Yusuph Mavura

Yield of reported results from genetic testing provides a proximal measure of clinical usefulness. While ACMG/AMP guidelines provide representations of uncertainty for individual genetic variant classification, additional factors are considered when determining whether results explain a patient's presentation. To standardize cross-consortium analysis, a working group of the Clinical Sequencing Evidence-Generating Research (CSER2) consortium iteratively identified factors used when contextualizing variant-level results to case-level interpretation (i.e., interpretation of an individual's genetic data with respect to the indication for testing). Sites independently categorized results; complex cases were discussed collaboratively, leading to revision of classification categories. Our metric incorporates factors beyond classification of reported variants. Analogous to variant-level results, "Definitive Positive" and "Probable Positive" represent certainty that results may be clinically explanatory. The category "Inconclusive" applies when results may or may not fully explain the patient presentation, with subdivision into multiple (non-exclusive) subcategories. Cases falling outside all of the other categories are considered "Negative". The overall diagnostic yield by this metric and use of categories for inconclusive results varied by CSER project, in part paralleling study design differences. This case-level categorization provides a meaningful assessment of diagnostic yield, and for inconclusive cases identifies potentially resolvable factors for case resolution.

Purpose: Diagnostic yield from exome and genome sequencing varies widely across studies. It remains unclear how much of this variation reflects patient-level factors (e.g., sex, clinical features, race/ethnicity, genetic ancestry) versus site-level practices such as sequencing modality or variant interpretation workflows. We aimed to quantify the contributions of these factors to diagnostic outcomes across five U.S. clinical sequencing sites. Methods: We performed a cross-sectional analysis of 3,008 prenatal, neonatal, and pediatric cases from the NHGRI Clinical Sequencing Evidence-Generating Research (CSER) consortium (2017–2023). Clinical indications spanned neurodevelopmental, neurological, immunological, metabolic, craniofacial, skeletal, cardiac, prenatal, and oncologic presentations. Genetic ancestry was inferred from sequencing data, and variants were interpreted using ACMG/AMP guidelines to classify DNA-based diagnoses. Generalized linear mixed models were used to estimate associations between diagnostic yield and fixed effects (sex, prenatal status, isolated cancer, number of clinical indications, sequencing modality, race/ethnicity, and genetic ancestry), while modeling study site as a random effect to quantify between-site variation. Results: The overall diagnostic yield was 19.0%. Multiple clinical indications (OR=1.47, 95% CI 1.20–1.80, p<0.001) were associated with higher diagnostic yield, and male sex (OR=0.80, 95% CI 0.66–0.96, p=0.017) and prenatal status (OR=0.63, 95% CI 0.44–0.90, p=0.012) were associated with lower yield. Sequencing modality, race/ethnicity, genetic ancestry, and isolated cancer were not statistically significantly associated with diagnostic outcomes.. A model without fixed effects attributed ∼10% of variance in diagnostic yield to between-site differences. After adjusting for covariates, site-level variance decreased to 5.7%, indicating consistent variation across sites not explained by measured patient factors. Conclusion: Across five sites, patient-level clinical features influenced diagnostic yield, but substantial site-level variation remained even after adjustment. Differences in variant interpretation, or case-classification practices may contribute to this residual variability. Further efforts to increase consistency in exome- and genome-sequencing diagnostic workflows may help reduce inter-site differences.

Purpose: Pathogenic DEGS1 variants have been reported in individuals with autosomal recessive hypomyelinating leukodystrophy 18 (HLD18; MIM# 618404). We sought to resolve a 5′ +4/+5 splice site variant of uncertain significance found in three individuals with HLD features. Methods: We used next-generation DNA and transcriptome sequencing, cell-based splicing assays, and tandem mass spectrometry to detect and characterize the splice site variant. We then performed RNA structure probing and conventional antisense oligonucleotide screening to investigate molecular mechanisms for potential therapeutic intervention. Results: A homozygous, DEGS1 5′ splice site variant, c.825+4_825+5delAGinsTT (NM_003676.4) was identified in all three participants. Although the gene has been associated with autosomal recessive hypomyelinating leukodystrophy, the variant has not been previously reported in any available databases or literature. We show that the splice site variant: 1) was sufficient to induce exon two skipping in most detected transcripts; 2) resulted in structural changes to the 5′ and 3′ splice site regions using RNA structure probing; and 3) corresponds to plasma sphingolipid profiles consistent with loss of sphingolipid delta(4)-desaturase activity. Discussion: Our RNA and lipidomic evidence proved that the DEGS1 variant c.825+4_825+5delAGinsTT is pathogenic and suggested a mechanistic model to explain how exon two skipping is induced.

It has been suggested that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental/subcontinental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Cases (N = 845) with suspected genetic disorders underwent ES for diagnosis. Continental/subcontinental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov–Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. We observed no reduction in overall DY associated with any genetic ancestry (African, Native American, East Asian, European, Middle Eastern, South Asian). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.

Purpose: It has been hypothesized that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Methods: Cases (N=845) with suspected genetic disorders underwent ES for diagnosis. Continental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. Results: We observed no reduction in overall DY associated with any continental genetic ancestry (Africa, America, East Asia, Europe, Middle East, South Asia). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. Conclusions: In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the ethical and equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.

Background: Men of African ancestry have disproportionately high incidence rates of prostate cancer (PCa) and have high mortality rates. While there is evidence for a higher genetic predisposition for incidence of PCa in men of African ancestry compared to men of European ancestry, there have been few transcriptomic studies on PCa in men of African ancestry in the African continent.Objective: We performed transcriptomic profiling and fusion analysis on bulk RNA sequencing (RNA‐seq) samples from 24 Nigerian PCa patients to investigate the transcriptomic and genomic rearrangement landscape of PCa in Nigerian men.Design: Bulk RNA‐seq was performed on 24 formalin‐fixed paraffin‐embeded (FFPE) prostatectomy specimens of Nigerian men. Transcriptomic analysis was performed on 11 high‐quality samples. Arriba Fusion and STAR Fusion were used for fusion detection.Results: 4/11 (36%) of the samples harbored an erythroblast transformation‐specific (ETS) fusion event; 1/11 (9%) had a TMPRSS2‐ERG fusion; 2/11 had a TMPRSS2‐ETV5 fusion, and 1/11 had a SLC45A3‐SKIL fusion. Hierarchical clustering of normalized and mean‐centered gene expression showed clustering of fusion positive samples. Furthermore, we developed gene set signatures for Nigerian PCa based on fusion events. By projecting the cancer genome atlas prostate adenocarcinoma (TCGA‐PRAD) bulk RNA‐seq data set onto the transcriptional space defined by these signatures derived from Nigerian PCa patients, we identified a positive correlation between the Nigerian fusion signature and fusion positive samples in the TCGA‐PRAD data set.Conclusions: Less frequent ETS fusion events other than TMPRSS2‐ERG such as TMPRSS2‐ETV5 and non‐ETS fusion events such as SLC45A3‐SKIL may be more common in PCa in Nigerian men. This study provides useful working transcriptomic signatures that characterize oncogenic states representative of specific gene fusion events in PCa from Nigerian men.