Article

The Personal Genome Project

Molecular Systems Biology (Impact Factor: 14.1). 02/2005; 1(1):2005.0030. DOI: 10.1038/msb4100040
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Available from: George Church, Mar 20, 2015
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    • "Apart from this, genotype information at sample level for a large number of individuals who participated in various genotype to phenotype association studies are available as part of the dbGAP (Mailman et al. 2007), though many of the datasets are not freely available but are secured under specific license restrictions. The personal genome project (PGP) (Church 2005) is a recent initiative spearheaded to create a publicly available repository of personal genomes for volunteers who would reveal their identity and genome to the public. It has been argued that such an approach with systematic collection of phenotypic correlates would be a valuable tool for research. "
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    ABSTRACT: Advances in technology have enabled understanding genetic makeup of individuals at a clinical timescale and affordable cost. This has brought about new challenges in the ability to decipher the information content of the genome and be able to act on relevant evidence especially in an environment where the information and evidence is dynamic. The availability of genomic sequences of identifiable individuals in public domain could have far-reaching advantages and open up interesting opportunities, not only to the individual, but also towards understanding the genomic biology. Nevertheless, a framework of social acceptance and regulatory oversight might add to the widespread acceptability of such an approach.The recent years have seen phenomenal developments in the scale, throughput and consequential unprecedented reduction in the cost of genome sequencing. This change has largely been brought about by an entire gamut of technologies which have enabled miniaturization, large-scale paralle ...
    Journal of Genetics 12/2014; 93(3):917-20. DOI:10.1007/s12041-014-0451-3 · 1.01 Impact Factor
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    • "and http://www.pgpstudy.org/ [Church, 2005; Lunshof et al., 2010]. Integrated datasets of linked genomic and phenotypic data on each individual are made available publicly as a free resource for the research community and to the study participants themselves. "
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    ABSTRACT: In the traditional medical genetics setting, metabolic disorders, identified either clinically or through biochemical screening, undergo subsequent single gene testing to molecularly confirm diagnosis, provide further insight on natural disease history, and inform on disease management, treatment, familial testing, and reproductive options. For decades now, this process has been responsible for saving many lives worldwide. Only recently, though, has it become possible to move in the opposite direction by starting with an individual's whole genome or exome, and, guided by this data, study more minor perturbations in the absolute values and substrate ratios of clinically important biochemical analytes. Genomic individuality can also be used to guide more detailed phenotyping aimed at uncovering milder manifestations of known metabolic diseases. Metabolomic phenotyping in the Personal Genome Project for our first 200+ participants-all of whom are scheduled to have full genome sequence at more than 40× coverage available by May 2012-is aimed at uncovering potential subclinical and preclinical disease states in carriers of known pathogenic mutations and in lesser known rare variants that are protein predicted to be pathogenic. Our initial focus targets 88 genes involved in 68 metabolic disturbances with established evidence-based nutritional and/or pharmacological therapy as part of standard medical care.
    Human Mutation 05/2012; 33(5):809-12. DOI:10.1002/humu.22073 · 5.05 Impact Factor
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    • "The rules of variation described here can be used to assess any study related to human polymorphisms such as the PGP (Church, 2005), the 1000 Genomes Project (SoRelle, 2008; Via et al., 2010), multiple cohort studies like ARIC, Oregon-SUDS, CHS, etc. (Arking et al., 2010), and for studies related to any other organism, for example in plants (Ruiz-Rojas et al., 2010), cattle (Snelling et al., 2010), birds (van Bers et al., 2010), bacteria (Huang et al., 2008), etc. "
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    ABSTRACT: General guidelines for the molecular basis of functional variation are presented while focused on the rotating circular genetic code and allowable exchanges that make it resistant to genetic diseases under normal conditions. The rules of variation, bioinformatics aids for preventative medicine, are: (1) same position in the four quadrants for hydrophobic codons, (2) same or contiguous position in two quadrants for synonymous or related codons, and (3) same quadrant for equivalent codons. To preserve protein function, amino acid exchange according to the first rule takes into account the positional homology of essential hydrophobic amino acids with every codon with a central uracil in the four quadrants, the second rule includes codons for identical, acidic, or their amidic amino acids present in two quadrants, and the third rule, the smaller, aromatic, stop codons, and basic amino acids, each in proximity within a 90 degree angle. I also define codifying genes and palindromati, CTCGTGCCGAATTCGGCACGAG.
    Journal of Theoretical Biology 04/2010; 264(3):711-21. DOI:10.1016/j.jtbi.2010.03.046 · 2.30 Impact Factor
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