title: Prediction of rare single-nucleotide causative mutations for muscular diseases in pooled next-generation sequencing experiments.
abstract: Next-generation sequencing (NGS) is a new approach for biomedical research, useful for the diagnosis of genetic diseases in extremely heterogeneous conditions. In this work, we describe how data generated by high-throughput NGS experiments can be analyzed to find single nucleotide polymorphisms (SNPs) in DNA samples of patients affected by neuromuscular disorders. In particular, we consider untagged pooled NGS data, where DNA samples of different individuals are combined in a single experiment, still providing information with an uncertainty limited to only two patients. At the moment, only few publications address the problem of SNPs detection in pooled experiments, and existing tools are often inaccurate. We propose a computational procedure consisting of two parts. In the first, data are filtered by means of decision rules. The second phase is based on a supervised classification technique. In the present work, we compare different de facto standard supervised and unsupervised procedures to identify and classify variants potentially related to muscular diseases, and we discuss results in terms of statistical and biological validation.
authors.affiliation: 1 Department of Statistical Sciences, Sapienza University of Rome , Rome, Italy .
authors.forename: Maria Brigida
authors.initials: MB
authors.lastname: Ferraro
authors.forename: Marco
authors.initials: M
authors.lastname: Savarese
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Di Fruscio
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Nigro
authors.forename: Mario Rosario
authors.initials: MR
authors.lastname: Guarracino
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D056726:Genetic Association Studies / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009135:Muscular Diseases / Q000175:diagnosis*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: damaging mutations; muscular diseases; next generation sequencing; prediction; single-nucleotide polymorphism