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We aimed to determine whether SNP-microarray genomic testing of saliva had a greater diagnostic yield than blood for pathogenic copy number variants (CNVs). We selected patients who underwent CMA testing of both blood and saliva from 23,289 blood and 21,857 saliva samples. Our cohort comprised 370 individuals who had testing of both, 224 with syndromic intellectual disability (ID) and 146 with isolated ID. Mosaic pathogenic CNVs or aneuploidy were detected in saliva but not in blood in 20/370 (4.4%). All 20 individuals had syndromic ID, accounting for 9.1% of the syndromic ID sub-cohort. Pathogenic CNVs were large in size (median of 46 Mb), and terminal in nature, with median mosaicism of 27.5% (not exceeding 40%). By contrast, non-mosaic pathogenic CNVs were 100% concordant between blood and saliva, considerably smaller in size (median of 0.65 Mb), and predominantly interstitial in location. Given that salivary microarray testing has increased diagnostic utility over blood in individuals with syndromic ID, we recommend it as a first-tier testing in this group.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172398 | PMC |
http://dx.doi.org/10.1038/s41431-022-01232-5 | DOI Listing |
BMC Pregnancy Childbirth
December 2024
Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Maternal and Child Health Care Hospital, Beijing, 100026, China.
Background: Blake's pouch cyst (BPC) is a midline cystic anomaly of the posterior fossa. BPC has been shown to have a risk of aneuploidy prenatally. Copy number variation (CNV) and/or genetic syndromes have been reported in a few prenatal/postnatal cases with BPC.
View Article and Find Full Text PDFComput Biol Med
December 2024
Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; Laboratory of Computational Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China. Electronic address:
Background: Interpreting the pathogenicity of genetic variants associated with rare diseases is a laborious and time-consuming endeavour. To streamline the diagnostic process and lighten the burden of variant interpretation, it is crucial to automate variant annotation and prioritization. Unfortunately, currently available variant interpretation tools lack a unified and comprehensive workflow that can collectively assess the clinical significance of these types of variants together: small nucleotide variants (SNVs), small insertions/deletions (INDELs), copy number variants (CNVs) and structural variants (SVs).
View Article and Find Full Text PDFMod Pathol
December 2024
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address:
Detecting somatic structural variants (SVs), copy number variants (CNVs), and mutations in bone and soft tissue tumors is essential for accurately diagnosing, treating, and prognosticating outcomes. Optical genome mapping (OGM) holds promise to yield useful data on SVs and CNVs but requires fresh or snap-frozen tissue. This study aimed to evaluate the clinical utility of data from OGM compared to current standard-of-care cytogenetic testing.
View Article and Find Full Text PDFAnn Med
December 2025
Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.
Objectives: The aim of the study was to evaluate the detection rate of genetic abnormalities in cases of foetal gallbladder (FGB) size abnormalities to determine whether these abnormalities justify prenatal diagnosis.
Methods: Two hundred and twenty-seven foetuses with gallbladder (GB) size anomalies who underwent prenatal diagnosis between January 2015 and June 2024 were included in the study. All these patients underwent chromosomal microarray and/or karyotyping, and 37 cases also underwent whole exome sequencing (WES).
Genet Med Open
January 2024
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.
Purpose: Structural variants such as multiexon deletions and duplications are an important cause of disease but are often overlooked in standard exome/genome sequencing analysis. We aimed to evaluate the detection of copy-number variants (CNVs) from exome sequencing (ES) in comparison with genome-wide low-resolution and exon-resolution chromosomal microarrays (CMAs) and to characterize the properties of de novo CNVs in a large clinical cohort.
Methods: We performed CNV detection using ES of 9859 parent-offspring trios in the Deciphering Developmental Disorders (DDD) study and compared them with CNVs detected from exon-resolution array comparative genomic hybridization in 5197 probands from the DDD study.
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