Integrated multi-omics for rapid rare disease diagnosis on a national scale

Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospit...

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Published inNature medicine Vol. 29; no. 7; pp. 1681 - 1691
Main Authors Lunke, Sebastian, Bouffler, Sophie E., Patel, Chirag V., Sandaradura, Sarah A., Wilson, Meredith, Pinner, Jason, Hunter, Matthew F., Barnett, Christopher P., Wallis, Mathew, Kamien, Benjamin, Tan, Tiong Y., Freckmann, Mary-Louise, Chong, Belinda, Phelan, Dean, Francis, David, Kassahn, Karin S., Ha, Thuong, Gao, Song, Arts, Peer, Jackson, Matilda R., Scott, Hamish S., Eggers, Stefanie, Rowley, Simone, Boggs, Kirsten, Rakonjac, Ana, Brett, Gemma R., de Silva, Michelle G., Springer, Amanda, Ward, Michelle, Stallard, Kirsty, Simons, Cas, Conway, Thomas, Halman, Andreas, Van Bergen, Nicole J., Sikora, Tim, Semcesen, Liana N., Stroud, David A., Compton, Alison G., Thorburn, David R., Bell, Katrina M., Sadedin, Simon, North, Kathryn N., Christodoulou, John, Stark, Zornitza
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.07.2023
Nature Publishing Group
Subjects
692/308/2056
692/308/575
692/699
Abnormalities
Biomedical and Life Sciences
Biomedicine
Cancer Research
Child
Children
Chromosome aberrations
Critical Illness
Decision analysis
Diagnosis
Diagnostic systems
Exome Sequencing
Gene sequencing
Genomes
Genomics
Humans
Infant
Infants
Infectious Diseases
Metabolic Diseases
Molecular Medicine
Multiomics
Neurosciences
Palliation
Patients
Proteomics
Rare diseases
Rare Diseases - diagnosis
Rare Diseases - genetics
Rare Diseases - therapy
Transcriptomes
Whole genome sequencing
Whole Genome Sequencing - methods
Online AccessGet full text

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Abstract Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner. A report from the Australian Acute Care Genomics programme shows that the integration of rapid whole-genome sequencing and multi-omic analyses informs diagnoses and treatment decisions in a prospective cohort of 290 critically ill infants and children.
AbstractList Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner. A report from the Australian Acute Care Genomics programme shows that the integration of rapid whole-genome sequencing and multi-omic analyses informs diagnoses and treatment decisions in a prospective cohort of 290 critically ill infants and children.
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.A report from the Australian Acute Care Genomics programme shows that the integration of rapid whole-genome sequencing and multi-omic analyses informs diagnoses and treatment decisions in a prospective cohort of 290 critically ill infants and children.
Author Lunke, Sebastian
Eggers, Stefanie
Stroud, David A.
Francis, David
Jackson, Matilda R.
Sadedin, Simon
Barnett, Christopher P.
Brett, Gemma R.
Scott, Hamish S.
Rakonjac, Ana
Conway, Thomas
Tan, Tiong Y.
Stallard, Kirsty
Sandaradura, Sarah A.
Sikora, Tim
Christodoulou, John
Phelan, Dean
Arts, Peer
Bell, Katrina M.
Wallis, Mathew
Freckmann, Mary-Louise
Bouffler, Sophie E.
Halman, Andreas
North, Kathryn N.
Kassahn, Karin S.
Chong, Belinda
Thorburn, David R.
Ha, Thuong
Springer, Amanda
Van Bergen, Nicole J.
Hunter, Matthew F.
Semcesen, Liana N.
Kamien, Benjamin
Compton, Alison G.
Pinner, Jason
Ward, Michelle
Simons, Cas
de Silva, Michelle G.
Boggs, Kirsten
Wilson, Meredith
Rowley, Simone
Stark, Zornitza
Patel, Chirag V.
Gao, Song
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/37291213$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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Snippet Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the...
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Abnormalities
Biomedical and Life Sciences
Biomedicine
Cancer Research
Child
Children
Chromosome aberrations
Critical Illness
Decision analysis
Diagnosis
Diagnostic systems
Exome Sequencing
Gene sequencing
Genomes
Genomics
Humans
Infant
Infants
Infectious Diseases
Metabolic Diseases
Molecular Medicine
Multiomics
Neurosciences
Palliation
Patients
Proteomics
Rare diseases
Rare Diseases - diagnosis
Rare Diseases - genetics
Rare Diseases - therapy
Transcriptomes
Whole genome sequencing
Whole Genome Sequencing - methods
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Title Integrated multi-omics for rapid rare disease diagnosis on a national scale
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