Clinical chemistry最新文献

Background: Genetic screening has advanced from prenatal cell-free DNA (cfDNA) screening for aneuploidies (cfDNA-ANP) to single-gene disorders (cfDNA-SGD). Clinical validation studies have been promising in pregnancies with anomalies but are limited in the general population.

Methods: Chart review and laboratory data identified pregnancies with cfDNA-SGD screening for 25 autosomal dominant conditions at our academic center. Screening was identified as routine by International Classification of Diseases (ICD) 10 codes and chart review. Ultrasound anomalies or known family history of a condition on the panel were excluded. Retrospective chart review investigated test concordance, outcomes, and phenotypes.

Results: cfDNA-SGD was completed for 3480/37 050 (9.4%) pregnancies, of which 2745 (78.9%) were for routine screening. Fourteen (0.51%, 14/2745) had high-risk results defined as pathogenic/likely pathogenic (P/LP) variants: 6 (0.22%) likely fetal variants, and 8 (0.29%) maternal variants with 50% risk for fetal inheritance. Diagnostic testing detected 6/6 fetal and 6/8 maternal cfDNA-SGD variants (2/8 pregnant individuals declined testing but had clinical features on physical exam). Variants were detected in 11/14 pregnancies/newborns and in 9/14 (64.3%) parents/gamete donors. There were no false positives identified by cfDNA-SGD; however, 2 variants were discrepantly classified between the cfDNA-SGD and diagnostic testing laboratories. All pregnancies had normal imaging and 9 had mild postnatal phenotypes. Three terminated pregnancy following diagnostic testing.

Conclusions: Our study demonstrated that 0.51% of routine cfDNA-SGD was high risk, prompting comprehensive evaluation for pregnancies and parents. Routine cfDNA-SGD allowed for early identification and intervention, but raises counseling challenges due to variable expressivity, limited genotype-phenotype correlations, and discrepant variant classification.

Background: Minimally invasive molecular profiling using cell-free DNA (cfDNA) is increasingly important to the management of cancer patients; however, low sensitivity remains a major limitation, particularly for brain tumor patients. Transiently attenuating cfDNA clearance from the body-thereby, allowing more cfDNA to be sampled-has been proposed to improve the performance of liquid biopsy diagnostics. However, there is a paucity of clinical data on the effect of higher cfDNA recovery. Here, we investigated the impact of collecting greater quantities of cfDNA on circulating tumor DNA (ctDNA) sensitivity in the "low-shedding" cancer type glioblastoma by analyzing up to approximately 15-fold more plasma than routinely obtained clinically.

Methods: We tested 70 plasma samples (median 17.0 mL, range 2.5-66.5) from 8 IDH-wild-type glioblastoma patients using an optimized version of the MAESTRO-Pool ctDNA assay. Results were compared with simulated single-blood-tube equivalents of cfDNA. ctDNA results were then compared with magnetic resonance imaging (MRI) and pathology assessments of true progression vs pseudoprogression in glioblastoma patients.

Results: Larger cfDNA yields exhibited a doubling in ctDNA-positivity while achieving a median specificity of 99% and more precise ctDNA quantification. In 8 glioblastoma patients, ctDNA was detected in 88%, including at multiple timepoints in 6/7. In the setting of indeterminate progression by MRI, our data suggested that MAESTRO-Pool with large plasma volumes can help distinguish true glioblastoma progression from pseudoprogression.

Conclusions: Our findings provide a proof-of-principle that most glioblastomas shed ctDNA into plasma and that greater ctDNA yields could help improve liquid biopsies for "low-shedding" cancer types such as glioblastoma.

Background: Prenatal cell-free DNA (cfDNA) screening is a success story of clinical genomics that has translated to and transformed obstetric care. It is a highly sensitive and specific method of screening for the most common fetal aneuploidies, including trisomies 13, 18, and 21. While primarily designed to detect fetal chromosomal abnormalities, the test also analyzes maternal cfDNA, which can complicate interpretation of results. Occasionally, abnormalities in cfDNA that do not align with fetal aneuploidy may indicate benign or malignant maternal disease states, presenting unique diagnostic challenges and opportunities.

Content: This review explores the methods and implications of incidental cancer detection through prenatal cfDNA screening. Early case reports noted instances in which abnormal cfDNA results, initially suggestive of fetal aneuploidies, led to post-pregnancy diagnoses of maternal cancers. Subsequent large retrospective studies have established significant correlations between atypical prenatal cfDNA results and undiagnosed maternal malignancies. Abnormal cfDNA profiles, particularly those indicating multiple aneuploidies, first require fetal diagnostic tests, such as amniocentesis. If the fetal studies are normal, further investigation into a maternal source should proceed. Clinical management of these findings may involve a multidisciplinary approach, incorporating advanced imaging techniques and genetic counseling to ensure timely and accurate maternal diagnoses.

Summary: The integration of genome-wide analysis and innovative bioinformatics tools into prenatal cfDNA screening has enhanced its ability to identify potential cancer cases. Developing standardized guidelines for reporting and managing incidental findings is crucial to optimizing patient outcomes and mitigating psychological impacts on expectant persons and their partners.

Background: Candida auris is an emerging multidrug-resistant pathogen. Interpretation of susceptibility testing can be difficult since minimum inhibitory concentration (MIC) breakpoints have not been fully established.

Methods: All C. auris isolates from unique patients identified at a large urban hospital between 2020 and 2024 (n = 66) underwent whole-genome sequencing (WGS). Genomic DNA was extracted from pure culture isolates and underwent PCR-free library preparation. WGS was performed on an Illumina platform (NextSeq2000) with an average coverage of 50×. Genomic analysis was conducted via an adapted GATK-based pipeline using the B11205 strain as the reference genome based on the CDC (MycoSNP) protocol. All isolates underwent FKS1 gene Sanger sequencing for confirmation of WGS results. Genotypic results were correlated with antifungal susceptibility testing.

Results: All clinical isolates were part of Clade I and carried azole resistance mutations in ERG11, TAC1b, and CDR1, consistent with 100% phenotypic fluconazole resistance. Across all isolates, 5 distinct missense variants in FKS1 were identified: one case with p.Ser639Tyr, one case with both a p.Arg1354Ser and a p.Asp642His, 7 cases with p.Met690Ile, and 9 cases with p.Val1818Ile. Isolates with known echinocandin resistance conferring mutations p.Ser639Tyr and p.Arg1354Ser were resistant to micafungin and anidulafungin. Two isolates with Met690Ile were resistant to caspofungin alone.

Conclusions: With potential resistance to all 3 major antifungal classes of drugs, C. auris is an emerging public health threat. Early detection of echinocandin resistance by molecular methods could impact treatment course to include novel antifungal agents. Further study of the FKS1 Met690Ile variant is warranted.

Background: Newborn hearing screening is a physiologic screen to identify infants who may be deaf or hard of hearing (DHH) and would benefit from early intervention. Typically, an infant who does not pass the newborn hearing screen is referred for clinical audiology testing, which may be followed by genetic testing to identify the etiology of an infant's DHH.

Content: The current newborn hearing screening paradigm can miss mild cases of DHH or later-onset DHH, leaving a child at risk for unrecognized DHH, which could impact long-term language, communication, and social development. Genomic technologies are improving the diagnosis of DHH in newborns who fail their newborn hearing screen, and a case is being made for genomic screening for DHH in all newborns.

Summary: The genomic era brings a wealth of opportunities to screen newborns for genetic causes of hearing loss on a population wide basis, some of which are already being implemented in a clinical setting.