Importance of EQA/PT for the detection of genetic variants in comprehensive cancer genome testing

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 7, 2025

Comprehensive genomic profiling (CGP) is increasingly used as a clinical laboratory test and being applied to cancer treatment; however, standardization external quality assessments (EQA) have not been fully developed. This study performed cost-effective EQA proficiency tests (PT) for CGP testing among multiple institutions those belong the working group of Japan Association Clinical Laboratory Science (JACLS). revealed that preanalytical processes, such derived nucleic acids (NA) extraction from formalin fixed paraffine embedded (FFPE) samples, are critical. First, with extracted DNA cell lines showed detection rate 100% (9 out 9) in KRAS (c.38G > A; p.G13D), PIK3CA (p.H1047R), B-Raf proto-oncogene, serine/threonine kinase (BRAF) (c.1799 T p.V600E) cases 10% variant allele frequency (VAF). However, BRAF decreased 67% (6 VAF 4.9%. Second, when was FFPE pathogenic variants companion diagnostic indications were detected all 10 participating laboratories. Each had < 20% VAFs on average (8.1–19.1%) wide variability laboratories observed (relative standard deviation, 13–60%). Nonetheless, (c.1798_1799delinsAA; p.V600K) 8.1% VAF, EGFR (c.2235_2249del; p.E746_A750del) 9.7% (c.2254_2277del; p.S752_I759del) 9.8% 70% (7/10), 60% (6/10) frequency, respectively. Therefore, pre-analytic processing critical analysis. Further, incorrect results reported case independent calling BRAF; c.1798_1799delinsAA (p.V600K) mistakenly interpreted c.1798G A, c.1799 A other strand. In conclusion, EQA/PT institutes common samples importance pre-analysis helped us understand significance pipeline pitfalls usually ignored by internal control single institute.

Language: Английский

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Mitral Valve Prolapse Caused by TLL1 Gain-of-Function Mutation

Canadian Journal of Cardiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Mitral valve prolapse (MVP) is a common cardiac valvular anomaly that can be caused by mutations in genes of various biological pathways. Individuals three generations kindred presented with apparently dominant heredity isolated MVP. Clinical evaluation and echocardiography for all complying family members (n=13). Whole exome genome sequencing data two affected individuals were analyzed, delineating shared heterozygous variants, further tested segregation within the (Sanger sequencing). Tolloid Like 1 (TLL1) enzymatic activity was assayed media HEK293 cells transfected wild-type versus mutant TLL1. The only variant segregating as expected MVP p.T253A, catalytic domain Of eight heterozygotes, six had trivial mitral regurgitation. Activity assay extra-cellular HEK293-transfected showed over time (12 hours), mutated TLL1 protein X3.4 higher than wild type. Our genetic biochemical studies show Gain-of-Function mutation, prolonging half-life active extracellular matrix (ECM), causes autosomal variable expressivity. encodes an metalloprotease regulating ECM composition maintenance. Heterozygous Loss-of-Function have been previously shown to cause atrial septal defects. findings enable novel insights into molecular pathways physiology disease, role human development, differing phenotypes same gene.

Language: Английский

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Unraveling MECP2 structural variants in previously elusive Rett syndrome cases through IGV interpretation

npj Genomic Medicine, Journal Year: 2025, Volume and Issue: 10(1)

Published: March 13, 2025

Rett syndrome (RTT) is a severe neurodevelopmental disorder, with MECP2 mutations accounting for 90–95% of classic and 50–70% atypical cases. However, many clinically diagnosed RTT patients remain without molecular diagnoses. While point large rearrangements in are well studied, the role small-intermediate structural variants (SVs) remains mostly elusive. Using standard short-read whole genome sequencing, we identified novel de novo SVs three out previously unresolved cases: complex SV two deletions ( ~ 5Kbp ~60Kbp) ~105Kbp inversion; ~200Kbp translocation; ~3Kbp deletion. These findings suggest that such elusive might be common cause "MECP2-negative" RTT. Incorporating detection into routine genetic testing through bioinformatic analysis sequencing or manual review using IGV could improve diagnostic rates expand our understanding similar disorders.

Language: Английский

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Novel BRAT1 Deep Intronic Variant Affects Splicing Regulatory Elements Causing Cerebellar Hypoplasia Syndrome: Genotypic and Phenotypic Expansion

Clinical Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 25, 2024

ABSTRACT Biallelic mutations in BRAT1 result lethal neonatal rigidity and multifocal seizure syndrome a milder neurodevelopmental disorder of cerebellar atrophy with or without seizures (NEDCAS, MIM 618056). Combining linkage analysis whole‐genome sequencing (WGS), we identified novel deep intronic variant, NC_000007.14 (NM_152743.4):c.128‐1585 T > G, 3 siblings consanguineous Bedouin family exhibiting NEDCAS. In silico analyses followed by molecular studies demonstrated this variant's impact on splice regulatory elements, forming cryptic exon, resulting deleterious frameshift aberrant transcript. Previously reported pathogenic splice‐site were adjacent to exons, affecting canonical consensus sites, identifiable whole‐exome sequencing. The disease‐causing variant is thus unique underscores the potential elements disease pathogenesis, demonstrating utility WGS identifying noncoding variants unresolved cases. affected individuals (deep into their twenties) are among longest‐surviving patients described date—delineating NEDCAS phenotype at these ages. Although sharing homozygosity same they show varying penetrance nystagmus extreme variability extent ataxia age onset developmental delay. Notably, summarize all documented date phenotypic associations.

Language: Английский

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Developmental dysplasia of the hip caused by homozygousTRIM33pathogenic variant affecting downstream BMP pathway

Journal of Medical Genetics, Journal Year: 2024, Volume and Issue: 61(10), P. 959 - 965

Published: July 25, 2024

Developmental dysplasia of the hip (DDH), formerly termed congenital dislocation hip, is most common disease musculoskeletal system in newborns. While familial predilection to DDH has been well documented, molecular genetics/pathways this disorder are poorly understood.

Language: Английский

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Importance of EQA/PT for the detection of genetic variants in comprehensive cancer genome testing

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 16, 2024

Comprehensive genomic profiling (CGP) is increasingly used as a clinical laboratory test and being applied to cancer treatment; however, standardization external quality assessments (EQA) have not been fully developed. This study performed cost-effective EQA proficiency tests (PT) for CGP testing among multiple institutions those belong the working group of Japan Association Clinical Laboratory Science (JACLS). revealed that preanalytical processes, such derived nucleic acids (NA) extraction from formalin fixed paraffine embedded (FFPE) samples, are critical. First, with extracted DNA cell lines showed detection rate 100% (9 out 9) in KRAS (c.38G > A; p.G12D), PIK3CA (p.H1047R), B-Raf proto-oncogene, serine/threonine kinase (BRAF) (c.1799T p.V600E) cases 10% variant allele frequency (VAF). However, BRAF decreased 67% (6 VAF 4.9%. Second, when was FFPE pathogenic variants or companion diagnostics were detected all 10 participating laboratories. Each had < 20% VAFs on average (8.1–19.1%) wide variability laboratories observed (relative standard deviation, 13–60%). Nonetheless, (c.1798_1799delinsAA; p.V600K) 8.1% VAF, EGFR (c.2235_2249del; p.E746_A750del) 9.7% (c.2254_2277del; p.S752_I759del) 9.8% 70% (7/10), 60% (6/10) probability, respectively. Therefore, pre-analytic processing critical analysis. Further, incorrect results reported case independent calling BRAF; c.1798_1799delinsAA (p.V600K) interpreted c.1798G A, c.1799T A other allele. In conclusion, EQA/PT institutes common samples importance pre-analysis helped us understand significance pipeline pitfalls usually ignored by internal control single institute.

Language: Английский

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GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries

Database, Journal Year: 2024, Volume and Issue: 2024

Published: Jan. 1, 2024

Originally developed to meet the challenges of genomic data deluge, GeniePool emerged as a pioneering platform, enabling efficient storage, accessibility, and analysis vast datasets, enabled due its lake architecture. Building on this foundation, 2.0 advances through integration cutting-edge variant databases, such CHM13-T2T, AlphaMissense, gnomAD V4, coupled with capability for co-occurrence queries. This evolution offers an unprecedented level granularity scope in analyses, from enhancing our understanding pathogenicity phenotypic associations facilitating research collaborations. The introduction CHM13-T2T provides more accurate reference human genetic variation, AlphaMissense enriches platform protein-level impact predictions missense mutations, V4 comprehensive view diversity. Additionally, innovative feature is pivotal exploring combined effects variations, advancing comprehension compound heterozygosity, epistasis, polygenic risk factors disease pathogenesis. scalable which aims enhance contribute research, potentially supporting new discoveries clinical innovations. Database URL: https://GeniePool.link.

Language: Английский

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