Gene gain and loss: aCGH ISA CGH

Genomic copy num ber
es tim ation
Sm oothing: variation of th e Ad ap tive Weigh ts Sm ooth in g m eth od im p lem en ted in th e p rogram
GLAD.
Binary s egm entation: ch ecks wh eth er every sin gle p oin t in th e d ata set is a breakp oin t in an
iterative way. It u ses a p erm u tation d istribu tion to test for m ean d ifferen ces between grou p s
d rawin g robu st in feren ces th at d o n ot rely u p on an y m od el of th e d ata
Regres s ion: u ses som e ch aracteristics of lin ear regression of in ten sity m easu re on p osition
alon g th e gen om e. Su ch a regression lin e h as slop e close to z ero wh en fitted in region s with
h om ogen eou s in ten sity levels bu t th e slop e d iffers form z ero wh en in ten sity m easures on
th e left- h an d sid e are h igh er or lower th an in ten sity m easu res in th e righ t- h an d sid e. Given
th e p oin ts of in ten sity m easu rem en ts ord ered by th eir p osition in th e
ch rom osom e, ou r p roced u re fits a regression lin e for each N con secu tive p oin ts. Th u s a vector
of slop es equ ivalen t in som e way to a d erived cu rve of th e origin al d ata is obtain ed .
t- test is u sed to to id en tify th e slop e- p eaks th at are big en ou gh to in d icate a break- p oin t in
th e in ten sity levels.
Is ow indow : tries to id en tify bord ers between region s with a sign ifican t ch an ge in th e valu es
of in ten sity of h ybrid iz ation . Given th e in ten sity m easu rem en t p oin ts from th e array ord ered
by th eir p osition in th e ch rom osom e, a first step fin d s th ose th at are good can d id ates of
bein g su ch bord ers. Rou gh ly sp eakin g, a p oin t will be a good can d id ate if th e p - valu e of
a t- test com p arin g som e close p oin ts located at its left an d righ t n eigh borh ood s is low
en ou gh .
Th e bin ary segm en tation m eth od u ses th e global d istribu tion of th e d ataset wh ile th e oth ers
are m ore based on th e local d istribu tion s of th e p oin ts.