1. Carrier Screening in ART 2014
The Value of Next-Generation DNA Sequencing
Stephanie Hallam, PhD, FACMG, MBA
VP Laboratory Operations & Medical Director, Good Start Genetics

2. Agenda Need for Carrier Screening Responsible Approach
Clinically relevant tests
Best in class technologies
The Need for Accurate Screening
Value of Next-Generation Sequencing Technology
Clinical Experience
Clinical benefits of sequencing-based assay

3. The Need for Carrier Screening

4. Importance of Carrier Screening
Recommended by leading medical societies
ACOG
ASRM
ACMG
Jewish advocacy organizations (e.g., NTSAD) 
Disorders should be prevalent, have severe forms, and be costly to treat
For all women for all women of reproductive age

5. The Need for Better Screening
1/100 babies are born with an inherited disease1
20-30% of all infant deaths are due to genetic disorders2
11.1% of pediatric hospital admissions are for children with genetic disorders3
Preconception screening for disease-causing mutations and genetic counseling for carriers can reduce the incidence of these diseases
Incidence of Tay Sachs disease was reduced by 90% in AJ due to awareness and screening4
1 Monogenic disorders, World Health Organization
2 Berry, et al, 1987
3 Scriver, et al, 1973
4 Kaback, et al, 2000

6. Cystic Fibrosis (CF)
CF is the most common life- threatening, genetic disorder in Caucasians
Despite widespread availability of carrier screening, more than 2,500 babies are born with cystic fibrosis each year
The average survival age is late 30’s¹
Individuals with CF endure chronic symptoms with lifetime treatment costs estimated over $2,000,000¹
1 in 25 Caucasians is a carrier of CF
¹CF foundation website

7. Spinal Muscular Atrophy (SMA)
SMA is the leading genetic cause of death in infants and toddlers.
1/6,000 to 1/10,000 children are born with the disease
The most severe form (Type I) manifests before 6 months of age and generally results in death before age two
One in 40 to one in 50 people (approximately 6 million Americans) are carriers of the SMA gene.
Spinal Muscular Atrophy (SMA) is a genetic neuromuscular disease characterized by muscle atrophy and weakness.
Data from SMA foundation website

8. Carrier Screening: Assessing Inherited Disease in Couples
Helps determine risk for conceiving a child with an inherited disease
About 1 in 16 Caucasians is a carrier for cystic fibrosis or spinal muscular atrophy, the most common autosomal recessive diseases.
Preconception carrier screening for pathogenic gene mutations and genetic counseling can reduce the incidence of disease
Fragile x syndrome does not follow this inheritance pattern.

9. Pre-Pregnancy Screening Provides Valuable Early Information
Multiple options
Proceed at-risk
Prenatal testing
IVF with pre-implantation genetic diagnosis (PGD) of embryos
Sperm or egg donation
Adoption
Prenatal Screening
Preparation, genetic counseling, support groups
Newborn Screening
Early detection enabling early treatment, genetic counselor, support groups

10. Responsible Approach

11. A Balanced Approach to Genetic Screening
Testing for society guideline recommended disorders using a comprehensive set of disease-causing mutations
Society
Guideline Recommended
Disorders
Disease-
Causing
Mutations
Balance drives clinical value and sets the new standard for excellence
Prevalent & Severe
Validated Pathogenicity

12. Guideline and Society-Recommended Disorders
Focus on society-recommended disorders:
Provides clinicians confidence that they are screening for relevant diseases
Assures payers that testing is justifiable
Jewish Societies
Every test that GSG offers is recommended by either ACOG and/or ACMG and/or societies supportive of the Ashkenazi Jewish population.
GSGs advisors and other opinion-leaders in the field have advised GSG to concentrate on the society-recommended disorders.
Concentrating on these 22 disorders has allowed GSG to develop tests that are both highly accurate and clinically actionable.
* Recommended if indicated by family history
** Recommended for individuals of French Canadian or Cajun descent AJ – Tests recommended by national Jewish advocacy societies.

13. The Best Technology for Each Test
Test Methodology
Disorder(s)
Next-Generation DNA Sequencing (comprehensive)
Bloom’s syndrome
Glycogen storage disease 1a
Canavan disease
Maple syrup urine disease 1A/1B
Cystic fibrosis
Mucolipidosis type IV
DLD deficiency
Niemann-Pick type A/B
Familial dysautonomia
Tay-Sachs disease
Familial hyperinsulinism
Usher syndrome type 1F
Fanconi anemia group C
Usher syndrome type III
Next-Generation DNA Sequencing
Joubert syndrome 2
(targeted)
Walker-Warburg syndrome
Multiplex Ligation-Dependent Probe Amplification (MLPA)
Alpha-thalassemia
Spinal muscular atrophy (SMA)
Tri-Nucleotide Repeat PCR &
Fragile X syndrome
Methylation Analysis
Enzyme Analysis
Tay-Sachs disease (Hex A)
Hemoglobin Capillary Electrophoresis
Beta-thalassemia
Sickle cell disease
Genotyping
Gaucher disease
Nemaline myopathy

14. The Need for Accurate Screening

15. Why is Accurate Screening Important?
Screen with ~100 mutations
Result = Negative
Not tested because partner is negative

16. Why is Accurate Screening Important?
Child affected with cystic fibrosis

17. Why is Accurate Screening Important?
Carrier of a rare mutation, not detected by test that was used
Carrier of a common mutation, but not tested

18. Why is Accurate Screening Important?
Carrier
identified by test with higher detection rate
Carrier
identified because his partner screened positive
Embryo
1 in 4 chance for each pregnancy to be affected
Reproductive Options Available

19. Next-Generation DNA Sequencing

20. DNA Sequencing: The “Old” Way
First human genome
~13 years
~ $3B
At completion, cost to repeat was $300M
Routine clinical sequencing was unaffordable

21. Next-Generation DNA Sequencing
Massively parallel chemistry and detection
Faster
Cheaper
Revolutionizing Clinical Molecular Testing
HS2500 rapid run dual flowcell 2x100, 27 hrs, reagent cost

22. Next-Generation Sequencing: Technology Matters
Genotyping
Used by many companies for routine carrier screening
Tests for a limited set of only common mutations
Provides limited utility beyond Caucasian and Jewish ethnicities
Next-Generation Sequencing
Comprehensively evaluates the gene
Detects all known common and rare disease-causing mutations
Delivers higher accuracy across ethnicities
Why what using isn’t “good enough”

23. Delivering Clinically Actionable Results
Comprehensive Set of Known Disease-Causing Mutations
Rigorous, multi-year process to catalogue and evaluate each gene for all documented disease-causing variants
Accurate, actionable results that do not include variants of unknown significance (VUS)

24. Evaluating Variants: Not all are pathogenic
Some have no detrimental effect
Some have a mild effect
Some cause severe disease

25. Mutation Database: Validating the Variants
Literature (PubMed)
Locus Specific Databases
Genetic Evidence
Experimental Evidence
Sequence Based Evidence
Focus on mutations that cause disease and clinically important. Not just what easy to detect with technology!
~ 1,700 variants
~1,000 variants classified as disease-causing

26. NGS Versus Genotyping: Mutations in the CFTR Gene
Each dot represents a disease-causing mutation. (illustrative purposes only)
ACMG 23
Standard genotype screening panels (≈100)
Previously publicly reported pathogenic mutations (550)
Novel truncating mutations detectable by next-generation DNA sequencing (unknown)
GoodStart Select™ detects all of the disease-causing mutations above

27. The Power of Sequencing
NGS Tests for 5-10 Times More Pathogenic Mutations Per Disease than traditional genotyping
DISEASE
CARRIER FREQUENCY*
LEADING COMPETITORS
GOOD START GENETICS
Bloom's Syndrome
1 in 134
1-2 51
Canavan Disease
1 in 55 4 44
Cystic Fibrosis
1 in 23
~ 100
560
Dihydrolipoamide Dehydrogenase Deficiency
1 in 107
0 - 2 3
Familial Dysautonomia
1 in 31
2 - 32 2
Familial Hyperinsulinism
1 in 68
0 - 3 65
Fanconi Anemia Group C
1 in 100
2 - 4 26
Glycogen Storage Disease Type 1A
1 in 64
2 - 10 69
Maple Syrup Urine Disease Type 1A/1B
1 in 97
3 - 4 40
Mucolipidosis Type IV
1 in 89 9
Niemann-Pick Disease Type A/B
1 in 115 45
Tay-Sachs Disease
1 in 27
7 - 11 73
Usher Syndrome 1F
1 in 147
0 - 1 16
Usher Syndrome III
1 in 120 5 1 3
1 Data on file as of 12/2013.
2 Third mutation reported by one competitor not confirmed by GSG to be of clinical significance.
3 According to most-recently updated version of the GSG mutation list (9/13/2013).
* Based on Ashkenazi Jewish population (population selected because figures are available for all disorders).
Updated 5/2014

28. Mutations Reported Uncommon Mutations Common Mutations High frequency
Previously reported in the literature
In Validated Database

29. Mutations Reported
Traditional genotyping tests for a limited set of mutations.
Carrier screening by genotyping
Common Mutations
Uncommon Mutations

30. Truncating mutations expected to disrupt protein function
Mutations Reported
Good Start’s NGS test for 5-10 times more mutations than carrier screening tests performed by genotyping.
Carrier screening by next-generation DNA sequencing
Uncommon Mutations
Novel Mutations
Common Mutations
Truncating mutations expected to disrupt protein function
Any two mutations from the same disorder can cause disease

31. Detection of New Pathogenic Mutations
NGS enables the discovery of rare and novel mutations in a pan-ethnic population
Case Study: New CFTR Mutation Found Using NGS
Normal
Normal working protein
Truncating Mutation
Definition of Novel:
Not yet described in the literature
Disrupts protein structure and will cause disease
Protein is cut off and does not work properly
*Data presented at the 2013 Annual Meeting of the Pacific Coast Reproductive Society

32. Clinical Experience

33. Clinical Experience
22,296 patients from infertility centers across the US
Screened for up to 14 disorders using next-generation DNA sequencing
Carrier status determined by the presence or absence of a pathogenic mutation
Analysis of results: Good Start’s NGS versus genotyping-based carrier screening tests
Self-reported Ethnicity
% of Total
Caucasian
44.7%
Not Provided
29.0%
African American
7.0%
Asian
6.3%
Hispanic
5.8%
Other
4.8%
Ashkenazi Jewish
2.5%
Not all sequencing is the same: anyone can buy the machine, but it is not as simple as that to have an accurate test.
NGS has been used in research much longer than in a clinical setting because it is not easy to obtain the level of accuracy that is necessary for clinical use. It takes time to develop and validate to obtain that level of accuracy.
Data up to 1/31/2014 .

34. Carriers Detected
Carriers Detected
Gene
Genotyping Assays
GSG Only
Total Carriers
Familial Hyperinsulinism 23 7 30
Canavan Disease 36 6 42
Maple Syrup Urine Disease Type 1A/1B 18 14 32
Bloom Syndrome 13 20 33
Cystic Fibrosis
952 51
1003
Usher Syndrome Type III 9 4
Dihydrolipoamide Dehydrogenase Deficiency 2 15
Fanconi Anemia Group C
Glycogen Storage Disease Type 1a 5 41
Tay-Sachs Disease 87
105
Familial Dysautonomia 34 43
Mucolipidosis Type 1V 8
Usher Syndrome Type IF 10 19
Niemann-Pick Disease Type A/B 26
Total
1294
169
1463
~12% of carriers would not have been identified using genotyping-based carrier screening1,2
CF has higher values because (1) more patients are being screened for it (2) it has a high carrier frequency
1 – Results based on analysis of 22,296 patients in IVF centers across the country screened for up to 14 disorders using GoodStart Select.
2 – Analysis was done by comparing the mutations found using GoodStart Select to competitors’ genotyping panels. If all competitors did not test for a particular mutation, then it was marked as GSG only.

35. Clinical Implications of NGS for Your Patients
Reduce the risk of having a child with a common, severe genetic disorder
High detection rate, regardless of ethnicity
Low residual risk, regardless of ethnicity
Confidence in a negative test result

36. Thank You!