Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data

Abstract

PurposeThe objective of this study was to assess the ability of our laboratory's exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test.MethodsWe developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test to detect known variants using a reference HapMap sample, and (ii) an interpretation-based approach that assessed our relative ability to identify and interpret disease-causing variants, by analyzing and comparing the results of 19 randomly selected patients previously tested by external laboratories.ResultsWe demonstrate that this approach is reproducible with >99% analytical sensitivity and specificity for single-nucleotide variants and indels <10 bp. Our findings were concordant with the reference laboratories in 84% of cases. A new molecular diagnosis was applied to three cases, including discovery of two novel candidate genes.ConclusionWe provide an assessment of critical areas that influence interpretation of an exome test, including comprehensive phenotype capture, assessment of clinical overlap, availability of parental data, and the addressing of limitations in database updates. These results can be used to inform improvements in phenotype-driven interpretation of medical exomes in clinical and research settings.

The Epilepsy Genetics Initiative: Systematic reanalysis of diagnostic exomes increases yield

“…Although, unquestionably, our data further support that periodic reinterrogation of unresolved exomes is critical to improving the diagnostic rate [3][4][5][6][7] it is important to note that 10 of the 13 new and revised diagnoses that arose from this analysis came from reassessment of a variant that was initially provided to the clinicians in the original clinical report (SATB2, STAG, PROSC, VHL, CHD4, both SMC1A diagnoses, one of two of the SCN8A diagnoses, and both PPP3CA diagnoses, assuming that PPP3CA would have been discovered eventually without the involvement of EGI). In these 13 instances, a clinician with experience interpreting genetic diagnoses would have the potential to perform a similar review.…”

“…Clinical diagnostic sequencing laboratories will often perform a one‐time reanalysis at no cost at the ordering physician's request; however, there are often limitations on when this request can be initiated. Although ongoing reanalysis is not standard for clinical diagnostic exome sequencing companies, reinterrogation of sequence data in unsolved exome cases can increase diagnostic yield …”

“…Although ongoing reanalysis is not standard for clinical diagnostic exome sequencing companies, reinterrogation of sequence data in unsolved exome cases can increase diagnostic yield. [3][4][5][6][7] Reanalysis can increase diagnostic yield in broad cohorts; however, it has not been investigated specifically in epilepsy. Reanalysis and diagnosis are particularly important in epilepsy due to the rapid rate of gene discovery and potential for treatment implications.…”

“…Randall Stewart, 5 Vicky Whittemore. 5 EGI Enrollment Group: Kaitlin Angione, 6 Carl W. Bazil, 7 Louise Bier, 2 Judith Bluvstein, 8 Elise Brimble, 9 Colleen Campbell, 10 Gianpiero Cavalleri, 11,12 Chelsea Chambers, 13 Hyunmi Choi, 7 Maria Roberta Cilio, 4,14 Michael Ciliberto, 15 Susannah Cornes, 4 Norman Delanty, 11,12 Scott Demarest, 6 Orrin Devinsky, 8 Dennis Dlugos, 16 Holly Dubbs, 16 Patricia Dugan, 8 Michelle E. Ernst, 2 Melissa Gibbons, 6 Howard P. Goodkin, 13 Ingo Helbig, 16 Laura Jansen, 13 Kaleas Johnson, 4 Charuta Joshi, 6 Natalie C. Lippa, 2 Eric Marsh, 16,17 Alejandro Martinez, 16 John Millichap, 18,19 Maureen S. Mulhern, 2 Adam Numis, 4,14 Kristen Park, 6 Tommaso Pippucci, 20 Annapurna Poduri, 21 Brenda Porter, 9 Brigid Regan, 1 Tristan T. Sands, 2,22 Ingrid E. Scheffer, 1,23,24 John M. Schreiber, 25 Beth Sheidley,…”

Variable Clinical Manifestations of Xia‐Gibbs syndrome: Findings of Consecutively Identified Cases at a Single Children's Hospital

“…Diagnostics at the Children's Hospital of Philadelphia as a trio with the proband and his or her biological parents for each patient (Gibson et al, 2018). Genomic DNA was extracted from peripheral blood.…”