CCEPAS: the creation and validation of a fast and sensitive clinical whole exome analysis pipeline based on gene and variant ranking

Abstract

Aim: Whole exome sequencing technology has permitted the discovery of genes that cause Mendelian disorders and was used in clinical laboratories. However, identifying the disease causing variant(s) for a specific disorder from thousands of variants is challenging. In this study, we describe the Cincinnati Clinical Exome Pipeline Analysis Suite (CCEPAS) that utilizes a four-level framework into one analysis procedure that rapidly identify the most likely causative gene variants to establish a clinical diagnosis.

Methods: We developed and validated CCEPAS using 100 clinical exome cases. We applied this pipeline to clinical cases by first translating phenotypic information into candidate gene lists using Pheno2Gene. This list of candidate genes was given to the VarEval algorithm to guide variant filtering and prioritization. Finally, a short list of filtered variants was produced for clinical interpretation.

Results: We demonstrated the development and implementation of CCEPAS to aid in the variant prioritization and filtering to produce a short list of candidate variants for clinical diagnosis. Its unique Pheno2Gene tool utilized an extensive list of resources and provided an accurate, sensitive and specific way to obtain gene lists from clinical feature keywords. In addition, VarEval narrowed down the variants from ~150,000 to the top 20 (trios) and top 50 (singleton) for further variant curation and candidate determination.

Conclusion: Significantly, employment of CCEPAS rapidly provided causative variants in the top 20 and top 50 variants for single and trio cases, respectively, thus, ending the diagnostic odyssey in more than 30% of our clinical exome cases.

Keywords

Exome / sequencing / bioinformatics / pipeline / ranking / weighing

References

[1] Antonarakis SE.Mendelian disorders deserve more attention..Nat Rev Genet2006;7:277-82

[2] Ng SB,Lee C,Tabor HK,Huff CD,Jabs EW,Shendure J.Exome sequencing identifies the cause of a mendelian disorder..Nat Genet2010;42:30-5 PMCID:PMC2847889

[3] Chen JM,Cooper DN.Revealing the human mutome..Clin Genet2010;78:310-20

[4] McCarthy MI.Learning from molecular genetics: novel insights arising from the definition of genes for monogenic and type 2 diabetes..Diabetes2008;57:2889-98 PMCID:PMC2570381

[5] McCarthy MI.Exploring the unknown: assumptions about allelic architecture and strategies for susceptibility variant discovery..Genome Med2009;1:66 PMCID:PMC2717392

[6] Choi M,Ji W,Tikhonova IR,Nayir A,Ozen S,Nelson-Williams C,Mane S.Genetic diagnosis by whole exome capture and massively parallel DNA sequencing..Proc Natl Acad Sci U S A2009;106:19096-101 PMCID:PMC2768590

[7] Boehnke M.Limits of resolution of genetic linkage studies: implications for the positional cloning of human disease genes..Am J Hum Genet1994;55:379-90 PMCID:PMC1918352

[8] Hoischen A,Gilissen C,van Lier B,de Vries P,Wieskamp N,Devriendt K,Revencu N,Barbosa M,Smith J,Henderson A,Thompson EM,de Vries BB.De novo mutations of SETBP1 cause Schinzel-Giedion syndrome..Nat Genet2010;42:483-5

[9] Johnson JO,Benatar M,Van Deerlin VM,Gibbs JR,Gronka S,Ding J,Martinez-Lage M,Hernandez DG,Chong S,Rothstein J,Wang YD,Mora G,Monsurrò MR,Salvi F,Sola P,Galassi G,Taylor JP,Chiò A.Exome sequencing reveals VCP mutations as a cause of familial ALS..Neuron2010;68:857-64 PMCID:PMC3032425

[10] Krawitz PM,Rödelsperger C,Kölsch U,Stephani F,Murakami Y,Isau M,Dahl A,Hecht J,Jäger M,de Condor BJ,Brunner HG,Passarge E,Cole DE,Roscioli T,Robinson PN.Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome..Nat Genet2010;42:827-9

[11] Lalonde E,Ha KCH,Bolduc N,Dechelotte P,Jabado N.Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing..Hum Mutat2010;31:918-23

[12] Musunuru K,Do R,Guiducci C,Garimella KV,Abreu J,Fennell T,Ambrogio L,Kernytsky A,Rudzicz N,DePristo MA,Cohen JC,Altshuler D,Gabriel SB,Kathiresan S.Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia..N Engl J Med2010;363:2220-7 PMCID:PMC3008575

[13] Ng SB,Buckingham KJ,McMillin MJ,Beck AE,Cooper GM,Lee C,Smith JD,Yoshiura K,Ohta T,Nickerson DA,Shendure J.Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome..Nat Genet2010;42:790-3 PMCID:PMC2930028

[14] Pierce SB,Chisholm KM,Thornton AM,Opitz JM,Klevit RE.Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome..Am J Hum Genet2010;87:282-8 PMCID:PMC2917704

[15] Majewski J,Lalonde E,Jabado N.What can exome sequencing do for you?.J Med Genet2011;48:580-9

[16] Maxmen A.Exome sequencing deciphers rare diseases..Cell2011;144:635-7

[17] Browning BL.A fast, powerful method for detecting identity by descent..Am J Hum Genet2011;88:173-82 PMCID:PMC3035716

[18] Rödelsperger C,Bauer S,Bigham AW,de Condor BJ,Robinson PN.Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders..Bioinforma Oxf Engl2011;27:829-36 PMCID:PMC3051326

[19] Abecasis GR,Cookson WO.Merlin--rapid analysis of dense genetic maps using sparse gene flow trees..Nat Genet2002;30:97-101

[20] Ng PC.Predicting the effects of amino acid substitutions on protein function..Ann Rev Genomics Hum Genet2006;7:61-80

[21] Teng S,Alexov E.Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions..Curr Pharm Biotechnol2008;9:123-33

[22] Kumar P,Ng PC.Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm..Nat Protoc2009;4:1073-81

[23] Adzhubei IA,Peshkin L,Gerasimova A,Kondrashov AS.A method and server for predicting damaging missense mutations..Nat Meth2010;7:248-9 PMCID:PMC2855889

[24] Chun S.Identification of deleterious mutations within three human genomes..Genome Res2009;19:1553-61 PMCID:PMC2752137

[25] Schwarz JM,Schuelke M.Mutation taster evaluates disease-causing potential of sequence alterations..Nat Meth2010;7:575-6

[26] Liu X,Boerwinkle E.dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions..Hum Mutat2011;32:894-9 PMCID:PMC3145015

[27] Wang K,Hakonarson H.ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data..Nucleic Acids Res2010;38:e164 PMCID:PMC2938201

[28] Farwell KD,El-Khechen D,Chao EC,Baxter RM,Mroske C,Gandomi SK,Li X,Lu HM,Ruble D,Fischbach S,Lee S,Dunlop CL.Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions..Genet Med2015;17:578-86

[29] Retterer K,Cho MT,Millan F,Vertino-Bell A,Neidich J,Bai R,Friedman B,Pineda-Alvarez D,Brandt T,Chung WK.Clinical application of whole-exome sequencing across clinical indications..Genet Med2016;18:696-704

[30] Yang Y,Reid JG,Willis A,Braxton A,Xia F,Hardison M,Bekheirnia MR,Kirby A,Scull J,Ding Y,Lupski JR,Gibbs RA.Clinical whole-exome sequencing for the diagnosis of mendelian disorders..N Engl J Med2013;369:1502-11 PMCID:PMC4211433

[31] Lee H,Dorrani N,Kantarci S,Das K,Harry B,Fox M,Martinez-Agosto JA,Chang VY,Palmer CG,Grody WW,Nelson SF.Clinical exome sequencing for genetic identification of rare Mendelian disorders..JAMA2014;312:1880-7 PMCID:PMC4278636

[32] Bone WP,Buske OJ,Davis J,Flynn ED,Godfrey R,Groden C,Köhler S,Links AE,Mungall CJ,Robinson PN,Soldatos AG,Toro C,Valkanas E,Wahl C,Boerkoel CF,Haendel MA,Smedley D.Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency..Genet Med2016;18:608-17 PMCID:PMC4916229

[33] Valencia CA,Holle J,Qian Y,Wei C,Zou F,Wang L,Fisher R,Hogart Begtrup A,Wusik KA,Burrow T,Hopkin R,Harley JB,Zhang K.Clinical impact and cost-effectiveness of whole exome sequencing as a diagnostic tool: a pediatric center's experience..Front Pediatr2015;3:67 PMCID:PMC4522872

[34] O'Fallon BD,Bayrak-Toydemir P.VarRanker: rapid prioritization of sequence variations associated with human disease..BMC Bioinformatics2013;14 Suppl 13:S1 PMCID:PMC3849749

[35] Yang Y,Xia F,Person R,Ward P,Wang M,Veeraraghavan N,Chiang T,Beuten J,He W,Willis A,Craigen WJ,Stray-Pedersen A,Wen S,Cui H,Reid J,Patel A,Beaudet AL,Plon SE,Eng CM.Molecular findings among patients referred for clinical whole-exome sequencing..JAMA2014;312:1870-9 PMCID:PMC4326249