Measurements for Reference Material Characterization Working Group Summary Aug2012

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Measurements for Reference Material Characterization Working Group Summary Aug2012

  1. 1. Measurements  for  Reference   Material  Characteriza4on   Develop  a  consensus  plan  for   experimental  characteriza4on  of   Reference  Materials   Genome  in  a  Bo;le  Working  Group  
  2. 2. Determine  library  prepara4on   protocols  •  Fosmid  and/or  a  BAC  library?  •  Need  to  keep  some  cells  for  plaGorm-­‐specific   DNA  purifica4on  needs  (e.g.,  to  get  high-­‐ molecular-­‐weight  DNA)  •  Include  sequencing  family  members  
  3. 3. Determine  sequencing  plaGorms  •  Illumina   –  300-­‐600bp  inserts   –  3ish  kb  mate-­‐pair   –  2x100bp  reads  on  HiSeq  •  PacBio   –  >10kbish  inserts   –  1x90m  “movies”   –  Who  will  do  it  and  pay  for  it?   –  PacBio  may  be  able  to  create  the  libraries   –  Chris  Mason  to  sequence?  •  Life  Tech   –  5500  data  at  NIST  (1,6,  and  10kb  mate  pairs)   –  Ion  Torrent/Proton  data  (who  to  generate?)  •  Complete   –  Standard  libraries  and  LFR  approach   –  Start  with  cells  •  454?   –  700-­‐800bp  reads?  •  Newer  technologies  –  are  they  used  for  verifica4on/valida4on  only?   –  Oxford  Nanopore?   –  GnuBio?  
  4. 4. “Error  Correc4on”  and  Verifica4on   (not  valida4on)  •  ArrayCGH  and  SNP  Chip  •  OpGen  (or  other  op4cal  mapping  approaches)  •  Targeted  sequencing  
  5. 5. Difficult  to  sequence  regions  •  Characterize  MHC  regions?   –  Use  454?  •  Other  parts  of  the  genome?  •  Approved  CLIA-­‐cer4fied  specific  tests?   –  Highly  mul4plexed  TaqMan/Sanger  style  assay  •  CLIA-­‐cer4fied  whole  exome  data  •  Do  we  pick  very  specific  well-­‐characterized   fosmids?    
  6. 6. Old  vs  New  Data  •  What  new  data  will  we  need  to  generate  on   the  actual  reference  sample?  •  Can  we  use  data  that  currently  exists?  •  Or  generate  data  now  or  vanilla  Coriell   samples?  
  7. 7. Other  Thoughts  •  BAC  by  BAC  approach?  •  Divide  the  genome  into  the  easy,  medium,   and  hard  bits   –  Easy  =  same  call  all  the  4me  on  every  plaGorm  •  How  do  we  account  for  technological/ algorithmic  improvements?  

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