Regions of Homozygosity on a Single Chromosome: Insights into Complex Diagnosis Caused by Imprinting Disorders, Recessive Disease, and Chromosomal Aberrations
Laboratory Genetics and Genomics
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Primary Categories:
- Genomic Medicine
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Secondary Categories:
- Genomic Medicine
Introduction:
Array comparative genomic hybridization (aCGH) with single nucleotide polymorphism (SNP) genotyping, is a powerful tool for detection of both copy number variants and copy-neutral aberrations, such as regions with long stretches of homozygosity (ROH). While the presence of ROH on multiple chromosomes undoubtfully suggests parental relatedness, ROH confined to a single chromosome (scROH) may indicate; uniparental disomy (UPD), shared ancestry between the parents, an error in chromosomal recombination, or chromosome rearrangements. Clinical significance and diagnostic impact of scROH remain inadequately explored. Herein, we investigated the clinical management and results of diagnostic testing in a cohort of patients with developmental delay and congenital structural birth defects and scROH detected by CGH+SNP microarray to assess the rate of imprinting disorders, recessive conditions, and chromosomal abnormalities.
Methods:
Microarray analysis was performed using the 180k CGH+SNP oligonucleotide array (Agilent). In order to identify cases with scROH of at least 8Mb in size, the results of chromosomal microarray analysis (CMA) were reviewed from patients referred to the UPMC Medical Genetics and Genomics Laboratories during 2012-2024 for a clinical testing. Findings of additional genetic assessment, including methylation studies, single gene sequencing, exome and genome sequencing were evaluated to investigate the clinical significance of scROH and to determine a follow-up management strategy.
Results:
Regions of homozygosity confined to a single chromosome were present in 56 cases among them UPD was identified in 23 patients (41.07%). Imprinting disorders were confirmed in 13 (23.2%) patients, including Prader-Willi syndrome (UPD15mat) in 7 cases (58.3%), Angelman syndrome (UPD15pat) in 2 cases (16.7%), Silver-Russel syndrome (UPD7mat) in 2 cases (16.7%), and 2 patients (16.7%) with UPD14. In 8 cases, microarray analysis revealed complete isodisomy involving chromosomes 2 (2 cases), 3, 4, 6 (2 cases), 8, and 21.
Out of 56 cases, 18 presented chromosome abnormalities (32.1%); additional chromosomal gains and losses were detected and consistent with their clinical phenotype. Notably, 2 patients exhibited mosaicism for whole chromosome aneuploidy, including UPD8 with trisomy 8 in 20% of cells, and UPD7 with mosaic monosomy 7 and isodisomy in a patient with myelodysplastic syndrome. Thus, in 30 patients (53.6%) either imprinting disorder and/or a chromosomal abnormality provided a diagnosis. Next generation or single gene sequencing studies were performed in 21 patients and detected pathogenic homozygous variants in 5/56 (9%) cases. Of the remaining cases, exome sequencing was either negative, or in 9 (16.1%) cases had homozygous or heterozygous variants of unknown significance (VUS), or de novo likely pathogenic or de novo VUS variants.
Conclusion:
Our study shows that scROHs are commonly associated with imprinting or chromosomal conditions explaining the cause of developmental delay and congenital birth defects. Finding of scROH may indicate an imprinting condition, recessive disease, chromosomal abnormality or a combination of all. Our findings underscore the importance of detecting UPD through advanced microarray techniques and the need for specific diagnostic strategies. The concurrent presence of chromosomal abnormalities, such as aneuploidy and CNVs, may further complicate the diagnostic landscape in patients with these genomic features.
Array comparative genomic hybridization (aCGH) with single nucleotide polymorphism (SNP) genotyping, is a powerful tool for detection of both copy number variants and copy-neutral aberrations, such as regions with long stretches of homozygosity (ROH). While the presence of ROH on multiple chromosomes undoubtfully suggests parental relatedness, ROH confined to a single chromosome (scROH) may indicate; uniparental disomy (UPD), shared ancestry between the parents, an error in chromosomal recombination, or chromosome rearrangements. Clinical significance and diagnostic impact of scROH remain inadequately explored. Herein, we investigated the clinical management and results of diagnostic testing in a cohort of patients with developmental delay and congenital structural birth defects and scROH detected by CGH+SNP microarray to assess the rate of imprinting disorders, recessive conditions, and chromosomal abnormalities.
Methods:
Microarray analysis was performed using the 180k CGH+SNP oligonucleotide array (Agilent). In order to identify cases with scROH of at least 8Mb in size, the results of chromosomal microarray analysis (CMA) were reviewed from patients referred to the UPMC Medical Genetics and Genomics Laboratories during 2012-2024 for a clinical testing. Findings of additional genetic assessment, including methylation studies, single gene sequencing, exome and genome sequencing were evaluated to investigate the clinical significance of scROH and to determine a follow-up management strategy.
Results:
Regions of homozygosity confined to a single chromosome were present in 56 cases among them UPD was identified in 23 patients (41.07%). Imprinting disorders were confirmed in 13 (23.2%) patients, including Prader-Willi syndrome (UPD15mat) in 7 cases (58.3%), Angelman syndrome (UPD15pat) in 2 cases (16.7%), Silver-Russel syndrome (UPD7mat) in 2 cases (16.7%), and 2 patients (16.7%) with UPD14. In 8 cases, microarray analysis revealed complete isodisomy involving chromosomes 2 (2 cases), 3, 4, 6 (2 cases), 8, and 21.
Out of 56 cases, 18 presented chromosome abnormalities (32.1%); additional chromosomal gains and losses were detected and consistent with their clinical phenotype. Notably, 2 patients exhibited mosaicism for whole chromosome aneuploidy, including UPD8 with trisomy 8 in 20% of cells, and UPD7 with mosaic monosomy 7 and isodisomy in a patient with myelodysplastic syndrome. Thus, in 30 patients (53.6%) either imprinting disorder and/or a chromosomal abnormality provided a diagnosis. Next generation or single gene sequencing studies were performed in 21 patients and detected pathogenic homozygous variants in 5/56 (9%) cases. Of the remaining cases, exome sequencing was either negative, or in 9 (16.1%) cases had homozygous or heterozygous variants of unknown significance (VUS), or de novo likely pathogenic or de novo VUS variants.
Conclusion:
Our study shows that scROHs are commonly associated with imprinting or chromosomal conditions explaining the cause of developmental delay and congenital birth defects. Finding of scROH may indicate an imprinting condition, recessive disease, chromosomal abnormality or a combination of all. Our findings underscore the importance of detecting UPD through advanced microarray techniques and the need for specific diagnostic strategies. The concurrent presence of chromosomal abnormalities, such as aneuploidy and CNVs, may further complicate the diagnostic landscape in patients with these genomic features.