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.
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Lee H, Deignan JL, Dorrani N, et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA. 2014;312:1880–7.
Gilissen C, Hoischen A, Brunner HG, Veltman JA. Unlocking Mendelian disease using exome sequencing. Genome Biol. 2011;12:228.
Need AC, Shashi V, Hitomi Y, et al. Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet. 2012;49:353–61.
Yang Y, Muzny DM, Xia F, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014;312:1870–9.
Wenger AM, Guturu H, Bernstein JA, Bejerano G. Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genet Med. 2017;19:209–14.
Smith ED, Radtke K, Rossi M, et al. Classification of genes: standardized clinical validity assessment of gene-disease associations aids diagnostic exome analysis and reclassifications. Hum Mutat. 2017;38:600–8.
Eldomery MK, Coban-Akdemir Z, Harel T, et al. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med. 2017;9:26.
Nambot S, Thevenon J, Kuentz P, et al. Clinical whole-exome sequencing for the diagnosis of rare disorders with congenital anomalies and/or intellectual disability: substantial interest of prospective annual reanalysis. Genet Med. 2018;20:645–54.
Gibson KM, Nesbitt A, Cao K, et al. Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data. Genet Med. 2018;20:329–36.
Need AC, Shashi V, Schoch K, Petrovski S, Goldstein DB. The importance of dynamic re-analysis in diagnostic whole exome sequencing. J Med Genet. 2017;54:155–6.
Pena LDM, Jiang YH, Schoch K, et al. Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. Genet Med. 2018;20:464–9.
Gilissen C, Hehir-Kwa JY, Thung DT, et al. Genome sequencing identifies major causes of severe intellectual disability. Nature. 2014;511:344–7.
Taylor JC, Martin HC, Lise S, et al. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet. 2015;47:717–26.
Lionel AC, Costain G, Monfared N, et al. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med. 2018;20:435–43.
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014;15:121–32.
Fang H, Wu Y, Narzisi G, et al. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med. 2014;6:89.
Shashi V, Pena LD, Kim K, et al. De novo truncating variants in ASXL2 are associated with a unique and recognizable clinical phenotype. Am J Hum Genet. 2016;99:991–9.
Schoch K, Meng L, Szelinger S, et al. A recurrent de novo variant in NACC1 causes a syndrome characterized by infantile epilepsy, cataracts, and profound developmental delay. Am J Hum Genet. 2017;100:343–51.
Pabinger S, Dander A, Fischer M, et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014;15:256–78.
Rare Disease Statistics. 2015.https://globalgenes.org. Global Genes, CA. Accessed January 30, 2018.
genome E. http://edicogenome.com/dragen-bioit-platform/. Illumina, CA. Accessed January 30, 2018.
Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 2013;9:e1003709.
Gussow AB, Petrovski S, Wang Q, Allen AS, Goldstein DB. The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. Genome Biol. 2016;17:9.
Lek M, Karczewski KJ, Minikel EV, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–91.
(ESP) NGESP. Exome Variant Server.: http://evs.gs.washington.edu/EVS/. University of Washington, WA. Accessed January 30, 2018.
Resource CG. https://www.clinicalgenome.org/. ClinGen. Accessed January 30, 2018.
Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901–13.
Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24.
Yang Y, Muzny DM, Reid JG, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369:1502–11.
Bick D, Fraser PC, Gutzeit MF, et al. Successful application of whole genome sequencing in a medical genetics clinic. J Pediatr Genet. 2017;6:61–76.
Stepensky P, Chacon-Flores M, Kim KH, et al. Mutations in EFL1, an SBDS partner, are associated with infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies in a Shwachman-Diamond like syndrome. J Med Genet. 2017;54:558–66.
Vlaskamp DR, Rump P, Callenbach PM, et al. Haploinsufficiency of the STX1B gene is associated with myoclonic astatic epilepsy. Eur J Paediatr Neurol. 2016;20:489–92.
Caspar SM, Dubacher N, Kopps AM, Meienberg J, Henggeler C, Matyas G. Clinical sequencing: from raw data to diagnosis with lifetime value. Clin Genet. 2017;93:508–19.
Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat. 2015;36:928–30.
Philippakis AA, Azzariti DR, Beltran S, et al. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015;36:915–21.
This work has received support by the National Institutes of Health (NIH) Common Fund through the Office of Strategic Coordination/Office of the NIH Director (U01HG007672, to Shashi V and Goldstein DB). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
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David Goldstein is a founder of and holds equity in Pairnomix and Praxis, serves as a consultant to AstraZeneca, and has research supported by Janssen, Gilead, Biogen, AstraZeneca, and UCB. The remaining authors declare no conflicts of interest.
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Unique bioinformatic approach and comprehensive reanalysis improve diagnostic yield of clinical exomes
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