title: Discovery of copy number variants by multiplex amplifiable probe hybridization (MAPH) in candidate pigmentation genes.
abstract: BACKGROUND
  Copy Number Variants (CNVs) contribute to a large fraction of genetic diversity and some of them have been reported to offer an evolutionary advantage.
  
  
  OBJECTIVE
  To identify CNVs in pigmentary loci that could contribute to human skin pigmentation diversity.
  
  
  METHODS
  This study assessed the existence of CNVs in every exon of candidate genes: TYR, TYRP1, DCT, MC1R and SLC24A5, using the Multiplex Amplifiable Probe Hybridization technique (MAPH). This study analysed a total of 99 DNA samples of unrelated individuals from different populations. Validation and further analysis in a larger Spanish sample were performed by RT-qPCR.
  
  
  RESULTS
  Five CNVs were identified by MAPH: DCT exons 4 and 8, TYR exon 1 and SLC24A5 exons 1 and 4. Real-time quantitative PCR (RT-qPCR) confirmed the CNV in exon 1 of SLC24A5. This study further analysed the 5' promoter region of SLC24A5 and found another CNV in this region. However, no association was found between the CNV and the degree of pigmentation.
  
  
  CONCLUSIONS
  Although the functional role of these structural variants in pigmentation should be the subject of future work, the results emphasize the need to consider all classes of variation (both SNPs and CNVs) when exploring the genetics of skin pigmentation.
authors.affiliation: a Genetics, Physical Anthropology and Animal Physiology and.
authors.forename: Saioa
authors.initials: S
authors.lastname: López
authors.affiliation: a Genetics, Physical Anthropology and Animal Physiology and.
authors.forename: Iker
authors.initials: I
authors.lastname: García
authors.affiliation: b Department of Zoology and Animal Cell Biology , University of the Basque Country UPV/EHU , Barrio sarriena s/n , Leioa , Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Smith
authors.affiliation: a Genetics, Physical Anthropology and Animal Physiology and.
authors.forename: Arrate
authors.initials: A
authors.lastname: Sevilla
authors.affiliation: a Genetics, Physical Anthropology and Animal Physiology and.
authors.forename: Neskuts
authors.initials: N
authors.lastname: Izagirre
authors.affiliation: a Genetics, Physical Anthropology and Animal Physiology and.
authors.forename: Concepción
authors.initials: C
authors.lastname: de la Rúa
authors.affiliation: a Genetics, Physical Anthropology and Animal Physiology and.
authors.forename: Santos
authors.initials: S
authors.lastname: Alonso
mesh_terms: D000293:Adolescent; D000328:Adult; D017920:Antiporters / Q000235:genetics; D044466:Asian People / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D044383:Black People / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D018628:Gene Dosage / Q000235:genetics*; D006801:Humans; D019746:Intramolecular Oxidoreductases / Q000235:genetics; D008297:Male; D008544:Melanocytes / Q000166:cytology / Q000201:enzymology*; D008562:Membrane Glycoproteins / Q000235:genetics; D008875:Middle Aged; D014442:Monophenol Monooxygenase / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques; D010088:Oxidoreductases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D044102:Receptor, Melanocortin, Type 1 / Q000235:genetics; D017422:Sequence Analysis, DNA; D012880:Skin Pigmentation / Q000235:genetics*; D044465:White People / Q000235:genetics; D055815:Young Adult
chemical_list: D017920:Antiporters; D008562:Membrane Glycoproteins; D044102:Receptor, Melanocortin, Type 1; C506584:SLC24A5 protein, human; D010088:Oxidoreductases; C489799:TYRP1 protein, human; D014442:Monophenol Monooxygenase; D019746:Intramolecular Oxidoreductases; C042501:dopachrome isomerase
keywords: Evolution; human diversity; mutation; natural selection