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Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

Human Subjects Research Protocol
Project title: Clinical  Center  Genomics  Opportunity  Secondary  Findings  Analysis  and  Return

Draft/version number: August  1,  2015

NHGRI Protocol Number: T-­‐HG-­‐0122

Principal Investigator: Leslie  G.  Biesecker

Title/Section/Branch/Institute: Head,  Clinical  Genomics  Section,  Chief,  Medical  Genomics  and  
Metabolic  Genetics  Branch,  NHGRI

Study Staff Roster
Medical Advisory Investigator: N/A

Associate Investigator(s):
Barbara  B.  Biesecker,  PhD,  MS,  NHGRI  Social  and  Behavioral  Research  Branch  
Jennifer  Johnston,  PhD,  NHGRI  Clinical  Genomics  Section  
James  Mullikin,  PhD,  NHGRI  –  NIH  Intramural  Sequencing  Center  
Julie  Sapp,  ScM,  NHGRI  Medical  Genomics  and  Metabolic  Genetics  Branch  

Collaborating Institutions: N/A

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

Table  of  Contents  
Main  Protocol  (Sections)   Page  
List  of  Abbreviations   4  
1  Precís   4  
2  Objectives  &  Specific  Aims   5  
3  Brief  Rationale  and  Background   5  
4  Description  of  Study  Design   8  
5  Description  of  Procedures   10  
6  Description  of  Study  Population   13  
7  Description  of  Statistical  Considerations   14  
8  Description  of  Potential  Benefits   15  
9  Description  of  Potential  Harms   16  
10  Privacy  and  Confidentiality   18  
11  Assessment  of  Risk/Benefit  Ratio   19  
12  Unanticipated  Problems/Adverse  Events   19  
13  Alternatives  to  Participation   21  
14.  Description  of  Consent  Process   21  
App  1  Adult  patient  with  positive  results  survey    
App  2  Parent  of  patient  with  positive  result  survey    
App  3  Adult  patient  with  negative  result  survey    
App  4  Parent  of  patient  with  negative  result  survey    
App  5  Example  Positive  Report    
App  6  Example  Negative  Report    
App  7  CLIA  Application    
App  8  Variant  Analysis  Standard  Oper.  Procedure    
App  9  Quality  Assessment  Plan    
App  10  NISC  CLIA  MPG  Validation    
App  11  DNA  Quality  Assessment    
App  12  List  of  CCGO  Approved  Investigators    
App  12  CCGO  Consent  Form    
App  13  Fact  Sheet    
App  14  Flowchart  of  Procedures    
App  15  Interview  Guide    
App  16  Assent  Form    
App  17  Genes  Currently  Reported  as  Secondary  Findings    
App  18  CCGO  Advisory  Group    

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

List of Abbreviations (as applicable)
AE     Adverse  Event/Adverse  Experience  
CCGO     Clinical  Center  Genomics  Opportunity  
CFR     Code  of  Federal  Regulations  
CLIA     Clinical  Laboratory  Improvement  Amendment  of  1988  
COI     Conflict  of  Interest  
CLIA     Clinical  Laboratory  Improvements  Amendment  
CRADA  Cooperative  Research  and  Development  Agreement  
DAC     Data  Access  Committee  
dbGaP     Database  of  Genotypes  and  Phenotypes  
DUC     Data  Use  Certificate  
DHHS     Department  of  Health  and  Human  Services  
DSMB     Data  Safety  and  Monitoring  Board  
FWA     Federal  Wide  Assurance  
GCP     Good  Clinical  Practice  
GINA     Genetic  Information  Nondiscrimination  Act  
GWAS     Genome-­‐Wide  Association  Study  
HIPAA   Health  Insurance  Portability  and  Accountability  Act  
ICF     Informed  Consent  Form  
IRB     Institutional  Review  Board  
MPG     Most  Probable  Genotype  
MTA     Material  Transfer  Agreement  
N     Number  (typically  refers  to  number  of  subjects/sample  size)  
NHGRI  National  Human  Genome  Research  Institute,  NIH  
NGS     Next  Generation  Sequencing  
NIH     National  Institutes  of  Health  
NISC     NIH  Intramural  Sequencing  Center  
OHRP     Office  for  Human  Research  Protections  
OHSRP  Office  of  Human  Subjects  Research  Program  
PHI     Protected  Health  Information  
PI     Principal  Investigator  
PK     Pharmacokinetics  
QA     Quality  Assurance  
QC     Quality  Control  
SAE     Serious  Adverse  Event/Serious  Adverse  Experience  
SOP     Standard  Operating  Procedure  
UP     Unanticipated  Problem  
UPnonAE   Unanticipated  Problem  that  is  not  an  Adverse  Event  

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

1. Precis: (In 400 words or fewer, describe the study objectives, population, design, and
outcome measures)
The   implementation   of   genome   and   exome   sequencing   creates   challenges   and   opportunities.  
We  propose  to  pilot  the  implementation  of  exome  sequencing  for  incidental/secondary  findings  
in   the   NIHCC   and   measure   its   perceived   utility.   Through   the   Clinical   Center   Genomics  
Opportunity   (CCGO),   we   have   offered   to   investigators   in   10   institutes   access   to   exome  
sequencing   for   gene   identification   studies   of   their   rare   disease   patients.   We   are   using   this  
research   resource   to   increase   the   research   use   of   genomics   outside   NHGRI,   to   begin   to   build  
the   NIHCC   clinical   laboratory   infrastructure   to   support   genome   scale   data,   and   to   familiarize  
clinicians  in  the  NIHCC  with  genomic  medicine.  To  accomplish  these  clinical  goals,  we  propose  
to   generate   exome   data   in   a   CLIA-­‐compliant   environment   at   NISC   and   use   those   data   to  
evaluate  patients  for  the  presence  of  variants  in  genes  recommended  by  the  American  College  
of   Medical   Genetics   and   Genomics   policy   on   incidental   and   secondary   findings,   which   is  
consistent   with   the   policy   recommendations   of   the   Presidential   Commission   for   the   Study   of  
Bioethical   Issues.   Thus,   the   exome   data   will   have   a   dual   purpose   –   the   entire   dataset   will   be  
available  for  research  to  the  ordering  principal  investigator  and  a  small  subset  of  those  data  will  
be   used   to   test   our   ability   to   identify   high   risk   variants   for   actionable   disorders,   coupled   to  
knowledgeable   clinical   interpretation,   genetic   counseling   and   referral   for   ongoing   care.   The  
human   subjects   review   and   approval   of   the   gene   identification   research   use   of   the   exome   data  
will  be  addressed  by  the  approved  PIs  through  their  own  IRBs.  Here,  we  are  requesting  review  
of   the   generation   of   the   sequence   data   by   next-­‐gen   technology   for   secondary   variants,   a  
bioinformatic   pipeline   for   filtering   those   variants,   manual   curation   of   the   variants,   and  
behavioral   follow   up   of   participants   who   receive   secondary   findings   results   to   measure   their  
utility  and  perceived  value.  Additional  and  critical  Specific  Aims  are  to  measure  the  efficacy  by  
which   we   communicate   1)   to   the   participants   who   do   not   receive   a   secondary   finding   the  
concept  that  a  secondary  findings  analysis  is  not  a  substitute  for  an  indicated  single  gene  and  2)  
explore  the  interpretation  and  outcomes  of  results  for  those  who  receive  a  secondary  finding.    
2. Objectives and specific aims. (List the objectives concisely; whenever possible, state
objectives as hypotheses.)
1. Pilot  a  process  for  exome  sequencing  of  DNA  from  research  participants  that  conforms  
to  CLIA  regulations  for  the  generation  of  clinically  useful  results.    
2. Understand  participant  perceptions  of  the  identification,  or  not,  of  a  secondary  finding  
Specific  Aims  
1. Generate   sequence   data   from   research   patient   samples,   filter   them   using  
bioinformatics,   and   manually   curate   them   to   generate   clinically   valid   secondary   findings  
2. Measure  the  frequency  and  distribution  of  secondary  findings  in  1,000  exome  samples.  
3. Explore   participant   understanding   and   response   to   a   positive   secondary   finding  
including   determination   of   whether   they   shared   it   with   family   with,   and   what,   if   any,  
health  care  interventions  they  undertook.  

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

4. Determine   if   individuals   who   receive   a   negative   secondary   findings   report   accurately  
understand  the  limitations  of  this  analysis.    
3. Brief Rationale and Background: Write a brief [no more than 5 pages in length] summary
of the clinical background, limits of current knowledge, and significance of this protocol. For
background on drugs and devices, cite animal studies, prior experience in humans, and
discuss potential toxicities. Include up to 20 key references.
The   NHGRI   has   committed   to   the   deployment   and   distribution   of   genomic   analysis   to  
investigators   across   the   intramural   research   program.   This   is   part   of   a   broader   vision   that  
proposes  that  the  NIH  Clinical  Center  (NIHCC)  should  become  a  test  platform  for  the  complete  
molecular  characterization  of  research  patients  to  facilitate  a  comprehensive  understanding  of  
biology  and  disease.  This  commitment  to  catalyzing  clinical  genomics  and  molecular  medicine  
arose  at  a  planning  retreat  in  the  fall  of  2012  following  the  NHGRI  blue  ribbon  panel  review  and  
has  been  carried  forward  by  the  NHGRI  leadership  and  enthusiastically  embraced  by  the  wider  
NIH  leadership.  The  overarching  goal  described  above  is  a  long-­‐term  one  and  will  take  years  to  
accomplish.   However,   technical   advances   provide   us   with   an   opportunity   to   start   this  
evolutionary   process   with   currently   available   technology,   which   is   exome   sequencing.   Exome  
sequencing   has   been   used   successfully   by   us   and   many   others   to   elucidate   the   causative  
mutation   for   a   large   number   of   disorders.   Thinking   more   broadly,   our   goal   is   to   establish   the  
foundations   of   predictive   medicine   (otherwise   referred   to   as   individualized,   personalized,  
precision  medicine)  in  the  NIHCC.  These  objectives  will  be  implemented  via  the  Clinical  Center  
Genomics  Opportunity  (CCGO),  which  was  a  competitive  program  which  is  funded  jointly  by  the  
Deputy   Director   of   Intramural   Research   and   NHGRI.   The   purpose   is   to   make   available   to  
investigators   outside   of   NHGRI   exome   analysis   through   the   NIH   Intramural   Research   Center  
(NISC)   to   apply   to   rare   disease   patients   to   identify   the   genes   causing   these   disorders.   In  
addition,  we  are  using  this  program  to  pilot  the  development  of  clinical  genomics  in  the  NIHCC.  
There  are  innumerable  tasks  to  accomplish  this  vision  –  the  goal  of  the  present  proposal  is  to  
take   the   first   steps   by   harnessing   available   technologies   to   existing   NIHCC   and   intramural  
resources   to   start   this   evolutionary   process.   Some   of   the   many   tasks   that   need   to   be  
accomplished   include   proper   sample   acquisition   and   processing,   CRIS   informatics,   CLIA  
processes,  variant  interpretation  algorithms  that  properly  balance  positive  value  and  sensitivity,  
maximizing   the   information   utility   from   genomic   assays,   effective   ways   to   communicate   clinical  
results   to   participants,   report   generation,   and   training   NIHCC   health   providers   to   properly  
interpret   and   use   genomics   results.   In   this   protocol   we   aim   to   focus   on   several   of   these  
challenges  by  implementing  the  direct  use  of  genomic  variant  testing  in  a  CLIA  environment  and  
to  study  the  meaning  and  utility  of  the  results  to  the  participants.  Our  initial  proposal  is  to  use  
exome  data  to  extract  and  report  variants  for  so  called  secondary  (formerly  termed  incidental)  
The   Presidential   Commission   on   the   Study   of   Bioethical   Issues   (PCSBI)   report   on   incidental  
findings  has  made  a  number  of  recommendations  regarding  this  issue,  which  serve  as  general  
basis  or  starting  point  from  which  investigators  can  use  the  principles  and  general  guidance  to  
fit   different   research   situations   (President's   Commission,   2013).   The   key   findings   from   this  
report   are   that   investigators   must   prospectively   address   how   they   will   approach   the   issues  

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

requirement   for   orthogonal   evaluation   would   prevent   negative   reports   from   being   issued,  
which  is  a  serious  problem  for  the  field.    
Beyond   these   laboratory   and   informatic   challenges   and   processes,   we   aim   to   understand  
participant   perceptions   of   secondary   findings.   This   is   critical   and   equally   important   for   those  
who  receive  as  it  is  for  those  who  do  not  receive  such  a  finding.    
Among   participants   who   receive   a   secondary   finding   we   plan   to   explore   the   impact   and  
usefulness  of  the  result:  
1. What  do  patient  participants  understand  about  their  secondary  finding  and  perceive  to  
be  the  value  of  that  finding?  
2. How  do  patients  respond  psychologically  to  the  secondary  finding,  given  that  they  may  
be  surprising?  
3. Was   the   secondary   finding   unsurprising   or   previously   known   to   the   patient   or   family?  
Has  it  been  found  among  any  of  the  patient’s  relatives?  
4. What   communication   of   secondary   findings   were   followed   within   the   family   and   with  
health  care  providers?  
5. What,  if  any,  changes  in  patients’  health  behaviors  or  care  resulted  from  the  secondary  
findings;  including  but  not  limited  to  screening,  evaluation,  or  interventions?  
Among  participants  without  a  secondary  finding  
1. What  do  participants  understand  about  the  analysis  of  secondary  variants  [Expectations  
for  receiving  results].  
2. What  do  participants  understand  about  the  limitations  of  a  negative  secondary  variant  
3. Did   participants   decline   any   recommended   health   care   assessments   because   of   the   lack  
of  any  secondary  findings    
An   understanding   of   these   issues   would   contribute   exploratory   data   to   our   understanding   of  
the   challenges   and   effective   approaches   to   the   identification   of   secondary   findings   from  
exomes,  specifically  how  research  participants  interpret  secondary  variant  finding  reports  and  
whether  they  are  useful  in  promoting  positive  health  care  behaviors.  These  data  will  be  used  to  
generate   hypotheses   for   further   research   and   with   follow   up   studies,   may   help   to   improve  
practice  in  this  new  and  challenging  area  of  genome  sequencing.    
4. Description of study design (Brief description of what study design has been selected)
This  is  exploratory  translational  implementation  science.  We  will  use  clinical  judgment  and  the  
lessons   from   ClinSeq®   to   carry   these   processes   over   from   research   to   a   clinical   environment.  
ClinSeq®  is  well  known  to  this  IRB  (07-­‐HG-­‐0002)  as  a  pilot  study  for  clinical  research  sequencing  
to   develop   approaches   to   the   generation   and   use   of   next   generation   sequencing   in   a   clinical  
research  environment.    
Samples  for  the  CCGO  participants  will  be  accessioned  and  processed  by  NISC  for  their  exome  
pipeline   (both   molecular   biologic   and   informatic)   according   to   a   freeze   of   those   processes   as  
described   in   the   CLIA   documentation.   In   brief,   exome   data   will   be   generated,   filtered   for  
general  attributes  of  pathogenicity,  remaining  variants  will  be  manually  curated,  reports  will  be  

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

generated   and   entered   into   the   NIHCC   chart   (See   Appendices   5   &   6).   These   reports   will   be  
generated   consistent   with   our   CLIA   application   (see   Appendix   7)   and   signed   by   Drs.   Johnston  
and   L   Biesecker.   We   have   convened   an   advisory   group   (Appendix   18)   to   help   us   to   make   bigger  
decisions   and   set   policy.   For   example,   this   group   will   advise   us   on   thresholds   to   be   used   for  
reporting   variants   and   which   variants   require   Sanger   validation.   We   will   update   our   gene  
reporting  list  (See  Appendix  17)  annually  with  the  advice  of  this  group  and  include  that  as  part  
of  our  annual  renewals  of  this  protocol.    
The   next   step   is   to   return   results   to   participants.   This   will   be   done   using   two   distinct  
approaches,   depending   on   whether   the   result   is   positive   or   negative.   If   negative,   the   report  
(example   report   is   Appendix   6)   will   be   uploaded   into   the   CRIS   system   (as   a   pdf),   which   will  
trigger  an  alert  to  the  clinician  managing  the  participant.  This  clinician  will  then  communicate  
that   negative   result   to   the   participant.   The   NHGRI   team   will   offer   training   to   the   CCGO   primary  
research  clinical  groups  on  how  to  return  these  results  to  their  participants  –  emphasizing  that  
the  analysis  does  not  include  all  variants  in  the  56  genes,  is  deliberately  designed  to  have  low  
sensitivity   and   high   predictive   value,   that   variants   of   unknown   significance   are   not   included,  
that   many   genes   that   may   cause   life-­‐threatening   disorders   are   not   included,   that   common,   low  
relative   risk   susceptibility   variants   are   not   included,   etc.   In   short   –   that   this   is   in   no   way   a   clean  
bill   of   genomic   health.   This   information   is   also   emphasized   in   the   consent   form   and   the   fact  
sheet  that  accompanies  it  (see  Appendices  12  and  13).    
If   the   result   is   positive,   we   will   provide   a   clinical   genetic   evaluation   through   a   special  
consultation   through   a   CRIS   request   to   the   NHGRI   consultation   service.   Each   CCGO   Principal  
Investigator   has   been   asked   to   identify   a   contact   person   with   whom   our   group   will   work   to  
coordinate  return  of  positive  results.    A  detailed  description  of  the  procedure  that  we  imagine  
will   most   often   be   employed   to   return   these   findings   is   outlined   below   in   Section   5   and  
Appendix  14.  This  will  be  performed  by  J  Sapp  with  support  from  L  Biesecker  (see  Section  5.8  
for  details).  Our  goal  is  to  offer  medical  and  genetic  counseling  to  CCGO  participants,  which  will  
include  an  assessment  of  the  pedigree  with  recommendations  and  referrals  to  providers  who  
can  carry  out  these  evaluations.  
Participants   who   receive   a   positive   secondary   finding   will   be   asked   to   answer   an   on-­‐line   survey  
and  participate  in  a  short,  recorded  telephone  interview  with  Dr.  Barb  Biesecker  three  months  
after   receipt   of   their   result   to   gather   descriptive   data   in   answer   to   research   questions   1-­‐5  
above.  Given  the  relatively  small  number  of  participants  expected  to  receive  secondary  results  
in   CCGO,   our   primary   approach   is   to   assess   responses   to   the   results   using   open–ended  
interview   questions.   Ultimately   we   will   report   on   findings   from   CCGO   alongside   data   from  
participants  in  other  NIH  studies,  including  ClinSeq®  participants  who  learn  unexpected  findings  
in  the  56  genes.    
We  propose  to  quantitatively  assess  questions  1-­‐3  listed  above  in  a  subset  of  250  participants  
who   do   not   receive   a   secondary   finding   through   an   online   survey   that   will   be   administered  
three  months  after  the  receipt  of  the  negative  secondary  findings  report.      
See  Section  5.7  below  for  additional  details.    

Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  


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Submitted  in  Response  to  IRB  Stipulations  –  August  1,  2015  

correlation  between  patient  characteristics  and  expectations  of  benefit  from  Phase  I  clinical  
trials."  Cancer  98(1):  166-­‐175.