scholarly journals MRSD: a novel quantitative approach for assessing suitability of RNA-seq in the clinical investigation of mis-splicing in Mendelian disease

2021 ◽  
Author(s):  
Charlie F. Rowlands ◽  
Algy Taylor ◽  
Gillian Rice ◽  
Nicola Whiffin ◽  
Hildegard Nikki Hall ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Diagnostic Yield ◽  
Clinical Investigation ◽  
Genetic Disorders ◽  
Splice Junction ◽  
Mendelian Disease ◽  
Gene Transcript ◽  
Relative Expression Level ◽  
Gene Panels ◽  
The Impact

Background: RNA-sequencing of patient biosamples is a promising approach to delineate the impact of genomic variants on splicing, but variable gene expression between tissues complicates selection of appropriate tissues. Relative expression level is often used as a metric to predict RNA-sequencing utility. Here, we describe a gene- and tissue-specific metric to inform the feasibility of RNA-sequencing, overcoming some issues with using expression values alone. Results: We derive a novel metric, Minimum Required Sequencing Depth (MRSD), for all genes across three human biosamples (whole blood, lymphoblastoid cell lines (LCLs) and skeletal muscle). MRSD estimates the depth of sequencing required from RNA-sequencing to achieve user-specified sequencing coverage of a gene, transcript or group of genes of interest. MRSD predicts levels of splice junction coverage with high precision (90.1-98.2%) and overcomes transcript region-specific sequencing biases. Applying MRSD scoring to established disease gene panels shows that LCLs are the optimum source of RNA, of the three investigated biosamples, for 69.3% of gene panels. Our approach demonstrates that up to 59.4% of variants of uncertain significance in ClinVar predicted to impact splicing could be functionally assayed by RNA-sequencing in at least one of the investigated biosamples. Conclusions: We demonstrate the power of MRSD as a metric to inform choice of appropriate biosamples for the functional assessment of splicing aberrations. We apply MRSD in the context of Mendelian genetic disorders and illustrate its benefits over expression-based approaches. We anticipate that the integration of MRSD into clinical pipelines will improve variant interpretation and, ultimately, diagnostic yield.

scholarly journals Role of percutaneous liver biopsy in infantile cholestasis: cohort from Arabs

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Amna Basheer M. Ahmed ◽  
Musa Ahmad Fagih ◽  
Muhammed Salman Bashir ◽  
Abdulrahman Abdullah Al-Hussaini
Keyword(s):  
Liver Biopsy ◽  
Diagnostic Yield ◽  
Molecular Testing ◽  
Gamma Glutamyl Transferase ◽  
High Gamma ◽  
Infantile Cholestasis ◽  
Glutamyl Transferase ◽  
Gene Panels ◽  
The Impact

Abstract Background Investigators from different parts of the world are calling for a re-evaluation of the role of liver biopsy (LB) in the evaluation of infantile cholestasis (IC), especially in the light of emerging non-invasive diagnostic technologies. Therefore, this retrospective single-center study was conducted to determine the impact of LB on the diagnosis and management of IC in a cohort from Arabs. Methods From 2007 until 2019, 533 cases of IC were referred for evaluation. All infants who underwent LB were included in the study. We categorized the yield of LB into: (1) defined specific diagnosis; (2) excluded an important diagnosis. A single pathologist reviewed and made the histology report. Results 122 LB specimens met the inclusion criteria. The main indication for LB was a high suspicion of biliary atresia (BA) [high gamma-glutamyl transferase (GGT) cholestasis and pale stool] in 46 cases (37.8%). Liver biopsy had sensitivity of 86.4%, specificity (66.7%), PPV (70.4%), NPV (84.2%) in diagnosing BA. LB had a direct impact on clinical management in 52 cases (42.6%): (1) The true diagnosis was suggested by LB in 36 cases; (2) LB excluded BA and avoided intraoperative cholangiogram in 16 cases with high suspicion of BA. Among the 76 cases with low suspicion of BA, LB suggested the true diagnosis or helped to initiate specific management in 8 cases only (10.5%). In contrast, molecular testing confirmed the diagnosis in 48 (63%). Conclusion LB continues to be an important tool in the workup of cases with a high suspicion of BA. The low yield of LB in cases with low suspicion of BA calls for a re-evaluation of its role in these cases in whom early incorporation of cholestasis sequencing gene  panels can have a better diagnostic yield.

Diagnostic and Clinical Utility of Clinical Exome Sequencing in Children With Moderate and Severe Global Developmental Delay / Intellectual Disability

2019 ◽  
Vol 35 (2) ◽  
pp. 116-131 ◽  
Author(s):  
Jelena Ruml Stojanovic ◽  
Aleksandra Miletic ◽  
Borut Peterlin ◽  
Ales Maver ◽  
Marija Mijovic ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Exome Sequencing ◽  
Developmental Delay ◽  
Clinical Utility ◽  
Diagnostic Yield ◽  
Genetic Disorders ◽  
Significant Proportion ◽  
Global Developmental Delay ◽  
Clinical Exome Sequencing ◽  
The Impact

Clinical exome sequencing is currently being used in diagnostics of various genetic disorders, but studies supporting its application in clinical setting are scarce. The aim of this study was to establish diagnostic and clinical utility of clinical exome sequencing in patients with moderate and severe global developmental delay/intellectual disability. Clinical diagnosis was made in 49 of 88 investigated patients, with overall diagnostic yield of 55.7%. Molecular findings are characterized in detail, including the impact of newly made diagnosis on clinical management. Several previously unreported genotype-phenotype correlations and 33 novel variants are described. Genetic and clinical data were shared through publicly available database. In conclusion, clinical exome sequencing allows identification of causative variants in a significant proportion of patients in investigated clinical subgroup. Compared to whole exome sequencing, it shows similar diagnostic and clinical utility with reduced costs, which could be of particular importance for institutions with limited resources.

scholarly journals Empirical prediction of variant-associated cryptic-donors with 87% sensitivity and 95% specificity

2021 ◽  
Author(s):  
Ruebena Dawes ◽  
Himanshu Joshi ◽  
Sandra T Cooper
Keyword(s):  
Rare Disease ◽  
Rna Sequencing ◽  
Genetic Variant ◽  
Genetic Disorders ◽  
Diagnostic Testing ◽  
Splice Junction ◽  
Empirical Method ◽  
Evidence Based ◽  
Empirical Prediction ◽  
Testing Strategies

Predicting which cryptic-donors may be activated by a genetic variant is notoriously difficult. Through analysis of 5,145 cryptic-donors activated by 4,811 variants (versus 86,963 decoy-donors not used; any GT or GC), we define an empirical method predicting cryptic-donor activation with 87% sensitivity and 95% specificity. Strength (according to four algorithms) and proximity to the authentic-donor appear important determinants of cryptic-donor activation. However, other factors such as auxiliary splicing elements, which are difficult to identify, play an important role and are likely responsible for current prediction inaccuracies. We find that the most frequent mis-splicing events at each exon-intron junction, mined from 40,233 RNA-sequencing samples, predict with remarkable accuracy which cryptic-donor will be activated in rare disease. Aggregate RNA-Sequencing splice-junction data provides an accurate, evidence-based method to predict variant-activated cryptic-donors in genetic disorders, assisting pathology consideration of possible consequences of a variant for the encoded protein and RNA diagnostic testing strategies.

scholarly journals Empirical prediction of variant-associated cryptic-donors with 87% sensitivity and 95% specificity

2021 ◽  
Author(s):  
Ruebena Dawes ◽  
Himanshu Joshi ◽  
Sandra Cooper
Keyword(s):  
Rare Disease ◽  
Rna Sequencing ◽  
Genetic Variant ◽  
Genetic Disorders ◽  
Diagnostic Testing ◽  
Splice Junction ◽  
Empirical Method ◽  
Evidence Based ◽  
Empirical Prediction ◽  
Testing Strategies

Abstract Predicting which cryptic-donors may be activated by a genetic variant is notoriously difficult. Through analysis of 5,145 cryptic-donors activated by 4,811 variants (versus 86,963 decoy-donors not used; any GT or GC), we define an empirical method predicting cryptic-donor activation with 87% sensitivity and 95% specificity. Strength (according to four algorithms) and proximity to the authentic-donor appear important determinants of cryptic-donor activation. However, other factors such as auxiliary splicing elements, which are difficult to identify, play an important role and are likely responsible for current prediction inaccuracies. We find that the most frequent mis-splicing events at each exon-intron junction, mined from 40,233 RNA-sequencing samples, predict with remarkable accuracy which cryptic-donor will be activated in rare disease. Aggregate RNA-Sequencing splice-junction data provides an accurate, evidence-based method to predict variant-activated cryptic-donors in genetic disorders, assisting pathology consideration of possible consequences of a variant for the encoded protein and RNA diagnostic testing strategies.

scholarly journals One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

2021 ◽  
Author(s):  
Stephen E. Lincoln ◽  
Tina Hambuch ◽  
Justin M. Zook ◽  
Sara L. Bristow ◽  
Kathryn Hatchell ◽  
...  
Keyword(s):  
Diagnostic Yield ◽  
Copy Number Variants ◽  
Low Complexity ◽  
Clinical Genetic ◽  
Clinical Sensitivity ◽  
Pathogenic Variants ◽  
Wide Range ◽  
Large Indels ◽  
Next Generation Sequencing Ngs ◽  
The Impact

Abstract Purpose To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. Methods An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)–based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. Results In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. Conclusion The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.

scholarly journals Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants

2021 ◽  
Vol 11 (2) ◽  
pp. 131
Author(s):  
Laura B. Scheinfeldt ◽  
Andrew Brangan ◽  
Dara M. Kusic ◽  
Sudhir Kumar ◽  
Neda Gharani
Keyword(s):  
In Silico ◽  
Drug Efficacy ◽  
Common Variant ◽  
Genomic Research ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Allele Frequency Distribution ◽  
Sequencing Data ◽  
Patient Race ◽  
The Impact

Pharmacogenomics holds the promise of personalized drug efficacy optimization and drug toxicity minimization. Much of the research conducted to date, however, suffers from an ascertainment bias towards European participants. Here, we leverage publicly available, whole genome sequencing data collected from global populations, evolutionary characteristics, and annotated protein features to construct a new in silico machine learning pharmacogenetic identification method called XGB-PGX. When applied to pharmacogenetic data, XGB-PGX outperformed all existing prediction methods and identified over 2000 new pharmacogenetic variants. While there are modest pharmacogenetic allele frequency distribution differences across global population samples, the most striking distinction is between the relatively rare putatively neutral pharmacogene variants and the relatively common established and newly predicted functional pharamacogenetic variants. Our findings therefore support a focus on individual patient pharmacogenetic testing rather than on clinical presumptions about patient race, ethnicity, or ancestral geographic residence. We further encourage more attention be given to the impact of common variation on drug response and propose a new ‘common treatment, common variant’ perspective for pharmacogenetic prediction that is distinct from the types of variation that underlie complex and Mendelian disease. XGB-PGX has identified many new pharmacovariants that are present across all global communities; however, communities that have been underrepresented in genomic research are likely to benefit the most from XGB-PGX’s in silico predictions.

scholarly journals Suitability of Bronchoscopic Biopsy Tissue Samples for Next-Generation Sequencing

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 391
Author(s):  
Shuji Murakami ◽  
Tomoyuki Yokose ◽  
Daiji Nemoto ◽  
Masaki Suzuki ◽  
Ryou Usui ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Success Rate ◽  
Rna Sequencing ◽  
Surface Area ◽  
Endobronchial Ultrasound ◽  
Next Generation ◽  
Endobronchial Ultrasonography ◽  
Tissue Surface ◽  
The Impact ◽  
Generation Sequencing

A sufficiently large tissue sample is required to perform next-generation sequencing (NGS) with a high success rate, but the majority of patients with advanced non-small-cell lung cancer (NSCLC) are diagnosed with small biopsy specimens. Biopsy samples were collected from 184 patients with bronchoscopically diagnosed NSCLC. The tissue surface area, tumor cell count, and tumor content rate of each biopsy sample were evaluated. The impact of the cut-off criteria for the tissue surface area (≥1 mm2) and tumor content rate (≥30%) on the success rate of the Oncomine Dx Target Test (ODxTT) was evaluated. The mean tissue surface area of the transbronchial biopsies was 1.23 ± 0.85 mm2 when small endobronchial ultrasonography with a guide sheath (EBUS-GS) was used, 2.16 ± 1.49 mm2 with large EBUS-GS, and 1.81 ± 0.75 mm2 with endobronchial biopsy (EBB). The proportion of samples with a tissue surface area of ≥1 mm2 was 48.8% for small EBUS-GS, 79.2% for large EBUS-GS, and 78.6% for EBB. Sixty-nine patients underwent ODxTT. The success rate of DNA sequencing was 84.1% and that of RNA sequencing was 92.7% over all patients. The success rate of DNA (RNA) sequencing was 57.1% (71.4%) for small EBUS-GS (n = 14), 93.4% (96.9%) for large EBUS-GS (n = 32), 62.5% (100%) for EBB (n = 8), and 100% (100%) for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) (n = 15). Regardless of the device used, a tissue surface area of ≥ 1 mm2 is adequate for samples to be tested with NGS.

A novel mitral stenosis assessment using projected transmitral gradient improves the diagnostic and prognostic yields of doppler-based gradient

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
N Kato ◽  
R Padang ◽  
C Pislaru ◽  
C.G Scott ◽  
V.T Nkomo ◽  
...  
Keyword(s):  
Mitral Valve ◽  
Mitral Stenosis ◽  
Diagnostic Yield ◽  
Cardiac Events ◽  
Final Formula ◽  
Hemodynamic State ◽  
Tertiary Center ◽  
Novel Concept ◽  
The Impact

Abstract Background Transmitral gradient (TMG) is highly dependent on hemodynamic state, leading to discordance between TMG and mitral valve area (MVA). The effect of heart rate (HR) and stroke volume (SV) on TMG among patients with mitral stenosis (MS) is poorly understood. Purposes We aimed to (1) develop a formula for projected TMG (proTMG) for assessment of MS severity under varying hemodynamics; (2) assess the prognostic value of proTMG in patients with MS. Methods All patients evaluated for suspected MS without ≥moderate other valve disorder at our tertiary center between 2001 and 2017 were analyzed. Projected TMG is the expected gradient under normal flow (SV 80–94 ml and HR 60–79 bpm), and was modeled based on the observed impact of HR and SV on TMG by multiple regression analysis. The data were randomly split (2:1) into training and testing sets. The improvement in agreement between MVA and proTMG was evaluated. Composite cardiac events including all-cause death and mitral valve interventions were compared according to TMG grade using TMG and proTMG. Severe and moderate MS were defined as MVA ≤1.5 cm2 and 1.5–2.0 cm2 respectively, by the continuity equation. MVA ≤1.0 cm2 was considered as very severe MS. Results Of 4973 patients with suspected MS (age 73±12 years, 33% male), severe MS was present in 437 (9%, including 98 with very severe MS) and moderate MS in 934 (19%). In 838 patients with normal HR and SV, very severe, severe and moderate MS corresponded to TMG ≥12 mmHg, ≥6 mmHg and 4–6 mmHg, respectively. In the training set (n=3315), the median [interquartile range] of HR and SV were 70 [61–80] bpm and 97 [83–113] mL in men (n=1120), and 72 [63–82] bpm and 84 [71–97] mL in women (n=2195), respectively. The impact of HR and SV on TMG for men and women were 0.07 and 0.08 mmHg per 1 bpm increase in HR (95% confidence interval [CI] 0.06–0.07 and 0.07–0.08), and 0.03 and 0.05 mmHg per 1 mL increase in SV (95% CI 0.03–0.03 and 0.04–0.05), respectively. Therefore, the final formula to calculate proTMG was: proTMG=TMG-0.07(HR-70)-0.03(SV-97) in men and proTMG=TMG-0.08(HR-72)-0.05(SV-84) in women. In the testing set (n=1658), the proTMG (kappa=0.63, 95% CI 0.60–0.66) had better agreement with MS severity by MVA than TMG (kappa=0.28, 95% CI 0.24–0.32). To explore the prevalence of patients reclassified using proTMG, in 98 with TMG ≥12 mmHg, proTMG remained ≥6 mmHg. Of 657 with TMG 6–12 mmHg, proTMG remained ≥6 mmHg in 356 (54%), and decreased to <6 mmHg in 301 (46%). In patients with TMG 6–12 mmHg, proTMG ≥6 mmHg was associated with higher probability of cardiac events compared with <6 mmHg during follow-up of 2.8±3.1 years (Figure). Conclusion We propose a novel concept of projected TMG defined as the expected transmitral gradient at normal HR and SV levels. This improved the diagnostic yield of Doppler TMG measurements for MS severity assessment and identified a low-risk subset of patients with elevated TMG due to high HR or SV. Funding Acknowledgement Type of funding source: None

scholarly journals The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Marczyk ◽  
Chunxiao Fu ◽  
Rosanna Lau ◽  
Lili Du ◽  
Alexander J. Trevarton ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Rna Sequencing ◽  
Rna Extraction ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
The Impact ◽  
Formalin Fixed

Abstract Background Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA. Methods Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance. Results Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96). Conclusions The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.

scholarly journals Whipple’s Disease Affecting Ileal Peyer’s Patches: The First Case Report

2019 ◽  
Vol 2019 ◽  
pp. 1-4
Author(s):  
Sabah Sid’Amar ◽  
Giacomo Puppa
Keyword(s):  
Lymphoid Tissue ◽  
Diagnostic Yield ◽  
Clinical Investigation ◽  
Periodic Acid ◽  
Disease Diagnosis ◽  
Peyer's Patches ◽  
Peyer’S Patches ◽  
Whipple’S Disease ◽  
Whipple's Disease ◽  
First Case

Whipple’s disease is a rare chronic systemic bacterial infectious disease which can affect multiple organs, with a wide clinical spectrum encompassing many symptoms presenting in various forms and combinations. In the cases where the gastrointestinal tract is implicated, the more frequent localizations involve the small bowel, especially the duodenum. A case of a 67-year-old man who underwent clinical investigation after presenting with a progressive weight loss and showing a hypercapting right paracoeliac adenopathy at PET-CT scan is reported herein. A gastroscopy and a colonoscopy were done. The biopsies of the endoscopically normal ileal mucosa encompassed some submucosal Peyer’s patches. Histological examination of this lymphoid tissue revealed several foamy macrophages which turned out positive on periodic acid-Schiff special staining. Polymerase chain reaction of the microdissected lymph follicles allowed for confirming Whipple’s disease diagnosis. A targeted antibiotic treatment administrated to the patient led to a rapid clinical improvement. This finding of a previously unreported localization of infected macrophages in Whipple’s disease suggests that sampling the organized mucosal-submucosal lymphoid tissue may increase the diagnostic yield in endoscopic biopsies.

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