Cambridge Healthtech Institute’s Second Annual
Non-Invasive Prenatal Testing
Advances in Cell-Free and Cell-Based Prenatal Screening and Diagnostics
August 18, 2017 | Grand Hyatt Washington | Washington, DC

Non-invasive prenatal testing continues to be a growing field in the prenatal diagnostic space, but there is much to be done to perfect these technologies for routine clinical use. Cambridge Healthtech Institute’s 2nd Annual Non-Invasive Prenatal Testing symposium will examine the latest advances in both cell-free and cell-based testing, including updates on the range of genetic conditions being tested for. Particular attention will be paid to characterizing, isolating, and extracting these cells, as well as fetal fraction considerations.

Final Agenda

Recommended Short Course(s)*

SC17: Mosaicism in NIPT: Challenges and Implications

*Separate registration required


8:00 am Registration & Morning Coffee


8:25 Chairperson’s Opening Remarks

Peter Benn, Ph.D., Department of Genomics and Genome Sciences, University of Connecticut Health Center


Mark_EvansMark Evans, M.D., President, Fetal Medicine Foundation of America; Professor of Obstetrics and Gynecology, Mt. Sinai School of Medicine; Comprehensive Genetics

Statistical performance of NIPT is excellent for T21 but is terrible for the microdeletions. Microarray technologies now detect 1% significant copy number variants (CNVs) in patients of all ages which is far above the age 35 threshold (1/200) for required offering of CVS or amniocentesis. For younger women the detection by microarray is 10x that of NIPT. All women, regardless of age should be offered CVS/amniocentesis with microarray.

9:00 Current Status of Expanded NIPS for Aneuploidy

Peter_BennPeter Benn, Ph.D., Department of Genomics and Genome Sciences, University of Connecticut Health Center

Non-invasive prenatal screening (NIPS) based on cell-free DNA in maternal plasma has expanded to include additional chromosome abnormalities beyond those involving chromosomes 21, 18, 13, X and Y. This includes unbalanced chromosome rearrangements, marker chromosomes, rare autosomal aneuploidies and also sets of specific microdeletion syndromes. In this presentation, I will review the current status of this testing, discuss clinical utility, and present some of the interpretation issues associated with expanded NIPT.

9:30 Validation Studies for the Launch of a CLIA-Compliant Fetal Cell-Based Noninvasive Prenatal Test

Art_BeaudetArt Beaudet, M.D., Department of Molecular & Human Genetics, Baylor College of Medicine

Steady progress has been achieved towards a fetal trophoblast-based form of NIPT. From 3-10 cells can be recovered at 8-14 weeks gestation in the majority of pregnancies. Individual cells are subjected to whole genome amplification and genotyping followed by copy number analysis using whole genome shotgun next-generation sequencing. Numerous sub-chromosomal abnormalities have been detected.

 Lifecodexx10:00 Taking NIPT to the Next Level: Detection of Fetal Trisomy Based on Quantitative Real-Time PCR

Michael Lutz, Ph.D., CEO, LifeCodexx AG

A newly developed NIPT assay based on qPCR (qNIPT technology) for the determination of fetal trisomy 21 showed a sensitivity and specificity of 100% when compared to NGS. First results from diagnostic routine indicate the potential to become the standard of care concerning cost-efficiency and turnaround time.

10:30 Coffee Break with Poster Viewing


11:00 NanoVelcro Chips for Isolation and Characterization of Circulating Fetal Nucleated Cells – Toward Noninvasive Prenatal Diagnostics

Hsian-Rong_TsengHsian-Rong Tseng, Ph.D., Professor, Department of Molecular and Medical Pharmacology, University of California, Los Angeles

In contrast to the existing rare-cell sorting approaches, our joint research team at UCLA pioneered the concept of “NanoVelcro” cell-affinity assay, in which a capture antibody-coated nanosubstrate substantially enhances the performance of rare cell enrichment from blood. The ways in which different generations of NanoVelcro Chips were employed in streamlined workflows to isolate and characterize single circulating fetal nucleated cells (CFNCs, including both trophoblast and fetal nucleated red blood cells) in maternal blood will be presented. Using maternal blood samples collected from expectant mothers who carried single fetuses, the CFNC-derived CGH microarray data were able to detect fetal genders and chromosomal aberrations, which had been confirmed by standard clinical practice. In addition to sharing our latest research progress in developing CFNC-based noninvasive prenatal diagnostic (NIPD) solutions, the challenges that still need to be resolved will be presented.

11:30 Acoustic Tweezers: An Innovative Tool for Non-Invasive Prenatal Testing

Tony_Jun_HuangTony Jun Huang, Ph.D., Professor, Mechanical Engineering and Materials Science (MEMS), Duke University

The ability to manipulate cells, micro/nano particles, and fluids in a biocompatible and dexterous manner is critical for many biomedical studies and applications. Here I will summarize our recent progress on an “acoustic tweezers” technology that utilizes acoustic waves to manipulate particles, cells, organisms, and fluids. In particular, my talk will focus on our results on using the acoustic tweezers technology to isolate extracellular vesicles and fetal cells from blood.

12:00 pm Development of a Noninvasive Prenatal Test for β-Hemoglobinopathies Utilizing NGS and a Novel Probe Capture Panel to Analyze Cell-Free Fetal DNA in Maternal Plasma

Katie_CarlbergKatie Carlberg, M.D., Clinical Hematology Oncology Fellow, Children’s Hospital Oakland Research Institute

We have developed a non-invasive prenatal test using probe hybrid capture and next-generation sequencing (NGS) for analysis of cell-free fetal DNA (cfFDNA) for β-hemoglobinopathies. Our approach to inferring fetal genotype is based upon counting reads of informative SNPs from a panel of >400 to estimate fetal fraction. We have shown proof of concept for analyzing cfFDNA by capturing both limited and degraded DNA as well as resolving mixtures.

12:30 Sponsored Presentation (Opportunity Available)

1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:30 Session Break


2:00 Chairperson’s Remarks

Art Beaudet, M.D., Department of Molecular & Human Genetics, Baylor College of Medicine

2:05 Clear Results, Confused Reporting: cfDNA Prenatal Screening and Lessons to Be Learned

Glenn_PalomakiGlenn E. Palomaki, Ph.D., Professor, Pathology and Laboratory Medicine, Women & Infants Hospital/Alpert School of Medicine at Brown University

Prenatal screening for open neural tube defects and Down syndrome is over 40 years old. Tests based on circulating cfDNA are the latest improvement but laboratories have not leveraged this long history in their communications. This leads to confusion in use of terms, content of reports and other issues that hamper uptake. These lessons may also be relevant for those introducing new technologies in transplantation and cancer screening/monitoring.

2:35 High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletion

David_PetersDavid Peters, Associate Professor, Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh

We tested the hypothesis that inter-individual genomic copy number variation in control samples is a confounding factor in the non-invasive prenatal detection of fetal microdeletions via the sequence-based analysis of maternal plasma DNA. The database of genomic variants (DGV) was used to determine the “Genomic Variants Frequency” (GVF) for each 50kb region in the human genome. We found strong correlation between high variance in read counts and GVF amongst controls. Consequently, we were unable to confirm the presence of the microdeletion via sequencing of maternal plasma samples obtained from two sequential affected pregnancies. It is vital to develop our understanding of the factors that impact the sensitivity and specificity of these approaches.

3:05 Refreshment Break with Poster Viewing

3:35 Cell-Free Fetal DNA Fraction and Inflammatory Conditions: Is There a Correlation?

Luis_GomezLuis Gomez, M.D., Assistant Professor, Division of Maternal Fetal Medicine, Perinatal Associates of Northern Virginia

This is a retrospective cohort study to evaluate if the cell-free fetal DNA fraction is affected by maternal inflammatory conditions, including autoimmune conditions such as rheumatoid arthritis, diabetes, and inflammatory bowel disease. A total of 389 subjects were included who underwent cell-free DNA testing at our institution and the fetal fraction was evaluated. Subjects with autoimmune conditions and BMI >40 had a higher fetal fraction as compared to healthy controls. Elevated fetal fraction is associated with fetal growth restriction.

4:05 Using Genome in a Bottle Benchmark Genomes with Targeted Sequencing Panels

Megan_ClevelandMegan H. Cleveland, Ph.D., Research Biologist, Applied Genetics Group, National Institute of Standards and Technology (NIST)

The Genome in a Bottle (GIAB) Consortium aims to highly characterize a small number of benchmark genomes. These genomes have been sequenced by several sequencing technologies, each with different biases in detection of INDEL, SNPs, and structural variants. GIAB has integrated these data to form high-confidence SNP, INDEL, and homozygous reference genotype calls. These GIAB materials can be used to evaluate targeted sequencing panels.

4:35 Close of Symposia Programs