Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing

Huayun Hou; Kyoko E Yuki; Gregory Costain; Anna Szuto; Sierra Barnes; Arun K Ramani; Alper Celik; Michael Braga; Meagan Gloven-Brown; Dimitri J Stavropoulos; Sarah Bowdin; Ronald D Cohn; Roberto Mendoza-Londono; Stephen W Scherer; Michael Brudno; Christian R Marshall; M Stephen Meyn; Adam Shlien; James J Dowling; Michael D Wilson; Lianna Kyriakopoulou

doi:10.1038/s41525-025-00505-4

Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing

NPJ Genom Med. 2025 Jul 1;10(1):51. doi: 10.1038/s41525-025-00505-4.

Authors

Huayun Hou^#¹, Kyoko E Yuki^#^{1

2}, Gregory Costain^{1

3

4

5}, Anna Szuto^{1

3

5}, Sierra Barnes², Arun K Ramani⁶, Alper Celik⁶, Michael Braga², Meagan Gloven-Brown², Dimitri J Stavropoulos^{2

7}, Sarah Bowdin^{2

8}, Ronald D Cohn^{1

4

5

9}, Roberto Mendoza-Londono^{3

4}, Stephen W Scherer^{1

5

10}, Michael Brudno^{1

11

12

13}, Christian R Marshall^{2

7}, M Stephen Meyn^{14

15}, Adam Shlien^{1

2

7}, James J Dowling^{1

5

16}, Michael D Wilson^{17

18}, Lianna Kyriakopoulou^{19

20}

Affiliations

¹ Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.
² Division of Genome Diagnostics, The Hospital for Sick Children, Toronto, ON, Canada.
³ Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
⁴ Department of Paediatrics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
⁵ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁶ Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON, Canada.
⁷ Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
⁸ Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
⁹ Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
¹⁰ The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
¹¹ University Health Network, Toronto, ON, Canada.
¹² Department of Computer Science, University of Toronto, Toronto, ON, Canada.
¹³ Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
¹⁴ Center for Human Genomics and Precision Medicine, University of Wisconsin, Madison, WI, USA.
¹⁵ Department of Pediatrics, University of Wisconsin, Madison, WI, USA.
¹⁶ Division of Neurology, The Hospital for Sick Children, Toronto, ON, Canada.
¹⁷ Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada. michael.wilson@sickkids.ca.
¹⁸ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. michael.wilson@sickkids.ca.
¹⁹ Division of Genome Diagnostics, The Hospital for Sick Children, Toronto, ON, Canada. lianna.kyriakopoulou@sickkids.ca.
²⁰ Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. lianna.kyriakopoulou@sickkids.ca.

^# Contributed equally.

Abstract

Despite advances in genome sequencing, many individuals with rare genetic disorders remain undiagnosed. Transcriptional profiling via RNA-seq can reveal functional impacts of DNA variants and improve diagnosis. We assessed blood-derived RNA-seq in the largely undiagnosed SickKids Genome Clinic cohort (n = 134), which has been subjected to multiple analyses benchmarking the utility of genome sequencing. Our RNA-centric analysis identifies gene expression outliers, aberrant splicing, and allele-specific expression. In one-third of diagnosed individuals (20/61), RNA-seq reinforced DNA-based findings. In 2/61 cases, RNA-seq revised diagnoses (EPG5 to LZTR1 in an individual with a Noonan syndrome-like disorder) and discovered an additional relevant gene (CEP120 in addition to SON in an individual with ZTTK syndrome). Additionally, ~7% (5/73) of undiagnosed cases had at least one plausible candidate gene identified. This study highlights both the benefits and limitations of whole-blood RNA profiling in refining genetic diagnoses and uncovering novel disease mechanisms.

Abstract

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