Length distribution of the CNVs in Negrito from Peninsular Malaysia.

<p>Length distribution of the CNVs in Negrito from Peninsular Malaysia.</p

General characteristics of CNV and CNVR among 34 Negrito genomes from Peninsular Malaysia.

<p>*Merged: stringent CNV calls by at least 2 out of 3 algorithms applied.</p

UCSC Genome Browser view of CNV on chromosome 3p22.2.

<p>Figure produced by custom tracks listing CNV call of Negrito and uploaded to <a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>.</p

Length distribution of the CNVs unique to the Negrito from Peninsular Malaysia.

<p>Length distribution of the CNVs unique to the Negrito from Peninsular Malaysia.</p

CNVR map of Negrito samples.

<p>The ideogram summarizes the distribution of CNVRs on each human chromosome. The red indicates copy number loss, the blue indicates copy number gain while the green indicates multi-allelic loci.</p

Candidate genes primer sequences and copy number amplified in SyBr Green qPCR assay.

<p>WDR4 and QCNV4 showed copy number normal and therefore considered as false positive. QCNV2 was detected as a CN gain by microarray, inconsistent with the qPCR validation, therefore considered as false positive. Parentheses, unrounded copy number values calculated using the relative quantification, standard deviation.</p

Gene Ontology and pathway analyses on the gene set within the Negrito-specific CNVs using PANTHER and DAVID.

<p>(a) PANTHER analysis suggests a major involvement of the genes harboring the population specific CNVs in the immune system process and response to stimulus, as well as the metabolic process; (b) DAVID analysis suggests the involvement of the genes harboring the population specific CNVs in the transcription and regulation of RNA metabolic processes.</p

Pathways and biological processes of the genes underlying the population specific CNvs in Negrito from Peninsular Malysia.

<p>Analysis was performed using PANTHER DAVID.</p

Common CNV with significant difference in allele frequencies compare to the HapMap3 dataset.

<p>Common CNV with significant difference in allele frequencies compare to the HapMap3 dataset.</p

Population specific CNVs in 34 genomes of Negrito from Peninsular Malaysia.

<p>Position of CNVs were coordinated based on Human Genome Assembly NCBI (hg18).</p><p>*CNV frequencies calculated based on the 34 Negrito genomes genotyped.</p