Mitochondrial DNA diversity in the African American population

Johnson, Derek C.; Shrestha, Sadeep; Wiener, Howard W.; Makowsky, Robert; Kurundkar, Ashish; Wilson, Craig M.; Aissani, Brahim

doi:10.3109/19401736.2013.840591

Cited by 19 publications

(17 citation statements)

References 27 publications

(48 reference statements)

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“…L2 for L2a) represented the majority of the observed ambiguities (about 7%); with the adopted grouping procedure, these haplogroups felt under the same macrohaplogroups. As reported in the early study [20], about 2.9% of self-reported Caucasian descents were re-classified by PCA as African American descents.…”

Section: Resultsmentioning

confidence: 91%

“…Principal component analysis (PCA) based on a validated set of 150 nuclear AIMs typed in the predominantly African American REACH cohort previously enabled us to identify and exclude study participants of admixed population descent, namely, other than non-Hispanic African or European descent [20]. In that study ( n =343), from which the present study sample was derived, we observed 17 out of the 18 mtDNA haplogroups reported so far for populations of African American descent, indicating a good representation of the African American population diversity in our studied REACH sample.…”

Section: Resultsmentioning

confidence: 99%

“…The experimental design and bioinformatics treatment of nucleotide sequence data have been described [20]. Briefly, DNA extracted from buffy coat samples (Qiagen DNA purification kit) was used as templates in PCR to amplify the hypervariable regions HV1 and HV2 as described [20].…”

Section: Methodsmentioning

confidence: 99%

“…Briefly, DNA extracted from buffy coat samples (Qiagen DNA purification kit) was used as templates in PCR to amplify the hypervariable regions HV1 and HV2 as described [20]. …”

Section: Methodsmentioning

confidence: 99%

“…HV1 and HV2 regions are the most rapidly evolving sequences within the D-loop. These highly polymorphic mtDNA regions define population-specific mitochondrial haplogroups, and we have sequenced them in the REACH cohort [20]. …”

Section: Introductionmentioning

confidence: 99%

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Mitochondrial DNA variation and virologic and immunological HIV outcomes in African Americans

Aissani¹,

Shrestha²,

Wiener³

et al. 2014

Aids

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Objective To evaluate the impact of mitochondrial DNA (mtDNA) haplogroups on virologic and immunological outcomes of HIV infection. Design HAART-naive African American adolescent participants to the Reaching for Excellence in Adolescent Care and Health study. Methods The mtDNA haplogroups were inferred from sequenced mtDNA hypervariable regions HV1 and HV2 and their predictive value on HIV outcomes were evaluated in linear mixed models, controlled for human leukocyte antigen (HLA)-B27, HLA-B57 and HLA-B35-Px alleles and other covariates. Results We report data showing that the mtDNA L2 lineage, a group composed of L2a, L2b and L2e mtDNA haplogroups in the studied population, is significantly associated (beta=−0.08; Bonferroni-adjusted P=0.004) with decline of CD4+ T cells (median loss of 8 ± 1 cells per month) in HAART-naive HIV-infected individuals of African American descent (n=133). No significant association (P<0.05) with set-point viral load was observed with any of the tested mtDNA haplogroups. The present data concur with previous findings in the AIDS Clinical Trials Group study 384, implicating the L2 lineage with slower CD4+ T-cell recovery after antiretroviral therapy in African Americans. Conclusions Whereas the L2 lineage showed an association with unfavorable immunological outcomes of HIV infection, its phylogenetic divergence from J and U5a, two lineages associated with accelerated HIV progression in European Americans, raises the possibility that interactions with common nucleus-encoded variants drive HIV progression. Disentangling the effects of mitochondrial and nuclear gene variants on the outcomes of HIV infection is an important step to be taken toward a better understanding of HIV/AIDS pathogenesis and pharmacogenomics.

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Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Briefly, DNA extracted from buffy coat samples (Qiagen DNA purification kit) was used as templates in PCR to amplify the hypervariable regions HV1 and HV2 as described [20]. …”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Mitochondrial DNA variation and virologic and immunological HIV outcomes in African Americans

Aissani¹,

Shrestha²,

Wiener³

et al. 2014

Aids

Self Cite

View full text Add to dashboard Cite

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Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier

Fleskes

Bruwelheide

West

et al. 2019

American J Phys Anthropol

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Objectives: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America. Materials and methods: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence. Results: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa. Discussion: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century.

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Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y‐chromosome lineages in the Guadeloupe archipelago

Mendisco

Pémonge

Romon

et al. 2019

American J Phys Anthropol

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Objectives: The history of the Caribbean region is marked by numerous and various successive migration waves that resulted in a global blending of African, European, and Amerindian lineages. As the origin and genetic composition of the current population of French Caribbean islands has not been studied to date, we used both mitochondrial DNA and Y-chromosome markers to complete the characterization of the dynamics of admixture in the Guadeloupe archipelago. Materials and Methods: We sequenced the mitochondrial hypervariable regions and genotyped mitochondrial and Y-chromosomal single nucleotide polymorphisms (SNPs) of 198 individuals from five localities of the Guadeloupe archipelago.Results: The maternal haplogroups revealed a blend of 85% African lineages (mainly traced to Western, West-Central, and South-Eastern Africa), 12.5% Eurasian lineages, and 0.5% Amerindian lineages. We highlighted disequilibria between European paternal contribution (44%) and European maternal contribution (7%), pointing out an important sexual asymmetry. Finally, the estimated Native American component was strikingly low and supported the near-extinction of native lineages in the region. Discussion:We confirmed that all historically known migratory events indeed left a visible genetic imprint in the contemporary Caribbean populations. The data gathered clearly demonstrated the significant impact of the transatlantic slave trade on the Guadeloupean population's constitution. Altogether, the data in our study confirm that in the Caribbean region, human population variation is correlated with colonial and postcolonial policies and unique island histories.

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Mitochondrial DNA diversity in the African American population

Cited by 19 publications

References 27 publications

Mitochondrial DNA variation and virologic and immunological HIV outcomes in African Americans

Mitochondrial DNA variation and virologic and immunological HIV outcomes in African Americans

Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier

Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y‐chromosome lineages in the Guadeloupe archipelago

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