Biology subjects

Chong, J. X.

Publications and source records attributed to Chong, J. X..

5 recordsLinked to original sources

bioRxiv2025

Cell modeling and rescue of a novel non-coding genetic cause of Glycogen Storage Disease IX

Delayed diagnosis of Mendelian disease substantially prevents early therapeutic intervention that could improve symptoms and prognosis. One major contributing challenge is the functional interpretation of non-coding variants that cause disease by altering splicing and/or gene expression. We identified two siblings with glycogen storage disease (GSD) type IX {gamma}2, both of whom had a classic clinical presentation, enzyme deficiency, and a known pathogenic splice acceptor variant on one allele of PHKG2. Despite the autosomal recessive nature of the disease, no variant on the second allele was identified by gene panel sequencing. To identify a potential missing second pathogenic variant, we completed whole genome sequencing (WGS) and detected putative deep intronic splicing variant in PHKG2 in both siblings. We confirmed the functional splicing effects of this variant using short-read and long-read RNA-seq on patient blood and a HEK293T cell model in which we installed the variant using CRISPR editing. Using the cell model, we demonstrated multiple biochemical and cellular impacts that are consistent with GSD IX {gamma}2, and a reversal of aberrant splicing using antisense splice-switching oligonucleotides. In doing so, we demonstrate a novel and robust pathway for detecting, validating, and reversing the impacts of novel non-coding causes of rare disease.

genetics↗

bioRxiv2020

Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants

BACKGROUNDDespite widespread availability of clinical genetic testing, many individuals with suspected genetic conditions do not have a precise diagnosis. This limits their opportunity to take advantage of state-of-the-art treatments. In such instances, testing sometimes reveals difficult-to-evaluate complex structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in specific genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. METHODSTargeted long-read sequencing (T-LRS) was performed on 33 individuals using Read Until on the Oxford Nanopore platform. This method allowed us to computationally target up to 100 Mbp of sequence per experiment, resulting in an average of 20x coverage of target regions, a 500% increase over background. We analyzed patient DNA for pathogenic substitutions, structural variants, and methylation differences using a single data source. RESULTSThe effectiveness of T-LRS was validated by detecting all genomic aberrations, including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences, previously identified by prior clinical testing. In 6/7 individuals who had complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, which led, in one case, to a change in clinical management. In nine individuals with suspected Mendelian conditions who lacked a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in five and variants of uncertain significance in two others. CONCLUSIONST-LRS can accurately predict pathogenic copy number variants and triplet repeat expansions, resolve complex rearrangements, and identify single-nucleotide variants not detected by other technologies, including short-read sequencing. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority candidate genes and regions or to further evaluate complex clinical testing results. The application of T-LRS will likely increase the diagnostic rate of rare disorders.

genomics↗

bioRxiv2020

Mutations in MYLPF cause a novel segmental amyoplasia that manifests as distal arthrogryposis

We identified ten persons in six consanguineous families with Distal Arthrogryposis (DA) who had congenital contractures, scoliosis, and short stature. Exome sequencing revealed that each affected person was homozygous for one of two different rare variants (c.470G>T, p.(Cys157Phe) or c.469T>C, p.(Cys157Arg)) affecting the same residue of myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF). In a seventh family, a c.487G>A, p.(Gly163Ser) variant in MYLPF arose de novo in a father, who transmitted it to his son. In an eighth family comprised of seven individuals with dominantly-inherited DA, a c.98C>T, p.(Ala33Val) variant segregated in all four persons tested. Variants in MYLPF underlie both dominant and recessively inherited DA. Mylpf protein models suggest that the residues associated with dominant DA interact with myosin whereas the residues altered in families with recessive DA only indirectly impair this interaction. Pathological and histological exam of a foot amputated from an affected child revealed complete absence of skeletal muscle (i.e., segmental amyoplasia). To investigate the mechanism for this finding, we generated an animal model for partial MYLPF impairment by knocking out zebrafish mylpfa. The mylpfa mutant had reduced trunk contractile force and complete pectoral fin paralysis, demonstrating that mylpf impairment most severely affects limb movement. mylpfa mutant muscle weakness was most pronounced in an appendicular muscle and was explained by reduced myosin activity and fiber degeneration. Collectively, our findings demonstrate that partial loss of MYLPF function can lead to congenital contractures, likely as a result of degeneration of skeletal muscle in the distal limb.

genetics↗

bioRxiv2019

Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes critical for an organisms function will be depleted for such variants in natural populations, while non-essential genes will tolerate their accumulation. However, predicted loss-of-function (pLoF) variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes1. Here, we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence pLoF variants in this cohort after filtering for sequencing and annotation artifacts. Using an improved human mutation rate model, we classify human protein-coding genes along a spectrum representing tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve gene discovery power for both common and rare diseases.

genomics↗

bioRxiv2017

Loss of function, missense, and intronic variants in NOTCH1 confer different risks for left ventricular outflow tract obstructive heart defects in two European cohorts

Loss of function variants in NOTCH1 cause left ventricular outflow tract obstructive defects (LVOTO) in a small percentage of families. Clinical surveys report an increased prevalence of missense variants in NOTCH1 in family members of individuals with LVOTO and other types of congenital heart disease (CHD). However, the risk conferred by rare variants in NOTCH1 for LVOTO remains largely uncharacterized. In a cohort of 49 families affected by hypoplastic left heart syndrome, a severe form of LVOTO, we discovered predicted loss of function NOTCH1 variants in 6% of individuals. Rare missense variants were found in an additional 16% of families. To make a quantitative estimate of the genetic risk posed by variants in NOTCH1 for LVOTO, we studied associations of 400 coding and non-coding variants in NOTCH1 in 271 adult cases and 333,571 controls from the UK Biobank. Two rare intronic variants in strong linkage disequilibrium displayed significant association with risk for LVOTO (g.chr9:139427582C>T, Odds Ratio 16.9, p=3.12e-6; g.chr9:139435649C>T, Odds Ratio 19.6, p = 2.44e-6) amongst European-ancestry British individuals. This result was replicated in an independent analysis of 51 cases and 68,901 controls of non-European and mixed ancestry. We conclude that carrying rare predicted loss of function variants or either of two intronic variants in NOTCH1 confer significant risk for LVOTO. Our approach demonstrates the utility of population-based datasets in quantifying the specific risk of individual variants for disease related phenotypes.\n\nAuthor summaryCongenital heart defects are the most common class of birth defect and are present in 1% of live births. Although CHD cases are often clustered in families, and thus the causal variant(s) are seemingly inherited, finding genetic variants causing these defects has been challenging. With the knowledge that variation in the NOTCH1 gene previously has been associated with CHDs affecting the left side of the heart, our aim was to further investigate the role of different types of NOTCH1 variants in left sided CHDs in two cohorts - a cohort of Finnish families with severe lesions affecting the left side of the heart, and the UK Biobank population including individuals with less severe left-sided lesions such as bicuspid aortic valve, congenital aortic stenosis, and coarctation of the aorta. We found a causal loss-of-function NOTCH1 variant in 6% of the families in the Finnish cohort and in the UK Biobank cohort, we identified two rare variants in the non-coding region of NOTCH1, associated with severe left-sided CHDs. These findings support screening of NOTCH1 loss-of-function variants in patients with severe left sided congenital heart defects and suggests that non-coding region variants in NOTCH1 play a role in CHDs.

genetics↗