NPJ Genomic Medicine最新文献

This study utilized single-tube long fragment read whole genome sequencing (stLFR WGS) to identify cryptic chromosomally balanced translocations in preimplantation genetic testing (PGT), aiming to improve outcomes for couples experiencing recurrent pregnancy loss (RPL). G-banded karyotyping initially revealed normal results for Family 1 and a reciprocal translocation for Family 2. However, PGT's low-coverage WGS uncovered recurrent copy number variations (CNVs) that contradicted the initial findings. Further analysis using stLFR WGS and Sanger sequencing precisely located the breakpoints, revealing a balanced translocation between chromosomes 7 and 13 in Family 1's male and a complex translocation involving chromosomes 9, 10, and 11 in Family 2's female. By selecting non-carrier embryos for transfer, the study resulted in successful births of healthy infants. These findings highlight the critical role of PGT in detecting concealed chromosomal rearrangements and demonstrate stLFR WGS as an effective diagnostic tool for breakpoint identification, significantly impacting reproductive decisions for couples with cryptic balanced translocations and RPL.

Exome sequencing is the current standard for diagnosing Mendelian disorders; however, it is generally not considered the first-line test for detecting copy number variants (CNVs). We retrospectively investigated the additional diagnostic yield by performing concurrent CNV analysis using exome data in a large and diverse pediatric cohort. Patients were referred from various sources with variable phenotypes. Human Phenotype Ontology terms were used to prioritize variants for analysis. Ancestry and CNV analyses were performed using Somalier and NxClinical, respectively. A total of 1538 patients were tested, with the majority being Admixed Americans. Diagnostic CNVs were identified in 70 patients (4.6%), ranging from exonic deletions to large, unbalanced rearrangements, aneuploidies, and mosaic findings. While no significant differences were identified in diagnostic yield, or rates of negative or uncertain diagnoses, between ancestries, our study demonstrates the feasibility and increased yield of CNV analysis of exome data, across multiple phenotypes, referral sources, and ancestries.

In pediatric cancer precision medicine clinical trials settings, parents proactively seeking treatment and answers to causation may request return of their child's raw data and/or biospecimen. To satisfy such requests, the ZERO Childhood Cancer Program required a guidance document. Literature review led to Version(V)1; Delphi consultation with 21/54 invited experts (V2-4) and parent consultations (V5-6). A final V7 was approved for implementation: Policy (purpose; background; ethical considerations), Process (nine steps), and consent form. Issues addressed included: child's best interests, clinical utility, non-maleficence, reciprocity between researchers and participants/parents; responsibility to genetic relatives; acknowledging potential value of subsequent analysis/interpretation but no obligation on treating clinicians to act on therapeutic recommendations arising; practical barriers to return; and supporting parental empowerment by facilitating meeting with a study genetic counselor, separate from their treating clinician, if preferred, to manage their request. This guide may be a model for other research groups and inform ethical guidelines.

This study aims to characterize the clinical spectrum and genetic landscape of IRDs in Portugal. Multicentre, cross-sectional, cohort study comprising consecutive patients with a clinical diagnosis of IRD and available genetic results, enroled in the IRD-PT registry (retina.com.pt). Among the 1369 patients enroled from 1125 families, the most frequently observed phenotype was non-syndromic retinitis pigmentosa (40.8%). A genetically confirmed diagnosis was achieved in 72.3% of families. Consanguinity was observed in one-fifth of cases, contributing to a higher frequency of homozygous variants within this cohort. Disease-causing genotypes were distributed across 136 different genes, with ABCA4 (13.0%), EYS (10.0%) and USH2A (6.9%) being the most frequently mutated genes. Overall, these results from a nationwide cohort significantly advance our understanding of the clinical and genetic spectrum of IRDs in Portugal, laying the groundwork for future studies to identify patients eligible for targeted therapies and to describe the natural history of these diseases.

Nail-Patella syndrome (NPS) is a rare autosomal dominant condition due to haploinsufficiency of LMX1B, caused by loss-of-function variants affecting the coding sequence, or partial/whole deletions of the gene. In here, we describe two familial cases of NPS, carrying novel variants of the LMX1B 5'UTR region (-174C>T and -226G>A). To verify their pathogenic role, we carried out a functional characterization, both by reporter gene assays in heterologous systems and in patient's derived cells. We demonstrated that both variants impair LMX1B expression at post-transcriptional level. They introduce two upstream open reading frames (uORFs), out-of-frame with the main LMX1B coding sequence, generating transcripts detected by the non-sense mediated decay (NMD). We also demonstrated that the escape of the altered mRNA from NMD, if any, may lead to the synthesis of an aberrant LMX1B protein.

Turner syndrome (TS) presents with multiple karyotypes, including 45,X monosomy and variants such as isochromosomes and mosaicism, and is characterized by several co-morbidities, including metabolic conditions and autoimmunity. Here, we investigated the genomic landscapes across a range of karyotypes. We show that TS have a common autosomal methylome and transcriptome, despite distinct karyotypic variations. All TS individuals lacked the X chromosome p-arm, and XIST expression from the q-arm did not affect the autosomal transcriptome or methylome, highlighting the critical role of the missing p-arm with its pseudoautosomal region 1. Furthermore, we show increased levels of neutrophils and increased neutrophil activation. The increase in neutrophils was linked to TS clinical traits and to increased expression of the X-Y homologous gene TBL1X, suggesting a genetic basis, which may lead to neutrophil-driven inflammatory stress in TS. Identifying TS individuals with increased neutrophil activation could potentially mitigate the progression towards more severe metabolic issues.

Junctional epidermolysis bullosa (JEB) is characterized by mucocutaneous fragility. We enrolled 69 cases of recessive JEB, with 13.0% of these cases remained genetically undiagnosed following an initial exome sequencing. Among cases carried COL17A1 variants, this proportion can reach 31.6%. We employed genome sequencing to genetically diagnosis these cases. Four deep intronic variants (c.4156+117 G > A, c.2039-104 G > A and c.1267+237dupC in the COL17A1 gene and c.-38 + 2 T > C in the LAMB3 gene) were identified in six cases. The c.4156+117 G > A variant was found in three of the five cases, suggesting it may be a common deep intronic variant in Chinese JEB. Splicing analysis revealed that these variants caused splicing defect by inducing exon skipping, or pseudoexon insertion into the transcript in HaCaT cells, not in HEK293 cells. Our results emphasize the importance of selecting the right cell line for mRNA analysis.

Human height prediction based on genetic factors alone shows positive correlation, but predictors developed for one population perform less well when applied to population of different ancestries. In this study, we evaluated the utility of incorporating non-genetic factors in height predictors for the Han Chinese population in Taiwan. We analyzed data from 78,719 Taiwan Biobank (TWB) participants and 40,641 Taiwan Precision Medicine Initiative (TPMI) participants using genome-wide association study and multivariable linear regression least absolute shrinkage and selection operator (LASSO) methods to incorporate genetic and non-genetic factors for height prediction. Our findings establish that combining birth year (as a surrogate for nutritional status), age at measurement (to account for age-associated effects on height), and genetic profile data improves the accuracy of height prediction. This method enhances the correlation between predicted and actual height and significantly reduces the discrepancies between predicted and actual height in both males and females.

We investigated the effectiveness of exome sequencing (ES) in diagnosing ethnically diverse patients with rare genetic disorders. A total of 18,994 patients referred to a single reference laboratory for ES between 2020 and 2022 were studied for the diagnostic rate and factors influencing the diagnostic rate. The overall diagnostic rate was 31.8%. Dermatological disorders, skeletal disorders, and neurodevelopmental disorders disease categories, early age-of-onset, presence of consanguinity, and the presence of parental sequencing data were found to be correlated with a higher diagnostic rate. Nearly 68K variants were identified in our dataset at a higher frequency than that observed in gnomAD 4.0. Of these, 507 variants could be classified as likely benign, representing 0.04% of non-benign variants in ClinVar (507/1,433,904) and 0.20% of the non-benign ClinVar variants observed at least once in our cohort (507/276,777). The overall diagnostic rate is comparable to that observed in other large cohort studies with less diverse ethnic backgrounds.

Multigene panel tests (MGPTs) revolutionized the diagnosis of Lynch syndrome (LS), however noncoding pathogenic variants (PVs) can only be detected by complementary methods including whole genome sequencing (WGS). Here we present a DNA-, RNA- and tumor tissue-based WGS prioritization workflow for patients with a suspicion of LS where MGPT detected no LS-related PV. Among the 100 enrolled patients, MGPT detected 28 simple PVs and an additional 3 complex PVs. Among the 69 MGPT-negative patients, the lack of somatic MLH1 promoter methylation in a patient with a distinguished MLH1 allelic imbalance selected this sample for WGS. This returned a germline deep intronic MLH1 variant, with further functional studies confirming its' pathogenicity. Interestingly, all three complex PVs and the MLH1 deep intronic PV were found to be recurrent at our center. Our straightforward and cost-effective prioritization workflow can optimally include WGS in the genetic diagnosis of LS.