A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease

Gavin R. Oliver, Xiaojia Tang, Laura E. Schultz-Rogers, Noemi Vidal-Folch, W. Garrett Jenkinson, Tanya L. Schwab, Krutika Gaonkar, Margot A. Cousin, Asha Nair, Shubham Basu, Pritha Chanana, Devin Oglesbee, Eric W. Klee

Research output: Contribution to journalArticle

Abstract

Background RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5–35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. Methods We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. Results We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. Conclusions The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis.

Original languageEnglish (US)
Article numbere0223337
JournalPloS one
Volume14
Issue number10
DOIs
StatePublished - Jan 1 2019

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Rare Diseases
Fusion reactions
prioritization
germ cells
RNA Sequence Analysis
Workflow
Sequence Alignment
Gene Fusion
Gene Expression Profiling
range improvement
Tumor Cell Line
cell lines
Computer Simulation
gene fusion
Alleles
sequence alignment
RNA
transcriptomics
Phenotype
Cell Line

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Oliver, G. R., Tang, X., Schultz-Rogers, L. E., Vidal-Folch, N., Garrett Jenkinson, W., Schwab, T. L., ... Klee, E. W. (2019). A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PloS one, 14(10), [e0223337]. https://doi.org/10.1371/journal.pone.0223337

A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. / Oliver, Gavin R.; Tang, Xiaojia; Schultz-Rogers, Laura E.; Vidal-Folch, Noemi; Garrett Jenkinson, W.; Schwab, Tanya L.; Gaonkar, Krutika; Cousin, Margot A.; Nair, Asha; Basu, Shubham; Chanana, Pritha; Oglesbee, Devin; Klee, Eric W.

In: PloS one, Vol. 14, No. 10, e0223337, 01.01.2019.

Research output: Contribution to journalArticle

Oliver, GR, Tang, X, Schultz-Rogers, LE, Vidal-Folch, N, Garrett Jenkinson, W, Schwab, TL, Gaonkar, K, Cousin, MA, Nair, A, Basu, S, Chanana, P, Oglesbee, D & Klee, EW 2019, 'A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease', PloS one, vol. 14, no. 10, e0223337. https://doi.org/10.1371/journal.pone.0223337
Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Garrett Jenkinson W, Schwab TL et al. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PloS one. 2019 Jan 1;14(10). e0223337. https://doi.org/10.1371/journal.pone.0223337
Oliver, Gavin R. ; Tang, Xiaojia ; Schultz-Rogers, Laura E. ; Vidal-Folch, Noemi ; Garrett Jenkinson, W. ; Schwab, Tanya L. ; Gaonkar, Krutika ; Cousin, Margot A. ; Nair, Asha ; Basu, Shubham ; Chanana, Pritha ; Oglesbee, Devin ; Klee, Eric W. / A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. In: PloS one. 2019 ; Vol. 14, No. 10.
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AU - Garrett Jenkinson, W.

AU - Schwab, Tanya L.

AU - Gaonkar, Krutika

AU - Cousin, Margot A.

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