Classic Galactosemia: Clinical and Computational Characterization of a Novel GALT Missense Variant (p.A303D) and a Literature Review.

Classic galactosemia is an autosomal recessive inherited liver disorder of carbohydrate metabolism caused by deficient activity of galactose-1-phosphate uridylyltransferase (GALT). While a galactose-restricted diet is lifesaving, most patients still develop long-term complications. In this study, we report on a two-week-old female patient who is a compound heterozygote for a known pathogenic variant (p.K285N) and a novel missense variant (p.A303D) in the GALT gene. Segregation analysis showed that the patient inherited the p.K285N pathogenic variant from her father and the p.A303D variant from her mother. A bioinformatics analysis to predict the impact of the p.A303D missense variant on the structure and stability of the GALT protein revealed that it may be pathogenic. Based on this finding, we performed a literature review of all GALT missense variants identified in homozygous and compound heterozygous galactosemia patients carrying the p.K285N pathogenic variant to explore their molecular effects on the clinical phenotype of the disease. Our analysis revealed that these missense variants are responsible for a wide range of molecular defects. This study expands the clinical and mutational spectrum in classic galactosemia and reinforces the importance of understanding the molecular consequences of genetic variants to incorporate genetic analysis into clinical care.

Tumor Testing and Genetic Analysis to Identify Lynch Syndrome Patients in an Italian Colorectal Cancer Cohort.

Lynch syndrome (LS) is an inherited cancer susceptibility syndrome caused by germline mutations in a DNA mismatch repair (MMR) gene or in the EPCAM gene. LS is associated with an increased lifetime risk of colorectal cancer (CRC) and other malignancies. The screening algorithm for LS patient selection is based on the identification of CRC specimens that have MMR loss/high microsatellite instability (MSI-H) and are wild-type for BRAFV600. Here, we sought to clinically and molecularly characterize patients with these features. From 2017 to 2023, 841 CRC patients were evaluated for MSI and BRAFV600E mutation status, 100 of which showed MSI-H. Of these, 70 were wild-type for BRAFV600. Among these 70 patients, 30 were genetically tested for germline variants in hereditary cancer predisposition syndrome genes. This analysis showed that 19 of these 30 patients (63.3%) harbored a germline pathogenic or likely pathogenic variant in MMR genes, 2 (6.7%) harbored a variant of unknown significance (VUS) in MMR genes, 3 (10%) harbored a VUS in other cancer-related genes, and 6 (20%) were negative to genetic testing. These findings highlight the importance of personalized medicine for tailored genetic counseling, management, and surveillance of families with LS and other hereditary cancer syndromes.

Bilateral Phyllodes Giant Tumor. A Case Report Analyzed by Array-CGH.

The breast phyllodes tumor is a biphasic tumor that accounts for less than of 1% of all breast neoplasms. It is classified as benign, borderline, or malignant, and can mimic benign masses. Some recurrent alterations have been identified. However, a precise molecular classification of these tumors has not yet been established. Herein, we describe a case of a 43-year-old woman that was admitted to the emergency room for a significant bleeding from the breast skin. A voluminous ulcerative mass of the left breast and multiple nodules with micro-calcifications on the right side were detected at a physical examination. A left total mastectomy and a nodulectomy of the right breast was performed. The histological diagnosis of the surgical specimens reported a bilateral giant phyllodes tumor, showing malignant features on the left and borderline characteristics associated with a fibroadenoma on the right. A further molecular analysis was carried out by an array-Comparative Genomic Hybridization (CGH) to characterize copy-number alterations. Many losses were detected in the malignant mass, involving several tumor suppressor genes. These findings could explain the malignant growth and the metastatic risk. In our study, genomic profiling by an array-CGH revealed a greater chromosomal instability in the borderline mass (40 total defects) than in the malignant (19 total defects) giant phyllodes tumor, reflecting the tumor heterogeneity. Should our results be confirmed with more sensitive and specific molecular tests (DNA sequencing and FISH analysis), they could allow a better selection of patients with adverse pathological features, thus optimizing and improving patient's management.

14q12q13.2 microdeletion syndrome: Clinical characterization of a new patient, review of the literature, and further evidence of a candidate region for CNS anomalies.

BACKGROUND: Chromosome 14q11-q22 deletion syndrome (OMIM 613457) is a rare contiguous gene syndrome. Two regions of overlap (RO) of the 14q12q21.1 deletion have been identified: a proximal region (RO1), including FOXG1(*164874), NKX2-1(*600635), and PAX9(*167416) and a distal region (RO2), including NKX2-1 and PAX9. We report a 6-year-old boy with mild dysmorphic facial features, global developmental delay, and hypoplasia of the corpus callosum. METHODS AND RESULTS: Array-CGH analysis revealed a 14q12q13.2 microdeletion. We compared the phenotype of our patient with previously published cases in order to establish a genotype-phenotype correlation. CONCLUSION: The study hypothesizes the presence of a new RO, not including the previously reported candidate genes, and attempt to define the associated molecular and psychomotor/neurobehavioral phenotype. This region encompasses the distal breakpoint of RO1 and the proximal breakpoint of RO2, and seems to be associated with intellectual disability (ID), hypotonia, epilepsy, and corpus callosum abnormalities. Although more cases are needed, we speculated on SNX6(*606098) and BAZ1A(*605680) as potential candidate genes associated with the corpus callosum abnormalities.

Genomic changes of chromosomes 8p23.1 and 1q21: Novel mutations in malignant mesothelioma.

INTRODUCTION: Malignant mesothelioma is an aggressive malignancy of the thoracic cavity caused by prior asbestos exposure. In the peritoneum the mesothelioma is an extremely rare condition. In the present preliminary study, high-resolution array-comparative genomic hybridization (a-CGH) was performed to identify genetic imbalances in a series of malignant peritoneal mesothelioma cases. MATERIALS AND METHODS: Between 1990 and 2008, among the cases recorded in the Apulia Mesothelioma Register, we found 22 peritoneal mesothelioma cases. CGH-array was performed on samples from all patients. RESULTS: The CGH-array analysis revealed multiple chromosomal imbalances. Interestingly, deletion at 8p23.1 was observed in 12 cases. Furthermore, another novel deletion at 1q21 was present in 11. Often, 1q21 and 8p23.1 losses were present in the same patient (7 cases). Losses of BAP1 and CDKN2A loci were not detected. DISCUSSION: The region at 8p23.1 contains the beta-defensin gene cluster (DEF) and 1q21 contains ubiquitin conjugating enzyme E2 (UBE2Q1). We hypotesized that the loss of function of ubiquitination, as well as of the defensins, could play an important role in the initial development and subsequent progression of mesothelioma.

Peritoneal Mesothelioma with Residential Asbestos Exposure. Report of a Case with Long Survival (Seventeen Years) Analyzed by Cgh-Array.

Malignant mesothelioma is a rare and aggressive tumor with limited therapeutic options. We report a case of a malignant peritoneal mesothelioma (MPM) epithelioid type, with environmental asbestos exposure, in a 36-year-old man, with a long survival (17 years). The patient received standard treatment which included cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). METHODS AND RESULTS: Molecular analysis with comparative genomic hybridization (CGH)-array was performed on paraffin-embedded tumoral samples. Multiple chromosomal imbalances were detected. The gains were prevalent. Losses at 1q21, 2q11.1→q13, 8p23.1, 9p12→p11, 9q21.33→q33.1, 9q12→q21.33, and 17p12→p11.2 are observed. Chromosome band 3p21 (BAP1), 9p21 (CDKN2A) and 22q12 (NF2) are not affected. Conclusions: the defects observed in this case are uncommon in malignant peritoneal mesothelioma. Some chromosomal aberrations that appear to be random here, might actually be relevant events explaining the response to therapy, the long survival and, finally, may be considered useful prognostic factors in peritoneal malignant mesothelioma (PMM).

14q13 distal microdeletion encompassing NKX2-1 and PAX9: Patient report and refinement of the associated phenotype.

Chromosome 14q11-q22 deletion syndrome (OMIM 613457) is a rare genomic disorder whose associated phenotype is heterogeneous, depending on the size, and, mostly, on the deleted region. We report the clinical and molecular characterization of a female newborn, whose phenotype was characterized by poor growth, dysmorphic facial features, subclinical hypothyroidism, and mild reduction of CD3CD8 Lymphocytes with increased CD4/CD8 ratio. By array-CGH, we identified a 4.08 de novo interstitial deletion of the 14q13.2q21.1 region, which includes 16 OMIM genes.Our patient phenotype is compared with other published cases, for a better classification of the 14q11-q22 deletion syndrome. We demonstrated that the 14q13.2q21.1 deletion, which encompasses NKX2-1, but not FOXG1 gene and HPE8 region, identifies a well defined, more benign, microdeletion syndrome. This report confirms that an early identification with accurate characterization of the genomic disorders is of great relevance, enabling proper genetic counseling of the reproductive risk, as well as disease prognosis, and patient management. © 2016 Wiley Periodicals, Inc.

Molecular cytogenetic characterization and genotype/phenotype analysis in a patient with a de novo 8p23.2p23.3 deletion/12p13.31p13.33 duplication.

Genomic copy number imbalances are being increasingly identified as an important cause of intellectual disability (ID) and behavioral disturbances. This article reports the clinical features, and long term follow-up of a patient with neurodevelopmental, cognitive, and behavioral abnormalities associated with facial dysmorphism, CNS anomalies, and epilepsy. The karyotype was normal; array CGH testing revealed a de novo cryptic aberration with a terminal 8p23.2p23.3 deletion, and a concomitant 12p13.31p13.33 duplication, of 6.86 Mb, and 8.49 Mb, respectively. Our patient clinical features are compared to those of partial 8 monosomy and/or partial 12p trisomy cases reported in literature, in order to establish genotype-phenotype correlations. For some features, for example, electroencephalogram (EEG) abnormalities and epilepsy, both abnormalities seem to make a contribution, while most phenotypic traits have been assigned to 8p monosomy or to 12p trisomy, contributing to a tentative phenotype map for partial monosomy of the short arm of chromosome 8, and trisomy of the short arm of chromosome 12.

High Wilms' tumour gene (WT1) expression and low mitotic count are independent predictors of survival in diffuse peritoneal mesothelioma.

AIMS: To evaluate the use of the Wilms' tumour gene (WT1) marker and histomorphological parameters as indicators of prognosis in malignant peritoneal mesothelioma (MPM). METHODS AND RESULTS: Histological samples of 31 MPM were stained immunohistochemically for the WT1 protein. The results were quantified by recording the number of stained nuclei, and then correlated with patient survival. Statistical correlation was evaluated for tumour histotype, mitotic count (MC), nuclear grade (NG), necrosis, lymphoid response (grade of inflammation) and desmoplasia with regard to survival. High-grade histology (solid epithelioid, pure sarcomatoid or biphasic tumours), high NG, MC more than five per 10 per high-power field (HPF), necrosis and desmoplasia were associated with a significantly worse prognosis. Patients with MPM with low WT1 expression (≤25% of positive cells) survived for a significantly shorter time compared to those with high WT1 expression (>25% of positive cells) (P = 0.0001). The 50% survival time of subjects with low WT1 expression was 2.9 months [95% confidence interval (CI): 2.05-3.71] versus 31.5 months (95% CI: 20.4-42.5) for those with high WT1 expression. On multivariate analysis, WT1 and MC were found to be associated independently with survival (P = 0.002; P = 0.005, respectively). CONCLUSIONS: Our study suggests that low WT1 expression and high MC may be indicative of an unfavourable prognosis in patients with advanced malignant peritoneal mesothelioma.

Characterization of a complex chromosome aberration in two cases of peritoneal mesothelioma arising primarily in the hernial sac.

Malignant mesotheliomas of the hernial sac are uncommon and only a few cases have been diagnosed incidentally during herniorrhaphy procedures. The prognosis is poor and patient management is difficult because current treatment modalities do little to prolong survival. Molecular markers could be useful to identify potential therapeutic targets. Using microarray-comparative genomic hybridization (aCGH), two cases of peritoneal mesothelioma that were found incidentally at the time of hernia repair, were investigated. A high number of genetic aberrations was detected in both cases. The gains were prevalent. The tumors showed identical lost regions at 2q13, 6q25.3, 6q26, 6q26-->q27, 9q31.1-->9q31.3, 10p15.3, 11q13.2, 13q14.2, 19q13.42-->q43, and gains at 1p36.33, 3q29, 5p15.33, 7p22.3, 10p15.1-->10p14, 11q13.2, 12q24.23, 12q24.33, 16p13.3, 17p13.3, 18p11.31, 19q13.43, 21q21.1-->q21.2, 22q11.1-->q11.22, Xp21.2, Xq28. Survival was longer in the patient with a lower total number of genetic defects. aCGH provides a high-resolution map of copy number changes that may be critical to mesothelioma progression.

Interstitial 1q43-q43 deletion with left ventricular noncompaction myocardium.

We describe a newborn infant with del(1)(q) syndrome, presenting with rare congenital cardiomyopathy and left ventricular noncompaction myocardium (LVNC), as well as typical clinical features such as facial dysmorphism and psychomotor retardation. Although conventional chromosome banding at 850 bands per haploid set indicated a karyotype of 46,XX,add(1)(q42.3), FISH analysis confirmed that the deleted portion was limited to within q43, and q44 was preserved. Therefore, the chromosome constitution is 46,XX,del(1)(q43q43), which has not previously been reported in the literature. Screening for the mutations in the candidate genes for LVNC, i.e. G4.5, CSX, Dystrobrevin, FKBP12, and Desmin, produced negative results. Interestingly, the deleted portion includes the locus for the cardiac ryanodine receptor type 2 gene (RyR2), that selectively binds to the FKBP12 homolog, FKBP12.6. The relationship between this rare myocardial abnormality and deletion of q43 is currently unknown and awaits further accumulation of cases with the same chromosomal aberration.

Prenatal diagnosis of chromosome 4 mosaicism: prognostic role of cytogenetic, molecular, and ultrasound/MRI characterization.

Trisomy 4 mosaicism is extremely rare: herein we report the cytogenetic and molecular characterization and prenatal US findings of a case diagnosed prenatally. The diagnosis of level III mosaicism was established in cultured amniotic fluid cells (22.5%). At 22 weeks gestation, micrognathia and hypotelorism were suspected at 2-D sonography, and confirmed at 3-D examination. In addition, 2-D US showed cerebellar hypoplasia associated with borderline ventriculomegaly (confirmed at magnetic resonance imaging, MRI), spine deformity (hemivertebra), and a complete atrioventricular septal defect (AVSD). The pregnancy was terminated. Trisomy 4 mosaicism was confirmed in placental and fetal skin cultured cells. The cord blood karyotype was normal. Molecular analysis excluded uniparental disomy of chromosome 4, and indicated that the trisomy 4 was of maternal meiotic origin. In presence of chromosome 4 mosaicism, accurate fetal sonography and echocardiography are mandatory. Low level mosaicism and normal echographic examinations seem to be associated with good prognosis. In postnatal life, chromosome 4 mosaicism should be suspected, and cytogenetic analysis proposed of further tissues (i.e., skin), in presence of craniofacial dysmorphism, cardiac defects, and abnormal hands/feet, even if mental development is appropriate or only slightly impaired.

22q11 deletions in fetuses with malformations of the outflow tracts or interruption of the aortic arch: impact of additional ultrasound signs.

OBJECTIVES: One hundred and forty-one consecutive cases of malformations of the outflow tracts or interrupted aortic arch (IAA), detected by fetal echocardiography, underwent detailed anatomy scan, karyotyping and fluorescence in situ hybridization analysis (FISH) to detect the prevalence of 22q11 microdeletion and to evaluate neonatal clinical findings and outcome according to the presence of the genetic defect. Then, we sought to investigate whether some prenatal ultrasound findings could help identify fetuses at higher risk of carrying the 22q11 microdeletion. METHODS: Echocardiography and FISH for the DiGeorge critical region (22q11) were performed in all cases. RESULTS: 22q11 microdeletion was detected in 28 of 141 fetuses (19.8%). Intrauterine growth restriction (IUGR) appeared to be associated with the worst prognosis, being present in 2/2 intrauterine fetal deaths and 5/6 post-natal deaths. IUGR, additional aortic arch anomalies and thymic hypo/aplasia were significantly more frequent in fetuses with 22q11 microdeletion (p=0.011, 0.011 and <0.0001, respectively). Prenatal ultrasound thymus examination, performed on the last 84 fetuses, showed 75% sensitivity and 94% specificity. The combination of 2 predictors, namely, thymus defects and IUGR associated with additional aortic arch anomalies reached more than 90% sensitivity and 100% specificity. CONCLUSIONS: Our study demonstrates that 22q11 microdeletion occurs in 20% of malformations of the outflow tracts and IAA type B, as detected in utero, and that this association is significantly predicted by the presence of associated ultrasound findings: thymic hypo/aplasia, IUGR and additional aortic arch anomalies. The feasibility of a correct prenatal diagnosis should enable clinicians to provide the couple with further informative counselling and to plan adequate post-natal medical interventions.