Actividades económicas del corregimiento de Toluca

                                                                         Haplotypes:  CD  or  cd                      Haplotypes:  Cd  or  cD    

A   θ   of   50%   specifies   unlinked   loci   distantly   located   on   the   same   chromosome   or   on   separate  chromosomes,  a  consequence  of  independent  assortment.  A  θ  less  than  50%   means  loci  are  linked  with  a  small  physical  distance  between  them.    

4.1.2  Linkage  models  in  complex  disease      

With  genetically  complex  traits,  there  is  unclear  evidence  of  a  single  locus  effect   with  a  specific  mode  of  inheritance,  such  that  the  unreliability  of  conventional   linkage  analysis  requires  distinct,  model  free  strategies  to  be  created  (Curtis  and   Sham   1995).   For   a   dichotomous   trait   genetic   complexity   is   causative   of   heterogeneity,   involvement   of   multiple   genetic   loci   and   environmental   exposures,  so  requires  a  method  where  the  precise  mechanism  of  disease  can   remain  unknown.  Affected  sibling  pair  methods  were  modelled  based  on  this,   followed   by   likelihood-­‐based   methods   in   which   the   observed   data   is   a   probability  of  θ  of  two  loci  by  way  of  reporting  a  logarithm  (base  10)  of  odds   (LOD)   score.     The   LOD   score   method   was   first   defined   in   parametric   models   where   allele   frequencies,   penetrances   and   inter-­‐marker   genetic   distances   (for   multipoint   analyses)   were   required   (Kruglyak,   Daly   et   al.   1996).   This   model   is   successful   where   a   clear   inheritance   pattern   is   observed,   for   example,   autosomal  dominant  or  recessive.  A  non-­‐parametric  model  (NPL,  or  model  free)  

C

D

c

d

C

D

c

d

is  used  for  disorders  of  unclear  inheritance  and  variable  penetrance.  It  assumes   that  linked  loci  shared  by  affected  relative  pairs  share  more  alleles  identical  by   descent  (IBD)  at  the  marker  locus  than  expected  by  chance  only  (Risch  1990).   The  test  looks  for  chromosomal  segments  shared  between  affected  individuals   by  distinguishing  IBD  alleles  from  identical  by  state  (IBS)  alleles.  Alleles  IBS  may   look   identical   but   their   common   ancestor   cannot   be   demonstrated,   whereas   IBD   alleles   can   be   (Ott   and   Bhat   1999).   Only   genotypic   information   from   the   affected   individuals   is   used   for   analysis,   following   the   assumption   that   the   affected   phenotype   is   more   likely   to   be   associated   with   the   presence   of   the   disease  allele.  Unaffected  individuals  are  used  to  provide  genotypic  information   on   any   un-­‐typed   parents.   Pedigree   relationships,   allele   frequencies   and   genotypes  of  all  individuals  are  needed  for  NPL.    

The  linkage  experiment  in  this  chapter  differs  to  other  combined  exome/whole   genome   sequencing   and   linkage   studies   in   monogenic   disease.   For   monogenic/Mendelian  diseases,  researchers  have  combined  exome  sequencing   in  pedigrees  where  positive  linkage  has  been  identified  to  find  the  causal  gene   (Louis-­‐Dit-­‐Picard,   Barc   et   al.   2012),   and   this   has   been   successful   for   many   autosomal  dominant  (Johnson,  Mandrioli  et  al.  2010;  Wang,  Yang  et  al.  2010),   recessive  (Bilguvar,  Ozturk  et  al.  2010)  and  quantitative  traits  (Bowden,  An  et  al.   2010).   Linkage   has   also   been   used   in   complex   traits.   Recently,   rare   missense   mutations   in   CARD14   have   been   implicated   in   psoriasis,   using   a   variety   of   strategies,   some   similar   to   ones   taken   in   this   study.   Linkage   was   identified   in   PSORS2   chromosomal   region,   containing   CARD14.   Target   capture   and   sequencing   then   identified   gain-­‐of-­‐function   mutations   in   CARD14   segregating   with  disease  (Bertin,  Wang  et  al.  2001;  Jordan,  Cao  et  al.  2012).  For  a  complete   mutation   profile   of   the   gene,   exon   4   of   CARD14   (where   most   clustering   rare   variants   were   located)   was   sequenced   in   1,856   cases   and   882   controls   of   European   ancestry   and   the   entire   case   (6,000)   control   (4,000)   cohort   was   genotyped  to  establish  allele  frequencies  of  all  rare  CARD14  variants.  This  study   was  successful  in  finding  a  potential  causal  gene  through  linkage,  establishing   that   mutations   in   the   gene   also   occurred   outside   of   families   with   a   genetic   predisposition  and  that  harbouring  rare  variants  are  likely  to  confer  a  high  risk  

for  the  phenotype  (Jordan,  Cao  et  al.  2012).  The  study  is  a  successful  one  for   complex   disease   and   mirrors   a   monogenic   disease   finding   in   that   one   gene   (others  genes  also  contribute  to  psoriasis  susceptibility)  containing  rare  variants   are   possibly   detrimental   to   disease   risk.   Furthermore,   monogenic   forms   of   complex   disease,   such   as   in   cutaneous   lupus   erythematosus,   where   an   autosomal   dominant   inheritance   pattern   was   described   by   findings   from   a   genome-­‐wide   linkage   search   in   a   large   kindred   (Lee-­‐Kirsch,   Gong   et   al.   2006)   provides  further  evidence  of  how  linkage  can  identify  a  single  gene  responsible   for  disease  susceptibility.    

In  this  chapter,  linkage  has  been  performed  in  large  multigenerational  coeliac   pedigrees  using  a  set  of  common  and  rare  SNP  markers  from  the  Immunochip   array.   In   order   the   link   this   information   with   the   exome   dataset   of   75   CD   subjects,  genomic  regions  under  the  linkage  peaks  were  then  inspected  for  rare   exome   variants   from   the   exome   sequencing   dataset   (data   from   Chapter   3,   phase  two),  in  the  hope  of  finding  segregating  variants  in  one  or  more  genes  to   take  forward  for  targeted  resequencing.    

4.2  Aims  and  hypotheses    

Specific  aims  and  hypothesis  for  three  analyses  are  outlined  below:    

i) Linkage   analysis   –   the   aim   is   to   perform   NPL   analysis   on   multiply  

affected  families  using  196,524  Immunochip  SNP  markers,  to  infer  if   a  rare  coding  disease  risk  variant  is  shared  by  affected  individuals  in   the   same   pedigree   under   a   linkage   peak.   The   linkage   information   here  provides  knowledge  of  shared  chromosomal  regions,  which  can   be   linked   to   exome   sequencing   data   to   search   for   rare   segregating   variants   carrying   a   disease   risk.   The   hypothesis   is   if   common   SNPs   are   segregating   more   than   expected   by   chance   then   there   will   be   some  rare  functional  variants  under  that  peak  also;  the  rare  variant   will  be  IBD  in  affected  individuals.