Teasing  out  the  VOLS  from  the  VOUS
-­‐
Christopher  E.  Mason
DNA   RNA   Protein

1)   Variant  calling
2)  Genome  InterpretaAon  /  Pharmacogenomics
3)  Data  Provenance  and  Management

Oliver  Hofmann  and  Brad  Chapman:   hPp://bcbio.wordpress.com/2013/05/06/framework-­‐for-­‐evaluaAng-­‐variant-­‐detecAon-­‐methods-­‐ comparison-­‐of-­‐aligners-­‐and-­‐callers/

Does  a  $1,000  genome  need  a  $100,000  interpretaAon?  At  least  a  big  phone  bill.
Genome,  NGS,   and  Clinical
Standards
Groups
Personalized
Medicine     using
Variant
AnnotaAon  and
ContextualizaAon
-­‐NGS   -SEQC
Cloud-­‐based
Approaches  to
InformaAcs  and
Sequencing
PaAent  and  Data
Sharing  IniAaAves   for  Treatment

R-­‐make  is  open  source  (under  review):   hPp://physiology.med.cornell.edu/faculty/mason/lab/data/r-­‐make/

Intra-­‐paAent  allelic  dynamics  detail  cell  heterogeneity:
Same  paAent  at  diagnosis  (D)  and  relapse  (R)

Paired  RNA-­‐Seq  reveals  a  seemingly  endless  ocean  of  private  mutaAons

Using  RNA-­‐Seq  to  find  chemo-­‐resistant  clones  in  ALL
Meyer  et  al,   Nature  Gene*cs ,  2013

Meyer  et  al,   Nature  Gene*cs ,  2013

We  see  enrichment  of  a  gene  for  nucleoAde   metabolism,  mutaAons  near  binding  pocket
NT5C2:  5'-­‐nucleoAdase  (purine),  cytosolic  type  II
Meyer  et  al,  Nature  GeneAcs,  2013

That  took  four  years.
What  if  we  did  it  again  today?

Lanvis,  GSK  (thioguanine)   Mercaptopurine

Only  Significantly  Associated  Clinical
Variable  Was  Early  Relapse
7  of  40
Meyer  et  al,   Nature  Gene*cs ,  2013

We  see  enrichment  of  a  gene  for  nucleoAde   metabolism,  mutaAons  near  binding  pocket
NT5C2:  5'-­‐nucleoAdase  (purine),  cytosolic  type  II
Meyer  et  al,  Nature  GeneAcs,  2013

NT5C2  Mutants  Confer  Chemoresistance  to
Purine  Nucleoside  Analogue  Treatment
6-­‐MP     6-­‐TG
Reh  cells  transiently  lenAviral  infected  with  WT,  GFP,  and  mutants
Meyer  et  al,  Nature  GeneAcs,  2013

Meyer  et  al,  Nature  GeneAcs,  2013

The NIH Undiagnosed Diseases Program (UDP)
•   Launched May 19, 2008
•   Supported by the Office of Rare Diseases, NHGRI and the NIH Clinical Center.
•   Goals:
–   Addresses unmet need for diagnosis of mysterious diseases.
–   Helps discover new diseases that provide insight into human physiology and genetics.

UDP441 spiny follicular hyperkeratosis case
•   50 year-old Caucasian woman.
•   Spiny follicular hyperkeratosis with alopecia, follicular plugging, abscesses.
•   Exacerbated by UV-A light and oral retinoid therapies.
•   Ruled out infections, hormone and paraneoplastic causes.
•   No known dermatological causes.
•   RNA-Seq and WGS

Already  we  may  have  been  able  to  predict   this  potenAal  from  the  germline  DNA

Found  mutaAons  in  gene  involved  in   follicle  development  and  cell  cycle

50Tb

More  genomes  are  coming…
100  TeraBytes  is  only  the  beginning
Current  -­‐  1,000  genomes            =  100  TeraB
WGS  for  all  new  U.S.  babies/year:
4,300,000  genomes                =  430  PetaB
WGS  for  everyone  >40  in  U.S.  in  2013
100  million  genomes              =  10  ExaB
Every  human  in  China
1.3  billion  genomes              =  130  ExaB
Each  biopsy/checkup/visit…  per  paAent
100  billion  genomes              =  10  ZePaB

And  that  is  only  the  Genome!
Family
Medical
History
Robust
Sample  Prep
&    Data
AcquisiAon
AnnotaAons,
TDBGV   miRbase,
TCGA,
1KG,dbSNP
StaAsAcal
Models  Built   from  Per-­‐
Base,  High-­‐
Res  Data
G
Bacteria
/Fungi
Virus
G
1.              Mass  spectrophotometry  data
1.
Protein-­‐Protein  InteracAons
2.
Polysome-­‐Associated  mRNAs
1.
2.
3.
mC  or  hmC  modificaAons
Histone  marks  (HXXX)
Regulatory  informaAon
Nucleosome   effects
Gene   regulaAon
1.
Variants  (SNVs,  indels)
2.
Structural  variants  (CNVs,  TxC)
3.
Ancestry  predicAon  from
AIMs
RNA  edits,   eQTLs
TFBS
mRNAs   degrade
1.
Small  Variants  (SNVs,  indels)
2.
DE  by  exon,  gene,  intron,  &  jxn
3.
PolyA  sites  and  miRNA   changes
4.
TARs  and  ORF  potenAal
5.
Gene  fusion  events
6.
Allele-­‐specific  expression
1.    Metabolic  changes   drugs   vitamin   hormone
N  other   species

Environment
T=0   T=1
Environment
T=N

hPp://www.allthingstechnology.net/2011/07/how-­‐much-­‐byte-­‐make-­‐yoPabyte.html

$100  for  one  terabyte
1YB=1  trillion  TB
1YB  =  $100  trillion
…

We  need     per-­‐base,  per-­‐allele,  per  generaAon     data   chr   pos   bcalls   chr10   79090   14   chr10   79091   13   chr10   79092   13   chr10   79093   12   chr10   79094   14   chr10   79095   14   chr10   79096   15   chr10   79097   15   chr10   79098   15   chr10   79099   15   chr10   79100   15   chr10   79101   15   chr10   79102   15   chr10   79103   13   chr10   79104   8   chr10   79105   8   chr10   79106   8   chr10   79107   8   chr10   79108   8   chr10   79109   8   chr10   79110   8   bcalls   filt
5
5
5
1
1
5
5
5
5
1
1
1
2
1
2
2
4
4
2
4
4   ref
Q
(snp)
GT
A   0
A   0
A   0
C   0
T   0
T   0
A   0
C   0
A   0
A   0
T   0
T   0
C   0
T   0
A   40   AG
A   0   AA
A   0
A   0
AA
AA
T   0
A   0
A   0
TT
AA
AA
AA
TT
TT
CC
TT
AA
AA
AA
CC
TT
TT
AA
CC
AA
AA
AA
AA
CC
TT
TT
AA
CC
AA
AG
AA
AA
AA
TT
AA
AA
AA
TT
TT
CC
TT
Q   max_gt   poly  site
Q  (max_gt
|poly_site)  As  used
75
69
54
54
54
54
54
54
54
40
75
75
75
75
75
75
72
69
69
66
72
42
36
21
21
21
21
21
21
21
73
42
42
42
42
42
42
39
36
36
33
39
0
0
0
15
13
8
8
0
8
8
15
15
15
0
15
15
14
0
0
0
0
Cs   used
8
0
0
0
0
0
0
8
0
0
0
0
0
0
0
0
0
0
0
12
0
Gs   used   Ts  used
0
0
0
0
0
0
0
0
0
0
0
0
0
0
6
0
0
0
0
0
0
0
8
8
0
0
0
0
0
0
15
0
0
0
0
0
0
0
13
13
0
14

We  can  now  observe  the  dynamics   and  evoluAon  of  cancers
Ding  L,  et.al,    Clonal  evoluAon  in  relapsed  acute  myeloid  leukemia  revealed  by  whole-­‐genome  sequencing.  Nature.  2012  Jan  11;481(7382):
506-­‐10.

A  Future  of  Publically  Personalized  Medicine

Today  I  am  even  more  sure  I  shouldn’t  smoke

“All  science  is  either  physics  or  stamp  collecAng”
Ernest  Rutherford
Awarded  Nobel  Prize  in  1908  for  Chemistry,  not  Physics.
“The   energy  produced   by  the   breaking  down  of  the  atom   is  a   very  poor   kind  of  thing.  Anyone   who  expects  a  source  of  power  from  the  transformaAon  of  these  atoms  is  talking  moonshine."
–  1933
“An  alleged  scienAfic  discovery  has  no  merit  unless  it  can  be  explained  to  a  barmaid.”

All  physicists  were  stamp  collectors  unAl  around
1935.
All  genomicists  will  have  to  be  stamp  collectors  for   a  few  years  more.
“When  we  have  found  how  the  nucleus  of  atoms  is   built  up  we  shall  have  found  the  greatest  secret  of   all  —  except  life.”   -­‐    Ernest  Rutherford