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Background: Chromosome 13q deletion syndrome shows variable clinical features related to the different potential breakpoints in chromosome 13q. The severely malformed phenotype is known to be associated with the deletion of a critical region in 13q32. However, esophageal atresia is a rare symptom and the relevant region is unknown. Thus, determining the association between accurate breakpoints and new clinical features is essential. Case presentation: A 28-year-old Japanese primigravid woman was referred for fetal growth restriction, absence of a gastric bubble, cerebellar hypoplasia, overlapping fingers, and polyhydramnios at 31 weeks gestation. At 38 + 0 weeks, she delivered a 1774 g female infant. The infant presented with isolated esophageal atresia (Gross type A), Dandy–Walker malformation, right microphthalmia, left coloboma, overlapping fingers, pleurocentrum in the thoracic vertebrae, reduced anogenital distance, and hearing loss. Her karyotype was diagnosed as 46,XX,del(13)(q32.1–qter) by amniocentesis, but array comparative genomic hybridization after birth revealed the deletion of 13q31.3–qter. At 48 days after birth, the infant underwent surgery for esophageal atresia and was later discharged from the hospital at 7 months of age. Conclusion: This case report and the literature reviews supports the previous findings on the pathological roles of haploinsufficiency of the ZIC2/ZIC5 in Dandy–Walker malformation and the EFBN2 haploinsufficiency in eye malformation and hearing loss. Furthermore, the possible involvement of IRS2, COLA1, and COLA2 in eye malformation were identified. This is the first case of 13q deletion syndrome with esophageal atresia (Gross A), but it may be a symptom of VATER/VACTER association (vertebral defects, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal malformations, and limb defects), as in the previous cases. These symptoms might also be associated with EFBN2 haploinsufficiency, although further research is required. [ABSTRACT FROM AUTHOR]

Background: Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare disorder of pulmonary vascular abnormality with persistent pulmonary hypertension of the newborn. The symptom usually presents within hours after birth, leading to an early demise. Heterozygous de novo point mutations and genomic deletions of the FOXF1 (forkhead box F1) gene or its upstream enhancer have been identified in most patients with ACD/MPV. Most cases of ACD/MPV are sporadic; however, familial cases are also reported in 10% of patients. Case presentation: We herein report a case of familial ACD/MPV that showed unusual glomeruloid proliferation of endothelial cells. In this family, three of the four siblings died within two to 3 days after birth because of persistent pulmonary hypertension and respiratory failure. Only the second child remains alive and healthy. An autopsy was performed for the third and fourth children, resulting in a diagnosis of ACD/MPV based on the characteristic features, including misalignment of smaller pulmonary veins and lymphangiectasis. In both of these children, glomeruloid endothelial proliferation of vessels was noted in the interlobular septa. The vessels were immunohistochemically positive for D2–40, CD31, Factor VIII, and ERG, suggestive of differentiation for both lymphatic and blood vessels. Conclusions: Unusual glomeruloid endothelial proliferation was observed in a familial ACD/MPV case. This histologic feature has not been described previously in ACD/MPV or any other pulmonary disease. Although the histogenesis of this histologic feature is unclear, this finding may suggest that ACD/MPV is a compound vascular and lymphovascular system disorder that exhibits various histologic features. [ABSTRACT FROM AUTHOR]

Background: Bilateral congenital diaphragmatic hernia (CDH) is very rare. A few studies have reported the pathogenic role of 5p in CDH.Case Presentation: A 23-year-old primigravida Japanese woman was referred for the following abnormal findings at 33 weeks of gestation: polyhydramnios, macroglossia, talipes equinovarus, and levocardia. A marker chromosome was detected by amniocentesis. Fluorescence in situ hybridization with whole chromosome paint 5 and nucleolus organizer region probes confirmed its origin from chromosome 5 and an acrocentric chromosome. The karyotype of the fetus was diagnosed as 47, XY, +mar. ish +mar(WCP5+). At 39 + 5 weeks, a 2462 g male infant was delivered, with a specific facial configuration. Bilateral CDH, hypoplasia of the corpus callosum, atrial septal defect, and hypothyroidism were also detected in the baby. The karyotype of the peripheral blood was consistent with that of the amniocentesis.Conclusion: Genes coded on 5p might be associated with the pathogenesis of CDH; however, further investigation is required. [ABSTRACT FROM AUTHOR]

Background: 5p deletion syndrome is known as cri-du-chat syndrome, but there are no reports on congenital diaphragmatic hernia complications associated with it.Case Presentation: A 28-year-old primigravida Japanese woman was referred for 5 mm of nuchal translucency. Fetal growth restriction was found at 20 weeks, and a left-sided congenital diaphragmatic hernia was diagnosed at 24 weeks. The karyotype of the fetus was diagnosed as 46, XX, del(5)(p14) and referred to our hospital. At 36 + 6 weeks, a 1524 g female infant was delivered after premature membrane rupture, with Apgar scores of 4 and 6 at 1 and 5 minutes, respectively. The baby was intubated immediately with sedation and muscle relaxation, after birth for initial treatment for congenital diaphragmatic hernia. The peripheral blood karyotype was consistent with the prenatal result. The infant was discharged alive, without any respiratory support, after the defect of the diaphragm was repaired.Conclusion: The results of this study may be helpful for antenatal genetic counseling. [ABSTRACT FROM AUTHOR]

Background: Gastrointestinal (GI) cancer including colorectal cancer, gastric cancer, pancreatic cancer, etc., are among the most frequent malignancies diagnosed annually and represent a major public health problem worldwide.Methods: This paper reports an aided curation pipeline to identify potential influential genes for gastrointestinal cancer. The curation pipeline integrates biomedical literature to identify named entities by Bi-LSTM-CNN-CRF methods. The entities and their associations can be used to construct a graph, and from which we can compute the sets of co-occurring genes that are the most influential based on an influence maximization algorithm.Results: The sets of co-occurring genes that are the most influential that we discover include RARA - CRBP1, CASP3 - BCL2, BCL2 - CASP3 - CRBP1, RARA - CASP3 - CRBP1, FOXJ1 - RASSF3 - ESR1, FOXJ1 - RASSF1A - ESR1, FOXJ1 - RASSF1A - TNFAIP8 - ESR1. With TCGA and functional and pathway enrichment analysis, we prove the proposed approach works well in the context of gastrointestinal cancer.Conclusions: Our pipeline that uses text mining to identify objects and relationships to construct a graph and uses graph-based influence maximization to discover the most influential co-occurring genes presents a viable direction to assist knowledge discovery for clinical applications. [ABSTRACT FROM AUTHOR]