Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions Article Swipe
Yong-Han Hank Cheng
,
Jane Ranchalis
,
Katherine M. Munson
,
Mitchell R. Vollger
,
Elsa Balton
,
Casie A. Genetti
,
Michael J. Bamshad
,
Chia‐Lin Wei
,
Katrina M. Dipple
,
Elizabeth Blue
,
Daniela Witten
,
Anne O’Donnell‐Luria
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.11.07.25339764
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.11.07.25339764
Identifying pathogenic non-coding variants that contribute to Mendelian conditions remains challenging as the functional impact of these variants on gene function is often unknown. We present IsoRanker, a long-read transcriptome sequencing-based framework that prioritizes functionally relevant non-coding variants by detecting genes and novel isoforms with outlier expression, allelic imbalance, and/or nonsense-mediated decay (NMD). We generated paired cycloheximide-treated and untreated fibroblast transcriptomes from 31 individuals (3 individuals with known transcript-altering rare variants and 28 individuals with unsolved conditions) and linked transcripts to phased long-read genomes. IsoRanker successfully recovered known transcript alterations in this cohort and remained robust in subsampling analyses to cohorts of 11 individuals and ∼5 million full-length transcripts per individual. However, performance was dependent upon de novo isoform caller choice, particularly for NMD-sensitive and novel isoforms. Among 28 previously unsolved cases, IsoRanker deprioritized most fibroblast-expressed candidate splice site variants while nominating new leads. In one individual, IsoRanker prioritized HARS1 , revealing biallelic non-coding variants that together produced a partial HARS1 loss-of-function and informed targeted therapy in this individual using histidine supplementation. These findings establish long-read, NMD-aware transcriptomics with IsoRanker as an effective approach for generating isoform-level functional evidence, improving classification of non-coding variants and supporting the diagnosis of individuals with rare diseases.
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.11.07.25339764
- https://www.medrxiv.org/content/medrxiv/early/2025/11/13/2025.11.07.25339764.full.pdf
- OA Status
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- References
- 31
- OpenAlex ID
- https://openalex.org/W4416247839
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- DOI
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https://doi.org/10.1101/2025.11.07.25339764Digital Object Identifier
- Title
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Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditionsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-11-13Full publication date if available
- Authors
-
Yong-Han Hank Cheng, Jane Ranchalis, Katherine M. Munson, Mitchell R. Vollger, Elsa Balton, Casie A. Genetti, Michael J. Bamshad, Chia‐Lin Wei, Katrina M. Dipple, Elizabeth Blue, Daniela Witten, Anne O’Donnell‐LuriaList of authors in order
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https://doi.org/10.1101/2025.11.07.25339764Publisher landing page
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https://www.medrxiv.org/content/medrxiv/early/2025/11/13/2025.11.07.25339764.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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-
greenOpen access status per OpenAlex
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https://www.medrxiv.org/content/medrxiv/early/2025/11/13/2025.11.07.25339764.full.pdfDirect OA link when available
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| abstract_inverted_index.rare | 70, 202 |
| abstract_inverted_index.site | 139 |
| abstract_inverted_index.that | 5, 33, 156 |
| abstract_inverted_index.this | 92, 168 |
| abstract_inverted_index.upon | 116 |
| abstract_inverted_index.with | 45, 67, 75, 179, 201 |
| abstract_inverted_index.∼5 | 106 |
| abstract_inverted_index.Among | 128 |
| abstract_inverted_index.HARS1 | 150, 161 |
| abstract_inverted_index.These | 173 |
| abstract_inverted_index.decay | 52 |
| abstract_inverted_index.genes | 41 |
| abstract_inverted_index.known | 68, 88 |
| abstract_inverted_index.novel | 43, 126 |
| abstract_inverted_index.often | 23 |
| abstract_inverted_index.these | 17 |
| abstract_inverted_index.using | 170 |
| abstract_inverted_index.while | 141 |
| abstract_inverted_index.(NMD). | 53 |
| abstract_inverted_index.and/or | 50 |
| abstract_inverted_index.caller | 120 |
| abstract_inverted_index.cases, | 132 |
| abstract_inverted_index.cohort | 93 |
| abstract_inverted_index.impact | 15 |
| abstract_inverted_index.leads. | 144 |
| abstract_inverted_index.linked | 79 |
| abstract_inverted_index.paired | 56 |
| abstract_inverted_index.phased | 82 |
| abstract_inverted_index.robust | 96 |
| abstract_inverted_index.splice | 138 |
| abstract_inverted_index.allelic | 48 |
| abstract_inverted_index.choice, | 121 |
| abstract_inverted_index.cohorts | 101 |
| abstract_inverted_index.isoform | 119 |
| abstract_inverted_index.million | 107 |
| abstract_inverted_index.outlier | 46 |
| abstract_inverted_index.partial | 160 |
| abstract_inverted_index.present | 26 |
| abstract_inverted_index.remains | 10 |
| abstract_inverted_index.therapy | 166 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.However, | 112 |
| abstract_inverted_index.analyses | 99 |
| abstract_inverted_index.approach | 184 |
| abstract_inverted_index.findings | 174 |
| abstract_inverted_index.function | 21 |
| abstract_inverted_index.genomes. | 84 |
| abstract_inverted_index.informed | 164 |
| abstract_inverted_index.isoforms | 44 |
| abstract_inverted_index.produced | 158 |
| abstract_inverted_index.relevant | 36 |
| abstract_inverted_index.remained | 95 |
| abstract_inverted_index.targeted | 165 |
| abstract_inverted_index.together | 157 |
| abstract_inverted_index.unknown. | 24 |
| abstract_inverted_index.unsolved | 76, 131 |
| abstract_inverted_index.variants | 4, 18, 38, 71, 140, 155, 194 |
| abstract_inverted_index.IsoRanker | 85, 133, 148, 180 |
| abstract_inverted_index.Mendelian | 8 |
| abstract_inverted_index.NMD-aware | 177 |
| abstract_inverted_index.biallelic | 153 |
| abstract_inverted_index.candidate | 137 |
| abstract_inverted_index.dependent | 115 |
| abstract_inverted_index.detecting | 40 |
| abstract_inverted_index.diagnosis | 198 |
| abstract_inverted_index.diseases. | 203 |
| abstract_inverted_index.effective | 183 |
| abstract_inverted_index.establish | 175 |
| abstract_inverted_index.evidence, | 189 |
| abstract_inverted_index.framework | 32 |
| abstract_inverted_index.generated | 55 |
| abstract_inverted_index.histidine | 171 |
| abstract_inverted_index.improving | 190 |
| abstract_inverted_index.isoforms. | 127 |
| abstract_inverted_index.long-read | 29, 83 |
| abstract_inverted_index.recovered | 87 |
| abstract_inverted_index.revealing | 152 |
| abstract_inverted_index.untreated | 59 |
| abstract_inverted_index.IsoRanker, | 27 |
| abstract_inverted_index.conditions | 9 |
| abstract_inverted_index.contribute | 6 |
| abstract_inverted_index.fibroblast | 60 |
| abstract_inverted_index.functional | 14, 188 |
| abstract_inverted_index.generating | 186 |
| abstract_inverted_index.imbalance, | 49 |
| abstract_inverted_index.individual | 169 |
| abstract_inverted_index.long-read, | 176 |
| abstract_inverted_index.nominating | 142 |
| abstract_inverted_index.non-coding | 3, 37, 154, 193 |
| abstract_inverted_index.pathogenic | 2 |
| abstract_inverted_index.previously | 130 |
| abstract_inverted_index.supporting | 196 |
| abstract_inverted_index.transcript | 89 |
| abstract_inverted_index.Identifying | 1 |
| abstract_inverted_index.alterations | 90 |
| abstract_inverted_index.challenging | 11 |
| abstract_inverted_index.conditions) | 77 |
| abstract_inverted_index.expression, | 47 |
| abstract_inverted_index.full-length | 108 |
| abstract_inverted_index.individual, | 147 |
| abstract_inverted_index.individual. | 111 |
| abstract_inverted_index.individuals | 64, 66, 74, 104, 200 |
| abstract_inverted_index.performance | 113 |
| abstract_inverted_index.prioritized | 149 |
| abstract_inverted_index.prioritizes | 34 |
| abstract_inverted_index.subsampling | 98 |
| abstract_inverted_index.transcripts | 80, 109 |
| abstract_inverted_index.functionally | 35 |
| abstract_inverted_index.particularly | 122 |
| abstract_inverted_index.successfully | 86 |
| abstract_inverted_index.NMD-sensitive | 124 |
| abstract_inverted_index.deprioritized | 134 |
| abstract_inverted_index.isoform-level | 187 |
| abstract_inverted_index.transcriptome | 30 |
| abstract_inverted_index.classification | 191 |
| abstract_inverted_index.transcriptomes | 61 |
| abstract_inverted_index.transcriptomics | 178 |
| abstract_inverted_index.loss-of-function | 162 |
| abstract_inverted_index.sequencing-based | 31 |
| abstract_inverted_index.supplementation. | 172 |
| abstract_inverted_index.nonsense-mediated | 51 |
| abstract_inverted_index.transcript-altering | 69 |
| abstract_inverted_index.fibroblast-expressed | 136 |
| abstract_inverted_index.cycloheximide-treated | 57 |
| cited_by_percentile_year | |
| countries_distinct_count | 1 |
| institutions_distinct_count | 12 |
| citation_normalized_percentile |