Request for Information: Whole Genome Sequencing, Data Analysis, Storage and Annotation
Release
Date: May 11, 2011
Response
Date: May 30, 2011
National Institute of Neurological Disorders and Stroke (NINDS)
This is a time sensitive Request for Information (RFI) issued by the National Institute of Neurological Disorders and Stroke (NINDS). The purpose of the RFI is to solicit information on the research needs of the NINDS community for whole genome sequencing services and accompanying data storage, analysis and annotation services. The responses to the RFI will be collected and evaluated by Institute staff to assess how best to meet the current and future needs for whole genome sequencing as it relates to neurologic disease.
Rapid and significant changes in technology continue to advance our understanding of human biology and disease with technological applications ranging from single molecule to whole genome approaches. One of these technologies, massively parallel sequencing or Next Generation Sequencing (NGS) has revolutionized our ability to identify rare variants and as yet unidentified Mendelian mutations related to disease. Although it is not clear which NGS technology will eventually dominate the genomic research field, technological developments are resulting in reductions in cost and rapid increases in sequencing speed with improved accuracy. The reality of these advancements in sequencing technology now enables re-sequencing of the whole human genome to be achieved within weeks instead of months to years with unprecedented accuracy. NGS technologies are leading to new strategies in the understanding of monogenic Mendelian diseases allowing the identification of causative mutations in disorders that were not amenable to linkage-based positional cloning [Lupski J.R. et al., 2010].
Although cost and availability of services may play a role
in determining the NGS approach (exome verses whole genome), understanding the
underlying complexity of the disease phenotype is a key to selection and
eventual success in identifying the causative mutation. Since the technologic
advancements in NGS have been rapid, the volume and complexity of the
information captured through NGS challenges the storage and processing
capabilities of many laboratories and institutions. If all roadblocks to
accessing NGS services and processing of NGS data were removed, perhaps the
greatest challenge will be the analysis and annotation of data to effectively
differentiate between the many rare benign variants detected by novel genomic
techniques and disease causing mutations.
This RFI is meant to solicit information from extramural research investigators regarding the type and availability of projects that can be advanced through whole genome sequencing services. The RFI also solicits information on institutional capabilities for sequence storage, data analysis and annotation. Responses to this RFI will be reviewed by NINDS staff and will help inform and complement their assessment of current and future whole genome sequencing needs. This RFI is for planning purposes only, and should not be construed as a solicitation for applications or proposals and/or as an obligation in any way on the part of the United States Federal Government.
1. Describe the whole genome sequencing services available or planned at your institution.
2. Describe the composition of your research cohort (e.g. small or large families, population based) which will utilize whole genome sequencing.
3. Indicate how you anticipate whole genome sequencing will contribute to your field of research.
4. Provide your rationale for choosing whole genome sequencing over whole exome sequencing.
5. If you plan to utilize whole genome sequencing, how many samples would you sequence within the next 12 months? How will these samples be chosen?
6. Outline the plans of your laboratory or institution regarding storage capacity for raw data generated from whole genome sequencing.
7. What are the plans of your laboratory or institution regarding analytical support for sequence assembly, variant identification and annotation?
8. Provide your perspective on the constraints regarding the public sharing of genomic sequences and associated phenotype for your research cohort.
1. Please identify the nature of your interest in the area of whole genome sequencing services (i.e. are you a biomedical or clinical researcher, a member of an advocacy or community group, or other?).
2. If you are a member of a particular advocacy or professional organization, please indicate the name of the organization.
3. Please indicate your main area of research interest.
4. Your name
5. Your email address
* Note: All of the preceding fields are optional. Proprietary, classified, confidential, or sensitive information should not be included in your response.
Responses must be submitted electronically using the web-based form (http://www.ninds.nih.gov/funding/areas/neurodegeneration/RFI-for-Whole-Genome-Sequencing.htm
and will be accepted through May 30, 2011. Replies to individual questions are optional, and the site will permit anonymous responses. The information provided will be analyzed and may appear in various reports.
Please direct all inquiries to:
Margaret Sutherland, PhD
Program Director, Neurodegeneration Cluster
NINDS / NIH
6001 Executive Blvd., Rm 2222
Bethesda, MD 20892
Phone: 301-496-5680
Fax: 301-480-1080
E-mail: sutherlandm@ninds.nih.gov
and Human Services (HHS)
