'Era of Personal Genomics May Have to Wait'
Genes Show Limited Value in Predicting Diseases
By NICHOLAS WADE
April 15, 2009
The era of personal genomic medicine may have to wait. The genetic analysis of common disease is turning out to be a lot more complex than expected.
Since the human genome was decoded in 2003, researchers have been developing a powerful method for comparing the genomes of patients and healthy people, with the hope of pinpointing the DNA changes responsible for common diseases.
This method, called a genomewide association study, has proved technically successful despite many skeptics’ initial doubts. But it has been disappointing in that the kind of genetic variation it detects has turned out to explain surprisingly little of the genetic links to most diseases.
A set of commentaries in this week’s issue of The New England Journal of Medicine appears to be the first public attempt by scientists to make sense of this puzzling result.
Read article.
Government Report Calls for
Overhaul of Forensic Science
SUMMARY: Scores of talented and dedicated people serve the forensic science community, performing vitally important work. However, they are often constrained by lack of adequate resources, sound policies, and national support. It is clear that change and advancements, both systematic and scientific, are needed in a number of forensic science disciplines to ensure the reliability of work, establish enforceable standards, and promote best practices with consistent application. Strengthening Forensic Science in the United States: A Path Forward provides a detailed plan for addressing these needs and suggests the creation of a new government entity, the National Institute of Forensic Science, to establish and enforce standards within the forensic science community.
The benefits of improving and regulating the forensic science disciplines are clear: assisting law enforcement officials, enhancing homeland security, and reducing the risk of wrongful conviction and exoneration. Strengthening Forensic Science in the United States gives a full account of what is needed to advance the forensic science disciplines, including upgrading of systems and organizational structures, better training, widespread adoption of uniform and enforceable best practices, and mandatory certification and accreditation programs.
While this book provides an essential call-to-action for congress and policy makers, it also serves as a vital tool for law enforcement agencies, criminal prosecutors and attorneys, and forensic science educators.
Sexy sons and sexy daughters: the influence of parents' facial characteristics on offspring
I.e., Why do sexy parents produce sexy daughters, but not sexy sons?
R. Elisabeth Cornwell, and David I. Perrett
Animal Behaviour doi: 10.1016/j.anbehav.2008.07.031
Abstract
Choosing a mate to maximize fitness underlies all sexual selection theories. Key to understanding mate choice is the inheritance of particular traits. Using family photos, we evaluated the predictions made by sexual selection theories for human mate choice concerning the inheritance of facial characteristics and assortment in facial appearance of parents. We found that both fathers' and mothers' attractiveness predicted the facial attractiveness of daughters: ‘sexy daughters’. Fathers and sons were related to each other in facial masculinity but not attractiveness, providing only partial evidence for ‘sexy sons’. Mothers and sons did not relate in masculinity–femininity; neither did fathers and daughters. Parents were similar in attractiveness but masculine men were not partnered to feminine women. Our findings support some predictions of Fisherian selection processes and ‘good genes’ theory but are less consistent with ‘correlated response theory’ and the immunocompetence handicap principle.
Writes blogger Dienekes Pontikos: "Interestingly, this may solve the paradox of non-inheritance of male attractiveness. While sexy parents have sexy daughters, apparently they don't tend to have especially attractive sons. This may be due to male-expressed maternally inherited traits. Such traits don't make their mothers' attractive (they are male expressed), and they are not inherited from their fathers.
Climate Change Helped to Cause Downfall
Of Chinese Tang and Classic Maya Civilizations
A Test of Climate, Sun, and Culture Relationships from an 1810-Year Chinese Cave Record
Pingzhong Zhang et al.
Science 7 November 2008:
Vol. 322. no. 5903, pp. 940 - 942
A record from Wanxiang Cave, China, characterizes Asian Monsoon (AM) history over the past 1810 years. The summer monsoon correlates with solar variability, Northern Hemisphere and Chinese temperature, Alpine glacial retreat, and Chinese cultural changes. It was generally strong during Europe's Medieval Warm Period and weak during Europe's Little Ice Age, as well as during the final decades of the Tang, Yuan, and Ming Dynasties, all times that were characterized by popular unrest. It was strong during the first several decades of the Northern Song Dynasty, a period of increased rice cultivation and dramatic population increase. The sign of the correlation between the AM and temperature switches around 1960, suggesting that anthropogenic forcing superseded natural forcing as the major driver of AM changes in the late 20th century.
My genome. So what.
According to an editorial in Nature with this title, recent additions to the growing database of personal genomes dictate that research be undertaken on how people are using the new genetic clues about their health.
Human genes are multitaskers
Up to 94% of human genes can generate different products.
Heidi Ledford
Nature 456, 7248 (5 November 2008)
Almost all human genes can generate more than one product. Although people often struggle to master more than one discipline, our genes are accomplished polymaths. Genome-wide surveys of gene expression in 15 different tissues and cell lines have revealed that up to 94% of human genes generate more than one product....
Related article in Science
Parsing the Genetics of Behavior
Constance Holden
It takes more than a gene, or even a few genes, to make a personality trait. But which ones?
Genomics takes hold in Asia
Genome Institute of Singapore head Edison Liu talks about how to make pan-Asian genomics research projects work.
David Cyranoski
Recruited in 2001 from the US National Cancer Institute, Edison Liu was the first big international catch for Singapore's burgeoning Biopolis research hub. He still heads the Genome Institute of Singapore there and had the leading role in the Pan-Asian SNP Initiative, an effort to compare subtle genetic variations across Asian populations. He is currently chairman of Singapore's Health Sciences Authority and president of the Human Genome Organisation (HUGO). He spoke with Nature's David Cyranoski about how to make pan-Asian genomics research projects work. . . .
Related story in Science
PERSONAL GENOMICS:
Number of Sequenced Human Genomes Doubles
Elizabeth Pennisi
Science 7 November 2008: 838
How to get the most from a gene test
New tools squeeze more research out of personal genomics.
Erika Check Hayden
Published in Nature 456, 11, 5 November 2008
According to two commercial gene-testing services — 23andMe and deCODEme — US Army medic Timothy Richard Gall of Fort Belvoir, Virginia, has a higher-than-average risk of basal cell carcinoma, type 2 diabetes and psoriasis. But much more enlightening than these results, which cost Gall more than $1,400, was a free online program called Promethease that he used to further analyse the data. By offering more in-depth information and interpreting of more of his genetic variants, Promethease "gives a much more realistic view of the usefulness of the information", Gall says.
Start-ups and services such as Promethease are now developing ways to improve the limited value of information provided by personal genomics companies for consumers and scientists alike . . . . Read Article.
$5,000 genome next year, company promises
Complete Genomics is about to release fast, cheap sequencing into a competitive market.
Erika Check Hayden
Published online 6 October 2008 in Nature magazine
The era of the $1,000 genome has arrived. That's the claim from Complete Genomics, a young company based in Mountain View, California, that revealed today that it plans to sequence 1,000 human genomes next year — and 20,000 in 2010.
Article on Genetic Diversity of Native Americans
Declared Most Viewed in Online PLoS Genetics
One Surprising Finding the Role of Circum-Pacific Population Movements
Citation: Wang S, Lewis CM Jr, Jakobsson M, Ramachandran S, Ray N, et al. (2007) Genetic Variation and Population Structure in Native Americans. PLoS Genet 3(11): e185. doi:10.1371/journal.pgen.0030185
Abstract
We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.
Author Summary
Studies of genetic variation have the potential to provide information about the initial peopling of the Americas and the more recent history of Native American populations. To investigate genetic diversity and population relationships in the Americas, we analyzed genetic variation at 678 genome-wide markers genotyped in 29 Native American populations. Comparing Native Americans to Siberian populations, both genetic diversity and similarity to Siberians decrease with geographic distance from the Bering Strait. The widespread distribution of a particular allele private to the Americas supports a view that much of Native American genetic ancestry may derive from a single wave of migration. The pattern of genetic diversity across populations suggests that coastal routes might have been important during ancient migrations of Native American populations. These and other observations from our study will be useful alongside archaeological, geological, and linguistic data for piecing together a more detailed description of the settlement history of the Americas.
It's Not Just in the Genes
A major new multidisciplinary study in the October issue of Genetics concludes that human variation and evolution was sped by learned behavior and culture, and that molecular variation and gene expression -- long thought to be the primary driving forces -- work in tandem with environment to shape human beings. The article is titled, "Explaining Human Uniqueness: Genome Interactions with Environment, Behaviour and Culture," and is contributed by Ajit Varki, Daniel H. Geschwind and Evan E. Eichler, all at the Center for Academic Research and Training in Anthropogeny (CARTA). "Rejecting any 'genes versus environment' dichotomy," they write, "we consider genomme interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture -- perhaps relaxing allowable thresholds for large-scale genomic diversity."
The new approach in evolutionary theory overcomes an oft-voiced criticism that the rate of spontaneous, random mutation is too slow to accomodate the changes in species, especially quantum leaps.
"Anthropogeny" is a newly dubbed field that seeks to explain the origin of humans.
High Density SNP Testing Is Transferred from Medicine to Forensics
An article titled "DNA has Nowhere to Hide" in October's Genetics (published by Nature magazine) describes how the technology of high-density SNP genotyping that has opened up vast horizons in genome-wide association studies is now transforming forensic science. The new techniques can detect trace quantities of a suspect's DNA in a complex mixture containing hundreds of other individuals, substituting a rifle for what was previously a shotgun approach to crime scene evidence. High-density SNP testing uses allele profile frequencies -- somewhat as a DNA fingerprint and population statistics are used to infer ethnicity in our DNA Fingerprint Test.
Population Geneticists and Forensic Scientists Construct the Genetic Map of Europe
A review by writer Nicholas Wade in the Science section of the New York Times, August 13, 2008, summarizes the recent work by Dr. Manfred Kayser and others published in Current Biology revealing the genetic relationship between 23 populations in Europe. With few exceptions, the DNA landscape with its clusters and clines and genetic distances follows the political and linguistic boundaries of European countries. Finns were found to be very different from everybody else, and the Italian population was shown to be extremely stable over the ages. Who would ever want to leave Italy anyway?