Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Genome Medicine, Journal Year: 2023, Volume and Issue: 15(1)

Published: Nov. 9, 2023

Abstract Background Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, diagnostic yields many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25–30%. This part because although entire genomes sequenced, analysis confined to silico gene panels or coding regions genome. Methods We undertook WGS on cohort 122 unrelated disease and their relatives (300 genomes) who had been pre-screened by arrays. Patients were recruited from broad spectrum clinical specialties. applied bioinformatics pipeline that would allow comprehensive all variant types. combined established tools phenotypic genomic our novel algorithms (SVRare, ALTSPLICE GREEN-DB) detect annotate structural, splice site non-coding variants. Results Our yield was 43/122 cases (35%), 47/122 (39%) considered solved when considering candidate genes supporting functional data into account. Structural, deep intronic variants contributed 20/47 (43%) cases. Five novel, time discovery, identified, whilst further three putative evidence causality. identified uncertain significance fourteen genes. The associated RMND1 expanded include polymicrogyria. Two secondary findings FBN1 KCNQ1 confirmed have previously unidentified Marfan long QT syndromes, respectively, referred interventions. Clinical diagnoses changed six treatment adjustments made eight individuals, which five life-saving. Conclusions Genome as first-line genetic test routine settings can make substantial contribution rapidly identifying causal aetiology patients, shortening odyssey. demonstrated significant essential maximise value sequencing.

Language: Английский

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Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases

Journal of Molecular Diagnostics, Journal Year: 2023, Volume and Issue: 25(3), P. 175 - 188

Published: Feb. 22, 2023

This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. included 50 negative controls and 359 samples from individuals (patients) suspected genetic conditions referred for cytogenetic testing. OGM was using the Saphyr system Bionano Access software version 1.7. Structural variants, including copy number aneuploidy, regions of homozygosity, were detected classified according to American College Medical Genetics Genomics guidelines. Repeated expansions FMR1 contractions facioscapulohumeral dystrophy 1 also analyzed. results compared SOC technical concordance, classification intrasite intersite reproducibility, ability provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) yielded successful data analysis interpretation. Overall, concordance detect previously reported 99.5% (399/401). The blinded variant agreement between 97.6% (364/373). Replicate 130 structural variations 100% concordant. On basis this demonstration analytic validity utility by multisite assessment, authors recommend technology as an alternative existing tests rapid detection diagnosis postnatal constitutional disorders.

Language: Английский

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PhenoScore quantifies phenotypic variation for rare genetic diseases by combining facial analysis with other clinical features using a machine-learning framework

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(9), P. 1598 - 1607

Published: Aug. 7, 2023

Language: Английский

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Genome sequencing as a generic diagnostic strategy for rare disease

Genome Medicine, Journal Year: 2024, Volume and Issue: 16(1)

Published: Feb. 14, 2024

Abstract Background To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increase efficiency. We assessed whether genome sequencing (GS) can replace these existing workflows aimed at germline diagnosis for rare disease. Methods performed short-read GS (NovaSeq™6000; 150 bp paired-end reads, 37 × mean coverage) on 1000 cases with 1271 known clinically relevant variants, identified across representative our tertiary diagnostic centers. Variants were categorized into small variants (single nucleotide indels < 50 bp), large (copy number short tandem repeats) other (structural aneuploidies). Variant calling format files queried per variant, which workflow-specific true positive rates (TPRs) detection determined. TPR ≥ 98% was considered threshold transition GS. GS-first scenario generated laboratory, using efficacy predicted false negative as primary outcome measures. As input, we modeled path all 24,570 individuals referred in 2022, combining clinical referral, underlying workflow(s) GS, variant type(s) be detected. Results Overall, 95% (1206/1271) Detection differed category: 96% (826/860), 93% (341/366), 87% (39/45). TPRs varied between (79–100%), 7/10 being replaceable by Models laboratory indicate that a strategy feasible 84.9% referrals (750/883), translating 71% (17,444/24,570) receiving their test. An estimated rate 0.3% could expected. Conclusions capture ‘GS-first strategy’ majority indications genetics lab.

Language: Английский

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Detection of Clinically Relevant Monogenic Copy-Number Variants by a Comprehensive Genome-Wide Microarray with Exonic Coverage

Clinical Chemistry, Journal Year: 2025, Volume and Issue: 71(1), P. 141 - 154

Published: Jan. 1, 2025

Abstract Background Disease-causing copy-number variants (CNVs) often encompass contiguous genes and can be detected using chromosomal microarray analysis (CMA). Conversely, CNVs affecting single disease-causing have historically been challenging to detect due their small sizes. Methods A custom comprehensive CMA (Baylor College of Medicine - BCM v11.2) containing 400k probes featuring exonic coverage for &gt;4200 known or candidate was utilized the detection at single-exon resolution. results across a consecutive clinical cohort more than 13 000 patients referred genetic investigation Baylor Genetics were examined. The genomic characteristics impacting protein-coding investigated. Results Pathogenic likely pathogenic (P/LP) (n = 190) in 188 patients, accounting 9.9% (188/1894) with P/LP findings. monogenic accounted 9.2% (190/2058) all nuclear by CMA. total 57.9% (110/190) smaller 50 kb size. Single exons affected 26.3% (50/190) while 13.2% (25/190) 2 exons. 107 unique associated predominantly autosomal dominant (AD) X-linked (XL) conditions but also contributed recessive (AR) conditions. Conclusions exon-targeted disease-associated facilitated genes, adding substantial sensitivity CNV investigation. This approach resolved etiologies yielded multiple significant Monogenic represent an underrecognized subset alleles Mendelian disorders.

Language: Английский

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The known structural variations in hearing loss and their diagnostic approaches: a comprehensive review

Molecular Biology Reports, Journal Year: 2025, Volume and Issue: 52(1)

Published: Jan. 17, 2025

Language: Английский

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Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping

Journal of Medical Genetics, Journal Year: 2022, Volume and Issue: 60(3), P. 274 - 284

Published: June 16, 2022

Chromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and risk miscarriage or delivering abnormal offspring with congenital malformations carrier couples is significantly increased. In present study, we aimed investigate potential single-molecule optical genome mapping (OGM) unravelling rearrangements.Eleven normal karyotypes that had abortions/affected unbalanced were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells processed via OGM. The assembly performed followed variant calling annotation. Meanwhile, multiple strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing Sanger implemented confirm results obtained OGM.High-resolution OGM successfully detected reciprocal translocation all recruited couples, which consistent FISH sequencing. All high-confidence translocations confirmed analysis rearrangement breakpoints. Moreover, revealed additional complex events such as inverted aberrations, further refining interpretation.To best our knowledge, this first study wherein facilitate rapid robust clinical practice. With excellent performance, findings suggest well qualified an accurate, comprehensive first-line method for detecting testing.

Language: Английский

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Optical genome mapping and revisiting short-read genome sequencing data reveal previously overlooked structural variants disrupting retinal disease−associated genes

Genetics in Medicine, Journal Year: 2022, Volume and Issue: 25(3), P. 100345 - 100345

Published: Dec. 16, 2022

Structural variants (SVs) play an important role in inherited retinal diseases (IRD). Although the identification of SVs significantly improved upon availability genome sequencing, it is expected that involvement IRDs higher than anticipated. We revisited short-read sequencing data to enhance gene-disruptive SVs.Optical mapping was performed improve SV detection sequencing-negative cases. In addition, reanalysis interpretation and re-establish prioritization criteria.In a monoallelic USH2A case, optical identified pericentric inversion (173 megabase), with 1 breakpoint disrupting USH2A. Retrospectively, variant could be observed but previously deemed false positive. Reanalysis (427 IRD cases) which yielded 30 pathogenic affecting, among other genes, (n = 15), PRPF31 3), EYS 2). Eight these (>25%) were overlooked during previous analyses.Critical evaluation our findings allowed us guidelines, will prevent missing events future analyses. Our suggest more attention should paid current contribution still underestimated.

Language: Английский

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Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing

Journal of Molecular Diagnostics, Journal Year: 2023, Volume and Issue: 25(4), P. 234 - 246

Published: Feb. 8, 2023

The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes chorionic villi sampling. However, each technology has its limitations: karyotyping low resolution (>5 Mb), FISH is targeted, CMA does not detect balanced structural variations (SVs). These limitations necessitate the use multiple tests, simultaneously sequentially, to reach genetic diagnosis. Optical genome mapping (OGM) an emerging that can several classes SVs single assay, but it been evaluated setting. This validation study analyzed 114 samples were received our laboratory for traditional analysis with FISH, and/or CMA. OGM was 100% concordant identifying 101 aberrations included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence heterozygosity regions, 3 triploid genomes, 4 isochromosomes, 1 translocation; method revealed identity marker chromosomes chromosome additional material determined by karyotyping. In addition, detected 64 clinically reportable 43 samples. standardized workflow reporting solution be adopted routine clinical laboratories demonstrates potential replace current methods testing.

Language: Английский

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A unifying model that explains the origins of human inverted copy number variants

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(1), P. e1011091 - e1011091

Published: Jan. 4, 2024

With the release of telomere-to-telomere human genome sequence and availability both long-read sequencing optical mapping techniques, identification copy number variants (CNVs) other structural is providing new insights into genetic disease. Different mechanisms have been proposed to account for novel junctions in these complex architectures, including aberrant forms DNA replication, non-allelic homologous recombination, various pathways that repair breaks. Here, we focused on a set include an inverted segment propose they share common initiating event: triplication with long, unstable palindromic junctions. The secondary rearrangement palindromes gives rise variants. We postulate this same mechanism (ODIRA: origin-dependent inverted-repeat amplification) creates CNVs inherited syndromes also generates found cancers.

Language: Английский

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