Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease

Purpose To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Design Case series. Participants A total of 562 patients diagnosed with IRD. Methods We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data. Main Outcome Measures Diagnostic yield of genomic testing. Results Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15–45) uplift in diagnostic yield. Conclusions We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS.

[1]  D. Mackey,et al.  RPGR ORF15 genotype and clinical variability of retinal degeneration in an Australian population , 2009, British Journal of Ophthalmology.

[2]  L. Vissers,et al.  Genome sequencing identifies major causes of severe intellectual disability , 2014, Nature.

[3]  Bale,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 , 2015, Genetics in Medicine.

[4]  M. Peplow.  The 100 000 Genomes Project , 2016, British Medical Journal.

[5]  Mohammed Alhashem,et al.  Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases , 2015, Genome Biology.

[6]  W. Berger,et al.  The molecular basis of human retinal and vitreoretinal diseases , 2010, Progress in Retinal and Eye Research.

[7]  E. Zrenner,et al.  Panel-based next generation sequencing as a reliable and efficient technique to detect mutations in unselected patients with retinal dystrophies , 2013, European Journal of Human Genetics.

[8]  Lei Shang,et al.  Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants , 2014, Proceedings of the National Academy of Sciences.

[9]  I. C. Lloyd,et al.  Pinpointing clinical diagnosis through whole exome sequencing to direct patient care: a case of Senior-Loken syndrome , 2015, The Lancet.

[10]  Kai Ye,et al.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..

[11]  Leo Goodstadt,et al.  EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa , 2008, Nature Genetics.

[12]  Robert B. Hartlage,et al.  This PDF file includes: Materials and Methods , 2009 .

[13]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[14]  Euan A Ashley,et al.  Clinical interpretation and implications of whole-genome sequencing. , 2014, JAMA.

[15]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[16]  Eric Vilain,et al.  Clinical exome sequencing for genetic identification of rare Mendelian disorders. , 2014, JAMA.

[17]  Jonathan E. Dickerson,et al.  A paradigm shift in the delivery of services for diagnosis of inherited retinal disease , 2012, Journal of Medical Genetics.

[18]  Nicholas W. Wood,et al.  A robust model for read count data in exome sequencing experiments and implications for copy number variant calling , 2012, Bioinform..

[19]  A. Toland,et al.  Use of Whole Genome Sequencing for Diagnosis and Discovery in the Cancer Genetics Clinic , 2014, EBioMedicine.

[20]  Christian Gilissen,et al.  Next-generation genetic testing for retinitis pigmentosa , 2012, Human mutation.

[21]  J. Shendure,et al.  Exome sequencing as a tool for Mendelian disease gene discovery , 2011, Nature Reviews Genetics.

[22]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Peter Saffrey,et al.  Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units , 2012, Science Translational Medicine.

[24]  Davis J. McCarthy,et al.  Factors influencing success of clinical genome sequencing across a broad spectrum of disorders , 2015, Nature Genetics.

[25]  Magalie S Leduc,et al.  Clinical whole-exome sequencing for the diagnosis of mendelian disorders. , 2013, The New England journal of medicine.

[26]  Jessica C. Ebert,et al.  Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads , 2012, J. Comput. Biol..

[27]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[28]  A. Fulton,et al.  Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing , 2014, Genetics in Medicine.

[29]  T. L. McGee,et al.  Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle , 2008, Nature Genetics.