Genomics  for  Rare  DiseasesDr.  Anna  Lehman

Provincial  Medical  Genetics  Program

Adult  Metabolic  Diseases  Clinic

Department  of  Medical  Genetics

BC  Children’s  Hospital  Research  Institute

Definitions

• Rare  Disease:  affecting  fewer  than  1  in  2000  people

• Mendelian  disease:  simple,  predictable  genetics

Not  all  Mendelian  diseases  are  Rare

• Familial  Hypercholesterolemia  (1  in  500)  Austin,  Am  J  Epidemiol  2004;160:407–420

• Familial  Cardiomyopathies  (Hypertrophic: 1  in  500;  Dilated: 1  in  500)  Gene  Reviews

• Hereditary  Cancer  (HBOC:  1  in  400;  Lynch  1  in  440)  Gene  Reviews,  2017

• Nonsyndromic Intellectual  Disability  (~  1  in  100)  my  estimate

Not  all  rare  diseases  are  Mendelian

• Polymyositis  (prevalence  1  in  14,000)

• Childhood  leukemia  (incidence  1  in  20,000)

• Congenital  diaphragmatic  hernia  (incidence  1  in  2500)

Rare  Diseases  are  Common

• 1  in  3  children  admitted  to  BCCH  have  a  rare  genetic  disease.

• More  than  1,500  rare  diseases  do  not  have  a  known  cause.

• Too  often,  children  and  families  affected  by  rare  diseases  must  undertake  a  frustrating,  time-­‐consuming,  expensive  and  painful  journey  in  search  for  a  diagnosis  – the  “diagnostic  odyssey”.

Rare  Diseases  Kill

January  7th,  2017 4,919 confirmed  genetic  disorders(phenotype  and  known  gene)

Heterogeneic disorders  are  broken  down  into  subtypes  for  each  different  gene

Growing  focus  on  genetic  subtypes,  because  many  new  therapies  are  gene-­‐specific,  or  even  mutation  specific

Retinitis  PigmentosaAn  endpoint  disease  resulting  from  many  different  molecular  mechanisms

National  Eye  Institute

67  genes  responsible  and  counting(RetNet)

1  in  3500  prevalence

Genetic  diagnostic  rate  2010:  50%(Berger  et  al  2010)

Genetic  diagnostic  rate  2015:  65%

Source:  RetNet

Test SNVs Indels CNVs Structural  rearrangement

Sanger   ✔ ✔ ✗ ✗

MLPA ✗ ✗ ✔ ✗

Next  Gen  panel ✔ ✔ ✗ ✗

Array ✗ ✗ ✔ ✗

Whole  genome  sequencing

✔ ✔ ✔ ✔

Genetic  Testing:  Faster,  Cheaper,  Better

First  medical  exome

• Wisconsin• Late  2009• $100,000• Life-­‐saving  diagnosis

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Panel  or  Exome?

• Previously,  panels  had  a  major  advantage  of  allowing  virtually  complete  sequencing  coverage  of  all  exons  (usually).

• Now,  a  high-­‐end  exome  can  provide  similar  coverage.  • So  main  reason  to  rely  on  panels  as  much  as  possible  is  cost.  • A  panel  $1  – 3K  and  a  trio  exome  is  $6K  – 11K• Second  reason  to  use  panel  is  to  avoid  VUS  and  IFs

When  to  order  an  exome

• Very  broad  differential  (eg.,  intellectual  disability  /  developmental  delay)

• “Weird”  presentation  (maybe  more  than  one  diagnosis)

• You  need  a  1  week  turn  around  time

• You  won’t  be  satisfied  by  a  negative  result-­‐-­‐-­‐you  want  to  discover  novel  genes  in  the  sequence  data  yourself

• Disease  discovery  pace  is  so  fast  right  now,  your  disease  panel  will  be  outdated  in  a  year.

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What’s  Next?  Resolving  uncertainty

Am  J  Hum  Genet.  2016  Jun 2;  98(6):  1067–1076.

651 kids  considered  for  exome  sequencing

401 approved  (total  will  be  500)

107 exomes  complete

56 diagnoses  made  (52%)

28 have  mutations  in  new  candidate  genes  

• Fewer  invasive  tests• More  effective  therapy• Anticipatory  screening

51  kids  remain  undiagnosed

CAUSES  Clinicas  of  September  2016

• Two  siblings  not  growing  well  &  behind  in  development• Both  had  abnormal  urine  biochemical  profile  with  results  suggestive  of  beta  ureidopropionase deficiency  – but  sequencing  of  UPB1  gene  – negative  – del/dup  negative

• MRI  – nonspecific  ventriculomegaly• Chromosomal  microarray  normal

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Siblingwt: 74v:       45

TKT(transketolase)

NM_001135055.2:c.1690_1692delTAT

NP_001128527.1:p.Tyr564del

autosomal recessive =  compound heterozygous

Childwt:      73v: 43

Motherwt: 52v:          62

SHORT STATURE,  DEVELOPMENTAL DELAY,  AND  CONGENITAL HEART DEFECTS• developmental delay

• global  developmental  delay• microcephaly

Child’s  phenotypeDisease  phenotype

Fatherwt: 120v:       0

Functional  impact• PROVEAN Genome  Variants  Result  (human37_66)  prediction  is  deleterious

• This  variant  results  in  a  single  amino  acid  deletion  564  of  623  in  exon  13  of  15.

Population  frequency• 0 in-­house• In  ExAC

• 6/121,242  alleles• 0  homozygous• African >MAF=9.612e-­05

• Not  in  DECIPHER or LOVD

Siblingwt: 84v:       70

TKT(transketolase)

NM_001135055:exon9:c.1202G>A:p.R401H

autosomal recessive =  compound heterozygous

Childwt:      82v: 55

Motherwt: 126v:              0

SHORT STATURE,  DEVELOPMENTAL DELAY,  AND  CONGENITAL HEART DEFECTS• developmental delay

• global  developmental  delay• microcephaly

Child’s  phenotypeDisease  phenotype

Fatherwt: 61v:       66 Functional  impact

• 4/4  in  silico programs  predict  an  impact

• CADD=35

Population  frequency• 0 in-­house• Not  in  dbSNP,  EVS,  or  ExAC• Not  in  DECIPHER or LOVD

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How  much  evidence  is  needed  for  a  gene  to  be  included  in  the  clinome?

• One  published  patient?• Ten  patients  in  a  database?• A  mouse?• A  Western  blot?• A  luciferase  assay?• An  odds  ratio?

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What  if  it  is  only  a  susceptibility  gene?

The  Deciphering  Developmental  Disorders  Study

• 1,133  children  with  severe,  undiagnosed  developmental  disorders,  and  their  parents,  underwent  a  combination  of  exome  sequencing and  microarray

• As  of  December  2014,  a  genetic  cause  had  been  found  for  31%

• The  study  went  on  to  recruit  14,000  probands

Nature 519, 223–228,  2015

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DDD  findings

April  2016  

Analysis  of  >4000  probands

$6ooo

What’s  Next?  Better  variant  calling

What’s  Next?          Genome  Diversity

Or,  alt.  title:  “75  million  new  dbSNP entries,  and  time  for  an  Hg  update”

Resolving  a  VUS

1. Decide  if  segregation  studies  in  your  family  will  be  

meaningfully  helpful.  Of  course,  for  many  conditions  with  

incomplete  penetrance,  you’re  really  only  wanting  to  test  

clearly  affecteds.  

2. Consider  doing  parents  (determine  if  cis or  trans  for  AR;  de  

novo  for  AD)

3. Consider  functional  studies

4. Wait  and  re-­‐visit  the  literature