Molecular Genetics & Genomic Medicine最新文献

Background: Li-Fraumeni syndrome is a rare autosomal dominant disorder caused by a pathogenic mutation of the tumor suppressor gene TP53. This disease starts at an early age and has been shown to be associated with multiple tumors. The study aims to discuss the clinical and genetic characteristics of Li-Fraumeni syndrome (LFS) and to provide therapeutic experience of LFS.

Materials and methods: We conducted a retrospective analysis of the clinicopathologic features, family history, treatment and follow-up in five LFS patients with germline TP53 (NCBI Gene: 7157, HGNC: 11998, OMIM: 191170) pathogenic/likely pathogenic (P/LP) variants. This research had been approved by the ethics committee and implemented.

Results: Our study involved five LFS patients with germline TP53 P/LP variants, including thyroid cancer, ovarian melanoma, colon cancer, fibrosarcoma, and lung cancer. Among this group of patients, the age at which tumors first appeared was between 24 and 53 years old. Three patients had a family history of tumors, and the other two were probands in the family. Traditional chemotherapy has limited effectiveness in clinical practice and may increase the risk of tumor development. However, immune checkpoint inhibitors (ICIs) have shown unexpected efficacy in patients with high programmed cell death ligand-1 (PD-L1) expression. Next-generation sequencing (NGS) and PD-L1 detection may provide more potential targets for LFS patients to achieve better therapeutic outcomes. In addition, we have added a new TP53 frameshift mutation spectrum, namely c.642_643delTA (p.H214Qfs*7), which belongs to the pathogenic variant. This mutant has not been described in the existing literature.

Conclusion: Patients with LFS may be potential beneficiaries of immune checkpoint inhibitors and targeted therapies.

Objective: Variants of the proto-cadherin 15 (PCDH15) gene are related to Usher syndrome type 1F (USH1F). The purpose of this study was to determine the genetic etiology of a USH1F family in China and to perform a minigene assay for the PCDH15 gene to explore the effect of variation on splicing and determine the pathogenicity of the identified variant.

Methods: Targeted next-generation sequencing of 127 hearing loss-related genes was performed for a 26-year-old proband to identify the candidate variants. Then, multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing were performed for all family members to confirm the variants. Further, to verify the pathogenicity of the intronic variant, a minigene splicing assay was performed.

Results: Compound heterozygous PCDH15 EX1_2DEL and c.3717+5G>A variants were identified in the proband. MLPA and Sanger sequencing confirmed these two variants and showed the same genotype of a paternally inherited c.3717+5G>A and a maternally inherited EX1_2DEL variation in both the proband and his affected sister. The minigene assay verified the pathogenicity of c.3717+5G>A and indicated that this variant possibly caused abnormal splicing, resulting in jump of exon 27 and retention of 51 bp at the 5' end of intron 27, leading to the formation of abnormal proteins.

Conclusion: This study reports a novel pathogenic variant c.3717+5G>A of PCDH15 in a proband for the first time. These findings offer evidence for the genetic counseling of USH1F. Minigene splicing assays are considered to be one of the most powerful methods for determining whether intron mutations lead to abnormal splicing.

Introduction: Fanconi anemia (FA) is the most prevalent inherited disorder leading to bone marrow failure, resulting from a rare autosomal recessive genetic condition that affects all three types of blood cells. A key characteristic of FA is the body's heightened sensitivity to DNA-damaging agents, particularly those that induce crosslinking, which serves as an important diagnostic marker. Children at higher risk-such as those with unexplained growth delays, congenital defects, or a family history of FA-can significantly benefit from genetic testing.

Methods: This study involved 140 pediatric patients aged 1 to 18 years who met specific inclusion criteria: unexplained short stature without identifiable endocrine or nutritional causes, congenital anomalies associated with FA (such as skeletal or craniofacial deformities), and a family history suggestive of FA or early-onset blood cancers. The screening and diagnostic approach included a Chromosomal Breakage Test and genetic analysis.

Results: The retrospective analysis revealed that 19 (13.57%) out of the 140 children had previously undiagnosed cases of Fanconi anemia. Among these cases, short stature was noted in 6.7% (5 of 75 patients with short stature), congenital anomalies in 13.3% (4 of 30 patients with congenital anomalies), and positive cases from family screening accounted for 28.6% (10 of 35 patients with positive family history). The findings from the chromosomal breakage test provided valuable insights into the rates of positive, mosaic, and negative outcomes. Notably, mutations in the FANCA gene were found to be the most common among confirmed cases.

Conclusion: Early genetic screening for Fanconi anemia in high-risk pediatric populations has proven to be an effective strategy for ensuring prompt diagnosis and timely management. Incorporating this screening into routine clinical practices could significantly enhance patient outcomes, reduce healthcare costs, and alleviate the impact of this serious genetic condition.

Background: Williams-Beuren syndrome (WBS; OMIM #194050), caused by 7q11.23 deletions, is well-characterized postnatally, but prenatal manifestations remain poorly defined. This study aims to delineate the prenatal phenotypes, inheritance patterns, and outcomes of 7q11.23 copy number variations (CNVs).

Methods: A retrospective study of 20 prenatal cases with 7q11.23 CNVs diagnosed by SNP array or CNV sequencing (CNV-seq) was conducted. Clinical data, including ultrasound findings, genetic results, and pregnancy outcomes, were analyzed.

Results: Classic 7q11.23 deletions (1.42 Mb median size) were associated with ultrasound anomalies in 100% of cases (11/11), predominantly cardiovascular defects (36.4%, 4/11) and growth restriction (18.2%, 2/11). While 7q11.23 duplications (1.42-3.03 Mb) were associated with anomalies in 50% of cases (3/6), including cleft palate and ventriculomegaly. Inheritance pattern analysis revealed 50% of deletions (6/12) and 42.9% of duplications (3/7) were inherited, either from phenotypically normal or abnormal parents. Termination of pregnancy (TOP) occurred in 76.5% (13/17) of ongoing pregnancies, primarily for de novo CNVs. Four live births involved inherited CNVs.

Conclusion: 7q11.23 CNVs exhibit significant prenatal phenotypic variability and inheritance heterogeneity. Advanced genomic testing and inheritance pattern analysis are critical for accurate diagnosis and counseling.

Background: Intellectual developmental disorder with autism and macrocephaly (IDDAM, OMIM #615032) is an autosomal dominant neurodevelopmental disorder characterized primarily by intellectual disability, autism spectrum disorder, macrocephaly, tall stature, gastrointestinal symptoms, and variable neurological manifestations. Most cases result from de novo pathogenic variants in CHD8.

Methods: We conducted genome sequencing through the Undiagnosed Diseases Network (UDN) in a female proband harboring a CHD8 variant of uncertain significance (VUS), whose clinical presentation was consistent with IDDAM but included atypical features such as ptosis and hearing loss. Variant pathogenicity was further evaluated using EpiSign DNA methylation analysis and structural biology modeling.

Results: Genome sequencing confirmed the CHD8 variant inherited from her father, who exhibited a subtle feature, including traits consistent with attention-deficit/hyperactivity disorder. Pathogenicity was confirmed through epigenetic signature testing (EpiSign), demonstrating characteristic methylation patterns and structural biology analysis, predicting significant protein destabilization.

Conclusion: We describe the case of IDDAM caused by a paternally inherited CHD8 variant. Our findings highlight the importance of considering parental inheritance in IDDAM diagnoses and suggest epigenetic and structural biology analyses as valuable tools for reclassifying VUS when variant pathogenicity remains uncertain.

Background: The calcium voltage-gated channel subunit alpha1 F (CACNA1F) gene-related retinal disorders have overlapping clinical symptoms and no definitive genotype-phenotype correlation, posing a challenge for diagnosis.

Methods: A comprehensive ocular examination was offered to a 6-year-old boy and his elder brother from a Chinese family. Exome sequencing and Sanger sequencing were applied to the family quads. A minigene assay was used to detect the aberrant splicing.

Results: The 6-year-old boy presented with low visual acuity, congenital nystagmus, and reduced photopic and scotopic responses in electroretinography, suggesting a clinical diagnosis of cone-rod dystrophy type 3 (CORDX3). By contrast, his elder brother merely had high myopia. A hemizygous splice-site variant CACNA1F NM_005183.4:c.4422-1G>T, inherited from their heterozygous carrier mother, was identified in the two brothers. Minigene assay showed that the variant resulted in intron 37 retaining or exon 38 skipping, leading to frameshift translation and early termination. This variant was absent from the public population databases and classified as pathogenic according to the ACMG guidelines.

Conclusion: A novel splice-site variant in CACNA1F with familial expression variability was identified. This study increases our understanding of the genotypic and phenotypic spectrum of CACNA1F-related disorders.

Background: DYNC1H1 is a critical gene implicated in neurodevelopmental and neuromuscular disorders with overlapping and variable phenotypes that challenge diagnosis.

Methods and results: Whole exome sequencing in patients presenting with motor neuron disease symptoms and a predominant pattern of lower-limb muscle weakness revealed pathogenic DYNC1H1 variants. This expands the known phenotypic spectrum to include rare features such as scapular winging and camptocormia. Clinical evaluations of affected individuals revealed features consistent with SMA-LED, reinforcing the role of DYNC1H1 in neuromuscular disorders. A review of 208 published DYNC1H1 variants highlighted significant clustering in the tail domain, primarily associated with neuromuscular conditions like SMA-LED. Approximately 28% of variants exhibited overlapping neuromuscular and neurodevelopmental features, emphasizing the diagnostic challenges posed by phenotypic overlap. These findings underscore the necessity of comprehensive clinical and genetic evaluations to address the variability observed within families and improve genotype-phenotype correlations.

Conclusion: This study reinforces the importance of DYNC1H1 in motor neuron function and its pivotal role in neurodevelopmental and neuromuscular disease mechanisms. The integration of exome sequencing in clinical practice is essential for identifying rare and novel variants, enhancing diagnostic accuracy. We recommend incorporating DYNC1H1 screening into diagnostic workflows to advance understanding and management of conditions with overlapping phenotypes.

Background: Hereditary pulmonary alveolar proteinosis (PAP) is a rare interstitial lung disease caused by variations in genes such as CSF2RA and CSF2RB, which disrupt granulocyte-macrophage colony-stimulating factor signaling and impair surfactant clearance. These defects lead to progressive surfactant accumulation in alveoli, resulting in respiratory dysfunction.

Methods: We describe a 3-year-old girl with Turner syndrome who presented with recurrent cough and dyspnea and was diagnosed with hereditary PAP. Diagnostic evaluation included high-resolution computed tomography (HRCT), lung biopsy, and whole-exome sequencing of peripheral blood cells. The patient received anti-inflammatory antibiotics and underwent therapeutic whole lung lavage via endobronchial endoscopy. A systematic literature review of CSF2RA-associated hereditary PAP was performed.

Results: HRCT demonstrated characteristic "crazy paving" patterns, and bronchoalveolar lavage fluid showed positive Periodic acid-Schiff staining. Genetic analysis identified a novel hemizygous variation in CSF2RA (NM_000402.4:c.200_204del, p.Asn67SerfsTer8), confirmed as a de novo pathogenic variant. Whole lung lavage resulted in marked clinical improvement.

Conclusions: We report the first documented case of hereditary PAP caused by the CSF2RA variant NM_000402.4:c.200_204del (p.Asn67SerfsTer8), expanding the genetic spectrum of this disease. Our findings reinforce that CSF2RA-related PAP exhibits phenotypic heterogeneity and confirm whole lung lavage as the cornerstone therapy. This case highlights the importance of genetic testing in diagnosing rare PAP subtypes.

Background: Prenatal diagnosis of X-linked hydrocephalus caused by variants in the L1CAM gene is often complicated by the identification of Variants of Uncertain Significance (VUSs). This study showcases an accelerated diagnostic workflow using artificial intelligence (AI) to rapidly interpret a novel missense variant for a family with a history of the disorder.

Methods: We performed exome sequencing (ES) on a male fetus with significant sonographic brain anomalies from a 29-year-old pregnant woman. To efficiently analyze the resulting VUSs, we used the AI tool AlphaMissense to predict their pathogenicity and prioritize them for validation. The top candidate variant was then assessed via Sanger sequencing for co-segregation across eight maternal relatives. The structural impact of the mutation was visualized using the AlphaFold 3 model.

Results: Exome sequencing identified four VUSs. AlphaMissense predicted only one, L1CAM c.1228C>G (p.His410Asp), as 'likely pathogenic'. Subsequent Sanger sequencing confirmed that this variant co-segregated perfectly with the disease phenotype in the family. Based on this strong genetic evidence, the variant was reclassified from a VUS to 'Likely Pathogenic'. Structural modeling revealed that the p.His410Asp substitution disrupts a critical salt bridge, likely compromising protein stability.

Conclusion: Our two-step approach-using AI for rapid VUS prioritization followed by targeted Sanger validation-proved to be a highly efficient strategy. It provided a definitive and clinically actionable diagnosis that facilitated genetic counseling and enabled the family to pursue Preimplantation Genetic Testing (PGT). This workflow significantly enhances the power of genomic testing in the prenatal setting.

Introduction: Meckel-Gruber syndrome (MKS, OMIM 24,900), also known as Meckel syndrome, is a rare and severe autosomal recessive disorder. The syndrome is typically characterized by a triad of occipital encephalocele, bilateral renal cystic dysplasia, and postaxial polydactyly. MKS shows significant clinical heterogeneity, which poses challenges for accurate prenatal diagnosis. Prenatal ultrasound is an important tool for detecting potential cases, but the complexity of MKS often requires additional advanced techniques such as prenatal whole-exome sequencing (WES) to provide more accurate molecular genetic evidence.

Methods: In this study, we used whole-exome sequencing (WES) to analyze the genetic causes of suspected MKS in a Chinese fetus. Sanger sequencing was used to confirm the origin of the variants. The classification of variants was carried out in accordance with the guidelines of the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP).

Results: A 26-year-old pregnant woman was referred to our antenatal centre for genetic diagnosis at 13 + 5 weeks of gestation due to fetal occipital encephalocele and renal cysts detected by ultrasound. Two novel heterozygous variants, c.1047delA (p.Val351fs*1) and c.1336C>T (p.Arg446*), were identified in TCTN2. Sanger sequencing revealed that the c.1047delA (p.Val351fs*1) variant was inherited from the mother and the c.1336C>T (p.Arg446*) variant was inherited from the father. According to the ACMG/AMP guidelines, these two variants were evaluated as pathogenic.

Conclusions: This study further expands the genetic mutation spectrum of TCTN2 and is conducive to further clarifying the relationship between the genotype and phenotype of MKS8. Severe variants in the TCTN2 gene appear to be more likely to lead to MKS8. Clinically, the triad is an important basis for the diagnosis of MKS8, while other variable phenotypes of MKS8 can provide additional information for prenatal diagnosis. The combination of prenatal ultrasound and WES can provide a more comprehensive and accurate diagnosis of MKS8, which will greatly aid support for early intervention and treatment.