- Presenting ENCODE (M. Skipper, R. Dhand, P. Campbell)
- Genomics: ENCODE explained (Joseph R. Ecker et al.)
- An integrated encyclopedia of DNA elements in the human genome (ENCODE Project Consortium)
Category Archives: global genetics
|From Supplemental Figure 1 – PC analysis|
As you can see in the PCA plot, the inter-population variation is most subtle, almost impossible to discern with so much overlap. The lack of structure repeats for the other components.
Copy number variation (CNV) is a type of global genetic variations in human genome, defined as a segment of DNA larger than one kilobase presenting copy-number differences by comparison of two or more genomes. One single or co-effects of multiple genomic rearrangements such as deletion, insertion, duplication and unbalanced translocation are likely to cause CNVs. By changing gene dosage, interrupting coding sequences, and influencing neighboring gene regulation, CNVs can impact on gene expression and phenotypes.
|Fig. 4 CNV sharing (click to expand)|
|Frequency of B006 worldwide|
In the available Neandertal sequence (Green et al. 2010), there is information on 20 out of 35 dys44 polymorphic sites. These represent eighteen ancestral and two derived alleles, fully matching the corresponding sites of B006 (Table 1). One of the derived alleles, C of rs6631517, is also shared with other dys44 haplotypes, whereas the second one, G of rs11795471, is unique to B006 (the information on two remaining B006-polymorphisms is not available).
ResultsHere, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection.
|Fig. 1 (click to enlarge)|
I understand that, in the case of Africa, the correlation is very strong, though not totally lineal. For instance the HbS (sickle cell) allele is lacking in wide areas of malaria endemism: The Horn, Southern Africa (including Bantu Mozambique but not Austronesian Madagascar), NW Africa…