Expanded Preimplantation Genetic Testing

Nathan R. Treff PhD, HCLD(ABB)

Cofounder, Chief Science Officer, and Clinical Laboratory Director

Disclosures

• Cofounder, Shareholder and CSO, Genomic Prediction Inc

• Director, Genomic Prediction Clinical Laboratory Inc

Stephen Hsu Laurent Tellier

SNP array (18)

qPCR (22) NGS

(19)

Monogenic Polygenic

e.g. Cystic Fibrosis e.g. Type 1 Diabetes 1% 15-25%

monogenic

polygenic

Power of Population Level Genetics

Principle Component Analysis

UK BioBank (500K Genome-wide Data)

Million Veterans Program

Polygenic Risk Score Publications

Modern Polygenic Risk Score Algorithms

Clinical Predictors (i.e. fracture risk assessment)

GWAS “one at a time”

Polygenic Risk Scores “machine learning”

Osteoporosis Variance Explained

Combined Testing?

Clinical Risk

Out of Sample Validation

Combined Risk

Family History

Common and Reliable Phenotype (applies to idiopathic short stature)

Methodology validation

Predicted Height (cm)

Act

ual

He

igh

t (c

m) Male

Female

Replication

Atrial Fibrillation

Inflammatory Bowel

Disease

Type 2 Diabetes

Breast Cancer

Disease Examples

“We propose that it is time to contemplate the inclusion of polygenic risk prediction in clinical care, and discuss relevant

issues.”

Accurate Genome-wide

Genotypes (PGT-M, PGT-P)

Accurate copy number

(PGT-A, PGT-SR)

Automated lysis and library

template prep DNA amplification 2

DNA amplification 1

Expanded Preimplantation Genomic Testing (ePGT) Methodology (>900K SNPs)

Accurate Genome-wide

Genotypes (PGT-M, PGT-P)

Accurate copy number

(PGT-A, PGT-SR)

Automated lysis and library

template prep

Expanded Preimplantation Genomic Testing (ePGT) Methodology (>900K SNPs)

96 samples per run

DNA amplification 3

ePGT Control Samples

Copy number

• Aneuploidy (PGT-A): 6-7 cells from samples with prior karyotyping (whole chromosome aneuploid and euploid)

• Structural (PGT-SR): 6-7 cells from samples with segmental aneuploidy

Genotyping

• Monogenic (PGT-M): 6-7 cells from samples with known CFTR delta F508 status

• Polygenic (PGT-P): cell free DNA from individuals with hypothyroidism (TSH)

Copy Number Accuracy PGT-A and PGT-S

PGT-A Examples (5-8 cells)

PGT-A Examples (Circos Plots)

PGT-A Performance (>99% Accuracy)

32% prevalence

PGT-SR Preliminary Results (>99% Accuracy)

n=42

ave

rage

co

py

nu

mb

er

size (Mbp) >900K SNPs = High Density

Translocation Carrier Status

Genotyping Accuracy PGT-M and PGT-P

Genotyping Accuracy on Limited Quantities

Large qty Small qty

Co

nco

rdan

ce

100%

99%

98%

97%

96%

95%

Copy number + genotyping for PGT-A

False Positives True Positives

AAA

AAB ABB

BBB

AB

BB

AA

BB

AA

Trisomy Disomy Monosomy

Mendelian Rules

PGT-M: Typical Number of Markers (~60)

PGT-M: CFTR delta F508 (>99.9% Accuracy)

47% prevalence

PGT-P Results: Hypothyroidism Risk (4945 SNPs)

eMERGE-GWAS Set

n=219,000 n=2,019

PGT-P Results: Hypothyroidism Risk (4945 SNPs)

n=219,000 n=36

PGT-P: Hypothyroidism Risk (83% Accuracy)

Note: Heritability studies suggest that up to 67% of hypothyroidism is genetically determined.

ePGT Initial Polygenic Risk Targets

Baade et al. BMJ Open 2015 CgvFactSheet. National Cancer Institute, 2012. Chen et al. BMC Medical Genetics 2017. American Speech-Language-Hearing Association. 2018. Lee et al. Nature Genetics 2018. Lello et al. Genetics 2018 .

https://www.ahajournals.org 2018 Lloyd-Jones et al. Circulation, August 31, 2004. Loukine et al. Population Health Metrics 2012. Patja et al. Journal of Intellectual Disability Research 2000 Sanchis-Gomar et al. Annals of Translational Medicine 2016. WebMD. 2018. Wit et al. Growth Hormone & IGF Research 2008.

Utilization • IVF population

• Higher risk of polygenic disorders (e.g. cancer risk in azoospermic males)

• Fewer embryos for selection

• General Population • Family History

• Greater number of embryos for selection

• Genetic Counseling

Aneuploidy and Polygenic Risk

45% 4% 19% 71%

Coronary Artery

Disease Risk

Aneuploidy Risk

Aneuploidy and Polygenic Risk

45% 4% 74% 71%

Type 1 Diabetes

Risk

Aneuploidy Risk

Intervention during honeymoon phase?

ePGT Conclusions and Implications

• Novel use of machine learning algorithms and molecular genetic methods to expand testing for common heritable disease risk

• First method for simultaneous and accurate PGT of: • Aneuploidy

• Monogenic Disease Risk

• Polygenic Disease Risk

• Structural Rearrangements (translocations)

• Polygenic risk scores may provide an additional embryo selection tool, increase utilization of IVF, and reduce the incidence of common genetic disease in humans

• Ethically justified when the condition is serious and no safe, effective interventions are available.

• Reproductive liberty arguments ethically allow for PGT-M for adult-onset conditions of lesser severity or penetrance.

• Strongly recommend that an experienced genetic counselor with knowledge about PGT-M play a major role in counseling patients considering such procedures.

• As of this time, testing is not available for multifactorial diseases

ASRM 2018

“CRISPR”

Bob Edwards 1996

National Surveys

• 74% of Americans support use of PGT for serious conditions1

• 72% of Americans2 and 66% of British3 were willing to gene edit their future children to reduce risk of serious disease

1. “Awareness and Knowledge about Reproductive Genetic Technology” Genetics and Public Policy Center, Johns Hopkins University, 2002

2. “The Public and Gene Editing, Testing, and Therapy” Harvard TH Chan School of Public Health, STAT, 2018 3. “Industry News: UK Public Cautiously Optimistic About Genetic Technologies” SelectScience, 2018

Future Directions

Acknowledgements

nathan@genomicprediction.com