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Mosaicism in PGT-A Is it a red herring?
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)
PGS 2.0 Mosaicism Publications “Have you published anything?”
“You’re cherry picking data”
“Do you have your own clinic?”
“You’re being dishonest”
“You can’t criticize a NEJM paper”
“You didn’t read the supplementary data”
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Treff Wells Fiorentino Munne
Debating Mosaicism
Truth
Only conflict of interest?
Laboratory Regulations Conflict of Interest
X X i.e. Germany
Laboratory Quality Conflict of Interest
Suboptimal Culture
Commercial Competition Conflict of Interest
Key Points
• Mosaicism exists, but is rare
• General lack of acknowledgement of technical limitations and artifacts
• Clinical diagnosis from a single biopsy provides poor predictive value
• Validation is extremely limited
Post implantation-primarily maternal meiotic (not mosaic)
Hassold and Hunt Nature 2001 2:280
n=358
Preimplantation-primarily maternal meiotic (not mosaic)
Why are some mosaicism estimates so high?
No meiotic aneuploidy?
Mosaicism or technical error?
aCGH False Positives
n=159 embryos
P=0.006
False Positive
Rate Single Cell < Multi Cell
Mosaicism or technical error?
9% FPR= 47% “mosaicism”
Mosaicism classification schemes
3-20%
Mosaicism is not common
~6%
Positive Controls?! (Mixture Model)
Comparison of methods to detect aneuploidy in a mixture
↑ sensitivity = ↓ specificity
33% False Positive Rate
Alternative Explanations
False Positive Mosaicism?
False Negative Uniform
Aneuploidy?
What is the true positive rate/predictive value?
?
?
?
Preimplantation stage
rebiopsy Amnio/CVS?
0 true positives Postimplantation stage
Mosaic
Predictive value for remaining embryo
~one third of embryos with a mosaic range chromosome were actually uniform aneuploid
<3% mosaicism rate on >20,000 embryos
Predictive value for remaining embryo
False negative uniform aneuploidy
Mosaic range trisomy 13
Uniform trisomy 13
Uniform trisomy 13
False negative uniform aneuploidy
Disomy
Trisomy
Mosaic +6, -13, +16?
Near Triploid Not Mosaic (using Allele Ratios)
AAA
AAB
ABB
BBB
AB
BB
AA
Allele Ratio
Mosaic +6, -13, +16 70,XXX,+6,-13,+16
AAAA
AAAB
ABBB
BBBB
AABB
AAAA
AAAB
ABBB
BBBB
AABB
Mosaicism Reporting
88% of clinics opt out of reporting mosaicism
74% of clinics do not use mosaicism testing
Non-invasive mosaicism prediction?
Micronuclei and genuine mosaicism
Time-lapse characterization of micronuclei?
Conclusions • Mosaicism exists, but is overestimated by imperfect methods and lax criteria
• Intermediate copy number can originate from phenomena other than mosaicism
• Results from a single biopsy should not be considered a definitive diagnosis of mosaicism
• Make raw data available
• Publish studies with rebiopsies of embryos classified as mosaic
• Perform systematic analysis of products of conception after transfer of “mosaic” embryos
• Develop time-lapse integrated analysis (machine learning algorithms)
Future Directions
References Cited
• Rosenwaks et al Fertil Steril 2018
• Hassold and Hunt Nature 2001
• Treff et al Fertil Steril 2008
• Mertzanidou et al Hum Reprod 2013
• Capalbo et al EJHG 2015
• Capalbo et al Hum Reprod 2017
• Goodrich et al JARG 2017
• Greco et al. NEJM 2015
• Scott et al Fertil Steril 2012
• Sachdev et al Fertil Steril 2017
• Katz-Jaffe et al Fertil Steril 2017
• Marin et al Curr Op OBGYN 2017
• Joshi et al Fertil Steril 2018
• Kim et al Am J Obstet Gynecology 2018
• Hong et al Fertil Steril 2014
• Kort et al Hum Reprod 2016
• Chavez et al Nature Comm 2012
Bold = Treff coauthor
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