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Advances in Prenatal Molecular Diagnostics Conference - Day 2

Conference Proceeding CD Now Available
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8:00 am Morning Coffee

8:30 Chairperson’s Remarks

8:35 Thinking about Selecting between Cell-Free and Fetal Cell Analysis, Now and in the Future 

Joe Leigh Simpson, M.D., Senior Vice President, Research and Global Programs, March of Dimes Foundation

Recovering fetal cells from maternal blood has been a vision for decades, long prior to the more recent advances using cell-free fetal DNA. In the early 1990’s our group and then others achieved prenatal detection of fetal trisomy using nucleated fetal red blood cells. Although a collaborative NICHD-funded trial generated 74% sensitivity for trisomy 21 (Bianchi, Simpson, Jackson et al 2002), informative results were not consistently achieved. Cell sorting technologies used in these studies were updated, but consistency was still lacking until recently. Now, trophoblasts and other embryonic cells can be recovered that are not admixed with maternal cells. Purity of sample has great potential for not only embryonic cytogenomic evaluation but also interrogating for a wide range of embryonic disorders. Analysis of the embryonic transcriptome should always be more facile.

9:05 Options for Analysis of Single Fetal Cells

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

Our objective is to develop a noninvasive prenatal diagnosis that is as complete as can be accomplished at present with invasive testing and ultimately to detect especially de novo seriously deleterious point mutations and CNVs. Cell-based analysis has far better potential to achieve these goals compared to analysis of cell free fetal DNA. Two goals must be achieved to accomplish these objectives; first, fetal cells must be reliably recovered noninvasively, and second, genetic analysis must be performed on single cells. The two most attractive cell types are fetal nucleated red cells and trophoblasts. The most attractive methods for analysis of single cells start with whole genome amplification followed by array comparative genomic hybridization (CGH) and/or next generation sequencing. We have compared multiple methods for whole genome amplification of single cells including the MALBAC method followed by array CGH.

9:35 Life at the Single Molecule Level: Single Cell Genomics

Xiaoliang (Sunney) Xie, Ph.D., Department of Chemistry and Chemical Biology, Harvard University

As the primary cause for failure in human pregnancy and genetic disorders, aneuploidy increases drastically with women’s age, and leads to low success rates of in vitro fertilization (IVF). To select ovum or embryo without aneuploidy in IVF, preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS) have been implemented with PCR, FISH, SNP and CGH arrays, but are limited in accuracy and resolution, thus often giving high false positives and negatives. Here we demonstrate highly accurate genome-wide PGS using multiple annealing and looping based amplification cycle (MALBAC) for single cell whole genome amplification and sequencing of oocytes and 8-cell embryos. By sequencing the two polar bodies of each oocyte, we deduced the ploidy of the female pronucleus, phased the maternal genome, and inferred the oocyte haplotype. In so doing, we show the proof of principle for selecting an embryo free of aneuploidy, particularly for women with recurrent implantation failure and miscarriages, as well as of maternal genetic diseases associated with point mutations.

10:05 Coffee Break with Exhibit and Poster Viewing


10:45 CGH Microarray Analysis of Fetal Cells Isolated from Maternal Blood   

Bhairavi Parikh, PhD, CEO and Co-Founder, CellScape Corp.

CellScape has developed a process suitable for collection and whole genome molecular analysis of fetal cells from maternal blood. The process includes a gentle approach to blood processing and enrichment, algorithms and optical methods to differentiate fetal cells from maternal ones, and the use of chromosomal microarrays to assess copy number variants which can cause cytogenetic syndromes relevant for prenatal testing.

11:15 Non-Invasive Prenatal Diagnosis through Genetic Analysis of Trophoblastic Cells, Isolated by ISET

Patrizia Paterlini-Brechot, M.D., Ph.D., Founder and CSO, RareCells; Professor of Cellular and Molecular Biology, University Paris Descartes

Trophoblasts are cells of epithelial origin thus consistently larger than leukocytes. We show that a highly efficient system of cell sorting by size (ISET: Isolation by Size of Epithelial Cells) is able to extract trophoblastic cells from blood and from cervical samples allowing their genotyping and genetic analysis. Trophoblastic cells are expected to provide the optimal DNA substrate for non-invasive prenatal diagnosis. In fact, they carry fetal DNA not mixed with maternal DNA, they are available at a very early term of pregnancy (from the 5th week of gestation, thus earlier than the current term for chorionic villus sampling), and their collection and analysis is easy, rapid and cheap. Results of a clinical validation study and potential implications of using trophoblasts and ISET for non-invasive prenatal diagnosis will be discussed.

11:45 A Workflow for the Isolation and Molecular Characterization of Individual Circulating Fetal Cells in Non-Invasive Prenatal Diagnosis

Francesca Fontana, Ph.D., R&D Biology Project Leader, Silicon Biosystems S.p.A.

Fetal cells circulating in maternal blood hold the promise to enable non-invasive prenatal diagnosis (NIPD); however, a trustful workflow comprising their identification, isolation and genetic analysis is still needed. A workflow for fetal cells isolation based on DEPArray™, a fluorescent image-based sorting platform will be presented. Results showing the achievement of the goal of isolating multiple, 100%-pure cells with single cell resolution from enriched suspensions will be described. In addition, with Ampli1™ Whole Genome Amplification for single-cells, we show that it is possible to confirm fetal origin by DNA fingerprinting, carry out array Comparative Genomic Hybridization as well as analysis of point mutations. The above capabilities can be the cornerstone for enabling 1) the set-up and validation of a dependable enrichment and staining method and 2) further bring this workflow into a routine clinical practice.

Agilent Technologies Logo12:15 pm Luncheon Presentation: Development of an Automated Agilent Microarray System to Detect Aneuploidy in Single Cells

Doug Blake, Clinical Field Application Scientist, Agilent Technologies

The aim of this study was to develop a reliable, cost effective and automated Agilent microarray hybridization and bioinformatics pipeline for aneuploidy detection. The ploidy detection results derived from the PacGenomics-developed Agilent pipeline has a 100% concordance with BlueGnome, NimbleGen platforms and Coriell cell line reports, respectively. The turn-around time is 13 hours, 4 hours shorter than NimbleGen. The PacGenomics-developed Agilent hybridization and automated pipeline is a reliable and less time-consuming tool for aneuploidy detection.



1:15 Chairperson’s Remarks

1:20 Highly Sensitive and Specific Serum Test for Risk of Preeclampsia

Matthew Cooper, Ph.D., CEO, Carmenta Biosciences

Carmenta Bioscience is currently developing a diagnostic test for preeclampsia, a condition impacting 5% of pregnancies and a leading cause of death in mothers and newborns in the US. Clinical symptoms of preeclampsia (hypertension and proteinuria) do not present in mothers until later in pregnancy, often unexpectedly and too late for preventative measures, resulting in complications such as preterm birth and death. Carmenta’s serum-based, multiplexed protein test can accurately detect preeclampsia enabling doctors to prescribe lifestyle, dietary, and pharmacological interventions demonstrated to improve clinical outcomes and yield economic benefit.

Perkin Elmer PNDX 1:50 First Trimester Screening for Early Onset Preeclampsia  

Garrett Lam, M.D., Associate Professor & Chairman, Department of Obstetrics and Gynecology, University of Tennessee School of Medicine at Chattanooga,
Associate Director, Perinatal Services, Regional Obstetrical Consultants, Chattanooga, TN

Early onset preeclampsia is less common than the late form of the disorder but contributes significantly more to the morbidity and mortality of pregnant mothers and babies.  PerkinElmer Labs/NTD has developed a first-of-its-kind serum screening test to aid in the accurate prediction of patient risk for early onset preeclampsia.

2:20 Triaging First-Time Pregnant Women into Different Strata of Personalized Prenatal Care – The Preeclampsia Case

Robin Tuytten, Ph.D., Vice President, Research & Development, Metabolomic Diagnostics Ltd.

Introduction to why biomarkers are key in developing personalized care for 1st time pregnant women. Developing a preeclampsia risk stratification test – what are the options? Review of the status of the metabolomics preeclampsia risk stratification test. Moving forward, outlook on a prenatal testing hub assisting care givers to deliver integrated and customized prenatal care.


2:50 Strategies towards Non-Invasive Prediction of Preterm Birth and Prenatal Diagnosis

Farideh Bischoff, Ph.D., Scientific Advisor, KellBenx, Inc.

Prevention of preterm birth (PTB) continues to be a major challenge in obstetrics. Evidence suggests that infection plays a crucial role in the onset of this process. The purpose of this presentation is to show that measurements of interleukin (IL-10), IL-1 receptor antagonist (IL-1Ra), and IL-13 in non-pregnant women can identify a subset of women at risk for future preterm delivery due to a dysfunctional immune response to infection. Utility of the 4B9 antibody for fetal cell enrichment and subsequent analysis will also be addressed.

3:20 Refreshment Break with Exhibit and Poster Viewing 


4:00 Serum-Based Exosomal Multiplexed Protein Assay for Pre-Term Birth

Alan Ezrin, Ph.D., President & CEO, NX PharmaGen

Microparticles (exosomes) shed from the placental syncytiotrophoblast into maternal circulation and the maternal response to such holds tremendous opportunity to develop a serum based “liquid biopsy” of stable protease resistant biomarkers for the detection of patients at risk for spontaneous preterm birth (SPTB). A gel-free LC/MS/MS proteomic assessment in 48 patients has resulted in the identification of 98 proteins observed in asymptomatic women at week 15 -17 of gestation that are early biomarkers differentiating between normal term outcomes and SPTB. A statistically valued subset of protein biomarkers that map to inflammatory and cell injury pathways have entered commercial development, and may aid in the early identification and management of at risk pregnancies.

4:30 Closing Panel Discussion: What Will the Prenatal Molecular Diagnostic Landscape Look Like in 3-5 Years?


Arthur Beaudet, M.D., Baylor College of Medicine

Diana W. Bianchi, M.D., Tufts University School of Medicine.

Joe Leigh Simpson, M.D., March of Dimes Foundation

Ronald J. Wapner, M.D., Columbia University Medical Center

5:30 Close of Conference

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