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A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants
Open accessAbstract
The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.
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An integrated map of genetic variation from 1,092 human genomes
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“0001).(51) A likely explanation of the disparity in results herein was the difference in experimental design: herein, trios were used to confirm phasing and de novo occurrence of likely causative variants detected by singleton sequencing, but not in the other studies.”
ResultSelf-citationLionel, A. C., Costain, G., Monfared, N., Walker, S., Reuter, M. S., Hosseini, S. M., Thiruvahindrapuram, B., Merico, D., Jobling, R., Nalpathamkalam, T., et al. (2018) · Genetics in Medicine · doi:10.1038/gim.2017.119 · Cited by 557
Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization
Farnaes, L., Hildreth, A., Sweeney, N. M., Clark, M. M., Chowdhury, S., Nahas, S., Cakici, J. A., Benson, W., Kaplan, R. H., Kronick, R., et al. (2018) · npj Genomic Medicine · doi:10.1038/s41525-018-0049-4 · Cited by 445
Self-citationClark, M. M., Hildreth, A., Batalov, S., Ding, Y., Chowdhury, S., Watkins, K., Ellsworth, K., Camp, B., Kint, C. I., Yacoubian, C., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aat6177 · Cited by 300
Self-citationPetrikin, J. E., Cakici, J. A., Clark, M. M., Willig, L. K., Sweeney, N. M., Farrow, E. G., Saunders, C. J., Thiffault, I., Miller, N. A., Zellmer, L., et al. (2018) · npj Genomic Medicine · doi:10.1038/s41525-018-0045-8 · Cited by 229
Self-citationMeeting the challenges of implementing rapid genomic testing in acute pediatric care.
Stark, Z., Lunke, S., Brett, G. R., Tan, N. B., Stapleton, R., Kumble, S., Yeung, A., Phelan, D. G., Chong, B., Fanjul-Fernandez, M., et al. (2018) · Genetics in Medicine · doi:10.1038/gim.2018.37 · Cited by 159
Self-citationRapid whole genome sequencing has clinical utility in children in the PICU
Sanford, E. F., Clark, M. M., Farnaes, L., Williams, M. R., Perry, J. C., Ingulli, E. G., Sweeney, N. M., Doshi, A., Gold, J. J., Briggs, B., et al. (2019) · Pediatric Critical Care Medicine · doi:10.1097/pcc.0000000000002056 · Cited by 150
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Dimmock, D., Caylor, S., Waldman, B., Benson, W., Ashburner, C., Carmichael, J. L., Carroll, J., Cham, E., Chowdhury, S., Cleary, J., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.05.008 · Cited by 259
Self-citationAustralian Genomics Health Alliance Acute Care Flagship, Lunke, S., Eggers, S., Wilson, M., Patel, C., Barnett, C. P., Pinner, J., Sandaradura, S. A., Buckley, M. F., Krzesinski, E. I., et al. (2020) · JAMA · doi:10.1001/jama.2020.7671 · Cited by 239
Self-citationEpilepsy in the mTORopathies: opportunities for precision medicine
Moloney, P. B., Cavalleri, G. L., & Delanty, N. (2021) · Brain Communications · doi:10.1093/braincomms/fcab222 · Cited by 125
The performance of genome sequencing as a first-tier test for neurodevelopmental disorders
van der Sanden, B. P. G. H., Schobers, G., Corominas Galbany, J., Koolen, D. A., Sinnema, M., van Reeuwijk, J., Stumpel, C. T. R. M., Kleefstra, T., de Vries, B. B. A., Ruiterkamp-Versteeg, M., et al. (2023) · European Journal of Human Genetics · doi:10.1038/s41431-022-01185-9 · Cited by 97
Nurchis, M. C., Altamura, G., Riccardi, M. T., Radio, F. C., Chillemi, G., Bertini, E. S., Garlasco, J., Tartaglia, M., Dallapiccola, B., & Damiani, G. (2023) · Archives of Public Health · doi:10.1186/s13690-023-01112-4 · Cited by 65
Metadata
- Authors
- Kingsmore, S. F., Cakici, J. A., Clark, M. M., Gaughran, M., Feddock, M., Batalov, S., Bainbridge, M. N., Carroll, J., Caylor, S. A., Clarke, C., Ding, Y., Ellsworth, K., Farnaes, L., Hildreth, A., Hobbs, C., James, K., Kint, C. I., Lenberg, J., Nahas, S., Prince, L., Reyes, I., Salz, L., Sanford, E., Schols, P., Sweeney, N., Tokita, M., Veeraraghavan, N., Watkins, K., Wigby, K., Wong, T., Chowdhury, S., Wright, M. S., Dimmock, D., Bezares, Z., Bloss, C., Braun, J. J. A., Diaz, C., Mashburn, D., Tamang, D., Orendain, D., Friedman, J., Gleeson, J., Barea, J., Chiang, G., Cohenmeyer, C., Coufal, N. G., Evans, M., Honold, J., Hovey, R. L., Kimball, A., Lane, B., Le, C., Le, J., Leibel, S., Moyer, L., Mulrooney, P., Oh, D., Ordonez, P., Oriol, A., Ortiz-Arechiga, M., Puckett, L., Speziale, M., Suttner, D., Van Der Kraan, L., Knight, G., Sauer, C., Song, R., White, S., Wise, A., & Yamada, C.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2019-10
- Volume
- 105
- Issue
- 4
- Pages
- 719-733
- ISSN
- 0002-9297 (ISSN-L)
- OpenAlex
- W2975298736
- Cited by
- 352
- References
- 9
- FWCI
- 22.89
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Kingsmore, S. F., Cakici, J. A., Clark, M. M., Gaughran, M., Feddock, M., Batalov, S., Bainbridge, M. N., Carroll, J., Caylor, S. A., Clarke, C., Ding, Y., Ellsworth, K., Farnaes, L., Hildreth, A., Hobbs, C., James, K., Kint, C. I., Lenberg, J., Nahas, S., . . . Yamada, C. (2019). A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants. The American Journal of Human Genetics. https://doi.org/10.1016/j.ajhg.2019.08.009
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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