title: H3M2: detection of runs of homozygosity from whole-exome sequencing data.
abstract: BACKGROUND
  Runs of homozygosity (ROH) are sizable chromosomal stretches of homozygous genotypes, ranging in length from tens of kilobases to megabases. ROHs can be relevant for population and medical genetics, playing a role in predisposition to both rare and common disorders. ROHs are commonly detected by single nucleotide polymorphism (SNP) microarrays, but attempts have been made to use whole-exome sequencing (WES) data. Currently available methods developed for the analysis of uniformly spaced SNP-array maps do not fit easily to the analysis of the sparse and non-uniform distribution of the WES target design.
  
  
  RESULTS
  To meet the need of an approach specifically tailored to WES data, we developed [Formula: see text], an original algorithm based on heterogeneous hidden Markov model that incorporates inter-marker distances to detect ROH from WES data. We evaluated the performance of [Formula: see text] to correctly identify ROHs on synthetic chromosomes and examined its accuracy in detecting ROHs of different length (short, medium and long) from real 1000 genomes project data. [Formula: see text] turned out to be more accurate than GERMLINE and PLINK, two state-of-the-art algorithms, especially in the detection of short and medium ROHs.
  
  
  METHODS
  [Formula: see text] is a collection of bash, R and Fortran scripts and codes and is freely available at https://sourceforge.net/projects/h3m2/.
  
  
  BACKGROUND
  albertomagi@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Alberto
authors: A
authors: Magi
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Lorenzo
authors: L
authors: Tattini
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Flavia
authors: F
authors: Palombo
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Matteo
authors: M
authors: Benelli
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Alessandro
authors: A
authors: Gialluisi
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Betti
authors: B
authors: Giusti
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Rosanna
authors: R
authors: Abbate
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Marco
authors: M
authors: Seri
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Gian Franco
authors: GF
authors: Gensini
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Giovanni
authors: G
authors: Romeo
authors: Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands Department of Experimental and Clinical Medicine, University of Florence, Florence 50019, Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Diagnostic Genetic Unit, Careggi Hospital, Florence 50019, Italy and Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen 6525 EN, The Netherlands.
authors: Tommaso
authors: T
authors: Pippucci
mesh_terms: D000465:Algorithms; D002877:Chromosomes, Human / Q000235:genetics; D059472:Exome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006720:Homozygote; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA