Novel mutations in genes causing hereditary spastic paraplegia and Charcot-Marie-Tooth neuropathy identified by an optimized protocol for homozygosity mapping based on whole-exome sequencing.
Homozygosity mapping is an effective approach for detecting molecular defects in consanguineous families by delineating stretches of genomic DNA that are identical by descent. Constant developments in next-generation sequencing created possibilities to combine whole-exome sequencing (WES) and homozygosity mapping in a single step.



Basic optimization of homozygosity mapping parameters was performed in a group of families with autosomal-recessive (AR) mutations for which both single-nucleotide polymorphism (SNP) array and WES data were available. We varied the criteria for SNP extraction and PLINK thresholds to estimate their effect on the accuracy of homozygosity mapping based on WES.



Our protocol showed high specificity and sensitivity for homozygosity detection and facilitated the identification of novel mutations in GAN, GBA2, and ZFYVE26 in four families affected by hereditary spastic paraplegia or Charcot-Marie-Tooth disease. Filtering and mapping with optimized parameters was integrated into the HOMWES (homozygosity mapping based on WES analysis) tool in the GenomeComb package for genomic data analysis.



We present recommendations for detection of homozygous regions based on WES data and a bioinformatics tool for their identification, which can be widely applied for studying AR disorders.Genet Med 18 6, 600-607.
Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.|Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.|Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria.
Daliya
0000-0001-6222-0461
D
Kancheva
Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.|Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
Derek
0000-0001-6097-3670
D
Atkinson
Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.
Peter
0000-0001-8558-9288
P
De Rijk
Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.|Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.|Current address: Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Magdalena
0000-0001-7255-6639
M
Zimon
Department of Neurology, Medical University-Sofia, Sofia, Bulgaria.
Teodora
T
Chamova
Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria.
Vanyo
V
Mitev
Department of Pediatrics, Dicle University School of Medicine, Diyarbakir, Turkey.
Ahmet
A
Yaramis
Department of Neurological, Neuropsychological, Morphological and Motor Sciences, University of Verona, Verona, Italy.
Gian
G
Maria Fabrizi
Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
Haluk
H
Topaloglu
Department of Neurology, Medical University-Sofia, Sofia, Bulgaria.|Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria.
Ivailo
I
Tournev
Yesim
Y
Parman
Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.
Yesim
Y
Parma
Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey.
Esra
E
Battaloglu
Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.|Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
Alejandro
0000-0001-9868-2465
A
Estrada-Cuzcano
Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, University of Antwerp, Antwerp, Belgium.|Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.|Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria.
Albena
A
Jordanova
D002352:Carrier Proteins / Q000235:genetics*; D002607:Charcot-Marie-Tooth Disease / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D002874:Chromosome Mapping; D003241:Consanguinity; D003598:Cytoskeletal Proteins / Q000235:genetics*; D005260:Female; D005962:Glucosylceramidase; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006720:Homozygote; D006801:Humans; D008297:Male; D009154:Mutation; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015419:Spastic Paraplegia, Hereditary / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D000073359:Exome Sequencing; D001617:beta-Glucosidase / Q000235:genetics*
D002352:Carrier Proteins; D003598:Cytoskeletal Proteins; C416508:GAN protein, human; C528699:ZFYVE26 protein, human; D001617:beta-Glucosidase; C517537:GBA2 protein, human; D005962:Glucosylceramidase