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Re: [R1b1c_U106-S21] Re: 1,000 Genomes Project paper to be published on Nov 1

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  • Joseph E. Carroll
    If one looks at the actual Nature paper some interpretation is certainly needed. I m not talking about genetic details, but about the printing of the paper.
    Message 1 of 5 , Nov 1, 2012
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      If one looks at the actual Nature paper some interpretation is certainly needed. I'm not talking about genetic details, but about the printing of the paper. One needs to study the text for awhile to understand that strings like
      FIN|[thinsp]||[minus]||[thinsp]|YRI
      means FIN - YRI
      and
      |[lsquo]|clan|[rsquo]|
      means 'clan'
      For me, at least, this was a significant distraction from trying to understand the paper. Is this only me or does this stuff happen all the time in these papers?
      ------------- Joe

      On Nov 1, 2012, at 12:14 AM, GTC wrote:

       

      An here's the abstract and link to the paper:

      ABSTRACT:

      By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.

      http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html

      --- In R1b1c_U106-S21@yahoogroups.com, "GTC" <gtc@...> wrote:
      >
      > 'tis certainly publishing season. 1K Genome paper to be published in Nature tomorrow:
      >
      > http://www.guardian.co.uk/science/2012/oct/31/genomes-project-inventory-human-genetic-variation?CMP=twt_gu
      >


    • GTC
      I noticed those distractions, too, but can t say I ve ever seen it before.
      Message 2 of 5 , Nov 1, 2012
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        I noticed those distractions, too, but can't say I've ever seen it before.

        --- In R1b1c_U106-S21@yahoogroups.com, "Joseph E. Carroll" <jcarroll2@...> wrote:
        >
        > If one looks at the actual Nature paper some interpretation is certainly needed. I'm not talking about genetic details, but about the printing of the paper. One needs to study the text for awhile to understand that strings like
        > FIN|[thinsp]||[minus]||[thinsp]|YRI
        > means FIN - YRI
        > and
        > |[lsquo]|clan|[rsquo]|
        > means 'clan'
        > For me, at least, this was a significant distraction from trying to understand the paper. Is this only me or does this stuff happen all the time in these papers?
        > ------------- Joe
        >
        > On Nov 1, 2012, at 12:14 AM, GTC wrote:
        >
        > > An here's the abstract and link to the paper:
        > >
        > > ABSTRACT:
        > >
        > > By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.
        > >
        > > http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html
        > >
        > > --- In R1b1c_U106-S21@yahoogroups.com, "GTC" <gtc@> wrote:
        > > >
        > > > 'tis certainly publishing season. 1K Genome paper to be published in Nature tomorrow:
        > > >
        > > > http://www.guardian.co.uk/science/2012/oct/31/genomes-project-inventory-human-genetic-variation?CMP=twt_gu
        > > >
        > >
        > >
        >
      • PDSnavely3
        That s the problem with reading these things online. Download the PDF and you ll be fine. Parke
        Message 3 of 5 , Nov 1, 2012
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          That's the problem with reading these things online. Download the PDF and you'll be fine.

          Parke
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