, striated skin pigmentations split-hand/foot (ectrodactyly), and major bone defects. A 3D reconstruction CT scan was directed mainly to further scrutinize children with pseudo cleft lip, submucus cleft, and cleft palate. Interstingly, they manifested massive demineralization of the cranium associated with severely defective dentition. A spine 3D reconstruction CT scan in two girls showed marked cystic cavitation of the upper jaw associated with excessive cavitation of the mastoid, causing tremendous frailty of the mastoid bone. A 3D sagittal CT scan showed odontoid hypoplasia and C1-2 instability associated with the rudimentary atlas and the persistence of extensive synchondrosis of the cervico-thoracic spine. The overall clinical and radiological phenotypic characterizations were consistent with the diagnosis of focal dermal hypoplasia (Goltz syndrome). Two children manifested heterozygous mutations in the PORCN gene, chromosome Xp11. In this study, we believe it's a good opportunity to share our novel scientific findings, which are intriguing and can be inspiring to readers, and to further aid the current scientific literature with exceptionally new unveiling results. This is the first comprehensive study of the cranio-skeletal malformation complex in children with GS.

STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review.

X-linked recessive ichthyosis (XLI) is clinically characterized by dark brown, widespread dryness with polygonal scales. We describe the identification of STS and PUDP deletions using targeted panel sequencing combined with copy-number variation (CNV) analysis in XLI. A 9-month-old infant was admitted for genetic counseling. Since the second day after birth, the infant's skin tended to be dry and polygonal scales had accumulated over the abdomen and upper extremities. The infant's maternal uncle and brother (who had also exhibited similar skin symptoms from birth) presented with polygonal scales on their trunks. CNV analysis revealed a hemizygous deletion spanning 719.3 Kb on chromosome Xp22 (chrX:7,108,996-7,828,312), which included a segment of the STS gene and exhibited a Z ratio of -2 in the proband. Multiplex ligation-dependent probe amplification (MLPA) confirmed this interstitial Xp22.31 deletion. Our report underscores the importance of implementing CNV screening techniques, including sequencing data analysis and gene dosage assays such as MLPA, to detect substantial deletions that encompass the STS gene region of Xq22 in individuals suspected of having XLI.

A-318 Pseudo-hypertriglyceridemia in a 2-year-old Male with Global Developmental Delay, Myopathy and Adrenal Hypoplasia

Abstract Background Pseudo-hypertriglyceridemia is an overestimation of serum triglyceride levels due to laboratory assays that measure free glycerol concentrations instead of triglycerides directly. Consequently, conditions presenting with elevated levels of endogenous or exogenous free glycerol, such as glycerol kinase deficiency, result in an overestimation of serum triglycerides. Glycerol kinase deficiency (GKD) is caused by pathogenic variants of the GK gene on chromosome Xp21. Three forms of GKD are recognized, characterized as infantile, juvenile, and adult forms. While the juvenile and adult forms are recognized as isolated GKD, the infantile form manifests itself as part of the Xp21.3 contiguous gene deletion syndrome, also known as complex GKD. This syndrome is composed of genes associated with Duchenne muscular dystrophy (DMD), X-linked congenital adrenal hypoplasia (NR0B1), and intellectual disability (IL1RAPL1). GKD is characterized biochemically by hyperglycerolaemia and glyceroluria. Case Description A 2-year-old male presented to the genetics clinic with a history of global developmental delay (gross motor and speech), axial hypotonia, poor head control and inability to sit unassisted or walk. Significant findings on examination included a startled appearance, absent eyebrows and temporal thinning, high forehead, frontal bossing, axial hypotonia and peripheral hypertonia. Laboratory findings included elevated creatine kinase (CK) of 14809 units/L (normal 27–160 units/L), aspartate aminotransferase (AST) of 307 (normal 20–60 units/L), alanine aminotransferase (ALT) 265 (normal 15–45 units/L), Adrenocorticotropic Hormone (ACTH) 156 (normal 6–48 pg/mL), and elevated triglycerides at 683 (normal 44–157 mg/dL). There was also a family history of developmental delay and intellectual disability in patient's mother and younger sister. Method Triglycerides are commonly measured indirectly with different enzyme reagents. The Triglycerides in this boy were measured by an automated chemistry analyzer based on a colorimetric serial enzymatic reaction including lipase, glycerol kinase and L-α-glycerol-phosphate oxidase1. Urinary organic acids profile including glycerol was extracted from acidified urine (pH 1-2) using diethyl ether. Organic extracts are then evaporated to dryness under nitrogen and trimethysilyl derivatized by the addition of N, O-bis (trimethylsilyl) trifluoroacetamide with 1% trimethylchorosilane (BSTFA/TMCS) and analyzed by gas chromatography-mass spectrometry (GC-MS). Results A comprehensive work-up including qualitative urinary organic acid analysis and chromosomal microarray was carried out. Urinary organic acids analysis revealed very abnormal accumulation of glycerol. Chromosomal microarray results showed a 4.2 Mb deletion of Xp21.3p21.1 (29296579-33551038) including complete copies of GK, DMD, and NR0B1 genes as well as multiple exons of IL1RAPL1. This confirmed his GKD as part of the Xp21 continuous gene deletion syndrome. Elevated triglycerides were then recognized as pseudo-hypertriglyceridemia after the diagnosis. Mild glyceroluria is also observed in the younger sister of this patient. Discussion and Conclusion This case highlights the importance recognizing pseudo-hypertriglyceridemia and diagnostic challenges. Earlier identification through urine organic acid analysis could have been made. The combination of clinical presentations and increased glycerol should cause suspicion for GKD. Female carriers of this X-linked disorder need to be evaluated for intellectual disability, as seen in this patient's mother and younger sister.

Investigation of (Epi)genetic causes in syndromic short children born small for gestational age

Intrauterine onset syndromic short stature constitutes a group of diseases that pose challenges in differential diagnosis due to their rarity and clinical as well as molecular heterogeneity. The aim of this study was to investigate the presence of (epi)genetic causes in children born small for gestational age (SGA) and manifesting clinically undiagnosed syndromic short stature. The study group comprised twenty-nine cases selected from the syndromic SGA cohort. Various analyses were performed, including chromosomal microarray (CMA), methylation-specific-multiple ligation probe amplification for chromosomes 6,14 and 20, and whole exome sequencing (WES). Pathogenic copy number variants (CNVs) on chromosomes 2q13, 22q11.3, Xp22.33, 17q21.31, 19p13.13 and 4p16.31 causing syndromic growth disturbance were detected in six patients. Maternal uniparental disomy 14 was identified in a patient. WES was performed in the remaining 22 patients, revealing pathogenic variants in nine cases; six were monoallelic (ACAN, ARID2, NIPBL, PIK3R1, SMAD4, BRIP1), two were biallelic (BRCA2, RFWD3) and one was hemizygous (HUWE1). Seven of these were novel. Craniofacial dysmorphism, which is an important clue for the diagnosis of syndromes, was very mild in all patients. This study unveiled, for the first time, that ARID2 mutatios can cause syndromic SGA. In conclusion, a high (55.2%) diagnosis rate was achieved through the utilization of CMA, epigenetic and WES analyzes; 15 rare syndromes were defined, who were born with SGA and had atypical and/or mild dysmorphic findings. This study not only drew attention to the association of some rare syndromes with SGA, but also introduced novel genes and CNVs as potential contributors to syndromic SGA.

Vascular endothelial growth factor-D plasma levels and VEGFD genetic variants are independently associated with outcomes in patients with cardiovascular disease.

The vascular endothelial growth factor (VEGF) family is involved in pathophysiological mechanisms underlying cardiovascular (CV) diseases. The aim of this study was to investigate the associations between circulating VEGF ligands and/or soluble receptors and CV outcome in patients with acute coronary syndrome (ACS) and chronic coronary syndrome (CCS). Levels of VEGF biomarkers, including bFGF, Flt-1, KDR (VEGFR2), PlGF, Tie-2, VEGF-A, VEGF-C, and VEGF-D, were measured in the PLATO ACS cohort (n = 2091, discovery cohort). Subsequently, VEGF-D was also measured in the STABILITY CCS cohort (n = 4015, confirmation cohort) to verify associations with CV outcomes. Associations between plasma VEGF-D and outcomes were analysed by multiple Cox regression models with hazard ratios (HR [95% CI]) comparing the upper vs. the lower quartile of VEGF-D. Genome-wide association study (GWAS) of VEGF-D in PLATO identified SNPs that were used as genetic instruments in Mendelian randomization (MR) meta-analyses vs. clinical endpoints. GWAS and MR were performed in patients with ACS from PLATO (n = 10 013) and FRISC-II (n = 2952), and with CCS from the STABILITY trial (n = 10 786). VEGF-D, KDR, Flt-1, and PlGF showed significant association with CV outcomes. VEGF-D was most strongly associated with CV death (P = 3.73e-05, HR 1.892 [1.419, 2.522]). Genome-wide significant associations with VEGF-D levels were identified at the VEGFD locus on chromosome Xp22. MR analyses of the combined top ranked SNPs (GWAS P-values; rs192812042, P = 5.82e-20; rs234500, P = 1.97e-14) demonstrated a significant effect on CV mortality [P = 0.0257, HR 1.81 (1.07, 3.04) per increase of one unit in log VEGF-D]. This is the first large-scale cohort study to demonstrate that both VEGF-D plasma levels and VEGFD genetic variants are independently associated with CV outcomes in patients with ACS and CCS. Measurements of VEGF-D levels and/or VEGFD genetic variants may provide incremental prognostic information in patients with ACS and CCS.

P118: Genotype-phenotype correlations in a female with a chromosome Xp11.23 deletion including PORCN and EBP

P118: Genotype-phenotype correlations in a female with a chromosome Xp11.23 deletion including PORCN and EBP

Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis.

Karyotyping and genome copy number variation sequencing (CNV-seq) are two techniques frequently used in prenatal diagnosis. This study aimed to explore the diagnostic potential of using a combination of these two methods in order to provide a more accurate clinical basis for prenatal diagnosis. We selected 822 pregnant women undergoing amniocentesis and separated them into six groups according to different risk indicators. Karyotyping and CNV-seq were performed simultaneously to compare the diagnostic performance of the two methods. Among the different amniocentesis indicators, abnormal fetal ultrasounds accounted for 39.29% of the total number of examinees and made up the largest group. The abnormal detection rate of non-invasive prenatal testing (NIPT) high risk was 37.93% and significantly higher than the other five groups (P<0.05). The abnormal detection rate of mixed indicators was significantly higher than the history of the adverse reproductive outcomes group (P = 0.0151). The two methods combined found a total of 119 abnormal cases (14.48%). Karyotyping detected 57 cases (6.93%) of abnormal karyotypes, 30 numerical aberrations, and 27 structural aberrations. CNV-seq identified 99 cases (12.04%) with altered CNVs, 30 cases of chromosome aneuploidies, and 69 structural aberrations (28 pathogenic, eight that were likely pathogenic, and 33 microdeletion/duplication variants of uncertain significance (VUS)). Thirty-seven cases were found abnormal by both methods, 20 cases were detected abnormally by karyotyping (mainly mutual translocation and mostly balanced), and 62 cases of microdeletion/duplication were detected by CNV-seq. Steroid sulfatase gene (STS) deletion was identified at chromosome Xp22.31 in three cases. Postnatal follow-up confirmed that babies manifested skin abnormalities one week after birth. Six fetuses had Xp22.31 duplications ranging from 1.5 Kb to 1.7 Mb that were detected by CNV-seq. Follow-up showed that five babies presented no abnormalities during follow-up, except for one terminated pregnancy due to a history of adverse reproductive outcomes. The combination of using CNV-seq and karyotyping significantly improved the detection rate of fetal pathogenic chromosomal abnormalities. CNV-seq is an effective complement to karyotyping and improves the accuracy of prenatal diagnosis.

EP005: Complex glycerol kinase deficiency and X-linked intellectual disability

Glycerol kinase deficiency (GKD) is caused by pathogenic variants of the GK gene on chromosome Xp21. Three forms of GKD are recognized, characterized as infantile, juvenile, and adult forms. While the juvenile and adult forms are recognized as isolated GKD, the infantile form manifests itself as part of the Xp21.3 contiguous gene deletion syndrome, also known as complex GKD. This syndrome is composed of genes associated with Duchenne muscular dystrophy (DMD), X-linked congenital adrenal hypoplasia (NR0B1), and intellectual disability (IL1RAPL1).