A genome blogger manifesto

Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger

CLU: A new algorithm for EST clustering

BACKGROUND: The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering, the process of grouping of original fragments according to their annotation, similarity to known genomic DNA or each other. Clustered EST data, accumulated in databases such as UniGene, STACK and TIGR Gene Indices have proven to be crucial in research areas from gene discovery to regulation of gene expression. RESULTS: We have developed a new nucleotide sequence matching algorithm and its implementation for clustering EST sequences. The program is based on the original CLU match detection algorithm, which has improved performance over the widely used d2_cluster. The CLU algorithm automatically ignores low-complexity regions like poly-tracts and short tandem repeats. CONCLUSION: CLU represents a new generation of EST clustering algorithm with improved performance over current approaches. An early implementation can be applied in small and medium-size projects. The CLU program is available on an open source basis free of charge. It can be downloaded fro

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicine

Background: Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. Methods: Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. Results: Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited 10 participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes. Conclusions: Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine

Comparative influences of parents, teachers and migrant workers on students\u27 moral values in three Fe Y Alegria schools in Peru

The study seeks to compare the influences of parents, teachers, and migrant workers on the moral values of high school students in three Fe y Alegria Schools in Peru. Two of these are the Fe y Alegria 16 and Fe y Alegria 30 which are located in the portland and where the participant graduating working students are closely associated with migrant workers. The third is F y Alegria 19, situated in the upland and which is not a converging place for migrant workers, unlike the communities in the portland.The study covered the first and fifth year students of the participant schools and their respective parents and teachers during the school year 2001. The study also included migrant co-workers with whom the fifth year working students closely associate with.Data were gathered through questionnaires and interviews. Parents and teachers validate the responses on the self-report of their children.This is a descriptive-comparative-correlational study, which made use of a cross-sectional survey to assess the moral values of students, teachers, parents and migrant workers and determines the extent to which the values of the students were influenced by their teachers, parents and migrant workers. Correlational and regression analysis were employed to determine the proportions in the variance of the students\u27 moral values that may be attributed to those of parents, teachers, and migrant workers.The study revealed the following significant findings: Across the three participant schools, the students were all at the prizing level of valuing across the nine values: love of God, respect for the dignity of man, love of truth, love of peace, respect for property, family solidarity, respect for life, freedom and justice, and work. The only exceptions were for the values: love of truth and love of peace for Fe y Alegria 16 respect for property for Fe y Alegria 19 and love of God for Fe y Alegria 30 where the fifth-year students were only at the choosing level.The teachers as well as the parents across the three participant schools were generally at the prizing level of valuing.Across the two schools in the portland, the migrant workers whom graduating students associate with were at the prizing level across the nine values.In general, length of exposure to the participant schools, particularly to the teachers did not make a difference in the levels of valuing of the fifth-year students.Across the schools, the students\u27 levels of valuing were significantly correlated with those of their parents for the values: love of God, respect for the dignity of man, respect for property, family solidarity, respect for life, freedom and justice, and work. Congruency in their values implies value transmission. The levels of valuing of the students do not vary with the civil status of their parents (legally or not).Exposure of the graduating working students to the migrant workers made a difference in their levels of valuing for two values: love of God and family solidarity.In sum, the parents had the greatest influence on the moral values of their children followed by both teachers and the migrant workers, the last, with respect only to the working, fifth-year students