link to RWJMS home page
obgyn

Research Opportunities for Fellows

Research

The clinical research team performs independent research on a variety of clinical questions.  It also has the responsibility of recruiting patients and collecting samples in support of the basic and translational research programs.  Over 1,000 patients per year participate in a wide variety of IRB approved research protocols.  Fellows will have access to all research projects.

The division has a highly competent and professional clinical research team which helps with all phases of the clinical research process including IRB preparation, consenting patients, protocol compliance, reporting, data collection, regulatory compliance, and limited data analysis.  These individuals represent an enormous asset to young investigators.

Research within the division is focused on understanding reproductive competence.  That includes studies of individual patients which are as far reaching as whole genome association studies, patterns of clinical response to various stimulation protocols, acupuncture, and mental health. 

The principal research has been directed towards evaluation of the competence of individual embryos.  Studies have ranged from a wide variety of clinical laboratory studies regarding culture conditions and decision making in the embryology and androlology laboratories to genomic, transcriptomic, proteomic, and metabolomic evaluation of individual embryos.  Our team has developed a reliable method for “DNA fingerprinting” individual embryos.  This provides an important and powerful new tool for clinical and scientific investigation.  For example, one patient may have two embryos transferred and in the case of a singleton pregnancy, it is possible to know with certainty which embryo developed into the baby. That provides an ideal opportunity for a paired analysis - same stimulation, same cycle, same culture conditions, same transfer, same endometrium, and same hormonal milieu. It is possible to then evaluate the transcriptome or proteome to determine how the competent embryo differs from the embryo that failed to develop.  These paired analyses allow investigators to answer critical questions with smaller sample sizes and greater precision. 

Molecular Genetics

The primary focus of the molecular genetics laboratory is to define markers of reproductive competence, develop technologies for embryo selection, and determine the genetic causes of infertility using state-of-the-art ‘omics’ technologies.  We have developed the most highly validated microarray based comprehensive chromosome PGD method and the only embryo DNA fingerprinting method capable of unequivocal sibling embryo discrimination.

Proteomics and Metabolomics

There are more than 50,000 embryo conditioned media samples that are characterized for outcome in the clinical database and that are available for analyses.  We currently evaluate SELDI-TOF, Raman, and infrared spectroscopy, and TaqMan protein expression, multiplex ELISA, and protein antibody array systems.  Oocyte and embryo gene expression microarray data is also available to evaluate transcription of secreted protein encoding genes and to identify targets for potential non-invasive diagnostics.  This portion of our research mission is expected to grow in the next year.

Transcriptomics

We house and run state-of-the-art gene and miRNA expression core facilities including a high throughput Affymetrix GeneChip System, and Applied Biosystems 7900HT and Fluidigm Microfluidic BioMark high-throughput TaqMan quantitiative real-time PCR (Q-PCR) Systems. There are more than 3,500 cumulus and corona samples with characterization including embryo specific outcomes through DNA fingerprinting and 24 chromosome oocyte aneuploidy diagnoses. 

Genomics

We have collected more than 15,000 oocyte and embryo biopsies for DNA analysis and have characterized more than 8,000 by genome-wide SNP microarray analyses (24 chromosome PGD).  Our Affymetrix microarray facility can process 192 GeneChips per week in support of 4 ongoing clinical trials.

We house and characterize the largest IVF DNA bank of currently more than 8,000 patients.  High throughput automated liquid handling instruments (epMotion VAC) provide for rapid DNA purification and subsequent evaluation of association of candidate polymorphisms and haplotypes with IVF outcomes.

Bioinformatics

Modern molecular biology techniques tend to generate large quantities of what is termed ‘high throughput data’ – biological data that is generated with thousands of data points per sample. RMA typically generates millions of high throughput data points per week from genetic and genomic assays.  This massive quantity of data requires specialized software and techniques for analysis.  For standard analyses, software is often provided by the assay manufacturers, and can be utilized by a skilled lab worker. However, some projects at RMA require that we develop specialized software to answer specific questions of the data. Data must be merged and managed appropriately, so that RMA research data can be merged with data from the clinical practice, and then enhanced with public repository data from sources such as the National Institutes of Health.  Further development of specialized analysis methods, software and research data management requires a good understanding of physiology, molecular biology, informatics, computer programming and statistics. This effort of data management, development and analysis is typically termed ‘bioinformatics’ and is a career for thousands of scientists world-wide.

There are many opportunities for trainees to become involved in the bioinformatics effort.   RMA has continuing bioinformatics projects in genomics, genetics, systems biology and assay development. Some ongoing research projects at RMA include:

  • Identifying genetic causes of infertility by genetic case-control analysis of infertile couples chosen for specific clinical outcomes
  • Studying novel methods for detecting aneuploidy in embryos through current biopsy techniques
  • Developing non-invasive genomic methods to detect aneuploidy in embryos

Because RMA utilizes high throughput data across several aspects of its research and practice,   many people are involved in various aspects of the bioinformatics effort at RMA including students, technicians, postdoctoral fellows, scientists, nurses and doctors. The ability to merge clinical and research data together in the study of human reproduction makes this an exciting time to be training at RMA. 

Fellows will have the opportunity to submit and present their research at the American Society Reproductive Medicine Annual Meeting and other relevant meetings.  

Summary

There are a wide variety of active research projects ongoing at the current time involving many areas of reproduction.  Fellows will be expected to participate actively in several projects and to focus on a particular area.  It is important to become a genuine expert in a particular methodology and scientific area of investigation when building an academic career.  A motivated fellow should be able to complete their fellowship with several clinical and basic science publications reflecting high quality prospective and novel investigations.  They will also have the knowledge and demonstrated experience to establish their own independent research program as they move forward in their academic career.