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Wojcik MH, Lemire G, Zaki MS, Wissman M, Win W, White S, Weisburd B, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Okur V, Oja KT, O'Leary M, O'Heir E, Morel C, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gazda HT, Ganesh VS, Ganapathy M, Gallacher L, Fu J, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bonnemann C, Beggs AH, Baxter SM, Agrawal PB, Talkowski M, Austin-Tse C, Rehm HL, O'Donnell-Luria A. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis. medRxiv 2023:2023.08.08.23293829. [PMID: 38328047 PMCID: PMC10849673 DOI: 10.1101/2023.08.08.23293829] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Background Causal variants underlying rare disorders may remain elusive even after expansive gene panels or exome sequencing (ES). Clinicians and researchers may then turn to genome sequencing (GS), though the added value of this technique and its optimal use remain poorly defined. We therefore investigated the advantages of GS within a phenotypically diverse cohort. Methods GS was performed for 744 individuals with rare disease who were genetically undiagnosed. Analysis included review of single nucleotide, indel, structural, and mitochondrial variants. Results We successfully solved 218/744 (29.3%) cases using GS, with most solves involving established disease genes (157/218, 72.0%). Of all solved cases, 148 (67.9%) had previously had non-diagnostic ES. We systematically evaluated the 218 causal variants for features requiring GS to identify and 61/218 (28.0%) met these criteria, representing 8.2% of the entire cohort. These included small structural variants (13), copy neutral inversions and complex rearrangements (8), tandem repeat expansions (6), deep intronic variants (15), and coding variants that may be more easily found using GS related to uniformity of coverage (19). Conclusion We describe the diagnostic yield of GS in a large and diverse cohort, illustrating several types of pathogenic variation eluding ES or other techniques. Our results reveal a higher diagnostic yield of GS, supporting the utility of a genome-first approach, with consideration of GS as a secondary or tertiary test when higher-resolution structural variant analysis is needed or there is a strong clinical suspicion for a condition and prior targeted genetic testing has been negative.
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Dawes R, Bournazos AM, Bryen SJ, Bommireddipalli S, Marchant RG, Joshi H, Cooper ST. SpliceVault predicts the precise nature of variant-associated mis-splicing. Nat Genet 2023; 55:324-332. [PMID: 36747048 PMCID: PMC9925382 DOI: 10.1038/s41588-022-01293-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/15/2022] [Indexed: 02/08/2023]
Abstract
Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity. Strikingly, ranking the four most common unannotated splicing events across 335,663 reference RNA-sequencing (RNA-seq) samples (300K-RNA Top-4) predicts the nature of variant-associated mis-splicing with 92% sensitivity. The 300K-RNA Top-4 events correctly identify 96% of exon-skipping events and 86% of cryptic splice sites for 140 clinical cases subject to RNA testing, showing higher sensitivity and positive predictive value than SpliceAI. Notably, RNA re-analyses showed we had missed 300K-RNA Top-4 events for several clinical cases tested before the development of this empirical predictive method. Simply, mis-splicing events that happen around a splice site in RNA-seq data are those most likely to be activated by a splice-site variant. The SpliceVault web portal allows users easy access to 300K-RNA for informed splice-site variant interpretation and classification.
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Affiliation(s)
- Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Adam M Bournazos
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Rhett G Marchant
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia.
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia.
- The Children's Medical Research Institute, Sydney, New South Wales, Australia.
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Lemerle J, Tournade MF, Marchant RG, Flamant R, Sarrazin D, Flamant F, Lemerle M, Jundt S, Zucker JM, Schweisguth O. Wilms' tumor: natural history and prognostic factors: a retrospective study of 248 cases treated at the Institut Gustave-Roussy 1952-1967. Cancer 1976; 37:2557-66. [PMID: 177189 DOI: 10.1002/1097-0142(197605)37:5<2557::aid-cncr2820370549>3.0.co;2-l] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A statistical analysis of 248 histologically proven cases of Wilms' tumor treated at the Institut Gustave-Roussy, Villejuif, France, from 1952 to 1967, is presented. Two years recurrence-free survival and five years survival have been selected as prognostic criteria. Patients under two years of age have significantly fewer metastases and a better five-year survival rate than those over two. Stage is stronly correlated with recurrences and survival. Influence of tumor size, number of tumor nodules, tumor rupture, adhesions, regional lymph node involvement, and renal vein infiltration is shown. Detailed analysis of histopathologic features indicates that a favorable clinical course is significantly related to the number of different varieties of epithelial differentiation (tubular, glomerular, microcystic) found in any tumor, whatever the abundance of each of them. Presence of striated muscular cells, however abundant, does not influence survival or metastatic rates. Cases where irradiation given prior to surgery resulted in complete destruction of tumor cells, form a distinctive group of very unfavorable prognosis. Relapse of tumor occurs in 54% of cases, 10% presenting with metastases. Involved sites are listed. No correlation is found between date of metastases and other parameters. The three major prognostic factors of age, stage, histologic pattern, bear prognostic value separately. Stage and age are linked, as well as histology and age. Stage and histology are not linked. Age in itself therefore seems less important. It is concluded that these well-defining treatment for each individual case.
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