Funding opportunities

Derivation of Novel Late Onset Disease-Specific Stem Cell Lines Using Highly Accurate Single Cell Genotyping Technology

Funding Type: 
New Cell Lines
Grant Number: 
RL1-00668
Funds requested: 
$1 315 032
Funding Recommendations: 
Not recommended
Grant approved: 
No
Public Abstract: 
The creation, propagation, and free distribution of novel human embryonic stem cell (hESC) lines are urgently needed in order to bring medical researchers one step closer to successfully treating many of the existing debilitating diseases. Although several federally approved embryonic stem cell lines exist, they are limited in their utility for a variety of reasons, most notably lack of genetic diversity. In order to fill this gap, we propose to derive novel hESC lines from embryos with inherited susceptibility to diseases that are relatively common and debilitating, such as cardiomyopathy, type II diabetes, early onset Alzheimer’s disease, and familial early onset breast cancer. Preimplantation genetic diagnosis (PGD) of embryos during in vitro fertilization (IVF) remains the most effective method for derivation of disease-specific hESC lines, and is the focus of this application. A major drawback of current PGD methods is their inability to simultaneously detect both aneuploidy (a change in the number of chromosomes) and multiple genes known to cause a disease. Most PGD screens for embryos with abnormal number of chromosomes to improve implantation rates and reduce spontaneous abortions, and in nearly all other cases, PGD only screens for diseases that develop during early childhood. As a result, none of the PGD screens for diseases that develop during adulthood. We will be able to create that opportunity with our {REDACTED} product, which is the only method that can simultaenously measure both disease-linked genes and aneuploidy in a single cell isolated from an embryo. In collaboration with our key California IVF clinic partners, we plan to first test our PSTM technology with unused embryos, and then apply the technology to screen hundreds to thousands of embryos per year. Given our ability to test for both chromosome abnormalities and genetic disease simultaneously, we will be in a unique position to screen each of these embryos for diseases that are not routinely tested by other PGD methods. With the parents’ consent, embryos that test positive for susceptibility to diseases of interest will be used to derive hESC lines and made available for free distribution to the research community worldwide. If funded, we will derive hESC lines that will make several critical contributions to the field of stem cell research, ranging from empowering scientists to answer fundamental biological questions to facilitating the development of safe targeted therapeutics.
Statement of Benefit to California: 
Our company is headquartered in {REDACTED}. We provide technical, high-salaried employment for dozens of California residents. With Series A venture backing from {REDACTED} we have outlined an ambitious plan for growth, promising to bring even more jobs to the state. Additionally, we have close strategic partnerships with three California-based IVF clinics: {REDACTED} These IVF clinics, and their patients, will be among the first beneficiaries of our groundbreaking technologies. Most importantly, if this grant is funded, our company will, in collaboration with the {REDACTED} Department of Genetics, help bring novel human embryonic stem cell lines to California scientists. These disease-specific lines will be a superb resource for California researchers working to understand, prevent, and cure debilitating genetic diseases. This resource will help keep California at the forefront of stem cell research worldwide, enriching our local economy and earning further prestige for nonprofit research institutions. Local drug companies will benefit from local resources in nonprofit stem cell research. Finally, California residents could eventually benefit from advances in medicine that result from this important local biological resource.
Review Summary: 
Executive Summary The applicant proposes to validate their proprietary and novel technology for Pre-implantation Genetic Diagnosis (PGD). The technology is designed to assess genetic information at a large number of disease-linked loci and to simultaneously measure chromosome copy number across all 24 chromosomes using single blastomeres extracted from human embryos. The applicant will also use embryos identified using this technology to generate human embryonic stem cell (hESC) lines carrying genetic risk factors for cardiomyopathy, familial early onset breast cancer, familial early onset Alzheimer’s disease and type 2 diabetes mellitus. The establishment of hESC bearing particular genetic risk variants is highly important as the availability of reliable human cell-based models for the diseases targeted in this application would provide valuable research tools and might even lead to new therapies. The applicant proposes to validate their pre-implantation genetic assessment technology. If this relatively untested technique were to work it would provide a leap forward in PGD. However, reviewers felt the method is unnecessary to discriminate affected embryos for the four diseases identified as targets for cell line derivation. These diseases would perhaps be better and more readily identified via traditional PGD approaches as they are all associated with very specific mutations. By relying on an un-validated PGD technique the overall feasibility of this proposal is therefore questionable. Furthermore, reviewers criticized that no independent quality assurance of the proprietary technology is presented or available, either through publication or through independent review by a third party, and critical experimental detail was lacking as well. This part of the proposal is thus hard to evaluate. For instance, a detailed description of the algorithm that enables the genetic assessment as proposed is minimally necessary if no independently evaluated data as to its effectiveness is to be presented. Reviewers noted that the principal investigator is highly entrepreneurial and has assembled an impressive network of collaborators, including an expert in hESC derivation. Concern was expressed that certain milestones described in the supporting material so far have not been met. Reviewer Synopsis The PI proposes the derivation of disease-specific human embryonic stem cell lines and using a new technology called Parental Support TM. Newly developed IVF PID tool This technology seems to screen for a range of different SNPs. Their method seems to be capable of measuring a large number of disease-linked loci and simultaneously measure chromosome copy number across all 24 chromosomes. Using this technology they will derive cell lines that have inherited susceptibility to more late onset diseases. They want to target diseases like cardiomyopathy, type II diabetes, Alzheimer’s, early onset breast cancer. They will do this by first “validating the power of PS TM” technology by looking at disease loci. Then, in a second step, they will derive specific cell lines Reviewer One Comments Significance: The establishment of human stem cell lines bearing particular genetic risk variants is highly important as detailed investigation may reveal new insights into how these mutations affect development and also provide opportunities for developing new therapeutics. Dr. Rabinowitz is highly entrepreneurial and has assembled an impressive network of collaborators. Feasibility: The proposal is divided into two Aims: validation of Genesecurity Network’s method for Pre-implantation Genetic Diagnosis using the Parental SupportTM product and to produce hESC lines with genetic risk factors for cardiomyopathy, familial early onset breast cancer, familial early onset Alzheimer’s disease and the Pro12Ala variant of PPARgamma2 that increases risk of type 2 diabetes mellitus Aim 1 is problematic for a number of reasons - No independent quality assurance of the Parental SupportTM product is presented or available, either through publication or by independent review by a third party. This part of the proposal is thus hard to evaluate. - Inadequate description of algorithms used. Although in principle Bayesian approaches using parental haplotypes to infer the presence of the risk haplotype in the blastomere, are feasible, even when there may be a failure rate of ~20% for any particular SNP in that haplotype, a detailed description of the implementation of the algorithm is minimally necessary if no independently evaluated data as to its effectiveness is to be presented. - Milestones described in the supporting material so far have not been met. For example, in the supporting material for the Stanford IVF, publication as part of Phase 2 to be completed Q2, 2007 has not occurred. - It is not clear how Aim 1 differs from the work already funded by the SBIR grants previously awarded to the PI. Aim 2 also lacks adequate description but the involvement of the Baker group is a strength. A lack of technical detail hampers evaluation. - Are the disease alleles to be inferred from the Illumina Infinium II array that will be used as part of the Parental SupportTM product. If so, how? - If instead a custom array will be used, what is the design? Will it be used for each potential mother and father? - If not, given that these are mostly early onset diseases, and given the aim of establishing only 6 hESC lines, wouldn’t it be most cost-effective to use this approach on those disease families who come forward for Pre-implantation Genetic Diagnosis; the probability of successfully identifying blastomeres with the genetic risk factor will be much higher and recruitment expenses much lower. Responsiveness to RFA: Aim 2 is responsive to the RFA, Aim 1 less so. Reviewer Two Comments Significance: The goal of this proposal is the creation of new human embryonic stem (hES) cells from embryos harboring genetic variants conferring susceptibility to cardiomyopathy, type II diabetes, early onset Alzheimer’s disease, and familial early onset breast cancer. Reliable human cell-based models for these diseases would provide valuable research tools and might even lead to new therapies. Feasibility: Rabinowitz and colleagues propose to validate their proprietary and novel technology designed to assess genetic information at thousands of loci across all chromosomes using single blastomeres extracted from a human embryo. If this relatively untested technique were to work it would provide a leap forward in preimplantation genetic diagnosis (PGD) but is wholly unnecessary to discriminate affected embryos for the four diseases identified as targets for cell line derivation. These diseases would perhaps be better and more readily identified via traditional PGD approaches as they are all associated with very specific mutations. By relying on an un-validated PGD technique the overall feasibility of this proposal is therefore questionable and the logic behind aim 1 is unclear. Responsiveness to RFA: This proposal is very responsive to the RFA.
Conflicts: 

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