1
Preconceptional Test For Monogenic
Diseases
Dr. José A. Horcajadas Associate Professor, U. Pablo de Olavide, Seville, Spain
Research Associate Professor, EVMS, Norfolk, Virginia, US CSO, Recombine Europe, Barcelona, Spain
The Human Genome Project started in 1990
² The Mission of the HGP: The quest to
understand the human genome and
the role it plays in both health and
disease.
“The true payoff from the HGP will be the ability to
better diagnose, treat, and prevent disease.” --- Francis Collins, Director of the HGP
and the National Human Genome
Research Institute (NHGRI)
1985-Human Genome Project 1985 2003
FINISHED!!! Lord, They discover the
complete Human Genome code!
Heavens!
Those … hackers!
I have to change
the password!
HUMAN GENOME PROJECT
+
NEW TECHNOLOGIES
=
THE “OMICS” REVOLUTION
Quackenbush 2006 N Engl J Med 354:2463-72
TRADITIONAL VERSUS OMICS APPROACHES
The Basic Paradigm of the Biology
PRECONCEPTIONAL
PGD/PGS PRENATAL
Complexity of the Human Genome
• 3.500 million pairs of bases
• Around 35.000 genes
• 3% are genes, 97% is “junk” DNA with some regulatory
acEvity over those genes (not anymore junk!)
• We all share >99% of geneEc informaEon, with >20 million
pairs of bases (SNPs) being different.
GENETIC BASIS OF DISEASE
• SNPs (single nucleoEde
polymorphisms) are one
base change (A,T,C,G) in the
DNA sequence.
• SNPs explain many geneEc
diseases and differences
between humans.
• Close to 20M SNPs
idenEfied
SNPs
§ 6000-‐7000 single gene disorders
§ Combined incidence: 1/300 births (U.S.)
§ Everyone carries severe recessive
mutaJons that can cause geneEc condiEons
§ Recessive mutaEons can pass down quietly
through many generaEons
§ Carriers may not have a family history or
symptoms of a geneEc disease
§ Hence, carrier tesJng is the only way to
determine carrier status
Autosomal Recessive
Inheritance
THE BURDEN OF GENETIC DISEASE
1. Bell, C.J., Dinwiddie, D.L., Miller, N.A., Hateley, S.L., Ganusova, E.E., Mudge, J., Langley, R.J., Zhang, L., Lee, C.C., Schilkey, F.D., Sheth, V., Woodward, J.E., Peckham, H.E., Schroth, G.P., Kim, R.W., Kingsmore, S.F., 2011.
Carrier tesEng for severe childhood recessive diseases by next-‐generaEon sequencing. Sci Transl Med. Jan 12;3(65):65ra4
2. Berry, R.J., Buehler, J.W., Strauss, L.T., Hogue, C.J., Smith, J.C., 1987. Birth weight-‐specific infant mortality due to congenital anomalies, 1960 and 1980. Public Health Rep. 102, 171–181.
3. Costa, T., Scriver, C.R., Childs, B., 1985. The effect of Mendelian disease on human health: a measurement. Am. J. Med. Genet. 21, 231–242.
4. Gukmacher, A.E., Collins, F.S., 2002. Genomic medicine: a primer. N. Engl. J. Med. 347, 1512–1520.
5. Kingsmore, S., 2012. Comprehensive carrier screening and molecular diagnosEc tesEng for recessive childhood diseases. PLoS Curr. May 2:e4f9877ab8ffa9.
6. Kumar, P., Radhakrishnan, J., Chowdhary, M.A., Giampietro, P.F., 2001. Prevalence and pakerns of presentaEon of geneEc disorders in a pediatric emergency department. Mayo Clin. Proc. 76, 777–783.
7. Scriver, C.R., Neal, J.L., Saginur, R., Clow, A., 1973. The frequency of geneEc disease and congenital malformaEon among paEents in a pediatric hospital. Can. Med. Assoc. J. 108, 1111–1115.
8. Srinivasan, B.S., Evans, E.A., Flannick, J., Pakerson, A.S., Chang, C.C., Pham, T., Young, S., Kaushal, A., Lee, J., Jacobson, J.L., Patrizio P., 2010. A universal carrier test for the long tail of Mendelian disease. Reprod
Biomed Online. Oct;21(4):537-‐51.
20%
infant deaths
PaEents affected by rare disorders face mulEple
challenges (survey by Eurodis 2006):
• 40% iniEally receive incorrect diagnosis
• DiagnosEc delay (5-‐30 years for 25% of paEents)
• 10% received Psychological care:
Wrong assumpEon of psychosomaEc basis
• 33% received inappropriate treatment:
16% unnecessary surgery
GENETIC DISORDERS AND SCREENING
Great, great, great, great, great
granduncle was the previous
affected family member
~175 years earlier
Why should we recommend
expanded carrier screening?
It has worked with other ethnic panels
It is recommended for the specialists
It is cheaper that the cost of maintaining the affected people
Because populaEon is homogenizing and ethnicity panels are
not valid
REASONS TO DO IT
17
Genomic TesJng for
Universal Carrier Status
Test every couple planning to conceive
for as many diseases as possible,
affordably.
NEW PARADIGM
What diseases
should be included in
expanded screening?
In the NIH meeEng on “PopulaEon-‐based Carrier Screening for Single
Gene Disorders,” the following criteria was recommended:
§ Impaired health in homozygous
affected offspring
§ High frequency of carriers in screened
populaEon
§ Technically and clinically valid
screening methods available
§ Screening is cost-‐effecEve
§ Consent is obtained
§ IVF, prenatal diagnosis and terminaEon
are reproducEve opEons
§ PotenEal benefits and risks of carrier
tesEng are explained pre-‐ and post-‐test
§ Privacy is protected
§ Experienced professionals are available
§ SEgmaEzaEon of carrier status in the
community is minimized
The meeEng concluded that the top three consideraEons are:
carrier frequency, disease burden and cost of screening.
1. hkp://www.genome.gov/27026048, Last accessed: 9/20/2012
CRITERIA FOR EXPANDED SCREENING: NIH
The meeEng concluded that the top three consideraEons are:
carrier frequency, disease burden and cost of screening.
ACMG & ACOG CURRENT GUIDELINES IN THE UNITED STATES
Cystic Fibrosis ACMG ACOG AJ
Fragile X ACMG ACOG AJ
Spinal Muscular Atrophy ACMG
Hemoglobinopathies ACOG
Bloom Syndrome ACMG AJ
Canavan Disease ACMG ACOG AJ
Familial Dysautonomia ACMG ACOG AJ
Fanconi Anemia Type C ACMG AJ
Gaucher Disease ACMG AJ
Mucolipidosis Type IV ACMG AJ
Niemann-Pick Type A ACMG AJ
Tay-Sachs Disease ACMG ACOG AJ
ACOG = American Congress of
Obstetricians & Gynecologists
ACMG = American College of Medical
Genetics & Genomics
AJ = Ashkenazi Jewish Screening
Recommendations by ACOG/ACMG
Screening methods:
SNP arrays
Simultaneous analysis of 15,000 of SNPs and/or mutations
Probes for each SNP allele are attached to a slide
DNA sample
SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MICROARRAYS
G
A
T
A
A
G
T
A
T
A
A
G
A
G
G
A
T
T
C
T
A
T
T
C
A G
C A A T T A
G
Homozygous for C allele Heterozygous C/T
SNP MICROARRAYS
HUMAN GENOME COST Decrease
The CarrierMap
• We have created a chip to determine carrier status
simultaneously for more than 300 geneEc condiEons by
screening nearly 2,000 mutaEons.
• Our pan-‐ethnic screen includes diseases that are more common
in specific ethnic groups as well as diseases that are less common
or occur more broadly in the general populaEon.
• Recombine’s test therefore provides the greatest reducEon to
the overall risk of having a child with a geneEc condiEon.
THE RECOMBINE TEST
>300 GENETIC DISEASES CARRIERMAP TESTS FOR
Copyright Recombine 2016
Cystic Fibrosis•
Common High Impact Conditions
•
Spinal Muscular Atrophy•
Fragile X Syndrome
Sickle-Cell Disease•
•
Tay-Sachs Disease•
Alpha and Beta Thalassemia
CarrierMap is the most comprehensive genetic carrier screen
available and follows all recommendations and guidelines from the
leading organizations in reproduction and genetics. Useful for all
patients, regardless of ethnicity.
10.05.2016 28
SELECTION CRITERIA DISEASE LIST
10.05.2016 Copyright Recombine 2014 29
INCLUSION: § Autosomal recessive and/or X-linked recessive inheritance pattern
§ Inclusion in ACOG/ACMG guidelines, and Jewish advocacy group recommendations
§ Inclusion in state newborn screening guidelines
§ Significant impact on life expectancy and/or quality of life, as defined by GC team
§ High carrier rate in at least one population
§ PGD previously performed for genetic disease
§ Meets population-based screening criteria1,2
§ Disease and/or mutation frequency studies published
§ Inclusion in other carrier screening panels
EXCLUSION: § Autosomal dominant and/or multifactorial inheritance pattern
§ Adult-onset disorder
§ Limited or no impact on reproductive decisions (e.g. MTHFR deficiency)
§ Low penetrance (e.g. HFE-related Hemochromatosis)
1. NIH meeting on “Population-based Carrier Screening for Single Gene Disorders” http://www.genome.gov/27026048, Last accessed: 9/2014.
2. Watson, M.S., Lloyd-Puryear, M.A., Mann, M.Y., Rinaldo, P., Howell, R.R., 2006. Newborn Screening: Toward a Uniform Screening Panel
and System. Genetics in Medicine. 8(5):12S-252S
INCLUSION: § Autosomal recessive and/or X-linked recessive inheritance pattern
§ Inclusion in ACOG/ACMG guidelines, and Jewish advocacy group recommendations
§ Inclusion in state newborn screening guidelines
§ Significant impact on life expectancy and/or quality of life, as defined by GC team
§ High carrier rate in at least one population
§ PGD previously performed for genetic disease
§ Meets population-based screening criteria1,2
§ Disease and/or mutation frequency studies published
§ Inclusion in other carrier screening panels
EXCLUSION: § Autosomal dominant and/or multifactorial inheritance pattern
§ Adult-onset disorder
§ Limited or no impact on reproductive decisions (e.g. MTHFR deficiency)
§ Low penetrance (e.g. HFE-related Hemochromatosis)
EVOLUTION CRITERIA DISEASE LIST
10.05.2016 Copyright Recombine 2014 30
NEW DISEASES ADDED BASED ON: § Emerging literature on natural history and frequency of diseases
§ High carrier frequency in at least one population, particularly in in less well-represented populations (e.g. African, Latin American, Asian, Middle Eastern)
§ Clinical impact affects areas that are less well-studied (e.g. ophthalmology)
NEW MUTATIONS FOR EXISTING DISEASES ADDED BASED ON: § Emerging literature on natural history and frequency of mutations
§ Associated with diseases for which detection rate is relatively low (<40%)
§ High frequency in at least one population
§ Highly penetrant mutation
DISEASES & MUTATIONS REMOVED BASED ON: § Emerging literature on relatively low impact of disease and/or mutation
§ Emerging literature on relatively low penetrance of disease and/or mutation
§ Found to be unrelated to reproductive decision-making
HAVE SIGNIFICANT IMPACT RECOMBINE CARRIERMAP DISEASES
10.05.2016 Copyright Recombine 2014 31
185+� Shortened � Lifespan�
α-Thalassemia Cystic Fibrosis
ARPKD
145+� Cognitive � Impairment�
Fragile X Smith-Lemli-Opitz
PKU
290+ � Physical� Impairment�
SCID FMF
β-Thalassemia
Detection Rates
10.05.2016 Genetic Testing. Simplified. 32
Disease Gene
(# Mutations) Ethnic Groups
Detection Rate
Carrier Rate
Residual Risk
Cystic Fibrosis CFTR (99)
African American Ashkenazi Jewish
Asian American European
Hispanic
~81% ~97%
~55% ~93%
~77%
1/61 1/23
1/94 1/25
1/59
1/316 1/767
1/205 1/343
1/257
Spinal Muscular Atrophy SMN1
(Ex7 deletion)
African American Ashkenazi Jewish
Asian American European
Hispanic
~71% ~90%
~93% ~95%
~91%
1/66 1/41
1/53 1/35
1/117
1/121 1/350
1/628 1/632
1/1,061
Bloom Syndrome BLM (2) Ashkenazi Jewish 97% 1/134 1/3,350
Canavan Disease ASPA (4) Ashkenazi Jewish European
99% 47%
1/55 Unknown
1/2,750 Unknown
Familial Dysautonomia IKBKAP (3) Ashkenazi Jewish ~>99% 1/31 <1/3,000
Fanconi Anemia Type C FANCC (6) Ashkenazi Jewish ~99% 1/101 1/10,100
Gaucher Disease GBA (9) Ashkenazi Jewish ~96% 1/15 1/375
Results: Carrier Rates Observed
10.05.2016 33 Copyright Recombine 2013
SAMPLE SIZE & DEMOGRAPHICS
10.05.2016 Copyright Recombine 2014 34
v Sample size: 6,636 samples
§ Analysis limited to samples tested on CarrierMap V3
§ Patient referrals from: endocrinologists, obstetricians, maternal-fetal medicine
specialists, and genetic counselors
§ 67% females, 33% males
Females
Males 67%
33%
DEMOGRAPHICS: ETHNICITY
10.05.2016 Copyright Recombine 2014 35
v Patient self-reported ethnicity
§ 10 broadly defined ethnic groups, including “Other”
67%
33%
6% 5%
36%
14%
13%
5%
2%
1%
4%
3% 11% African
East Asian
European
Jewish
Latin American
Mediterranean
Middle Eastern
Native American
South Asian
South East Asian
Other
RESULTS: QUICK OVERVIEW
10.05.2016 Copyright Recombine 2014 36
56% of patients identified as carriers
for any disease
39% of patients identified as carriers
for high impact disease
172 diseases, 534 mutations
detected in total
1.9% of couples identified as carriers
for same disease
RESULTS: HIGH IMPACT DISEASES
10.05.2016 Copyright Recombine 2014 37
Disease Counts Percentage
Familial Mediterranean Fever 1/10 10.0%
Spinal Muscular Atrophy 1/17 5.9%
Cystic Fibrosis 1/19 5.2%
Nonsyndromic Hearing Loss & Deafness: GJB2-Related 1/31 3.2%
Alpha Thalassemia 1/51 2.0%
Congenital Disorder of Glycosylation: Type 1A: PMM2 Related 1/51 2.0%
Phenylalanine Hydroxylase Deficiency 1/77 1.3%
Smith-Lemli-Opitz Syndrome 1/77 1.3%
Autosomal Recessive Polycystic Kidney Disease 1/77 1.3%
Beta Thalassemia 1/77 1.3%
10.05.2016 Copyright Recombine 2013 38
Disease Carrier Rate in General Population Observed Reported
Smith-Lemli-Opitz Syndrome 1/47 1/71
GSD Type II: Pompe Disease 1/72 1/97
Nonsyndromic Hearing Loss & Deafness: GJB2 Related 1/19 1/43
Gaucher Disease 1/75 1/112
Bardet-Biedl Syndrome: BBS1 Related 1/168 1/376
Walker-Warburg Syndrome 1/59 1/150
OBSERVED > REPORTED FREQUENCIES
CARRIER OF THE SAME DISEASE
COUPLES
Couples are carriers of the same disease 1,9%�~
*Kumar, N., Bisignano, A., Asgari, S., Chu, B., Munne, S., Grifo, J., Berkeley, A., Licciardi, F., Chen, S., Hoffman, D., Barrionuevo, M., Prates, R.
October 2014. From Carrier Screening to Single Gene PGD: An Analysis of 1/479 Couples Screened via an Expanded Carrier Screening
Platform. ASRM 2014.
29/1479 �
PGD for gene disorders
Disease tested: Acetil Co Oxidase type I defficiency, Adrenoleucodistrophy, Alpha-thalassemia, Alport syndrome,
Autosomal Dominant Polycystic Kidney Disease (ADPKD), Autosomal Recesive Polycystic Kidney Disease (ARPKD),
Beta-thalassemia, Branchio-Oto-Renal syndrome (BOR), BRCA1 breast cancer predisposition, BRCA2 breast cancer
predisposition, CanavanCharcot-Marie-Tooth type IA (CMT1a), Choroideremia, Congenital adrenal hyperplasia (CAH),
Congenital neutropenia, Connexin 26 hearing loss, Cystic fibrosis, Duchenne/Becker Muscular Dystrophy (DMD),
Ectrodactyly, Ectodermal dysplasia, and Cleft lip/palate syndrome (EEC1), Fabry Disease, Familial adenomatous
poliposis coli (FAP), Familial dysautonomia, Familial intrahepatic cholestasis 2, Fanconi anemia, Fragile site mental
retardation , Gangliosidosis type 1 (GM1), Gaucher disease, Glomuvenous malformations (GVM), Glycogen-storage
disease type I (GSD1), Glycosylation type 1C, Hemoglobin SC disease, Hemophilia A, Hemophilia B, Hereditary
nonpolyposis colon cancer (HNPCC), Hereditary pancreatitis, HLA matching Huntington disease, Hurler syndrome,
Hypophosphatasia, Incontinential pigmenti, Krabbe disease (Globoid cell leukodystrophy), Long QT syndrome, Marfan
syndrome, Meckle gruber, Metachromatic leukodystrophy (MLD), Methylmalonic aciduria cblC type (MMACHC), Myotonic
Dystrophy 1, Myotubular myopathy, Neurofibromatosis 1, Neurofibromatosis 2, Niemann-Pick Disease, Noonan
syndrome, Oculocutaneous albinism 1 (OCA1), Ornithine carbamoyltransferase deficiency (OTC), Osteogenesis
Imperfecta 1, Rapp Hodgkin ectodermal dysplasia, Retinitis pigmentosa, Retinoblastoma, Sickle Cell Anemia, Smith-
Lemli-Opitz syndrome (SLOS), Spinal bulbar muscular atrophy (SBMA), Spinal Muscular Atrophy Type 1 (SMA1), Tay
Sachs, Tuberous sclerosis 1 (TSC1), Tuberous sclerosis 2 (TSC2), Von Hippel-Lindau Syndrome (vHL), X-linked
dominant Charcot–Marie–Tooth (CMTX), etc…… (see review Gutierrez et al. (2008))
We can do PGD for any of the 6000 diseases provided the mutaJon is known
DISEASES FOUND IN COUPLES
SUMMARY
High impact disease Carrier
Couples
PGD Cases
Initiated
ALPORT SYNDROME : COL4A4 1 0
CARNITINE PALMITOILTRANSFERASE II 1 0
GLYCOSILATION DEFICIENCY: TYPE 1A, PMM2 1 1
CYSTIC FIBROSIS 6 3
GAUCHER 1 0
MEDITERRANEAN FEVER 2 1
MIOPATHY ON INCLUSION BODIES: TYPE 2 1 1
NIEMANN-PICK : TYPE A 1 1
NON SYNDROMIC DEAFNESS RELATED TO GJB2 7 1
SICKLE CELL DISEASE 4 1
SPINAL MUSCULAR ATROPHY: SMN1 3 2
TAY-SACHS 1 1
Total 29 12
*Kumar, N., Bisignano, A., Asgari, S., Chu, B., Munne, S., Grifo, J., Berkeley, A., Licciardi, F., Chen, S., Hoffman, D., Barrionuevo, M., Prates,
R. October 2014. From Carrier Screening to Single Gene PGD: An Analysis of 1/479 Couples Screened via an Expanded Carrier Screening
Platform. ASRM 2014.
Couple Report
FOR OOCYTE DONATION
OLD PARADIGM
• “we have healthy donors”
• Only few diseases
• Some characterisEcs selected by phenotype
NEW PARADIGM
• Test donors and couples for as much diseases as possible
• Don’t rule out affected donors (40%) but avoid matching (2.4%)
DONOR TESTS
Validation Phase
1 test.
30+ causes of infertility
70+ genes.
700+ variants.
Recombine FertilityMap
The unique test based on the Genetics of Infertility
Designed to provided to patients and
doctors the best options for a success
pregnancy
Validation Phase
Dr. Howard Jones (July 31st 2015)
Thank you Dr. Jones!