Jul 2026· American Journal of Medical Genetics. Part A· 0 citations· 46 references
Medicine
TL;DR
A variety of genomic rearrangement mechanisms contribute to copy number variations at the 17p11.2 locus driven in part by its complex genomic architecture which is characterized by low copy repeats (LCRs) and other repetitive elements, and genomic variations found in 11 families included simple copy number gains, higher order amplifications, and complex genomic rearrangements.
Abstract
A variety of genomic rearrangement mechanisms contribute to copy number variations at the 17p11.2 locus driven in part by its complex genomic architecture which is characterized by low copy repeats (LCRs) and other repetitive elements. These copy number variants are primarily mediated by nonallelic homologous recombination (NAHR) leading to recurrent tandem duplications and reciprocal deletions of the genomic interval mapping between the repeats. Two notable neurodevelopmental genomic disorders: Potocki-Lupski Syndrome (PTLS; MIM: 610883) and Smith-Magenis Syndrome (SMS; MIM: 182290) are driven by LCRs that undergo NAHR between the directly oriented repeats causing a duplication (PTLS) or deletion (SMS) encompassing the dosage-sensitive gene RAI1. We observed that other uncommon gains of varying sizes and extent at the 17p11.2 locus, which do not include the RAI1 gene, could be found in patients ascertained with a neurodevelopmental delay (NDD) phenotype. We ascertained 15 individuals from 11 families with copy number gains at the 17p11.2 locus not encompassing the driver gene-RAI1; such individuals manifested a broad spectrum of neurodevelopmental phenotypes. To validate our genomic findings, investigate DNA rearrangement mechanism(s), and refine our understanding at the breakpoint junctions, we performed a combination of high-resolution array CGH (n = 15), short-read whole-genome sequencing (sr-GS, n = 4), long-read GS (lr-GS; ONT; n = 4 and PacBio HiFi; n = 4), and breakpoint junctional analysis on this subset. Phenotypes in each individual were systematically studied. The phenotypes noted in these 15 individuals from 11 families primarily included developmental delay, intellectual disability, and behavioral problems. The genomic variations found in these 11 families included simple copy number gains (n = 7), higher order amplifications (n = 2), and complex genomic rearrangements (n = 2) at the 17p11.2 locus, surrounding the RAI1 gene and not encompassing it. Individuals from 4/11 families carried inherited variants. Identification of such rearrangement gains at the 17p11.2 locus that do not include the driver gene RAI1 and yet research subjects still exhibit neurodevelopmental phenotypes creates an opportunity to (i) dissect the gene(s) and genetic mechanisms that might contribute to phenotypic variability at the PTLS locus and (ii) uncover previously unrecognized genes or disease pathways and mechanisms.
Copy number variants (CNVs) are a major source of genetic diversity and could contain some of the missing heritability for mouse models of human disease. However, mouse CNVs have not been comprehensively characterized because they are difficult to resolve in repeat-rich, segmentally duplicated or reference sequence-absent regions of the genome. Here we analyzed long range sequence (LRS) data for 40 inbred mouse strains and characterized CNVs using pangenome graph-based (and other) methods and a C57BL/6J telomere to telomere (T2T) genome reference sequence. We resolved 1,594 high-confidence CNVs that often overlap tandem repeats (60.3%), segmental duplications (44.8%) or pericentromeric regions (11.5%); and 131 CNVs were T2T sequence-specific. CNVs affected 384 protein-coding genes, which spanned a range of important functional classes. The 40-strain pangenome map expanded the genome sequence from 2.29 to 3.32 Gb, with the wild-derived strains accounting for the largest sequence increments. Two different AIs were sequentially used to analyze this database and identify a 29-kb deletion CNV within the Nlrp1b locus of KK mice that contributed to the metabolic syndrome they develop. Human NLRP1 alleles also were associated with metabolic syndrome features in human populations. Hence, AI analyses of this comprehensive T2T pangenome-based resource could uncover some of the missing heritability for mouse models of human diseases and biomedical traits.
Wenlong Ren, Zhuanfen Cheng, Gary Peltz· bioRxiv· 0 citations
Copy-number variants (CNVs) are major contributors to human disease. In Alzheimer disease (AD), APP duplications cause autosomal-dominant forms, but the role of CNVs in non-monogenic AD remains poorly characterized. We analyzed rare CNVs (frequency <1%) from 22,319 exomes (4,150 early-onset AD [EOAD, ≤65 years], 8,519 late-onset AD [LOAD], 9,650 unaffected control subjects) using harmonized calling and quality control. After identifying 17 individuals with a pathogenic CNV, we performed exome-wide and gene-set burden analyses. EOAD-affected individuals showed increased burdens of rare CNVs affecting coding genes, particularly deletions in AD-related genes. Integrated loss-of-function (LoF) analysis gathering short truncating variants with deletions showed that ABCA1 (odds ratio [OR] = 5.77 [95% confidence interval 2.25; 17.06], p = 0.0002) and ABCA7 deletions contribute to this deletion burden (OR = 2.29 [1.44; 3.65], p = 0.0006), while CTSB LoF alleles appear as candidates (OR = 5.03 [1.50; 20.71], p = 0.0089). We then performed exome-wide gene-level dosage analysis and highlighted 18 genes across five loci with a false discovery rate of <10%, including the 22q11.21 central region, where deletions were restricted to EOAD (including one de novo event) and duplications were enriched in control individuals, with intermediate frequencies in LOAD. We narrowed this locus to the SCARF2-KLHL22-MED15 region after integrating short truncating variants. Replication in 33,977 affected individuals and 362,322 control subjects confirmed association for 22q11.21 dosage with exome-wide significance (ORSCARF2 = 0.34 [0.21; 0.53]; mega-p value = 5.52 × 10-7). SCARF2 overexpression significantly increased amyloid-β uptake, congruent with duplication-associated decreased AD risk. We conclude that rare coding CNVs in a proportion of AD-associated genes and 22q11.21 deletions, including some found in DiGeorge syndrome, increase AD risk. Conversely, we identify 22q11.21 duplication as a strong AD-risk-decreasing factor.
O. Quenez, Catherine Schramm, K. Cassinari et al.· American Journal of Human Ge...· 0 citations
This work provides mechanistic evidence that a position effect at the SOX3 locus can cause hereditary spastic paraplegia and identifies a 3D regulatory rewiring of SOX3 and transcriptional dysregulation of SOX3 targets in iPSC-derived neurons.
T. Terkelsen, V. Yumiceba, Joshua Kim et al.· American Journal of Human Ge...· 0 citations
Ongoing need for chromosome microarray analysis (CMA) characterization prompted the description of all 16,138 copy number variants (CNVs) found in 3832 patients studied from 2009 to 2024, 92% of them with developmental disabilities and/or autism. Detailed reporting shows the overlap of variants qualified as benign (15,083 CNVs, sizes 0.1 Kb–3 Mb) or of uncertain significance (216 CNVs, sizes 11 Kb–20 Mb) with pathogenic CNVs (836, 11 Kb–31 Mb), which are emphasized in most studies. Further distinguishing pathogenic CNVs were 88 recurring microdeletion/duplications and 86 in single patients, with all of the former and 66 of the latter having previous syndrome associations. Diagnoses were provided in 749 (20% of) patients, increasing to 21% among the 2470 patients (2015–2024) with their karyotypes recorded. Diagnoses included 61 known chromosomal syndromes, with CMA confirming or clarifying the abnormal karyotype in 187 (7.6%) or 55 (2.2%). The 90 microdeletions averaged 6439 kb in length (with chromosomes 6, 8, 17, and 22 accounting for most cases), while the 90 microduplications averaged 6895 kb (with chromosomes 8, 14, 17, 22, and X accounting for most cases). Together, these represent an average imbalance of 798,000 nucleotides per patient (0.75% of their genome). Continued reporting that match detailed CNV findings with patient profiles, especially symptom spectra, is needed to optimize CMA potential for presymptomatic diagnosis and therapy.
Santosh Chaval, Sahil S. Tonk, Golder N. Wilson et al.· Current Issues in Molecular...· 0 citations
ASXL3 patient truncations in neurodevelopmental condition Bainbridge-Ropers syndrome are shown to mediates gain-of-function (GOF) by escaping nonsense-mediated decay and Cullin 4-dependent degradation, resulting in aberrant protein accumulation, widespread transcriptional dysregulation, and altered chromatin accessibility.
Y. Nakamura, T. Nguyen, N. Mor et al.· medRxiv· 0 citations
ABSTRACT Background Deletions involving the 1q43q44 region are among the most recurrent terminal chromosomal imbalances and are associated with a recognizable neurodevelopmental phenotype. These deletions may occur as isolated events or in the context of more complex rearrangements. Case Presentation We describe presumed monozygotic twin sisters (patients 1 and 2) with a de novo 1q43q44 deletion and an unrelated patient (patient 3) carrying a similar deletion combined with a 21q22.3 duplication derived from a t(1;21)(q43;q22.3)mat. All three patients exhibited features consistent with the distal 1q43q44 deletion syndrome, including microcephaly, corpus callosum abnormalities, developmental delay, intellectual disability, language impairment, hypotonia, micro−/retrognathia, and congenital heart defects. Results Cytogenetics and FISH analyses confirmed distal 1q deletions in all patients. Chromosomal microarray analysis identified a ~9.5 Mb deletion in patient 1 (her twin was not tested) and a ~12.1 Mb deletion in patient 3. Despite differences in deletion size and genomic context, both rearrangements disrupted a largely overlapping interval containing 171 genes, including the dosage‐sensitive neurodevelopmental genes AKT3, HNRNPU, and ZBTB18 as well as other monoallelic expressed genes (GREM2 and NLRP3) and, in patient 3 only, RYR2. Functional enrichment analyses highlighted pathways related to neurodevelopment, epilepsy, and cardiac function. Although the twins showed similar congenital manifestations, patient 1 later developed seizures whose origin could not be assessed. Conclusion These findings further support the role of haploinsufficient genes within the distal 1q43q44 region, particularly AKT3, HNRNPU, and ZBTB18, to the core neurodevelopmental phenotype and highlight the value of high‐resolution genomic analysis for patient characterization.
Ma. Guadalupe Domínguez-Quezada, H. Rivera, L. E. Figuera et al.· Journal of clinical laborato...· 0 citations
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