Blepharophimosis sequence and diaphragmatic hernia associated with interstitial deletion of chromosome 3 (46,XY,del(3)(q21q23))

A novel 3q interstitial deletion including GATA2 and ZNF148: A case report

GATA2 and ZNF148 have both been mapped to chromosome 3q. Pathogenic variants in GATA2 have been associated with immunodeficiency and high risk for myelodysplasia, acute myeloid leukemia, and chronic myelomonocytic leukemia. Gain-of-function variants in ZNF148 have previously been suggested as a mechanism for agenesis of the corpus callosum (ACC). Here, we report a novel 10.4 Mb interstitial deletion on 3q12.33q22.1 including GATA2 and ZNF148 in a child with developmental delay, agenesis of the corpus callosum, and vertebral segmentation defects. With this diagnosis, we were able to suggest preemptive referrals to hematology/oncology and allergy/immunology for close monitoring of early myelodysplasia. We also propose a possible link between ZNF148 loss of function variants and ACC.

Interstitial Deletion of 3q21 in a Kuwaiti Child with Multiple Congenital Anomalies-Expanding the Phenotype

Interstitial deletions in the long arm of chromosome 3, although relatively rare, have previously been reported to be associated with several congenital anomalies and developmental delays. Around 11 individuals with interstitial deletion spanning the region 3q21 were reported to have overlapping phenotypes, including craniofacial dysmorphism, global developmental delay, skeletal manifestations, hypotonia, ophthalmological abnormalities, brain anomalies (mainly agenesis of corpus callosum), genitourinary tract anomalies, failure to thrive and microcephaly. We present a male individual from Kuwait with a 5.438 Mb interstitial deletion of the long arm of chromosome 3 (3q21.1q21.3) detected on the chromosomal microarray with previously unreported features, including feeding difficulties, gastroesophageal reflux, hypospadias, abdomino-scrotal hydrocele, chronic kidney disease, transaminitis, hypercalcemia, hypoglycemia, recurrent infections, inguinal hernia and cutis marmorata. Our report expands the phenotype associated with 3q21.1q21.3 while summarizing the cytogenetics and clinical data of the previously reported individuals with interstitial deletions involving 3q21, thus providing a comprehensive phenotypic summary.

Shared genetic architecture of hernias: A genome-wide association study with multivariable meta-analysis of multiple hernia phenotypes

Abdominal hernias are common and characterised by the abnormal protrusion of a viscus through the wall of the abdominal cavity. The global incidence is 18.5 million annually and there are limited non-surgical treatments. To improve understanding of common hernia aetiopathology, we performed a six-stage genome-wide association study (GWAS) of 62,637 UK Biobank participants with either single or multiple hernia phenotypes including inguinal, femoral, umbilical and hiatus hernia. Additionally, we performed multivariable meta-analysis with metaUSAT, to allow integration of summary data across traits to generate combined effect estimates. On individual hernia analysis, we identified 3404 variants across 38 genome-wide significant (p < 5×10-8) loci of which 11 are previously unreported. Robust evidence for five shared susceptibility loci was discovered: ZC3H11B, EFEMP1, MHC region, WT1 and CALD1. Combined hernia phenotype analyses with additional multivariable meta-analysis of summary statistics in metaUSAT revealed 28 independent (seven previously unreported) shared susceptibility loci. These clustered in functional categories related to connective tissue and elastic fibre homeostasis. Weighted genetic risk scores also correlated with disease severity suggesting a phenotypic-genotypic severity correlation, an important finding to inform future personalised therapeutic approaches to hernia.

Management of Congenital Diaphragmatic Hernia (CDH): Role of Molecular Genetics

Congenital diaphragmatic hernia (CDH) is a relatively common major life-threatening birth defect that results in significant mortality and morbidity depending primarily on lung hypoplasia, persistent pulmonary hypertension, and cardiac dysfunction. Despite its clinical relevance, CDH multifactorial etiology is still not completely understood. We reviewed current knowledge on normal diaphragm development and summarized genetic mutations and related pathways as well as cellular mechanisms involved in CDH. Our literature analysis showed that the discovery of harmful de novo variants in the fetus could constitute an important tool for the medical team during pregnancy, counselling, and childbirth. A better insight into the mechanisms regulating diaphragm development and genetic causes leading to CDH appeared essential to the development of new therapeutic strategies and evidence-based genetic counselling to parents. Integrated sequencing, development, and bioinformatics strategies could direct future functional studies on CDH; could be applied to cohorts and consortia for CDH and other birth defects; and could pave the way for potential therapies by providing molecular targets for drug discovery.

Unraveling the Genetics of Congenital Diaphragmatic Hernia: An Ongoing Challenge

Congenital diaphragmatic hernia (CDH) is a congenital structural anomaly in which the diaphragm has not developed properly. It may occur either as an isolated anomaly or with additional anomalies. It is thought to be a multifactorial disease in which genetic factors could either substantially contribute to or directly result in the developmental defect. Patients with aneuploidies, pathogenic variants or de novo Copy Number Variations (CNVs) impacting specific genes and loci develop CDH typically in the form of a monogenetic syndrome. These patients often have other associated anatomical malformations. In patients without a known monogenetic syndrome, an increased genetic burden of de novo coding variants contributes to disease development. In early years, genetic evaluation was based on karyotyping and SNP-array. Today, genomes are commonly analyzed with next generation sequencing (NGS) based approaches. While more potential pathogenic variants are being detected, analysis of the data presents a bottleneck-largely due to the lack of full appreciation of the functional consequence and/or relevance of the detected variant. The exact heritability of CDH is still unknown. Damaging de novo alterations are associated with the more severe and complex phenotypes and worse clinical outcome. Phenotypic, genetic-and likely mechanistic-variability hampers individual patient diagnosis, short and long-term morbidity prediction and subsequent care strategies. Detailed phenotyping, clinical follow-up at regular intervals and detailed registries are needed to find associations between long-term morbidity, genetic alterations, and clinical parameters. Since CDH is a relatively rare disorder with only a few recurrent changes large cohorts of patients are needed to identify genetic associations. Retrospective whole genome sequencing of historical patient cohorts using will yield valuable data from which today's patients and parents will profit Trio whole genome sequencing has an excellent potential for future re-analysis and data-sharing increasing the chance to provide a genetic diagnosis and predict clinical prognosis. In this review, we explore the pitfalls and challenges in the analysis and interpretation of genetic information, present what is currently known and what still needs further study, and propose strategies to reap the benefits of genetic screening.

The emerging role of genomics in the diagnosis and workup of congenital urinary tract defects: a novel deletion syndrome on chromosome 3q13.31-22.1

BACKGROUND

Copy number variants (CNVs) are increasingly recognized as an important cause of congenital malformations and likely explain over 16% of cases of congenital anomalies of the kidney and urinary tract (CAKUT). Here, we illustrate how a molecular diagnosis of CNV can be beneficial to the clinical management of a pediatric patient presenting with CAKUT and other organ defects.

METHODS

We describe a 14-year-old girl with a large de novo deletion of chromosome 3q13.31-22.1 that disrupts 101 known genes. The patient presented with CAKUT, neurodevelopmental delay, agenesis of corpus callosum (ACC), cardiac malformations, electrolyte and endocrine disorders, skeletal abnormalities and dysmorphic features. We performed extensive annotation of the deleted region to prioritize genes for specific phenotypes and to predict future disease risk.

RESULTS

Our case defined new minimal chromosomal candidate regions for both CAKUT and ACC. The presence of the CASR gene in the deleted interval predicted a diagnosis of hypocalciuric hypercalcemia, which was confirmed by the serum and urine chemistries. Our gene annotation explained clinical hypothyroidism and predicted that the index case is at increased risk of thoracic aortic aneurysm, renal cell carcinoma and myeloproliferative disorder.

CONCLUSIONS

Extended annotation of CNV regions refines the diagnosis and uncovers previously unrecognized phenotypic features. This approach enables personalized treatment and prevention strategies in patients harboring genomic deletions.

Identification of TCTE3 as a gene responsible for congenital diaphragmatic hernia using a high-resolution single-nucleotide polymorphism array

PURPOSE

Congenital diaphragmatic hernia (CDH) is a birth defect of the diaphragm associated with pulmonary hypoplasia. Although genetic factors have been suggested to play a role, the etiology of CDH is still largely unknown. In this study, we analyzed copy number variants (CNVs) using a single-nucleotide polymorphism (SNP) array to examine whether microdeletions contribute to the pathogenesis of this disease.

METHODS

A total of 28 CDH patients, including 24 isolated and 4 non-isolated cases, were available. We performed CNV analysis using high-resolution SNP arrays (370K, 550K, 660K; Illumina Inc.) and CNstream software. Deletions in loci that have been suggested in previous studies to contain candidate genes affecting CDH were analyzed.

RESULTS

We detected 335, 6 and 133 deletions specific for patients in 14 (350K array), 3 (550K) and 11 (660K) cases, respectively. Among these deletions, no segments included the previously suggested candidate genes with the exception of an 18-kb deletion observed in the candidate locus 6q27 in two non-isolated patients. This deleted region contains exon 4 of the t-complex-associated-testis-expressed 3 (TCTE3) gene.

CONCLUSION

Because TCTE3 encodes a putative light chain of the outer dynein arm of cilia and human diseases caused by ciliary dysfunction show various phenotypes including skeletal defect, TCTE3 may be a genetic candidate influencing CDH.

Further molecular and clinical delineation of the Wisconsin syndrome phenotype associated with interstitial 3q24q25 deletions

Deletions of the distal 3q22.3 region encompassing the gene forkhead transcription factor FOXL2 (FOXL2) usually result in intellectual disability (ID) and the highly recognizable blepharophimosis-ptosis-epicanthus inversus syndrome (BPES). We encountered three patients with molecularly defined interstitial deletions distal to the FOXL2 gene. They present with remarkably similar manifestations comprising variable ID, a coarse facial appearance, including prominent nose and eyebrows, hypogonadism and skin pigmentation abnormalities, and they share an approximately 8.8 Mb overlapping 3q24q25 deletion. Interestingly, one of the present patients was described previously in a clinical report with emphasis on her clinical similarity to the Wisconsin syndrome, suggesting that Wisconsin syndrome might be caused by a (micro) deletion within the 3q24q25 region.

Genetic factors in congenital diaphragmatic hernia

Congenital diaphragmatic hernia (CDH) is a relatively common birth defect associated with high mortality and morbidity. Although the exact etiology of most cases of CDH remains unknown, there is a growing body of evidence that genetic factors play an important role in the development of CDH. In this review, we examine key findings that are likely to form the basis for future research in this field. Specific topics include a short overview of normal and abnormal diaphragm development, a discussion of syndromic forms of CDH, a detailed review of chromosomal regions recurrently altered in CDH, a description of the retinoid hypothesis of CDH, and evidence of the roles of specific genes in the development of CDH.

Interstitial deletion in 3q in a patient with blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) and microcephaly, mild mental retardation and growth delay: clinical report and review of the literature

We present a boy with blepharophimosis, ptosis, epicanthus inversus, microcephaly, mild mental retardation, and growth delay. Chromosomal analysis revealed a male karyotype with an interstitial deletion in the long arm of chromosome 3. DNA-analysis showed that the deletion is of maternal origin and encompasses the region between markers D3S1535 and D3S1593. The deletion contains not only the FOXL2 gene, but also the gene encoding ataxia-telangiectasia and Rad3-related protein (ATR). Mutations in FOXL2 have been shown to cause blepharophimosis-ptosis-epicanthus inversus syndrome (BPES). ATR has been identified as a candidate gene for Seckel syndrome, an autosomal recessive syndrome that comprises growth retardation, microcephaly, and mental retardation. We hypothesize that our patient has a contiguous gene syndrome and that the non-BPES-associated abnormalities (microcephaly, mild mental retardation, and growth delay) are the result of the deletion of the maternal ATR gene. However, it has not yet been excluded that haploinsufficiency of some other gene in this region plays a role.

The genetics of congenital diaphragmatic hernia

Congenital diaphragmatic hernia (CDH) is a common birth defect with a high mortality and morbidity. A clear understanding of the pathogenesis of CDH is critical for determining prognosis and planning treatment, but to date, information on the genetic etiology of both nonsyndromic and syndromic CDH is limited. This paper summarizes the current knowledge concerning the genes, syndromes, and chromosome aberrations associated with CDH in humans and in animal model systems. Mutations in several different genes have been described in syndromic CDH, but there is only one mutation that has been reported in non-syndromic CDH to date. However, animal models suggest that genes involved in cell migration, myogenesis, and connective tissue formation are critical to normal diaphragm formation, and these data provide a starting point for the search for other genes involved in the pathogenesis of CDH.

FOXL2 inactivation by a translocation 171 kb away: analysis of 500 kb of chromosome 3 for candidate long-range regulatory sequences

A translocation breakpoint 171 kb 5' of the transcription start of FOXL2 causes blepharophimosis/ptosis/epicanthus inversus syndrome (BPES) and associated premature ovarian failure. The breakpoint falls within another gene, MRPS22, that has been sequenced in 500 kb of continuous DNA. MRPS22 encodes 20 exons and a number of alternative transcripts. Three CpG islands (>91% identical) are followed by noncoding exons 4-12 and coding exons 13-20. The 3'UTR extends into the 3'UTR of COPB2. Based on the sequence, three reported translocations that cause BPES all fall within intron 6 of MRPS22. Comparisons reveal conserved segments in introns 6, 11, and 12 of human and mouse. Notably intron 11 sequence is also deleted in goat PIS syndrome (which combines craniofacial defects, female infertility, and XX sex reversal). The conserved sequences are candidates for models in which they are distant enhancers or otherwise affect higher order chromatin structure to impose long-range cis regulation of FOXL2 expression.

Bilateral cataracts, retinal detachment and vitreous hemorrhage in a newborn with congenital diaphragmatic hernia

Congenital diaphragmatic hernia (CDH) is associated with a wide range of other malformations. We describe a patient with CDH who also had significant eye findings noted at birth.

Closing in on the BPES gene on 3q23: mapping of a de Novo reciprocal translocation t(3;4)(q23;p15.2) breakpoint within a 45-kb cosmid and mapping of three candidate genes, RBP1, RBP2, and beta'-COP, distal to the breakpoint

BPES is a genetic disorder presenting with blepharophimosis, ptosis of the eyelids, epicanthus inversus, and telecanthus. BPES type I is associated with female infertility, whereas type II presents without additional symptoms. Hitherto, it remains unknown whether BPES type I results from a defect in a single gene or from a contiguous gene syndrome. Previous cytogenetic and linkage analyses have assigned a BPES locus to 3q23, in a 5-cM interval between D3S1615 and D3S1316. In this report, we describe the molecular and physical characterization of the 3q23 breakpoint in a BPES patient with a t(3;4)(q23;p15.2) translocation. Eight YACs located around and within the D3S1615-D3S1316 interval were mapped relative to the 3q23 breakpoint; 5 YACs spanning the 3q23 breakpoint were identified. Thirteen STSs and ESTs were localized on the YAC map. Subsequent hybridization of 2 YACs spanning the breakpoint to the Human RPCI1 PAC Library and the Human Chromosome 3 LLNL Cosmid Library resulted in the identification of 12 PACs and 50 cosmids respectively, allowing the construction of a detailed PAC and cosmid physical map. A refined position-telomeric to the breakpoint-of 3 candidate genes, cellular retinol-binding proteins 1 and 2 (RBP1, RBP2) and the coatomer beta' subunit (beta'-COP), was obtained on this physical map. Furthermore, a PAC and cosmid contig encompassing the breakpoint was constructed. PAC 169-C 10 and cosmid 11-L 10 crossing the breakpoint have sizes of 110 and 45 kb, respectively. The isolation of coding sequences in these clones and in the rest of the contig will greatly facilitate further efforts toward positional cloning of the gene(s) involved in BPES.

Refinement of a translocation breakpoint associated with blepharophimosis-ptosis-epicanthus inversus syndrome to a 280-kb interval at chromosome 3q23

Blepharophimosis syndrome (BPES) is an autosomal dominant disorder of craniofacial development, the features of which include blepharophimosis, ptosis, and epicanthus inversus. Although it has been suggested that BPES is genetically heterogeneous, a major locus for this condition resides at chromosome 3q23. We have previously mapped a translocation breakpoint associated with BPES to the D3S1316-D3S1615 interval. The markers in this region have subsequently been shown to lie in a different order, with the BPES locus mapping to the 1-cM D3S1576 and D3S1316 interval. In the current investigation, a physical map, consisting of 60 yeast artificial chromosome (YAC) clones and 1 bacterial artificial chromosome, that spans this region has been constructed. Ten expressed sequence tags and the cellular retinol-binding protein I locus have been mapped to the contig. YAC end isolation has led to the creation of novel STSs that have been used to reduce the size of the BPES critical region to a 280-kb interval, which has been cloned in two nonchimeric YACs.

Deletion 3q in two patients with blepharophimosis-ptosis-epicanthus inversus syndrome (BPES)

BACKGROUND

Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is an autosomal dominant condition mapped to chromosome 3q23. There are several reports of chromosomal abnormalities involving this region with a resultant phenotype that includes BPES.

METHOD

We reassessed two unrelated boys ages 3 and 5 with BPES and associated nonocular abnormalities. Karyotype, which had been previously reported as normal, was repeated using high-resolution banding techniques, to look specifically at 3q23. Clinical findings were tabulated and compared with previously reported cases.

RESULTS

Both patients proved to have interstitial deletions of chromosome 3, the first involving bands q22.2q25.1 and the second q22.2q24. The first patient exhibited prenatal and postnatal growth retardation, with global developmental delay, while the second patient had normal growth and development except for speech delay. Both had dysmorphic facies with BPES, flat philtrum, a thin upper lip, and small chin. In addition, the first boy had an inguinal hernia and hypospadius; the second boy had abnormal auricles and metatarsus adductus. The eight cases of interstitial deletions of 3q2 and six rearrangements involving this region have a remarkably similar phenotype.

CONCLUSIONS

Deletion of 3q23 is a recognizable contiguous gene syndrome. Microdeletions of 3q23 should be ruled out in any sporadic case of BPES especially if there are associated nonocular abnormalities.

A novel case of unilateral blepharophimosis syndrome and mental retardation associated with de novo trisomy for chromosome 3q

We have evaluated a 3 2/12 year old girl who presented with unilateral blepharophimosis, ptosis of the eyelid, and mental retardation. Additional dysmorphic features include microcephaly, high, narrow forehead, short stubby fingers, and adduction of the right first toe. Cytogenetic analysis showed an unbalanced karyotype consisting of 46,XX,add(7)(q+) that was de novo in origin. Fluorescence in situ hybridisation (FISH) using microdissected library probe pools from chromosomes 1,2,3,7, and 3q26-qter showed that the additional material on 7q was derived from the distal end of the long arm of chromosome 3. Our results indicate that the patient had an unbalanced translocation, 46,XX,der(7)t(3;7)(q26-qter;q+) which resulted in trisomy for distal 3q. All currently reported cases of BPES (blepharophimosis-ptosis-epicanthus inversus syndrome) with associated cytogenetic abnormalities show interstitial deletions or balanced translocations involving 3q22-q23 or 3p25.3. Our patient shares similar features to BPES, except for the unilateral ptosis and absence of epicanthus inversus. It is possible that our patient has a contiguous gene defect including at least one locus for a type of blepharophimosis, further suggesting that multiple loci exist for eyelid development.

A gene for blepharophimosis-ptosis-epicanthus inversus syndrome maps to chromosome 3q23

Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is an autosomal dominant malformation of the eyelids that may severely impair visual function. Chromosomal aberrations involving chromosomes 3q23, 3p25 and 7p34 have been reported in BPES but the disease gene has not been hitherto localized by linkage analysis. We have mapped a gene for BPES to chromosome 3q23 in a large French pedigree (Zmax = 4.62 at Theta = 0 for probe AFM 182yc5 at locus D3S1549). The best estimate for the location of the disease gene is at locus D3S1549, between the loci D3S1292 and D3S1555 (maximum lod score of 5.10).