A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative

• Published in: Genetics in medicine Vol. 21; no. 1; pp. 161 - 172
• Main Authors: Schoch, Kelly, Spillmann, Rebecca, Tan, Queenie K.-G., McConkie-Rosell, Allyn, Jiang, Yong-Hui, Goldstein, David B., Adams, David R., Allard, Patrick, Ashley, Euan A., Bacino, Carlos A., Beggs, Alan H., Birch, Camille L., Bonner, Devon, Boone, Braden E., Brown, Donna M., Chen, Shan, Coakley, Terra R., Cogan, Joy D., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., Davidson, Jean M., Dayal, Jyoti G., Dell’Angelica, Esteban C., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Draper, David D., Dries, Annika M., Eckstein, David J., Emrick, Lisa T., Enns, Gregory M., Esteves, Cecilia, Estwick, Tyra, Fernandez, Liliana, Ferreira, Carlos, Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Gourdine, Jean-Philippe F., Haendel, Melissa, Handley, Lori H., Krasnewich, Donna M., Krier, Joel B., Lazar, Jozef, Levy, Shawn E., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., MacRae, Calum A., Majcherska, Marta M., Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, Martin G., McCormack, Colleen E., Might, Matthew, Morimoto, Marie, Mulvihill, John J., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Pallais, J. Carl, Palmer, Christina GS, Parker, Neil H., Phillips, John A., Postlethwait, John H., Reuter, Chloe M., Sampson, Jacinda B., Scott, Daryl A., Sharma, Prashant, Shashi, Vandana, Silverman, Edwin K., Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vogel, Tiphanie P., Wahl, Colleen E., Walsh, Chris A., Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Wheeler, Matthew T., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, Yaping, Yu, Guoyun, Zhao, Chunli, Zheng, Allison
• Format: Journal Article
• Language: English
• Published: New York Elsevier Inc 01.01.2019; Nature Publishing Group US; Elsevier Limited
• Subjects: Bioinformatics; Biomedicine; Child; Developmental Disabilities - diagnosis; Developmental Disabilities - epidemiology; Developmental Disabilities - genetics; Exome - genetics; Exome sequencing; Exome Sequencing - methods; Female; Genetic Predisposition to Disease; Genome sequencing; Genomics; Human Genetics; Humans; Laboratory Medicine; Male; Phenotype; Phenotyping; Rare diseases; Sequence Analysis, DNA; Undiagnosed diseases; Whole Genome Sequencing; Rare diseases; Genome sequencing; Undiagnosed diseases; Exome sequencing; Phenotyping
• ISSN: 1098-3600; 1530-0366; 1530-0366
• DOI: 10.1038/s41436-018-0044-2

Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES reanalysis resolving 10–15% of the ES negatives, further approaches are necessary to maximize diagnoses in these individuals. In 38 ES negative patients an individualized genomic–phenotypic approach was employed utilizing (1) phenotyping; (2) reanalyses of FASTQ files, with innovative bioinformatics; (3) targeted molecular testing; (4) genome sequencing (GS); and (5) conferring of clinical diagnoses when pathognomonic clinical findings occurred. Certain and highly likely diagnoses were made in 18/38 (47%) individuals, including identifying two new developmental disorders. The majority of diagnoses (>70%) were due to our bioinformatics, phenotyping, and targeted testing identifying variants that were undetected or not prioritized on prior ES. GS diagnosed 3/18 individuals with structural variants not amenable to ES. Additionally, tentative diagnoses were made in 3 (8%), and in 5 individuals (13%) candidate genes were identified. Overall, diagnoses/potential leads were identified in 26/38 (68%). Our comprehensive approach to ES negatives maximizes the ES and clinical data for both diagnoses and candidate gene identification, without GS in the majority. This iterative approach is cost-effective and is pertinent to the current conundrum of ES negatives.