Discovery of copy number variants by multiplex amplifiable probe hybridization (MAPH) in candidate pigmentation genes

<div><p></p><p><i>Background</i>: Copy Number Variants (CNVs) contribute to a large fraction of genetic diversity and some of them have been reported to offer an evolutionary advantage.</p><p><i>Aim</i>: To identify CNVs in pigmentary loci that could contribute to human skin pigmentation diversity.</p><p><i>Subjects and methods</i>: This study assessed the existence of CNVs in every exon of candidate genes: <i>TYR, TYRP1, DCT, MC1R</i> and <i>SLC24A5</i>, 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.</p><p><i>Results</i>: Five CNVs were identified by MAPH: <i>DCT</i> exons 4 and 8, <i>TYR</i> exon 1 and <i>SLC24A5</i> exons 1 and 4. Real-time quantitative PCR (RT-qPCR) confirmed the CNV in exon 1 of <i>SLC24A5</i>. This study further analysed the 5′ promoter region of <i>SLC24A5</i> and found another CNV in this region. However, no association was found between the CNV and the degree of pigmentation.</p><p><i>Conclusion</i>: 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.</p></div

Multidimensional Scaling (MDS), considering the Fst genetic differences calculated according to the distribution of the mtDNA haplogroup frequencies of different populations; Chalcolithics in the Basque Country (purple), Neolithics (green), present-day Near East and northern Caucasus (orange) and Europeans (blue).

<p>Abbreviations for populations. Hunter-gatherer groups: Scandinavia (HG_SCA), Central Europe (HG_CE) and Cantabrian fringe (HG_CANT: La Chora, La Pasiega, Aizpea and Erralla). <b>Neolithic populations:</b> Catalonia (NEO_CAT), Central Europe (NEO_CE), France (NEO_FR) and Navarre (Los Cascajos and Paternanbidea) (NEO_NAVARRE). <b>Chalcolithic </b><b>populations in the Basque Country:</b> Longar, SJaPL and Pico Ramos. <b>Present-day populations in Europe:</b> Eastern Mediterranean (MdE), Central Mediterranean (MdC), Western Mediterranean (MdW), Northeast Europe (NE), North-Central Europe (NC), Northwest Europe (NW), Southeast Europe (SE), Scandinavia (SCA), Alps (ALP), Iberian Peninsula (Ib_Pen), and Cantabrian Fringe populations (Cant_F) (that includes the Basque Country)</p

Geographic location of the ancient human remains analysed in the present study.

<p>All sites are located in the North of the Iberian Peninsula.</p

Median Joining Network of European Paleolithic, Neolithic and Bronze Age sequences.

<p>Data encompass mtDNA HVR-I (nps 15999-16399). <b>Hunter-gatherer groups</b>: Scandinavia (HG_SCA) in pink, Central Europe (HG_CE) in orange, and the Cantabrian fringe (HG_CANT: La Chora, La Pasiega, Aizpea and Erralla) in blue. <b>Neolithic populations</b>: Catalonia (NEO_CAT) in green, Central Europe (NEO_CE) in purple, Northwest France (NEO_FR_NW) in brown, South of France (NEO_FR) in white, and the Cantabrian fringe (NEO_Cant_F: Los Cascajos, Paternanbidea, Fuente Hoz and Marizulo) in light blue. Urtiaga (Bronze Age) in black.</p

Chronology, subsistence pattern and geographical origin of the prehistoric samples analysed in the present study.

<p>Minimal number of individuals at each sites (MNI), number of individuals analysed (N).</p

Proposed mechanism for the involvement of ribosomal proteins, MDM2 and p53 signaling pathway in the response to UVB irradiation.

<p>Proposed mechanism for the involvement of ribosomal proteins, MDM2 and p53 signaling pathway in the response to UVB irradiation.</p

Gene expression of genes <i>FDX6</i>, <i>RPL6</i>, <i>MDM2</i>, <i>TP53I3</i>, <i>ATP6VOB</i> and <i>MIF</i> assessed by RT-qPCR.

<p>Unpaired t-test; *** p<0.0001; ** p<0.001; * p<0.01.</p

Multidimensional Scaling Analysis performed by haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink hunter-gatherer groups and in yellow ancient and present-day Romanian groups, present-day European population in blue and present-day Near East population in orange. Stress: 0.07553 and RSQ: 0.99071.</p

Top 50 upregulated genes in LM vs DM at 6 hours after UVB irradiation (non-coding RNAs are indicated with *) (Bonferroni-adjusted p-value <0.0001).

<p>Top 50 upregulated genes in LM vs DM at 6 hours after UVB irradiation (non-coding RNAs are indicated with *) (Bonferroni-adjusted p-value <0.0001).</p

Principal Component Analysis (47% of the total variance) performed considering mtDNA haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink Hunter-Gatherer groups (HG), in yellow ancient and present-day Romania groups, present-day European population in blue and present-day Near East population in orange. Interpretation based on the haplogroup frequency has been written on both PC (Absence of haplogroups D, M, C and N on one side of the first component and absence of haplogroup H on the top of the second component). PC1 represents 30% of variance and PC2 represents 17% of variance.</p