Beyond the Genome: genomics research ten years after the human genome sequence

A report on the meeting 'Beyond the Genome', Boston, USA, 11-13 October 2010

Striving Towards Authenticity in the Self Through Dress and Appearance: Stories of Latina Adolescent Immigrants

We sought to explore how Latina adolescent immigrants experience immigration across adolescence as they seek to know and express their authentic selves through dress and appearance. Our work was informed by theories of acculturation, identity, and authenticity. Participants included 12 immigrant women who identified as Latina and who immigrated before age 16. Open-ended interviews focused on participants’ memories of their immigration experiences during adolescence. Data were analyzed using constant comparison processes. Findings revealed that, for participants, the typical challenges of adolescence were complicated by immigration that included constructing an authentic identity at the intersection of two cultures. Immigration produced a disjointed dance towards authenticity with many uneven steps, sharp turns, and the occasional reversal. Dress was a key means for the expression of the authentic self; a self that communicated to the culture of settlement who they were and how their culture of origin was part of their authentic self

A Tale of Two Haplotypes: The \u3cem\u3eEDA2R/AR\u3c/em\u3e Intergenic Region is the most Divergent Genomic Segment between Africans and East Asians in the Human Genome

Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the Out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly-differentiated SNPs. Using a publicly-available dataset of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed using a subset of individuals sequenced to high coverage. The first of these haplotypes, the α haplotype, is at high frequencies in most of the African populations surveyed and likely arose prior to the separation of African populations into distinct genetic entities. The second, the β haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa prior to the Out-of-Africa migration. We also observed a small group of rare haplotypes with no clear relationship to the α and β haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, like the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α and β haplotypes. We suggest that the rise of the α and β haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the Out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α and β haplotypes and of purifying selection against α/β recombinants

Characterization of X-Linked SNP genotypic variation in globally distributed human populations

An analysis of X-linked genetic variation in human populations provides insights into population structure and demographic patterns

Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji

Genome-Wide Association Study SNPs in the Human Genome Diversity Project Populations: Does Selection Affect Unlinked SNPs with Shared Trait Associations?

Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human fitness, including many immunological, metabolic, cardiovascular, and behavioral phenotypes. Given the polygenic nature of complex traits, selection may exert its influence on them by altering allele frequencies at many associated loci, a possibility which has yet to be explored empirically. Here we use 38 different measures of allele frequency variation and 8 iHS scores to characterize over 1,300 GWAS SNPs in 53 globally distributed human populations. We apply these same techniques to evaluate SNPs grouped by trait association. We find that groups of SNPs associated with pigmentation, blood pressure, infectious disease, and autoimmune disease traits exhibit unusual allele frequency patterns and elevated iHS scores in certain geographical locations. We also find that GWAS SNPs have generally elevated scores for measures of allele frequency variation and for iHS in Eurasia and East Asia. Overall, we believe that our results provide evidence for selection on several complex traits that has caused changes in allele frequencies and/or elevated iHS scores at a number of associated loci. Since GWAS SNPs collectively exhibit elevated allele frequency measures and iHS scores, selection on complex traits may be quite widespread. Our findings are most consistent with this selection being either positive or negative, although the relative contributions of the two are difficult to discern. Our results also suggest that trait-SNP associations identified in Eurasian samples may not be present in Africa, Oceania, and the Americas, possibly due to differences in linkage disequilibrium patterns. This observation suggests that non-Eurasian and non-East Asian sample populations should be included in future GWAS

A Re-Envisioned Multicultural STEM Education for All

This conceptual article calls for the transformation of the antiquated educational system into an innovative PreK-12 model that embraces the goals of multicultural education and the pedagogical strategies commonly associated with a holistically integrated STEM curriculum. Teaching STEM through a multicultural lens creates rich opportunities where all students, especially those who have been historically marginalized in STEM fields, can develop identities such as scientists, mathematicians, creative artists, and valued citizens as part of a global team effort. Recommendations are made to educational policymakers, curriculum developers, school administrators, teacher educators, and PreK-12 teachers to collectively create a STEM educational model that is equitable, pluralistic, and a path to social justice