Copy number alteration (CNA) is a significant genetic change in pediatric B-cell acute lymphoblastic leukemia (B-ALL), with CDKN2A/B deletions, PAX5 deletions, and IKZF1 deletions being the most common. Recent studies have increasingly highlighted the potential prognostic significance of these gene deletions and multiple co-deletions in pediatric B-ALL. This paper reviews the main detection methods for CNA, as well as the prognostic characteristics and treatment approaches for common CNA in pediatric B-ALL.
Humans ; DNA Copy Number Variations ; Child ; PAX5 Transcription Factor/genetics* ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics* ; Cyclin-Dependent Kinase Inhibitor p15/genetics* ; Ikaros Transcription Factor/genetics* ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics* ; Gene Deletion ; Cyclin-Dependent Kinase Inhibitor p16/genetics* ; Prognosis

OBJECTIVE: To investigate the relationship between CDKN2A copy number deletion and clinical features of patients with diffuse large B-cell lymphoma (DLBCL) and its prognostic value. METHODS: 155 newly diagnosed DLBCL patients with complete clinical data in the Department of Hematology of People's Hospital of Xinjiang Uygur Autonomous Region from March 2009 to March 2022 were included, formalin-fixed paraffin-embedded tumor tissues were obtained and DNA was extracted from them, and next-generation sequencing technology was applied to target sequencing including 475 lymphoma-related genes, the relationship between CDKN2A copy number deletion and clinical features, high-frequency mutated genes and overall survival (OS) of DLBCL patients were analyzed. RESULTS: CDKN2A copy number deletion was present in 12.9% (20/155) of 155 DLBCL patients, grouped according to the presence or absence of copy number deletion of CDKN2A, and a higher proportion of patients with IPI≥3 were found in the CDKN2A copy number deletion group compared to the group with no CDKN2A copy number deletion (80% vs 51.5%, P =0.015) and were more likely to have bulky disease (20% vs 5.2%, P =0.037). Survival analysis showed that the 5-year OS of patients in the CDKN2A copy number deletion group was significantly lower than that of the non-deletion group (51.3% vs 69.2%, P =0.047). Multivariate Cox analysis showed that IPI score≥3 (P =0.007), TP53 mutation (P =0.009), and CDKN2A copy number deletion (P =0.04) were independent risk factors affecting the OS of DLBCL patients. CONCLUSION CDKN2A copy number deletion is an independent risk factor for OS in DLBCL, and accurate identification of CDKN2A copy number deletion can predict the prognosis of DLBCL patients.
Humans ; Lymphoma, Large B-Cell, Diffuse/genetics* ; Prognosis ; Cyclin-Dependent Kinase Inhibitor p16/genetics* ; DNA Copy Number Variations ; Female ; Male ; Middle Aged ; Gene Deletion ; Adult ; Aged

BACKGROUND: Mitochondria, which harbor their own genome (mtDNA), have attracted attention due to the potential of mtDNA copy number (mtDNA-CN) as an indicator of mitochondrial dysfunction. Although mtDNA-CN has been proposed as a simple and accessible biomarker for metabolic disorders such as metabolic dysfunction-associated steatotic liver disease, the underlying mechanisms and the causal relationship remain insufficiently elucidated. In this investigation, we combined longitudinal epidemiological data, animal studies, and in vitro assays to elucidate the potential causal relationship between reduced mtDNA-CN and the development of steatotic liver disease (SLD). METHODS: We conducted a longitudinal study using data from a health examination cohort initiated in 1981 in Yakumo, Hokkaido, Japan. Data from examinations performed in 2015 and 2022 were analyzed, focusing on 76 subjects without SLD at baseline (2015) to assess the association between baseline mtDNA-CN and subsequent risk of SLD development. In addition, 28-day-old SD rats were fed ad libitum on a 45% high-fat diet and dissected at 2 and 8 weeks of age. Blood and liver mtDNA-CN were measured and compared at each feeding period. Additionally, in vitro experiments were performed using HepG2 cells treated with mitochondrial function inhibitors to induce mtDNA-CN depletion and to examine its impact on intracellular lipid accumulation. RESULTS: Epidemiological analysis showed that the subjects with low mtDNA-CN had a significantly higher odds ratio for developing SLD compared to high (odds ratio [95% confidence interval]: 4.93 [1.08-22.50]). Analysis of the animal model showed that 8 weeks of high-fat diet led to the development of fatty liver and a significant decrease in mtDNA-CN. A further 2 weeks of high-fat diet consumption resulted in a significant decrease in hepatic mtDNA-CN, despite the absence of fatty liver development, and a similar trend was observed for blood. Complementary in vitro experiments revealed that pharmacologically induced mitochondrial dysfunction led to a significant reduction in mtDNA-CN and was associated with increases in intracellular lipid accumulation in HepG2 cells. CONCLUSIONS Our findings suggest that reduced mtDNA-CN may contribute causally to SLD development and could serve as a convenient, noninvasive biomarker for early detection and risk assessment.
Animals ; DNA, Mitochondrial/genetics* ; Humans ; Male ; DNA Copy Number Variations ; Female ; Fatty Liver/blood* ; Rats ; Middle Aged ; Longitudinal Studies ; Rats, Sprague-Dawley ; Adult ; Japan/epidemiology* ; Aged ; Biomarkers/blood* ; Hep G2 Cells ; Diet, High-Fat/adverse effects*

In light of the lack of reliable molecular markers for odontogenic myxoma (OM), the detection of copy number variation (CNV) may present a more objective method for assessing ambiguous cases. In this study, we employed multiregional microdissection sequencing to integrate morphological features with genomic profiling. This allowed us to reveal the CNV profiles of OM and compare them with dental papilla (DP), dental follicle (DF), and odontogenic fibroma (OF) tissues. We identified a distinct and robustly consistent CNV pattern in 93.75% (30/32) of OM cases, characterized by CNV gain events in chromosomes 4, 5, 8, 10, 12, 16, 17, 20, and 21. This pattern significantly differed from the CNV patterns observed in DP, DF, and OF. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated potential links between this CNV patterns and the calcium signaling pathway and salivary secretion, while Gene Ontology (GO) term analysis implicated CNV patterns in tumor adhesion, tooth development, and cell proliferation. Comprehensive CNV analysis accurately identified a case that was initially disputable between OF and OM as OM. Our findings provide a reliable diagnostic clue and fresh insights into the molecular biological mechanism underlying OM.
Humans ; DNA Copy Number Variations ; Odontogenic Tumors/diagnosis* ; Myxoma/genetics* ; Female ; Male ; Adult ; Adolescent ; Middle Aged ; Dental Papilla ; Young Adult ; Fibroma/genetics* ; Dental Sac ; Child

OBJECTIVE: To assess the application value of copy number variation sequencing (CNV-seq) for women with a high risk for fetal anomalies. METHODS: Based on the results of non-invasive prenatal testing (NIPT), 271 high-risk pregnant women were divided into NIPT positive group (n = 83) and other anomaly group (advanced age, high risk by serological screening, repeated NIPT failure, adverse pregnancy history, abnormal ultrasound finding, and abnormal phenotype) (n = 188). CNV-seq was carried out to detect copy number variations (CNVs) in amniocytic DNA from the two groups of pregnant women, and karyotyping analysis of the amniotic cells was carried out for verification and comparison. RESULTS: The amniocytes from 271 pregnant women were detected. The detection rate was 20.66% (56/271) for pathogenic CNVs by CNV-seq and 19.19% (52/271) for pathogenic karyotypes by karyotyping analysis. The difference was statistically significant (P < 0.05). CNV-seq had shown that, compared with NIPT positive group, the detection rates for likely pathogenic CNVs and variants of unknown significance (VUS) in other abnormality group were significantly higher [2.41%(2/83) vs. 5.32%(10/188)](P < 0.05). CONCLUSION CNV-seq can well suit the first-tier diagnosis for pregnant women suspected for fetal abnormality. In prenatal diagnosis settings, CNV-seq can identify additional and clinically significant cytogenetic abnormalities. In those with other abnormalities, the detection rates for likely pathogenic CNVs and VUS are higher than with the NIPT positive cases.
Female ; Pregnancy ; Humans ; DNA Copy Number Variations ; Pregnancy, High-Risk ; Prenatal Diagnosis/methods* ; Chromosome Aberrations ; Chromosome Disorders/genetics*

OBJECTIVE: To explore the genetic etiology of a Chinese pedigree featuring non-simplex blepharocheilodontic syndrome. METHODS: Whole exome sequencing was carried out to detect genetic variant and copy number variations (CNVs) in the pedigree. Suspected variants were verified by Sanger sequencing and qPCR. RESULTS: The fetus and its elder brother, father and grandfather were found to harbor a heterozygous c.83delG (p.A29Rfs*55) variant of the CTNND1 gene, which was unreported previously. In addition, its elder brother was also found to be a double heterozygote for a c.235delC (p.L79Cfs*3) variant of GJB2 gene and a c.538C>T (p.R180X) variant of GJB3 gene, which were respectively inherited from his mother and father. CNVs analysis revealed a de novo heterozygotic deletion (1.46 Mb) at 17q12 in the mother, which was confirmed by qPCR. Based on American College of Medical Genetics and Genomics guidelines, the c.83delG variant, the c.235delC variant and the 17q12 microdeletion were predicted as pathogenic, while the c.538C>T variant was of uncertain significance. CONCLUSION The c.83delG (p.A29Rfs*55) variant of the CTNND1 gene probably underlay the pathogenesis of non-simplex blepharocheilodontic syndrome in this pedigree. The double heterozygous variants of c.235delC (p.L79Cfs*3) of GJB2 gene and c.538C>T (p.R180X) of GJB3 gene probably underlay the hearing loss in the elder brother. The bilateral renal cysts in the mother may be attributed to the 17q12 microdeletion. Above results have provided guidance for genetic counseling and prenatal diagnosis for this pedigree.
Male ; Pregnancy ; Female ; Humans ; Aged ; Pedigree ; Mutation ; DNA Copy Number Variations ; East Asian People ; China

OBJECTIVE: To explore the genetic basis for two patients from a family with BCL11A-related intellectual disability (BCL11A-ID). METHODS: Clinical data of the proband and her family members was analyzed. Chromosomal karyotyping analysis, trio-whole exome sequencing (trio-WES) and copy number variation sequencing (CNV-seq) were carried out. For the suspected genetic variants, Sanger sequencing was used to verify, and pathogenicity assessment was conducted. RESULTS: The proband and her mother both had intellectual and language impairment, and their fetal hemoglobin (HbF) was significantly elevated. A heterozygous c.1327_c.1328delTC (p.Ser443Hisfs*128) variant was found in exon 4 of the BCL11A gene by WES, which has resulted in truncated expression of the encoded protein, and Sanger sequencing has verified that the variant was inherited from the mother. The variant was not found in related databases. The variant was predicted as pathogenic according to the guidelines from the American College of Medical Genetics and Genomics (ACMG) (PVS1+PM2+PP1). No karyotypic abnormality was found in the proband, her parents and brother, and no pathogenic CNVs was found in the proband and her parents. CONCLUSION The c.1327_c.1328delTC (p.Ser443Hisfs*128) variant may underlay the BCL11A-ID in the proband and her mother. This de novo variant has expanded the mutational spectrum of the BCL11A gene.
Humans ; Male ; Female ; Intellectual Disability/genetics* ; DNA Copy Number Variations ; Pedigree ; Mutation ; Transcription Factors/genetics* ; Mothers ; Repressor Proteins/genetics*

OBJECTIVE: To explore the genetic basis for a child with Aspartylglucosaminuria (AGU). METHODS: Clinical data of the patient was analyzed. The child was subjected to trio-whole exome sequencing (WES) and copy number variation sequencing (CNV-seq), and candidate variant was verified by Sanger sequencing. RESULTS: The child was found to harbor homozygous c.319C>T (p.Arg107*) nonsense variant of the AGA gene, for which both of his parents were heterozygous carriers. No abnormality was found by CNV-seq analysis. The c.319C>T (p.Arg107*) variant was not found in population database, HGMD and other databases. Based on guidelines of the American College of Medical Genetics and Genomics, the variant was predicted to be pathogenic (PVS1+PM2+PP3). CONCLUSION The c.319C>T variant of the AGA gene probably underlay the autosomal recessive AGU in this child. Above finding has enabled genetic counseling and prenatal diagnosis for his parents.
Female ; Pregnancy ; Humans ; Child ; Aspartylglucosaminuria ; DNA Copy Number Variations ; Genetic Counseling ; Genomics ; Heterozygote ; Mutation

OBJECTIVE: To explore the genetic basis for a fetus with club foot detected upon mid-pregnancy ultrasonography. METHODS: Amniotic fluid of the fetus and peripheral blood samples of its parents were collected and subjected to G-banding karyotype analysis and copy number variation sequencing (CNV-seq). The result was verified by fluorescence in situ hybridization (FISH). RESULTS: The fetus and its parents all had a normal karyotype. CNV-seq analysis revealed that the fetus has harbored a 23.12 Mb on chromosome 5 and a 21.46 Mb duplication on chromosome 7. FISH assay has verified that its mother has carried a cryptic t(5;7)(p14.3;q33) translocation. CONCLUSION CNV-seq combined with FISH can effectively detect cryptic chromosome aberrations, and can help to reduce severe birth defects and provide a basis for prenatal genetic counseling.
Pregnancy ; Female ; Humans ; Cri-du-Chat Syndrome ; In Situ Hybridization, Fluorescence ; DNA Copy Number Variations ; Prenatal Diagnosis ; Fetus ; Amniotic Fluid ; Chromosome Deletion

Chromosomal aberrations including numerical abnormalities and segment duplications/deletions, as genome-wide copy number variations (CNVs), are a leading cause for spontaneous abortion. Analysis of abortive tissues for such CNVs can detect potential genomic variations in the couple and provide guidance for the choice of appropriate method to avoid further miscarriage or birth of child with chromosomal disorders. With evidence-based clinical data, an expert group jointly formed by the Genetic Disease Prevention and Control Group, Committee for Birth Defects Prevention and Control, Chinese Association of Preventive Medicine; the Clinical Genetics Group, the Society of Medical Genetics, Chinese Medical Association; the Professional Committee for Prenatal Diagnosis of Genetic Diseases, the Society of Medical Geneticists, Chinese Medical Doctor Association has discussed and formulated this consensus, with an aim to provide guidance for the application of genomic CNVs detection for the abortive tissue and genetic counseling for family reproduction.
Pregnancy ; Child ; Female ; Humans ; DNA Copy Number Variations ; Consensus ; Chromosome Aberrations ; Chromosome Disorders/genetics* ; Abortion, Spontaneous/genetics*