Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation
We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis -irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform t...
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| Vydáno v: | Nature communications Ročník 16; číslo 1; s. 10615 - 15 |
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| Médium: | Journal Article |
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Nature Publishing Group UK
22.11.2025
Nature Publishing Group Nature Portfolio |
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| ISSN: | 2041-1723, 2041-1723 |
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| Abstract | We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS,
n
= 2622) discovery, we identify over 1.1 million
cis
-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts,
P
< 5 × 10
−8
) across 4,971 genes. Among 11,425 sentinel
cis
-irQTLs, 72% replicate (
P
< 1 × 10
−4
) in the Women’s Health Initiative (WHI;
n
= 2005). Notably, 20% of
cis
-irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci (
P
< 1 × 10
−10
). We also identify 1870 sentinel
trans
-irQTLs (MAF ≥ 0.01,
P
< 1.5 × 10
−13
) for 1,084 isoforms across 590 genes, and 2327 rare
cis
-irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in
ULK3
, which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits.
Here the authors use a genome-wide approach to identify genetic variants associated with RNA isoform variation, uncovering new links between transcriptional regulation and complex traits. The findings can advance understanding of disease mechanisms. |
|---|---|
| AbstractList | Abstract We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10−8) across 4,971 genes. Among 11,425 sentinel cis-irQTLs, 72% replicate (P < 1 × 10−4) in the Women’s Health Initiative (WHI; n = 2005). Notably, 20% of cis-irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci (P < 1 × 10−10). We also identify 1870 sentinel trans-irQTLs (MAF ≥ 0.01, P < 1.5 × 10−13) for 1,084 isoforms across 590 genes, and 2327 rare cis-irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3, which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits. We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10 ) across 4,971 genes. Among 11,425 sentinel cis-irQTLs, 72% replicate (P < 1 × 10 ) in the Women's Health Initiative (WHI; n = 2005). Notably, 20% of cis-irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci (P < 1 × 10 ). We also identify 1870 sentinel trans-irQTLs (MAF ≥ 0.01, P < 1.5 × 10 ) for 1,084 isoforms across 590 genes, and 2327 rare cis-irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3, which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits. We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10−8) across 4,971 genes. Among 11,425 sentinel cis-irQTLs, 72% replicate (P < 1 × 10−4) in the Women’s Health Initiative (WHI; n = 2005). Notably, 20% of cis-irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci (P < 1 × 10−10). We also identify 1870 sentinel trans-irQTLs (MAF ≥ 0.01, P < 1.5 × 10−13) for 1,084 isoforms across 590 genes, and 2327 rare cis-irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3, which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits.Here the authors use a genome-wide approach to identify genetic variants associated with RNA isoform variation, uncovering new links between transcriptional regulation and complex traits. The findings can advance understanding of disease mechanisms. We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis -irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10 −8 ) across 4,971 genes. Among 11,425 sentinel cis -irQTLs, 72% replicate ( P < 1 × 10 −4 ) in the Women’s Health Initiative (WHI; n = 2005). Notably, 20% of cis -irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci ( P < 1 × 10 −10 ). We also identify 1870 sentinel trans -irQTLs (MAF ≥ 0.01, P < 1.5 × 10 −13 ) for 1,084 isoforms across 590 genes, and 2327 rare cis -irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3 , which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits. Here the authors use a genome-wide approach to identify genetic variants associated with RNA isoform variation, uncovering new links between transcriptional regulation and complex traits. The findings can advance understanding of disease mechanisms. We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10-8) across 4,971 genes. Among 11,425 sentinel cis-irQTLs, 72% replicate (P < 1 × 10-4) in the Women's Health Initiative (WHI; n = 2005). Notably, 20% of cis-irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci (P < 1 × 10-10). We also identify 1870 sentinel trans-irQTLs (MAF ≥ 0.01, P < 1.5 × 10-13) for 1,084 isoforms across 590 genes, and 2327 rare cis-irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3, which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits.We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10-8) across 4,971 genes. Among 11,425 sentinel cis-irQTLs, 72% replicate (P < 1 × 10-4) in the Women's Health Initiative (WHI; n = 2005). Notably, 20% of cis-irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci (P < 1 × 10-10). We also identify 1870 sentinel trans-irQTLs (MAF ≥ 0.01, P < 1.5 × 10-13) for 1,084 isoforms across 590 genes, and 2327 rare cis-irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3, which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits. We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis -irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10 −8 ) across 4,971 genes. Among 11,425 sentinel cis -irQTLs, 72% replicate ( P < 1 × 10 −4 ) in the Women’s Health Initiative (WHI; n = 2005). Notably, 20% of cis -irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci ( P < 1 × 10 −10 ). We also identify 1870 sentinel trans -irQTLs (MAF ≥ 0.01, P < 1.5 × 10 −13 ) for 1,084 isoforms across 590 genes, and 2327 rare cis -irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3 , which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits. |
| Author | Orchard, Peter Munson, Peter Li, Yun Hwang, Shih-Jen Huan, Tianxiao Sun, Quan Franceschini, Nora Raffield, Laura M. Heard-Costa, Nancy L. Wen, Jia Auer, Paul L. Joehanes, Roby Ma, Jiantao O’Connor, George Kooperberg, Charles Murabito, Joanne M. Liu, Chunyu Demirkale, Cumhur Y. Haessler, Jeffrey W. Yang, Jian Levy, Daniel Wang, Mengyao Carson, April P. Xie, Jiuyong Reiner, Alex P. |
| Author_xml | – sequence: 1 givenname: Chunyu orcidid: 0000-0002-9160-0153 surname: Liu fullname: Liu, Chunyu email: liuc@bu.edu organization: Department of Biostatistics, School of Public Health, Boston University, Framingham Heart Study – sequence: 2 givenname: Roby orcidid: 0000-0001-5549-9054 surname: Joehanes fullname: Joehanes, Roby email: roby.joehanes@nih.gov organization: Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health – sequence: 3 givenname: Jiantao surname: Ma fullname: Ma, Jiantao organization: Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and Policy, Tufts University – sequence: 4 givenname: Jiuyong orcidid: 0000-0003-2909-1033 surname: Xie fullname: Xie, Jiuyong organization: Physiology and Pathophysiology, University of Manitoba – sequence: 5 givenname: Jian orcidid: 0009-0009-7801-2021 surname: Yang fullname: Yang, Jian organization: Department of Biostatistics, School of Public Health, Boston University – sequence: 6 givenname: Mengyao orcidid: 0009-0005-5135-0224 surname: Wang fullname: Wang, Mengyao organization: Department of Biostatistics, School of Public Health, Boston University – sequence: 7 givenname: Tianxiao orcidid: 0000-0001-5840-9413 surname: Huan fullname: Huan, Tianxiao organization: Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health – sequence: 8 givenname: Shih-Jen orcidid: 0000-0002-2129-5704 surname: Hwang fullname: Hwang, Shih-Jen organization: Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health – sequence: 9 givenname: Jia orcidid: 0000-0003-3273-7704 surname: Wen fullname: Wen, Jia organization: Department of Genetics, University of North Carolina at Chapel Hill – sequence: 10 givenname: Quan orcidid: 0000-0001-8324-2803 surname: Sun fullname: Sun, Quan organization: Department of Biostatistics, University of North Carolina at Chapel Hill, Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, University of Pennsylvania – sequence: 11 givenname: Cumhur Y. surname: Demirkale fullname: Demirkale, Cumhur Y. organization: Critical Care Medicine Department, Clinical Center, National Institutes of Health – sequence: 12 givenname: Nancy L. orcidid: 0000-0001-9730-0306 surname: Heard-Costa fullname: Heard-Costa, Nancy L. organization: Framingham Heart Study, Departments of Neurology, Boston University Schools of Medicine – sequence: 13 givenname: Peter surname: Orchard fullname: Orchard, Peter organization: Department of Computational Medicine and Bioinformatics, University of Michigan – sequence: 14 givenname: April P. orcidid: 0000-0002-7970-6756 surname: Carson fullname: Carson, April P. organization: Department of Medicine, University of Mississippi Medical Center – sequence: 15 givenname: Jeffrey W. surname: Haessler fullname: Haessler, Jeffrey W. organization: Division of Public Health Sciences, Fred Hutchinson Cancer Center – sequence: 16 givenname: Laura M. orcidid: 0000-0002-7892-193X surname: Raffield fullname: Raffield, Laura M. organization: Department of Genetics, University of North Carolina at Chapel Hill – sequence: 17 givenname: Alex P. orcidid: 0000-0002-1427-4470 surname: Reiner fullname: Reiner, Alex P. organization: Division of Public Health Sciences, Fred Hutchinson Cancer Center, Department of Epidemiology, University of Washington – sequence: 18 givenname: Nora orcidid: 0009-0001-8346-3662 surname: Franceschini fullname: Franceschini, Nora organization: Department of Genetics, University of North Carolina at Chapel Hill, Department of Epidemiology, University of North Carolina at Chapel Hill – sequence: 19 givenname: Paul L. orcidid: 0000-0003-1735-8044 surname: Auer fullname: Auer, Paul L. organization: Division of Biostatistics, Data Science Institute and Cancer Center, Medical College of Wisconsin – sequence: 20 givenname: Charles orcidid: 0000-0002-7986-8560 surname: Kooperberg fullname: Kooperberg, Charles organization: Division of Public Health Sciences, Fred Hutchinson Cancer Center – sequence: 21 givenname: Yun orcidid: 0000-0002-9275-4189 surname: Li fullname: Li, Yun organization: Department of Biostatistics, University of North Carolina at Chapel Hill – sequence: 22 givenname: George surname: O’Connor fullname: O’Connor, George organization: Framingham Heart Study, Pulmonary Center, Boston University School of Medicine – sequence: 23 givenname: Joanne M. orcidid: 0000-0002-0192-7516 surname: Murabito fullname: Murabito, Joanne M. organization: Framingham Heart Study, Section of General Internal Medicine, Department of Medicine, Boston University Chobanian and Avedisin School of Medicine, Boston Medical Center – sequence: 24 givenname: Peter surname: Munson fullname: Munson, Peter organization: Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health – sequence: 25 givenname: Daniel surname: Levy fullname: Levy, Daniel email: levyd@nih.gov organization: Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health |
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| Snippet | We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham... Abstract We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In... |
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| SubjectTerms | 38 49/23 631/208/1792 631/208/205 692/499 692/699/75 Blood pressure Body mass index Diabetes DNA methylation Female Gene expression Gene Expression Profiling Gene Frequency Gene regulation Gene sequencing Genes Genetic diversity Genetic variance Genome, Human Genome-wide association studies Genome-Wide Association Study Genotype & phenotype Health promotion Heart High density lipoprotein Humanities and Social Sciences Humans Hypertension Isoforms Male Middle Aged multidisciplinary Polymorphism, Single Nucleotide Protein Isoforms - genetics Proteins Quantitative trait loci Quantitative Trait Loci - genetics Regulatory mechanisms (biology) Science Science (multidisciplinary) Transcriptome - genetics Transcriptomes Whole Genome Sequencing Womens health |
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| Title | Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation |
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