title: exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels.
abstract: Exome and whole-genome analyses powered by next-generation sequencing (NGS) have become invaluable tools in identifying causal mutations responsible for Mendelian disorders. Given that individual exomes contain several thousand single nucleotide variants and insertions/deletions, it remains a challenge to analyze large numbers of variants from multiple exomes to identify causal alleles associated with inherited conditions. To this end, we have developed user-friendly software that analyzes variant calls from multiple individuals to facilitate identification of causal mutations. The software, termed exomeSuite, filters for putative causative variants of monogenic diseases inherited in one of three forms: dominant, recessive caused by a homozygous variant, or recessive caused by two compound heterozygous variants. In addition, exomeSuite can perform homozygosity mapping and analyze the variant data of multiple unrelated individuals. Here we demonstrate that filtering of variants with exomeSuite reduces datasets to a fraction of a percent of their original size. To the best of our knowledge this is the first freely available software developed to analyze variant data from multiple individuals that rapidly assimilates and filters large data sets based on pattern of inheritance.
authors.affiliation: Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address: bmaranha@ucsd.edu.
authors.forename: B
authors.initials: B
authors.lastname: Maranhao
authors.affiliation: Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA. Electronic address: pbiswas@ucsd.edu.
authors.forename: P
authors.initials: P
authors.lastname: Biswas
authors.affiliation: Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA. Electronic address: duncanj@vision.ucsf.edu.
authors.forename: J L
authors.initials: JL
authors.lastname: Duncan
authors.affiliation: Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address: haag@med.umich.edu.
authors.forename: K E
authors.initials: KE
authors.lastname: Branham
authors.affiliation: Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Neurosciences Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address: gsilva@ucsd.edu.
authors.forename: G A
authors.initials: GA
authors.lastname: Silva
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: M A
authors.initials: MA
authors.lastname: Naeem
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: S N
authors.initials: SN
authors.lastname: Khan
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: S
authors.initials: S
authors.lastname: Riazuddin
authors.affiliation: Ophthalmic Genetics and Visual Function Branch, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: f3h@helix.nih.gov.
authors.forename: J F
authors.initials: JF
authors.lastname: Hejtmancik
authors.affiliation: Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address: jrheck@umich.edu.
authors.forename: J R
authors.initials: JR
authors.lastname: Heckenlively
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
authors.forename: S A
authors.initials: SA
authors.lastname: Riazuddin
authors.affiliation: Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA. Electronic address: plee@scripps.edu.
authors.forename: P L
authors.initials: PL
authors.lastname: Lee
authors.affiliation: Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA. Electronic address: rayyagari@ucsd.edu.
authors.forename: R
authors.initials: R
authors.lastname: Ayyagari
mesh_terms: D000483:Alleles; D004252:DNA Mutational Analysis / Q000379:methods; D066264:Datasets as Topic; D059472:Exome; D005260:Female; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D012984:Software
keywords: Exome; Filtering; Homozygosity mapping; Mendelian disease; Software