Ancestry informative markers in Amerindians from Brazilian Amazon

Abstract

Ancestry informative markers (AIMs) are genetic loci with large frequency differences between the major ethnic groups and are very useful in admixture estimation. However, their frequencies are poorly known within South American indigenous populations, making it difficult to use them in admixture studies with Latin American populations, such as the trihybrid Brazilian population. To minimize this problem, the frequencies of the AIMs FY-null, RB2300, LPL, AT3-I/D, Sb19.3, APO, and PV92 were determined via PCR and PCR-RFLP in four tribes from Brazilian Amazon (Tikúna, Kashinawa, Baníwa, and Kanamarí), to evaluate their potential for discriminating indigenous populations from Europeans and Africans, as well as discriminating each tribe from the others. Although capable of differentiating tribes, as evidenced by the exact test of population differentiation, a neighbor-joining tree suggests that the AIMs are useless in obtaining reliable reconstructions of the biological relationships and evolutionary history that characterize the villages and tribes studied. The mean allele frequencies from these AIMs were very similar to those observed for North American natives. They discriminated Amerindians from Africans, but not from Europeans. On the other hand, the neighbor-joining dendrogram separated Africans and Europeans from Amerindians with a high statistical support (bootstrap = 0.989). The relatively low diversity (G(ST) = 0.042) among North American natives and Amerindians from Brazilian Amazon agrees with the lack of intra-ethnic variation previously reported for these markers. Despite genetic drift effects, the mean allelic frequencies herein presented could be used as Amerindian parental frequencies in admixture estimates in urban Brazilian populations.

Insights on human evolution: an analysis of Alu insertion polymorphisms

“…Among them, APO, PV92 and Sb19.3 have also been used earlier in AIM panels. 55,56 Interestingly, PV92 is the only Alu marker with a d value of over 20% in the ASI/EUR comparison. On the other hand, APO, Sb19.3, A25, COL3A1 and NBC4 show moderate d levels (20%odo30%) in the SSA/ASI and SSA/EUR comparisons.…”

Self-declared ethnicity and genomic ancestry in prostate cancer patients from Brazil

“…To estimate genomic ancestry, 11 AIMs were selected based on frequency differences greater than 40% between the parental groups (Hoggart et al, 2003;Luizon et al, 2008). These AIMs exhibited many differences in allele frequencies (δ) between parental populations; therefore, they can be used to characterize the genetic composition of admixed populations Beuten et al, 2011;Pena et al, 2011).…”

“…These AIMs exhibited many differences in allele frequencies (δ) between parental populations; therefore, they can be used to characterize the genetic composition of admixed populations Beuten et al, 2011;Pena et al, 2011). Genotyping was performed as described by Shriver et al (2003) and Luizon et al (2008). Conventional polymerase chain reaction (PCR) was used to identify insertions/deletions and Alu insertions APOA1 -rs3138522, SB19.3*1 -rs3138524, MID-52 -rs16344, PV92 -rs3138523, MID-575 -rs140864, AT3 -rs3138521, while PCR-restriction fragment length polymorphism was employed to detect LPL-rs285, RB2300 -rs2252544, DRD2 -rs1079598, and CKMM -rs4884 SNPs.…”

Ancestry indicative markers in HIV positive patients in the state of Mato Grosso, Brazil

“…Peripheral blood samples from seronegative controls (2-4 ml) were collected as described above; the DNA was extracted according to Higuchi & Ochman, 10 with modifications, or through the use of two commercial extraction kits (GE Healthcare Life Sciences of Brazil ® and Invitrogen -Thermo Fisher Scientific).…”

“…Such markers make it possible to recover the socio-historical and demographic events of the country. [8][9][10] There is a scarcity of studies for the State of Mato Grosso (total area: 900.000 km 2 , population 3.3 million; HDI: 0.72, equatorial/tropical climate) evaluating the incidence of AIDS according to the race/color variable. In order to overcome some of this deficiency, this study aimed to analyze the prevalence of ancestral informational marker polymorphisms in samples in HIV-free and HIV-1 virus carriers within the population of the state…”