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SUMMARY:SNP arrays in heterogeneous tissue: highly accurate collection of 
 both germline and somatic genetic information from unpaired single tumor s
 amples. - Oscar Rueda (Cancer Research UK\, Cambridge Research Institute)
DTSTART:20100322T153000Z
DTEND:20100322T163000Z
UID:TALK23693@talks.cam.ac.uk
CONTACT:Stefan Gräf
DESCRIPTION:\nhttp://www.ncbi.nlm.nih.gov/pubmed/18355774\n\n\nAm J Hum Ge
 net. 2008 Apr\;82(4):903-15. Epub 2008 Mar 20.\n\n\nSNP arrays in heteroge
 neous tissue: highly accurate collection of both\ngermline and somatic gen
 etic information from unpaired single tumor\nsamples.\n\n\n\nAssié G\, La
 Framboise T\, Platzer P\, Bertherat J\, Stratakis CA\, Eng C.\n\n\n\nGenom
 ic Medicine Institute\, Lerner Research Institute\, Cleveland Clinic\nFoun
 dation\, Cleveland\, Ohio 44195\, USA.\n\n\n\n\nSNP arrays provide reliabl
 e genotypes and can detect chromosomal aberrations\nat a high resolution. 
 However\, tissue heterogeneity is currently a major\nlimitation for somati
 c tissue analysis. We have developed SOMATICs\, an\noriginal program for a
 ccurate analysis of heterogeneous tissue samples.\nFifty-four samples (42 
 tumors and 12 normal tissues) were processed through\nIllumina Beadarrays 
 and then analyzed with SOMATICs. We demonstrate that\ntissue heterogeneity
 -related limitations not only can be overcome but can\nalso be turned into
  an advantage. First\, admixture of normal cells with\ntumor can be used a
 s an internal reference\, thereby enabling highly\nsensitive detection of 
 somatic deletions without having corresponding normal\ntissue. Second\, th
 e presence of normal cells allows for discrimination of\nsomatic from germ
 line aberrations\, and the proportion of cells in the tissue\nsample that 
 are harboring the somatic events can be assessed. Third\,\nrelatively earl
 y versus late somatic events can also be distinguished\,\nassuming that la
 te events occur only in subsets of cancer cells. Finally\,\nadmixture by n
 ormal cells allows inference of germline genotypes from a\ncancer sample. 
 All this information can be obtained from any cancer sample\ncontaining a 
 proportion of 40-75% of cancer cells. SOMATICs is a\nready-to-use open-sou
 rce program that integrates all of these features into\na simple format\, 
 comprehensively describing each chromosomal event.
LOCATION:Room 132\, CRI
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