Thursday, September 25, 2008

Protective factor against breast cancer in Black women?

Breast cancer incidence has been found to be higher in those with higher SES, and incidence is highest among Whites, followed by Blacks, then Asians and Hispanics. Using several previous studies, this study finds that the disparity in breast cancer risk between ethnic groups can be accounted for by differences in SES, except for the disparity between Blacks and others.
"In contrast, for the black population, seven of the eight
analyzed datasets showed no difference in the incidence
of breast cancer at highest level of SES compared to the
lowest level, with only one dataset demonstrating a statistically significant disparity (data set 1: IRR 1.39, lower limit of 95% CI=1.04). This suggests that, as opposed to the apparent contributory effect of high SES on breast cancer risk in white, Hispanic and Asian/Pacific-Islander women, the risk of breast cancer in black women may not be significantly modified by SES."
in the conclusion:
"As for black women, the overall lack of statistically significant incidence rate ratios in Table 1 suggests that SES effects do not play an important role in modifying the risk of breast cancer in this population. This suggestion is supported by Chlebowski’s analysis, in which adjustment for SES-correlated breast cancer risk factors failed to eliminate the differencein hazard ratio of between black women and women of other races. Taken together, these findings imply the presence of a protective factor, which is not modified by SES, against breast cancer in black women."
There's a brief mention at the end about the grade and aggressiveness of breast cancer among Black women.

Disparities in breast cancer incidence across racial/ethnic strata and socioeconomic status: a systematic review
Vainshtein J.
J Natl Med Assoc. 2008 Jul;100(7):833-9.
OBJECTIVES: A higher incidence of breast cancer has been reported both in white women and women of higher socioeconomic status (SES) compared to women of other races and lower SES, respectively. We explored whether differences in SES can account for disparities in breast cancer incidence between races. METHODS: We identified several studies published between 1990 and 2007 that addressed disparities in breast cancer incidence across racial and socioeconomic strata. For each study, we calculated incidence rate ratios (IRRs) for breast cancer incidence in the highest strata to lowest strata of SES for white, black, Hispanic and Asian/Pacific-Islander populations. We then used these IRRs to compare trends in SES and breast cancer incidence between races and across studies. RESULTS: The studies we identified revealed that the magnitude of the disparity in breast cancer incidence between races decreases with increasing SES. While individual census-tract based studies' methods of assessing the association between SES and breast cancer incidence did not identify consistent trends between races, adjustment for risk factors closely correlated with SES eliminated the statistical differences in breast cancer incidence between women of white, Hispanic and Asian/Pacific-Islander, but not black, ethnicity. CONCLUSION: We found that racial differences in breast cancer incidence can largely be accounted for by ethnic differences in SES among white, Hispanic and Asian/Pacific-Islander women, but not between these populations and black women. We further highlight important differences in methodology between previously published studies that may account for their disparate findings.

Wednesday, September 24, 2008

Four Stone Hearth Anthropology Blog Carnival

I'm happy to be hosting the 50th edition of the Four Stone Hearth Anthropology Blog Carnival!
We've got a wide array of Anthropology topics. I'll go from social/cultural anthropology, then into archaeology, and then into biological anthropology.

Daniel at Neuroanthropology shares with us Alesha Sivartha's collection of drawings representing the domains of life and culture that brains might be devoted to dealing with. This is interesting in the sense that evolutionary psychologists have argued that the brain is not like a general purpose computer, but rather like a Swiss army knife with domain specific mechanisms evolved to deal with specific problems such as face recognition, social relationships, mental maps, etc..

Daniel has another interesting post about Race in the Race for President of the US, which reminds us that racial dynamics are never far from the lived experience of Americans.

Magnus Reuterdahl at Testimony at the Spade discusses Mark Twain's visit to Jonkoping, Sweden.

Terry Toohill, guest blogger at Remote Central, discusses the evidence and misconceptions surrounding the processes of evolution, and might I add, provides plenty of references.

Martin at Aardvarchaeology shares his experience with the trials and tribulations of archaeological digs in Sweden.

At the Southeast Asian Archaeology Newblog, we see that six new Neolithic burials from Sarawak from the Niah cave complex have been recently put on display.
"More significantly, the skeletons are of the Australomelanasoid affinity, which means they were natives of Sundaland (the geological land shelf on which much of island Southeast Asia sits on) and possibly represent the continuous habitation of the cave site rather part of the migratory group originating from Southern China that is thought to populate Southeast Asia in this period" (from 2-3 thousand years ago)
The past couple of weeks has seen several stories about Neanderthals.
As usual, John Hawks has a wealth of information and insight:
Still on the Neanderthal topic, Julien at A Very Remote Period Indeed reviews the new National Geographic series on Neanderthals. He focuses on the evidence for whether there were hostile or peaceful relations between modern Humans and Neanderthals, on the relative (and complementary) merit of fossil, archaeological and genetic data in interpreting what happened in the past. He closes with a discussion about the reconstruction of a face of a Neanderthal female, discussed on other blogs as well.

Afarensis also discusses a paper about Neanderthal brain size and maturation which argues that Neanderthals grew quickly but matured later than modern humans, suggesting that their overall life history was perhaps slower paced than that of modern humans. Afarensis also discusses the use of marine food resources by Neanderthals, before the most recent piece of evidence came out in PNAS.

Dienekes has his usual dizzying array of posts from a wide variety of topics in evolutionary and molecular anthropology.
I'll just point out the post on Stonehenge and how it has been dated more accurately, and how it has been suggested that it was a healing center.

Razib at GNXP has a great post on a recent NYT article about David Goldstein on the HapMap, selection and race. Many other bloggers (John Hawks, Genetic Future etc...) have also commented on this article. In this article David Goldstein questions the efficiency of the process by which we currently look for the genetic basis for disease (and intelligence).

Finally, let me point you to Kambiz's always excellent and thorough blog. He has recently posted about a new study published in PLoS Genetics that examines how genes involved in the immune system can predict human mating patterns.

Monday, September 22, 2008

Calling for Four Stone Hearth Anthropology Blog Carnival submissions

It's time for the 50th edition of the Four Stone Hearth Anthropology Blog Carnival, so please email your submissions to me at yannatunmdotedu.

The Fourth Stone Hearth is a blog carnival that specializes in anthropology in the widest (American) sense of that word. Here, anthropology is the study of humankind, throughout all times and places, focusing primarily on four lines of research:

  • archaeology
  • socio-cultural anthropology
  • bio-physical anthropology
  • linguistic anthropology

Each one of these subfields is a stone in our hearth.

You need not be a blogger that specializes in anthropology to host or participate, but the posts submitted should relate to some aspect of anthropology.

Are Indians destined to be diabetic?

I came across this interesting commentary paper that discusses whether there any particularities about diabetes risk among Indians (in India that is; living in New Mexico forces me to make that clarification). It discusses diabetes from an evolutionary perspective, as well as the link between mitochondrial function and the etiology of diabetes.

Sunday, September 21, 2008

Comparing genetic admixture methods

Comparison of Statistical Methods for Estimating Genetic Admixture in a Lung Cancer Study of African Americans and Latinos.
Aldrich MC, Selvin S, Hansen HM, Barcellos LF, Wrensch MR, Sison JD, Quesenberry CP, Kittles RA, Silva G, Buffler PA, Seldin MF, Wiencke JK.
Am J Epidemiol. 2008 Sep 12. [Epub ahead of print]
Abstract: A variety of methods are available for estimating genetic admixture proportions in populations; however, few investigators have conducted detailed comparisons using empirical data. The authors characterized admixture proportions among self-identified African Americans (n = 535) and Latinos (n = 412) living in the San Francisco Bay Area who participated in a lung cancer case-control study (1998-2003). Individual estimates of genetic ancestry based on 184 informative markers were obtained from a Bayesian approach and 2 maximum likelihood approaches and were compared using descriptive statistics, Pearson correlation coefficients, and Bland-Altman plots. Case-control differences in individual admixture proportions were assessed using 2-sample t tests and logistic regression analysis. Results indicated that Bayesian and frequentist approaches to estimating admixture provide similar estimates and inferences. No difference was observed in admixture proportions between African-American cases and controls, but Latino cases and controls significantly differed according to Amerindian and European genetic ancestry. Differences in admixture proportions between Latino cases and controls were not unexpected, since cases were more likely to have been born in the United States. Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors.

Monday, September 15, 2008

Admixed EUR-EAS population

Apparently, an admixed population where the admixture event happened 120 generations ago can be useful for admixture mapping, and for studying diseases that differ in prevalence between Europeans and East Asians. For some reason, my university is not giving me full text access which is frustrating.

A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery.
Am J Hum Genet. 2008 Aug 27. [Epub ahead of print]
Xu S, Jin L.
Abstract: Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (F(ST) greater than 0.25, mean F(ST) = 0.43) but small frequency differences (7999 AIMs validated) within both populations (F(ST) less than 0.05, mean F(ST) less than 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations.

Wednesday, September 10, 2008

New issue of Annual Review of Genomics and Human Genetics

There's several interesting review papers in this new issue:

Genetic Predisposition to Breast Cancer: Past, Present, and Future
Clare Turnbull and ­Nazneen Rahman­
In recent years, our understanding of genetic predisposition to breast cancer has advanced significantly. Three classes of predisposition factors, categorized by their associated risks of breast cancer, are currently known. BRCA1 and BRCA2 are high-penetrance breast cancer predisposition genes identified by genome-wide linkage analysis and positional cloning. Mutational screening of genes functionally related to BRCA1 and/or BRCA2 has revealed four genes, CHEK2, ATM, BRIP1, and PALB2; mutations in these genes are rare and confer an intermediate risk of breast cancer. Association studies have further identified eight common variants associated with low-penetrance breast cancer predisposition. Despite these discoveries, most of the familial risk of breast cancer remains unexplained. In this review, we describe the known genetic predisposition factors, expound on the methods by which they were identified, and consider how further technological and intellectual advances may assist in identifying the remaining genetic factors underlying breast cancer susceptibility.
African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping
Michael C. Campbell and ­Sarah A. Tishkoff
Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.
this one looks especially good:
Positive Selection in the Human Genome: From Genome Scans to Biological Significance
Joanna L. Kelley and ­Willie J. Swanson
Vol. 9: 143-160

Here we review the evidence for positive selection in the human genome and its role in human evolution and population differentiation. In recent years, there has been a dramatic increase in the use of genome-wide scans to identify adaptively evolving loci in the human genome. Attention is now turning to understanding the biological relevance and adaptive significance of the regions identified as being subject to recent positive selection. Examples of adaptively evolving loci are discussed, specifically LCT and FOXP2. Comprehensive studies of these loci also provide information about the functional relevance of the selected alleles. We discuss current studies examining the role of positive selection in shaping copy number variation and noncoding genomic regions and highlight challenges presented by the study of positive selection in the human genome.

Wednesday, September 03, 2008

Evolutionary ecology of "hot" in chilies

Green chile season is underway here in New Mexico, so this paper is fitting.
They find that variation in production of Capsaicinoids (hot stuff) is explained by variation in the damage caused by a fungal pathogen of chili the hot stuff protects the plants from pathogens. I assume they discuss other ecological factors (climate, maybe) that explain why other species of plants don't do this also. I bet green chile farmers in New Mexico would know a lot about this since they maintain lines of varying hotness (hot, medium, mild) and have to deal with "pests".

Evolutionary ecology of pungency in wild chilies
Joshua J. Tewksbury, Karen M. Reagan, Noelle J. Machnicki, Tomás A. Carlo, David C. Haak, Alejandra Lorena Calderón Peñaloza, and Douglas J. Levey
PNAS 2008 105:11808-11811
Abstract: The primary function of fruit is to attract animals that disperse viable seeds, but the nutritional rewards that attract beneficial consumers also attract consumers that kill seeds instead of dispersing them. Many of these unwanted consumers are microbes, and microbial defense is commonly invoked to explain the bitter, distasteful, occasionally toxic chemicals found in many ripe fruits. This explanation has been criticized, however, due to a lack of evidence that microbial consumers influence fruit chemistry in wild populations. In the present study, we use wild chilies to show that chemical defense of ripe fruit reflects variation in the risk of microbial attack. Capsaicinoids are the chemicals responsible for the well known pungency of chili fruits. Capsicum chacoense is naturally polymorphic for the production of capsaicinoids and displays geographic variation in the proportion of individual plants in a population that produce capsaicinoids. We show that this variation is directly linked to variation in the damage caused by a fungal pathogen of chili seeds. We find that Fusarium fungus is the primary cause of predispersal chili seed mortality, and we experimentally demonstrate that capsaicinoids protect chili seeds from Fusarium. Further, foraging by hemipteran insects facilitates the entry of Fusarium into fruits, and we show that variation in hemipteran foraging pressure among chili populations predicts the proportion of plants in a population producing capsaicinoids. These results suggest that the pungency in chilies may be an adaptive response to selection by a microbial pathogen, supporting the influence of microbial consumers on fruit chemistry.

Monday, September 01, 2008

European genetic structure

There's been two recent papers that look at the relationship between geography/ethnicity and genetics in Europe. Dienekes has some excellent posts and pictures of these two papers (here, here), as well as at GNXP (here, here, here).

from the Nature paper:
an individual's DNA can be used to infer their geographic origin with surprising accuracy--often to within a few hundred kilometres.
and from a news story:
The map was so accurate that when Novembre's team placed a geopolitical map over their genetic "map", half of the genomes landed within 310 kilometres of their country of origin, while 90% fell within 700 km.
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