Data AnalysisNCT00339508
Exploratory Data Analysis for Disease Pedigrees and Cancer Genetics
An observational study of Data Analysis and Cancer Genetics, run by National Human Genome Research Institute (NHGRI) at 1 site in United States.
Trial summary
The researchers have developed and distributed several software packages for pedigree analysis (FAST, CASPAR, PedHunter, IIC) and cancer genetics (oncotree, METREX). Users who need assistance with the software or who want to see new features added often send the researchers data files that include human data. Read more about this study
- Who is it for?
- Any age
- Conditions the study is for
- Data Analysis, Cancer Genetics
- How many people
- 13,385 participants
- Where
- 1 siteUnited States
- Study dates
- 19 Mar 2002to 9 May 2017
- Phase
- Observational
- Are there results?
- None posted in the registry
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages Any age
- All sexes
- No healthy volunteers
- Child, Adult, Older adult
Who may be able to join
- User Requests:
- When receiving data sets for problem reports and/or new feature requests, all data sets would be accepted. We would not consider how the data were collected. The reasons for this are: the medical aspects of the data set are irrelevant to the reason we receiving the data; we cannot respond promptly to problem reports, if we have to get details on how the data were collected; the data are never used by us for any research into the traits being studies by the researchers who collected data.
- Collaborations:
- For collaborative studies, we would request details of how the data were collected, including evidence of approval by a local ethics board. We would submit to the NHGRI IRB an amendment describing the new collaboration. That amendment would necessarily include a formal indication that the collaborating research group has permission to collect and analyze the human data that they present to us (in coded and summarized format). For collaborators in the United States that permission would consist of an IRB-approved protocol or exemption from the collaborator's institution. For collaborators outside the United States the permission would be one of the types of agreements currently supported by the NIH Office of Human Subjects Research.
- If we do not see evidence of appropriate permission to collect the data or the IRB turns down our proposed amendment, then we would exclude ourselves from participating in the proposed collaboration.
- There are two other circumstances under which we have also excluded collaborating on analysis of data sets in the past and may do so in the future. One circumstance was where we did not feel that the proposed data set could possibly give sufficient statistical power to detect anything interesting. The other circumstance was where we had an existing collaboration with one research group, and a competing group asked us to collaborate also.
Who cannot join
None listed.
Trial locations and contacts
1 site in 1 country.
United States1 site
National Human Genome Research Institute (NHGRI), 9000 Rockville Pike
Bethesda, Maryland, 20892
About this study
The researchers have developed and distributed several software packages for pedigree analysis (FAST, CASPAR, PedHunter, IIC) and cancer genetics (oncotree, METREX). Users who need assistance with the software or who want to see new features added often send the researchers data files that include human data. The information is normally coded, and the researchers do not have access to the identification of the people whose information is in the files. Sometimes the content of the files gives rise to collaborations between the software developers and the providers of the files. Because concerns over the confidentiality of medical information have increased significantly over the past few years, the researchers must apply for exemptions from detailed ethics committee oversight for every data set they receive. This process is cumbersome and makes it difficult to assist software users. The amount of information required to apply for an exemption also poses a barrier to collaborations.
A full protocol will subject all data sets to ethics committee oversight without the need for individual exemption requests, enabling the researchers to assist users with software problems and to collaborate with other researchers.
Read more
From January 1, 2000, through December 15, 2001, the researchers received 71 requests for assistance, 19 of which included data files. None of the data files had any names or patient identifiers. Of these 19, in 8 cases the researchers sent back modified output files. In two of these eight cases, the researchers could see results of research interest; one of them concerned human data. In 2 of the 19 cases, the researchers sent back modified input files; in one such case, they established a collaboration with the originator of the files. In sum, most requests come under the heading of customer service, with no research contents. A few, however, do lead to research results or collaborations, for which ethics committee oversight is required.
Over the three-year time frame of this protocol, the researchers anticipate receiving data on a maximum of 10,000 individuals. They have modified their software documentation to explicitly instruct users to make sure the data files they send have no names. Should they receive files with names, they will delete the files and ask the originator to resubmit them with names encoded. Users submit data through unencrypted e-mail. The data are stored in password-protected computers at the National Institutes of Health.
Read the detailed description
We have developed software packages for pedigree analysis (FAST, CASPAR, PedHunter, IIC) and cancer genetics (oncotrees, METREX). The purpose of this protocol is to allow us to work on software problems reports that may contain human subjects data in them. The data should be coded, by which we mean that if there are any links between identifiers and names, we do not possess the links to decode the names. Occasionally our assistance leads to a more formal research collaboration. This protocol seeks to clarify the guidelines under which we can provide assistance to users of our human genetics software and to establish a formal procedure under which we can seek IRB approval for the serendipitous collaborations that arise from providing that assistance. We cannot predict the sizes of samples or the diseases studied in the data sets sent to us, so most of the medical aspects of this protocol are necessarily general. We rely on the data being coded and the collectors of the data having their own institutional approvals to protect against most risks. The scientific aspects of investigating problem reports cannot be hypothesis driven because we cannot guess what problems will arise. On the engineering side, the basic hypotheses are that: 1) our software is likely to contain some bugs or other weaknesses, which cannot be easily found except by having others use the software and 2) a good way to improve the functionality of the software is to encourage users to submit problem reports and other suggestions.
This protocol has been in effect since early 2002. The only amendments during that time were to set up three collaborations, as described in Sections 4.6 and 4.7 and 4.8. The protocol has been quite useful and no changes are proposed in procedures.
- Conditions
- Data Analysis, Cancer Genetics
- Keywords
- Linkage Analysis, Cancer Genetics, Software, Bug Reports, Computer Programs, Data Analysis
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted21 Jun 2006 (estimated)
- Study start19 Mar 2002
- Study completion9 May 2017
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (3)Papers the sponsor has linked to this study.
- Other trials for Data AnalysisStudies of the same condition, open and under way.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Enrolment
- 13,385 participants (actual)
Sponsor and investigators
- Lead sponsor
- National Human Genome Research Institute (NHGRI)
- Sponsor type
- US National Institutes of Health
- Responsible party
- Sponsor
- Investigators
- Alejandro A Schaffer, Ph.D., Principal investigator, National Human Genome Research Institute (NHGRI)
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT00339508
- Sponsor's protocol ID
- 999902152
- Other IDs
- 02-HG-N152
- Status last verified
- 9 May 2017
- First submitted
- 19 Jun 2006
- Last updated
- 5 Apr 2018
- Results posted
- No
Publications
Buhler J, Owerbach D, Schaffer AA, Kimmel M, Gabbay KH. Linkage analyses in type I diabetes mellitus using CASPAR, a software and statistical program for conditional analysis of polygenic diseases. Hum Hered. 1997 Jul-Aug;47(4):211-22. doi: 10.1159/000154415.
PubMed 9239508Desper R, Jiang F, Kallioniemi OP, Moch H, Papadimitriou CH, Schaffer AA. Inferring tree models for oncogenesis from comparative genome hybridization data. J Comput Biol. 1999 Spring;6(1):37-51. doi: 10.1089/cmb.1999.6.37.
PubMed 10223663Atkinson TP, Schaffer AA, Grimbacher B, Schroeder HW Jr, Woellner C, Zerbe CS, Puck JM. An immune defect causing dominant chronic mucocutaneous candidiasis and thyroid disease maps to chromosome 2p in a single family. Am J Hum Genet. 2001 Oct;69(4):791-803. doi: 10.1086/323611. Epub 2001 Aug 21.
PubMed 11517424
Study at a glance
From the registry record, last updated by the sponsor on 5 Apr 2018. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Exploratory Data Analysis for Disease Pedigrees and Cancer Genetics
- ClinicalTrials.gov ID
- NCT00339508
- Acronym / sponsor ID
- 999902152
- Conditions
- Data Analysis, Cancer Genetics
- Keywords
- Linkage Analysis, Cancer Genetics, Software, Bug Reports, Computer Programs, Data Analysis
- Study type
- Observational
- Recruitment status
- Completed
- Enrolment
- 13,385 participants (actual)
- Lead sponsor
- National Human Genome Research Institute (NHGRI)US National Institutes of Health
- Study start
- 19 Mar 2002
- Study completion
- 9 May 2017
- First posted
- 21 Jun 2006 (estimated)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
The researchers have developed and distributed several software packages for pedigree analysis (FAST, CASPAR, PedHunter, IIC) and cancer genetics (oncotree, METREX). Users who need assistance with the software or who want to see new features added often send the researchers data files that include human data. The information is normally coded, and the researchers do not have access to the identification of the people whose information is in the files. Sometimes the content of the files gives rise to collaborations between the software developers and the providers of the files. Because concerns over the confidentiality of medical information have increased significantly over the past few years, the researchers must apply for exemptions from detailed ethics committee oversight for every data set they receive. This process is cumbersome and makes it difficult to assist software users. The amount of information required to apply for an exemption also poses a barrier to collaborations.
A full protocol will subject all data sets to ethics committee oversight without the need for individual exemption requests, enabling the researchers to assist users with software problems and to collaborate with other researchers.
From January 1, 2000, through December 15, 2001, the researchers received 71 requests for assistance, 19 of which included data files. None of the data files had any names or patient identifiers. Of these 19, in 8 cases the researchers sent back modified output files. In two of these eight cases, the researchers could see results of research interest; one of them concerned human data. In 2 of the 19 cases, the researchers sent back modified input files; in one such case, they established a collaboration with the originator of the files. In sum, most requests come under the heading of customer service, with no research contents. A few, however, do lead to research results or collaborations, for which ethics committee oversight is required.
Over the three-year time frame of this protocol, the researchers anticipate receiving data on a maximum of 10,000 individuals. They have modified their software documentation to explicitly instruct users to make sure the data files they send have no names. Should they receive files with names, they will delete the files and ask the originator to resubmit them with names encoded. Users submit data through unencrypted e-mail. The data are stored in password-protected computers at the National Institutes of Health.
Detailed description
We have developed software packages for pedigree analysis (FAST, CASPAR, PedHunter, IIC) and cancer genetics (oncotrees, METREX). The purpose of this protocol is to allow us to work on software problems reports that may contain human subjects data in them. The data should be coded, by which we mean that if there are any links between identifiers and names, we do not possess the links to decode the names. Occasionally our assistance leads to a more formal research collaboration. This protocol seeks to clarify the guidelines under which we can provide assistance to users of our human genetics software and to establish a formal procedure under which we can seek IRB approval for the serendipitous collaborations that arise from providing that assistance. We cannot predict the sizes of samples or the diseases studied in the data sets sent to us, so most of the medical aspects of this protocol are necessarily general. We rely on the data being coded and the collectors of the data having their own institutional approvals to protect against most risks. The scientific aspects of investigating problem reports cannot be hypothesis driven because we cannot guess what problems will arise. On the engineering side, the basic hypotheses are that: 1) our software is likely to contain some bugs or other weaknesses, which cannot be easily found except by having others use the software and 2) a good way to improve the functionality of the software is to encourage users to submit problem reports and other suggestions.
This protocol has been in effect since early 2002. The only amendments during that time were to set up three collaborations, as described in Sections 4.6 and 4.7 and 4.8. The protocol has been quite useful and no changes are proposed in procedures.
Study design
Who may qualify
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Child, Adult, Older adult
Key inclusion criteria (6 listed)
- When receiving data sets for problem reports and/or new feature requests, all data sets would be accepted. We would not consider how the data were collected. The reasons for this are: the medical aspects of the data set are irrelevant to the reason we receiving the data; we cannot respond promptly to problem reports, if we have to get details on how the data were collected; the data are never used by us for any research into the traits being studies by the researchers who collected data.
- For collaborative studies, we would request details of how the data were collected, including evidence of approval by a local ethics board. We would submit to the NHGRI IRB an amendment describing the new collaboration. That amendment would necessarily include a formal indication that the collaborating research group has permission to collect and analyze the human data that they present to us (in coded and summarized format). For collaborators in the United States that permission would consist of an IRB-approved protocol or exemption from the collaborator's institution. For collaborators outside the United States the permission would be one of the types of agreements currently supported by the NIH Office of Human Subjects Research.
- If we do not see evidence of appropriate permission to collect the data or the IRB turns down our proposed amendment, then we would exclude ourselves from participating in the proposed collaboration.
- There are two other circumstances under which we have also excluded collaborating on analysis of data sets in the past and may do so in the future. One circumstance was where we did not feel that the proposed data set could possibly give sufficient statistical power to detect anything interesting. The other circumstance was where we had an existing collaboration with one research group, and a competing group asked us to collaborate also.
Key exclusion criteria (0 listed)
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Primary outcome
Not reported in the source record.
Results and safety
The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 5 Apr 2018.
- Background: PubMed 9239508Buhler J, Owerbach D, Schaffer AA, Kimmel M, Gabbay KH. Linkage analyses in type I diabetes mellitus using CASPAR, a software and statistical program for conditional analysis of polygenic diseases. Hum Hered. 1997 Jul-Aug;47(4):211-22. doi: 10.1159/000154415.
- Background: PubMed 10223663Desper R, Jiang F, Kallioniemi OP, Moch H, Papadimitriou CH, Schaffer AA. Inferring tree models for oncogenesis from comparative genome hybridization data. J Comput Biol. 1999 Spring;6(1):37-51. doi: 10.1089/cmb.1999.6.37.
- Background: PubMed 11517424Atkinson TP, Schaffer AA, Grimbacher B, Schroeder HW Jr, Woellner C, Zerbe CS, Puck JM. An immune defect causing dominant chronic mucocutaneous candidiasis and thyroid disease maps to chromosome 2p in a single family. Am J Hum Genet. 2001 Oct;69(4):791-803. doi: 10.1086/323611. Epub 2001 Aug 21.
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
Alejandro A Schaffer, Ph.D. principal investigator
National Human Genome Research Institute (NHGRI)
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Data Analysis and Cancer Genetics, run by National Human Genome Research Institute (NHGRI) at 1 site in United States.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 6 inclusion and 0 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: finished, as of the sponsor's last update on 5 Apr 2018. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in United States. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
Where can I read the original study information?
On the ClinicalTrials.gov record for NCT00339508, which also lists 3 linked publications.
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 5 Apr 2018.