Fc gamma receptors: Their evolution, genomic architecture, genetic variation, and impact on human disease DOI Creative Commons
Sarah E. Frampton, Rosanna Smith,

Lili Ferson

et al.

Immunological Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 30, 2024

Summary Fc gamma receptors (FcγRs) are a family of that bind IgG antibodies and interface at the junction humoral innate immunity. Precise regulation receptor expression provides necessary balance to achieve healthy immune homeostasis by establishing an appropriate threshold limit autoimmunity but respond effectively infection. The underlying genetics FCGR gene central achieving this regulating affinity for IgG, signaling efficacy, expression. locus was duplicated during evolution, retaining very high homology resulting in genomic region is technically difficult study. Here, we review recent evolution mammals, its complexity variation through copy number single‐nucleotide polymorphism, impact these on disease incidence, resolution, therapeutic antibody efficacy. We also discuss progress limitations current approaches study emphasize how new genomics technologies will likely resolve much confusion field. This lead definitive conclusions genetic within function disease.

Language: Английский

Significantly improving the quality of genome assemblies through curation DOI Creative Commons
Kerstin Howe, William Chow, Joanna Collins

et al.

GigaScience, Journal Year: 2021, Volume and Issue: 10(1)

Published: Jan. 1, 2021

Abstract Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free is therefore ultimate, but sadly still unachieved goal a multitude research projects. Despite ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near genome eukaryotes. Whilst working towards improved datasets fully evaluation curation actively used to bridge this shortcoming significantly reduce number errors. In addition increase product value, insights gained from are fed back into strategy contribute notable quality. We describe tried tested using gEVAL, browser. outline procedures applied gEVAL also recommendations gEVAL-independent context facilitate uptake wider community.

Language: Английский

Citations

1304
Optical genome mapping enables constitutional chromosomal aberration detection DOI
Tuomo Mantere, Kornelia Neveling,

Céline Pebrel‐Richard

et al.

The American Journal of Human Genetics, Journal Year: 2021, Volume and Issue: 108(8), P. 1409 - 1422

Published: July 7, 2021

Language: Английский

Citations

172
Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping DOI Creative Commons
Kornelia Neveling, Tuomo Mantere,

Susan Vermeulen

et al.

The American Journal of Human Genetics, Journal Year: 2021, Volume and Issue: 108(8), P. 1423 - 1435

Published: July 7, 2021

Language: Английский

Citations

148
Beyond the exome: What’s next in diagnostic testing for Mendelian conditions DOI Creative Commons
Monica H. Wojcik, Chloe M. Reuter, Shruti Marwaha

et al.

The American Journal of Human Genetics, Journal Year: 2023, Volume and Issue: 110(8), P. 1229 - 1248

Published: Aug. 1, 2023

Language: Английский

Citations

67
Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies DOI Creative Commons
Xuefang Zhao, Ryan L. Collins, Wan‐Ping Lee

et al.

The American Journal of Human Genetics, Journal Year: 2021, Volume and Issue: 108(5), P. 919 - 928

Published: March 30, 2021

Language: Английский

Citations

100
Towards improved genetic diagnosis of human differences of sex development DOI
Emmanuèle C. Délot, Éric Vilain

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(9), P. 588 - 602

Published: June 3, 2021

Language: Английский

Citations

67
Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases DOI Creative Commons
M. Anwar Iqbal,

Ulrich Broeckel,

Brynn Levy

et al.

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

Citations

29
The Clinical Utility of Optical Genome Mapping for the Assessment of Genomic Aberrations in Acute Lymphoblastic Leukemia DOI Open Access
Jonathan Lukas Lühmann,

Marie Stelter,

Marie Wolter

et al.

Cancers, Journal Year: 2021, Volume and Issue: 13(17), P. 4388 - 4388

Published: Aug. 30, 2021

Acute lymphoblastic leukemia (ALL) is the most prevalent type of cancer occurring in children. ALL characterized by structural and numeric genomic aberrations that strongly correlate with prognosis clinical outcome. Usually, a combination cyto- molecular genetic methods (karyotyping, array-CGH, FISH, RT-PCR, RNA-Seq) needed to identify all relevant for risk stratification. We investigated feasibility optical genome mapping (OGM), DNA-based method, detect these an all-in-one approach. As proof principle, twelve pediatric samples were analyzed OGM, results validated comparing OGM data obtained from routine diagnostics. All including translocations (e.g., dic(9;12)), aneuploidies high hyperdiploidy) copy number variations IKZF1, PAX5) known other techniques also detected OGM. Moreover, was superior well-established resolution more complex structure translocation t(12;21) had higher sensitivity detection alterations. Importantly, new unknown gene fusion JAK2 NPAT due t(9;11) detected. demonstrate as well putative prognostic markers approach ALL. hope limited will be confirmed testing future.

Language: Английский

Citations

49
The role of structural variations in Alzheimer’s disease and other neurodegenerative diseases DOI Creative Commons
Hui Wang, Li‐San Wang, Gerard D. Schellenberg

et al.

Frontiers in Aging Neuroscience, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 8, 2023

Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer’s disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion the genetic component AD can be explained SNPs observed from GWAS. Structural variation (SV) major contributor missing heritability AD; while SV in remains largely unexplored as accurate detection SVs widely used array-based and short-read technology are still far perfect. Here, we briefly summarized strengths weaknesses available methods. We reviewed current landscape analysis that found associated with AD. Particularly, importance currently less explored SVs, including insertions, inversions, short tandem repeats, transposable elements neurodegenerative diseases were highlighted.

Language: Английский

Citations

18
Improving laboratory animal genetic reporting: LAG-R guidelines DOI Creative Commons
Lydia Teboul, James Amos‐Landgraf, Fernando Benavides

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 2, 2024

The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. ARRIVE guidelines outline documentation standards for laboratory animals experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals' makeup scientific publications, providing essential details replication appropriate model use. While verifying complete compositions may be impractical, better reporting validation efforts enhance reliability of research. standardization will bolster reproducibility, peer review, overall rigor.

Language: Английский

Citations

8