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Rapid Whole Genome Sequencing Decreases Morbidity and Healthcare Cost of Hospitalized Infants

Lauge Farnaes, Amber Hildreth, Nathaly M. Sweeney, Michelle M. Clark, Shimul Chowdhury, Shareef Nahas, Julie A. Cakici, Wendy Benson, Robert H. Kaplan, Richard Kronick, Matthew N. Bainbridge, Jennifer Friedman, Jeffrey J. Gold, Yan Ding, Narayanan Veeraraghavan, David Dimmock, Stephen F. kingsmore, on behalf of the RCIGM Investigators
doi: https://doi.org/10.1101/253534
Lauge Farnaes
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
2Department of Pediatrics, University of California San Diego, San Diego, CA, USA;
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Amber Hildreth
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
2Department of Pediatrics, University of California San Diego, San Diego, CA, USA;
Roles: DO
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Nathaly M. Sweeney
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
2Department of Pediatrics, University of California San Diego, San Diego, CA, USA;
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Michelle M. Clark
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Shimul Chowdhury
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Shareef Nahas
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Julie A. Cakici
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Wendy Benson
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Robert H. Kaplan
3Torrey Pines Health Group Inc., San Diego, CA, USA;
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Richard Kronick
4Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA;
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Matthew N. Bainbridge
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Jennifer Friedman
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
2Department of Pediatrics, University of California San Diego, San Diego, CA, USA;
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Jeffrey J. Gold
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Yan Ding
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Narayanan Veeraraghavan
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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David Dimmock
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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Stephen F. kingsmore
1Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA;
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ABSTRACT

BACKGROUND Genetic disorders are a leading cause of morbidity and mortality in infants. Rapid Whole Genome Sequencing (rWGS) can diagnose genetic disorders in time to change acute medical or surgical management (clinical utility) and improve outcomes in acutely ill infants.

METHODS Retrospective cohort study of acutely ill inpatient infants in a regional children’s hospital from July 2016–March 2017. Forty-two families received rWGS for etiologic diagnosis of genetic disorders. Probands received standard genetic testing as clinically indicated. Primary end-points were rate of diagnosis, clinical utility, and healthcare utilization. The latter was modelled in six infants by comparing actual utilization with matched historical controls and/or counterfactual utilization had rWGS been performed at different time points.

FINDINGS The diagnostic sensitivity was 43% (eighteen of 42 infants) for rWGS and 10% (four of 42 infants) for standard of care (P=.0005). The rate of clinical utility for rWGS (31%, thirteen of 42 infants) was significantly greater than for standard of care (2%, one of 42; P=.0015). Eleven (26%) infants with diagnostic rWGS avoided morbidity, one had 43% reduction in likelihood of mortality, and one started palliative care. In six of the eleven infants, the changes in management reduced inpatient cost by $800, 000 to $2,000,000.

DISCUSSION These findings replicate a prior study of the clinical utility of rWGS in acutely ill inpatient infants, and demonstrate improved outcomes and net healthcare savings. rWGS merits consideration as a first tier test in this setting.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 26, 2018.
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Rapid Whole Genome Sequencing Decreases Morbidity and Healthcare Cost of Hospitalized Infants
Lauge Farnaes, Amber Hildreth, Nathaly M. Sweeney, Michelle M. Clark, Shimul Chowdhury, Shareef Nahas, Julie A. Cakici, Wendy Benson, Robert H. Kaplan, Richard Kronick, Matthew N. Bainbridge, Jennifer Friedman, Jeffrey J. Gold, Yan Ding, Narayanan Veeraraghavan, David Dimmock, Stephen F. kingsmore, on behalf of the RCIGM Investigators
bioRxiv 253534; doi: https://doi.org/10.1101/253534
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Rapid Whole Genome Sequencing Decreases Morbidity and Healthcare Cost of Hospitalized Infants
Lauge Farnaes, Amber Hildreth, Nathaly M. Sweeney, Michelle M. Clark, Shimul Chowdhury, Shareef Nahas, Julie A. Cakici, Wendy Benson, Robert H. Kaplan, Richard Kronick, Matthew N. Bainbridge, Jennifer Friedman, Jeffrey J. Gold, Yan Ding, Narayanan Veeraraghavan, David Dimmock, Stephen F. kingsmore, on behalf of the RCIGM Investigators
bioRxiv 253534; doi: https://doi.org/10.1101/253534

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