| 1. |
- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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| 2. |
- Vickers, Andrew, et al.
(författare)
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Properties of the 4-Kallikrein Panel Outside the Diagnostic Gray Zone : Meta-Analysis of Patients with Positive Digital Rectal Examination or Prostate Specific Antigen 10 ng/ml and Above
- 2017
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Ingår i: Journal of Urology. - : Ovid Technologies (Wolters Kluwer Health). - 0022-5347 .- 1527-3792. ; 197, s. 607-613
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The 4-kallikrein panel, commercially available as the 4Kscore™, is a reflex test for prostate cancer early detection that has been extensively validated in multiple international cohorts. It has been suggested that use of such reflex tests be limited to those with prostate specific antigen less than 10 ng/ml and negative digital rectal examination. We aimed to determine the value of the panel in men outside this "diagnostic gray zone.". Materials and Methods: We performed an individual patient data meta-analysis using data from prior studies on the 4-kallikrein panel. We calculated the properties of the panel for predicting high grade (Gleason 7+) cancer in a subgroup of men with either positive digital rectal examination or prostate specific antigen 10 to 25 ng/ml. Results: A total 2,891 men from 8 cohorts were included. An important proportion of patients, including 32% in the United States validation study, had prostate specific antigen 10 to 25 ng/ml or a positive digital rectal examination. For men with prostate specific antigen 10 to 25 ng/ml the fixed-effects estimate for the discrimination of the kallikrein model was 0.84 vs 0.69 for the base model (difference 0.128, 95% CI 0.098-0.159). In the positive digital rectal examination group discrimination was 0.82 vs 0.72 (difference 0.092, 95% CI 0.069-0.115). Decision analysis showed a clinical net benefit for use of the panel in this subgroup with a reduction in biopsy rates of about 20% and only a small number of high grade cancers missed, fewer than 3% of those not biopsied. Conclusion: The use of the kallikrein panel in men with a positive digital rectal examination or prostate specific antigen 10 to 25 ng/ml is justified.
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| 3. |
- Vickers, Andrew, et al.
(författare)
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Value of Intact Prostate Specific Antigen and Human Kallikrein 2 in the 4 Kallikrein Predictive Model : An Individual Patient Data Meta-Analysis
- 2018
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Ingår i: Journal of Urology. - : Ovid Technologies (Wolters Kluwer Health). - 0022-5347 .- 1527-3792. ; 199:6, s. 1470-1474
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The 4 kallikrein panel, commercially available as the 4Kscore®, is a statistical model that has been shown to accurately predict Gleason Grade Group 2 or greater (high grade) cancer on biopsy and the long-term risk of distant prostate cancer metastases. The panel includes 2 novel markers, namely intact prostate specific antigen and hK2. It has been questioned whether these 2 additional markers add discrimination to the clinical predictors of patient age, digital rectal examination and prior biopsy, and the established molecular markers total and free prostate specific antigen. Materials and Methods: We performed an individual patient data meta-analysis of published studies in which the 4 kallikrein panel was measured in men undergoing prostate biopsy. We assess the improvement in discrimination associated with including intact prostate specific antigen and hK2 along with total and free prostate specific antigen in the statistical model. Results: Included in analysis were 14,510 men from a total of 10 studies. The fixed effects meta-analytical estimate of the discrimination of the model without intact prostate specific antigen and hK2 was 0.742 (95% CI 0.727–0.756) compared to 0.813 (95% CI 0.801–0.825) for the full kallikrein model. The 95% CIs did not overlap and the difference in discrimination was highly statistically significant (0.069, 95% CI 0.057–0.080, p <0.0001). Intact prostate specific antigen (increase in discrimination 0.059, 95% CI 0.050–0.069) and hK2 (increase in discrimination 0.024, 95% CI 0.020–0.029, each p <0.0001) added independently to the model. Conclusions: The clinical value of the panel could not be replicated using data readily available to urologists without measuring intact prostate specific antigen and hK2.
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