Pages

June 23, 2010

PopAffiliator

Luisa Pereira from IPATIMUP and a group of contributors have developing an internet tool to  predict of an individual affiliation to a major population group, based on information from a small set of autosomal STRs. The application can found here: http://cracs.fc.up.pt/popaffiliator

To calculate the assignment of an individual to a major population group (Asia, Eurasia, sub-Saharan Africa) the values in the form bellow should be provided. The range for the allele size was restricted to the ones published in the Short Tandem Repeat DNA Internet DataBase.

The probabilities are computed using a machine learning model built as described in:
Pereira et al (2010)  PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal STR genotype profile. Int J Legal Med. DOI 10.1007/s00414-010-0472-2. (in press)


Abstract
Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on  genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Keywords: Online calculator, genotype,  profile, autosomal STRs, individual affiliation
Conclusion: So the paper concludes that …our confirmation of an 86% accuracy of individual population affiliation for the common 17 STR genotype profiles shows that this well-known forensic set of STRs has also a considerable amount of information for population assignment, besides being excellent for individual identification. We believe that our online calculator will be a valuable tool in helping forensic researchers to predict population affiliation in a specific forensic casework. However, researchers should always be aware that this information is just a first indication, which should be confirmed by other genetic and nongenetic evidence if the population affiliation is really essential to resolve a case. This is especially true for populations that result from a high miscegenation between population groups, such as populations from the Near East or America, for which, in any case, most individuals will have a real mixed ancestry.

June 16, 2010

Does Using Mobile Phones Increase Brain Tumour Risk?

Recently, an interesting paper has been published in the International Journal of Epidemiology about this theme.
 
Brain tumour risk in relation to mobile telephone use: results of the INTERPHONE international case–control study, by The INTERPHONE Study Group, published in International Journal of Epidemiology 2010;39:675–694.
 
Mobile phone (cell phone) use is increasing extraordinarily rapidly worldwide. There are now 4.6 billion mobile phone subscribers worldwide. In many lowand middle-income countries use of cell phones has made communications possible in vast areas lacking cable connections. Increasingly, in high-income countries, cell phones have replaced ‘land lines’ for personal telecommunications. Users of mobile phones are exposed to electromagnetic radiation, which has long been hypothesized to have adverse health effects, including increased risk of cancer.  
 
Research on biological mechanisms of cellular and tissue injury by electromagnetic radiation has been inconclusive, and consequently epidemiological studies have been the principal source of evidence on potential health risks of mobile phone use. Brain tumours have been of particular concern because the electromagnetic radiation generated by mobile phones passes through the brain when the phones are used without a hands-free device. To date, findings of diverse studies on mobile phone use and brain tumour risk have been reported with mixed findings, but with no clear indication of increased risk for cancer. To provide needed evidence on the potential risk of brain cancer associated with mobile phone use, the International Agency for Research on Cancer (IARC) initiated a multi-centre case–control study, the INTERPHONE study, in 1998–99.
 
INTERPHONE is the largest case–control study of mobile phone use and brain tumours yet and includes the largest numbers of users with at least 10 years of exposure. A reduced OR for glioma and meningioma related to ever having been a regular mobile phone user possibly reflects participation bias or other methodological limitations.No elevated OR for glioma or meningioma was observed after first phone use. There were suggestions of an increased risk of glioma, and much less so meningioma, in the highest decile of cumulative call time, in subjects who reported usual phone use on the same side of the head as their tumour and, for glioma, for tumours in the temporal lobe. Biases and errors limit the strength of the conclusions that can be drawn from these analyses and prevent a causal interpretation.
 
Here is the abstract of the paper:
 
Background: The rapid increase in mobile telephone use has generated concern about possible health risks related to radiofrequency electromagnetic fields from this technology.         Methods:  An interview-based case–control study with 2708 glioma and 2409 meningioma cases and matched controls was conducted in 13 countries using a common protocol.   Results:  A reduced odds ratio (OR) related to ever having been a regular mobile phone user was seen for glioma [OR 0.81; 95% confidence interval (CI) 0.70–0.94] and meningioma (OR 0.79; 95% CI 0.68–0.91), possibly reflecting participation bias or other methodological limitations. No elevated OR was observed 510 years after first phone use (glioma: OR 0.98; 95% CI 0.76–1.26; meningioma: OR 0.83; 95% CI 0.61–1.14). ORs were <1.0 for all deciles of lifetime number of phone calls and nine deciles of cumulative call time. In the 10th decile of recalled cumulative call time, 51640 h, the OR was 1.40 (95% CI 1.03–1.89) for glioma, and 1.15 (95% CI 0.81–1.62) for meningioma; but there are implausible values of reported use in this group. ORs for glioma tended to be greater in the temporal lobe than in other lobes of the brain, but the CIs around the lobe-specific estimates were wide. ORs for glioma tended to be greater in subjects who reported usual phone use on the same side of the head as their tumour than on the opposite side.
Conclusions: Overall, no increase in risk of glioma or meningioma was observed with use of mobile phones. There were suggestions of an increased risk of glioma at the highest exposure levels, but biases and error prevent a causal interpretation. The possible effects of long-term heavy use of mobile phones require further investigation.
It can see a comment on this paper in the next link: Comment by Rodolfo Saracci and Jonathan Samet