NPJ Genomic Medicine最新文献

Inherited retinal diseases (IRDs) are a group of rare Mendelian disorders that often result in progressive vision loss and potentially to complete blindness at the end stage. In this study, we investigated a large cohort of patients with IRDs from Pakistan, the world's fifth most populous country, which is also characterized by distinctive demographic features, such as a high prevalence of consanguinity, endogamy, and a wide variety of ethnic groups. Specifically, we examined a total of 213 unrelated families (722 affected individuals) from three very large geographical regions. We achieved precise molecular diagnosis in 171 pedigrees (80.3%) and detected causative variants in 60 different IRD-associated genes, revealing a mutational landscape that differed substantially from previous data from other European or Asian populations, heavily shaped by endogamy and rare or recurrent founder mutational events. To our knowledge, this work represents the largest genetic study on IRDs within the Pakistani population.

Familial adenomatous polyposis (FAP) is caused by pathogenic germline variants in the tumor suppressor gene APC. Confirmation of diagnosis was not achieved by cancer gene panel and exome sequencing or custom array-CGH in a family with suspected FAP across five generations. Long-read genome sequencing (PacBio), short-read genome sequencing (Illumina), short-read RNA sequencing, and further validations were performed in different tissues of multiple family members. Long-read genome sequencing resolved a 6 kb full-length intronic insertion of a heterozygous LINE-1 element between exons 7 and 8 of APC that could be detected but not fully resolved by short-read genome sequencing. Targeted RNA analysis revealed aberrant splicing resulting in the formation of a pseudo-exon with a premature stop codon. The variant segregated with the phenotype in several family members allowing its evaluation as likely pathogenic. This study supports the utility of long-read DNA sequencing and complementary RNA approaches to tackle unsolved cases of hereditary disease.

Individuals affected by a rare disease often experience a long and arduous diagnostic odyssey. Delivery of genetic answers in a timely manner is critical to affected individuals and their families. Multi-omics, a term which usually encompasses genomics, transcriptomics, proteomics, metabolomics and lipidomics, has gained increasing popularity in rare disease research and diagnosis over the past decade. Mass spectrometry (MS) is a technique allowing the study of proteins, metabolites and lipids and their fragments at scale, enabling researchers to effectively determine the presence and abundance of thousands of molecules in a single test, accurately quantify their specific levels, identify potential therapeutic biomarkers, detect differentially expressed proteins in patients with rare diseases, and monitor disease progression and treatment response. In this review, we focus on mass spectrometry (MS)-based omics and survey the literature describing the utility of different MS-based omics and how they have transformed rare disease research and diagnosis.

In patients with complex congenital heart disease (CHD) pathogenic SMAD6 variants have been described previously. The aim of this study was to analyze if pathogenic SMAD6 variants also occur in patients with CHD associated with pulmonary arterial hypertension (CHD-APAH) or idiopathic PAH. A PAH gene panel with up to 64 genes including SMAD6 was used to sequence 311 patients with idiopathic PAH (IPAH) and 32 with CHD-APAH. In 4 of 32 (12.5%) CHD-APAH and in 2 out of 311 (0.64%) IPAH patients we identified likely pathogenic or rare SMAD6 missense variants. All CHD-APAH patients with a rare SMAD6 variant had complex CHD. One patient had bi-allelic SMAD6 variants, combined pulmonary valve defect and supravalvular aortic stenosis, craniosynostosis and radioulnar synostosis. This is the first description of potentially disease-causing SMAD6 variants in patients with IPAH and complex CHD-APAH. Further studies are needed to assess pathogenesis and prevalence of pathogenic SMAD6 variants in PAH.

Rapid genomic diagnostics in the Neonatal Intensive Care Unit represents a paradigm shift in medicine with increasing evidence of the utility of early diagnosis, impacting management. The goal of the Utah NeoSeq Project was to implement and evaluate a multidisciplinary and longitudinal rapid sequencing program while transitioning to CLIA-certified sequencing. Enrollment of 65 infants resulted in 26 (40%) with a diagnostic variant(s) and 7 (11%) harboring a strong candidate. This includes re-analyses resulting in four additional diagnoses. Parental surveys indicated that 7% (4/59) of parents had a decisional conflict after consent, and 3% (2/59) experienced decisional regret after the results. Fifty-two provider surveys were conducted. Seventy-nine percent (41/52) of results and 86% (19/22) of diagnostic results were "very useful" or "useful" and associated with management changes. The NeoSeq Project demonstrates that a multidisciplinary collaborative approach to diagnosis is feasible. We have developed a generalizable, collaborative protocol that addresses the need for expedited genetic evaluation with emerging technologies.

Individuals with heritable thoracic aortic disease (HTAD) face a high risk of deadly aortic dissections, but genetic testing identifies causative variants in only a minority of cases. We explored the contribution of non-canonical splice variants (NCVAS) to thoracic aortic disease (TAD) using SpliceAI and sequencing data from diverse cohorts, including 551 early-onset sporadic dissection cases and 437 HTAD probands with exome sequencing, 57 HTAD pedigrees with whole genome sequencing, and select sporadic cases with clinical panel testing. NCVAS were identified in syndromic HTAD genes such as FBN1, SMAD3, and COL3A1, including intronic variants in FBN1 in two Marfan syndrome (MFS) families. Validation in the Penn Medicine BioBank and UK Biobank showed enrichment of NCVAS in HTAD-associated genes among dissections. These findings suggest NCVAS are an underrecognized contributor to TAD, particularly in sporadic dissection and unsolved MFS cases, highlighting the potential of advanced splice prediction tools in genetic diagnostics.

In immunocompromised pediatric patients, diagnosing invasive pulmonary aspergillosis (IPA) poses a significant challenge. Next-Generation Sequencing (NGS) shows promise for detecting fungal DNA but lacks standardization. This study aims to advance towards clinical evaluation of liquid biopsy NGS for Aspergillus detection, through an evaluation of wet-lab procedures and computational analysis. Our findings support using both CHM13v2.0 and GRCh38.p14 in host-read mapping to reduce fungal false-positives. We demonstrate the sensitivity of our custom kraken2 database, cRE.21, in detecting Aspergillus species. Additionally, cell-free DNA sequencing shows superior performance to whole-cell DNA sequencing by recovering higher fractions of fungal DNA in lung fluid (bronchoalveolar lavage [BAL] fluid) and plasma samples from pediatric patients with probable IPA. In a proof-of-principle, A. fumigatus was identified in 5 out of 7 BAL fluid samples and 3 out of 5 plasma samples. This optimized workflow can advance fungal-NGS research and represents a step towards enhancing diagnostic certainty by enabling more sensitive and accurate species-level diagnosis of IPA in immunocompromised patients.

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

Programmed cell death protein 1 (PD-1) is a critical immune checkpoint receptor and a target for cancer immune checkpoint inhibitors (ICI). We investigated PD-1 transcript expression across cancer types and its correlations to clinical outcomes. Using a reference population, PD-1 expression was calculated as percentiles in 489 of 514 patients (31 cancer types) with advanced/metastatic disease. PD-1 RNA expression varied across and within cancer types; pancreatic and liver/bile duct malignancies displayed the highest rates of high PD-1 (21.82% and 21.05%, respectively). Elevated CTLA-4, LAG-3, and TIGIT RNA expression were independently correlated with high PD-1. Although high PD-1 was not associated with outcome in immunotherapy-naïve patients (n = 272), in patients who received ICIs (n = 217), high PD-1 transcript expression was independently correlated with prolonged survival (hazard ratio 0.40; 95%CI, 0.18-0.92). This study identifies PD-1 as an important biomarker in predicting ICI outcomes, and advocates for comprehensive immunogenomic profiling in cancer management.