title: The Use of Non-Variant Sites to Improve the Clinical Assessment of Whole-Genome Sequence Data.
abstract: Genetic testing, which is now a routine part of clinical practice and disease management protocols, is often based on the assessment of small panels of variants or genes. On the other hand, continuous improvements in the speed and per-base costs of sequencing have now made whole exome sequencing (WES) and whole genome sequencing (WGS) viable strategies for targeted or complete genetic analysis, respectively. Standard WGS/WES data analytical workflows generally rely on calling of sequence variants respect to the reference genome sequence. However, the reference genome sequence contains a large number of sites represented by rare alleles, by known pathogenic alleles and by alleles strongly associated to disease by GWAS. It's thus critical, for clinical applications of WGS and WES, to interpret whether non-variant sites are homozygous for the reference allele or if the corresponding genotype cannot be reliably called. Here we show that an alternative analytical approach based on the analysis of both variant and non-variant sites from WGS data allows to genotype more than 92% of sites corresponding to known SNPs compared to 6% genotyped by standard variant analysis. These include homozygous reference sites of clinical interest, thus leading to a broad and comprehensive characterization of variation necessary to an accurate evaluation of disease risk. Altogether, our findings indicate that characterization of both variant and non-variant clinically informative sites in the genome is necessary to allow an accurate clinical assessment of a personal genome. Finally, we propose a highly efficient extended VCF (eVCF) file format which allows to store genotype calls for sites of clinical interest while remaining compatible with current variant interpretation software.
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Ferrarini
authors.affiliation: Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Xumerle
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy; Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Griggio
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy.
authors.forename: Marianna
authors.initials: M
authors.lastname: Garonzi
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy; Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Cantaloni
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy.
authors.forename: Cesare
authors.initials: C
authors.lastname: Centomo
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy.
authors.forename: Sergio Marin
authors.initials: SM
authors.lastname: Vargas
authors.affiliation: Functional Genomics, Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment G, 1015, Lausanne, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Descombes
authors.affiliation: Functional Genomics, Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment G, 1015, Lausanne, Switzerland.
authors.forename: Julien
authors.initials: J
authors.lastname: Marquis
authors.affiliation: Molecular Biomarkers, Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment H, 1015, Lausanne, Switzerland.
authors.forename: Sebastiano
authors.initials: S
authors.lastname: Collino
authors.affiliation: Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy; Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Via S. Giacomo 12, 40126, Bologna, Italy; Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, Piazza di Porta S. Donato 1, 40126, Bologna, Italy; IRCCS, Institute of Neurological Sciences of Bologna, Ospedale Bellaria, Via Altura 3, 40139, Bologna, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Franceschi
authors.affiliation: Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy; Department of Experimental, Diagnostic and Specialty Medicine Experimental Pathology, University of Bologna, Via S. Giacomo 12, 40126, Bologna, Italy; Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, Piazza di Porta S. Donato 1, 40126, Bologna, Italy; Center for Applied Biomedical Research, St. Orsola-Malpighi University Hospital, 40138, Bologna, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Garagnani
authors.affiliation: Knome Inc., Waltham, Massachusetts, 02451, United States of America.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Salisbury
authors.affiliation: Knome Inc., Waltham, Massachusetts, 02451, United States of America.
authors.forename: John Max
authors.initials: JM
authors.lastname: Harvey
authors.affiliation: Functional Genomics Center, Department of Biotechnology, University of Verona, 37134, Verona, Italy; Personal Genomics s.r.l, Strada le Grazie 15, 37134, Verona, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
mesh_terms: D000483:Alleles; D059472:Exome; D005260:Female; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D006801:Humans; D008133:Long QT Syndrome / Q000235:genetics*; D008297:Male; D020641:Polymorphism, Single Nucleotide