Gene Alteration Clinical Condition And Intervention

$79 / year

The Clinical Genomic Database (CGD) purpose is to correlate genetic data with clinical settings, matching diseases with their genetic cause. The database includes all diseases with a known genetic cause of a single gene alteration. The dataset includes descriptions for the gene and inheritance, as well as for the manifestations and interventions to consider. The dataset does not contain contiguous gene syndromes or somatic alterations unless these result from a same gene germline change. The genetic conditions are ordered and categorized by organ system.

Complexity

“The Clinical Genomic Database (CGD) has been constructed to reflect the multisystemic nature of many genetic conditions in order to allow more comprehensive browsing by clinical categories. In the CGD, genes were first categorized into Manifestation categories, or the organ system(s) primarily affected by mutations in the corresponding gene. For many of these organ systems, recognition of the condition’s effects and related supportive care may be clinically beneficial. Conditions not grouped within a specific organ system under the Manifestation categories were included in the General category.

Next, genes were separately categorized under Intervention categories by the organ system(s) for which specific medical interventions were available. In determining the Intervention categories, the following points were considered: 1) the condition must be clinically significant (i.e., at least some manifestations must result in morbidity and mortality); 2) there must be a currently available, potentially beneficial intervention (this intervention may include preventive measures, surveillance, or medical and/or surgical treatments, though experimental/research-based interventions were not included); 3) there should be advantage to early (“genomic”) diagnosis as opposed to discovery of the condition on purely clinical grounds (i.e., without genetic/genomic testing). Regarding this last point, precise diagnosis is challenging for many conditions, and correct recognition based on genetic/genomic diagnosis may allow interventions related to specific manifestations. The efficacy of these interventions would be diminished or lost with later diagnosis, such as might occur based primarily upon clinical presentation.

For the Intervention categories, all genes not meeting the above criteria were included in the General category. As described, for many such conditions, while a more specific intervention may not be currently available, genetic knowledge may be beneficial related to a number of issues, including the selection of optimal supportive care, prognostic considerations related to medical-decision making, informing reproductive decisions, and avoidance of unnecessary testing as part of the diagnostic process.

A key barrier to translating the power of genomic sequencing to the clinical setting involves the time and resources required for clinically-relevant analysis. To help address this barrier, we constructed the Clinical Genomic Database (CGD), a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.

All conditions with identified genetic causes are included in the CGD. For each entry, the database includes the gene symbol, condition(s), allelic conditions, inheritance, age (pediatric or adult) in which interventions are indicated, clinical categorization, and a general description of interventions/rationale. The contents are not intended to serve as nor substitute for comprehensive clinical guidelines, but are rather intended to briefly describe the types of interventions that might be considered.

The database includes only single gene alterations (it does not include contiguous gene syndromes, although some conditions with, for example, digenic inheritance are included), and does not include genetic associations or susceptibility factors related to more complex diseases, such as identified through association-based studies. Somatic alterations, such as commonly occur in cancerous processes, are not included unless a germline change in the same gene results in disease.”

Description source: National Human Genome Research Institute, N.H.G.R.I. (2016). NIH.gov. Retrieved 12 November, 2016.

Date Created

2013-05-21

Last Modified

2016-10-13

Version

2016-10-13

Update Frequency

Continuous

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs => National Human Genome Research Institute

Source License URL

John Snow Labs Standard License

Source License Requirements

N/A

Source Citation

Solomon BD. Clinical Genomic Database. Proc Natl Acad Sci U S A. 2013 May 21.

Keywords

Genetic Correlation, Genetic Association, Genetic Diseases, Gene Syndrome, Genetic Association, Organ Systems, Genomics, Disease Interventions, Disease Manifestation

Other Titles

Organ Systems Genetic Conditions, Clinical Genomic Database, Clinical Conditions With Genetic Causes

Name Description Type Constraints
GeneSymbol of the gene associated with a clinical conditionstringunique : 1 required : 1
HGNC_IDIdentification number of the gene given by HUGO Gene Nomenclature Committee (HGNC)integerunique : 1 required : 1 level : Nominal
Entrez_Gene_IDA unique integer identifier or ID assigned by Entrez Gene which is the gene-specific database at the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM).integerunique : 1 required : 1 level : Nominal
ConditionConditions with known genetic causesstringrequired : 1
InheritanceType of genetic transmission of traits from parents to offspring. Types are: AR means autosomal recessive, AD means autosomal dominant, XL means sex linked, Digenic, methylation, BG means Blood group relatedstringrequired : 1
Age_GroupAge (pediatric or adult) in which interventions are indicatedstring-
Allelic_ConditionsConditions also resulting from mutations in the same gene, but which would otherwise be categorized in the "general" category for intervention categoriesstring-
Manifestation_CategoriesThe organ system(s) primarily affected by mutations in the corresponding gene. For many of these organ systems, recognition of the condition's effects and related supportive care may be clinically beneficial. Conditions not grouped within a specific organ system under the Manifestation categories were included in the General categorystringrequired : 1
Intervention_CategoriesThe organ system(s) for which specific medical interventions were available. In determining the Intervention categories, the following points were considered: 1) the condition must be clinically significant (i.e., at least some manifestations must result in morbidity and mortality); 2) there must be a currently available, potentially beneficial intervention (this intervention may include preventive measures, surveillance, or medical and/or surgical treatments, though experimental/research-based interventions were not included); 3) there should be advantage to early (“genomic”) diagnosis as opposed to discovery of the condition on purely clinical grounds (i.e., without genetic/genomic testing). For the Intervention categories, all genes not meeting the above criteria were included in the General category.stringrequired : 1
CommentsSome important information about the conditionstring-
Intervention_Or_RationaleSignificance of early intervention based on the genetic information in this particular conditionstringrequired : 1
ReferencesPubmed ID numbers from the NCBI website for referring the articlestringrequired : 1
GeneHGNC_IDEntrez_Gene_IDConditionInheritanceAge_GroupAllelic_ConditionsManifestation_CategoriesIntervention_CategoriesCommentsIntervention_Or_RationaleReferences
DGCR228459993SchizophreniaADNeurologicGeneralEvidence or clinical applicability unclear21822266
ZIM21287523619SchizophreniaADNeurologicGeneralEvidence or clinical applicability unclear21743468
CHD419191108SchizophreniaADNeurologicGeneralEvidence or clinical applicability is unclear21743468
LRP166924035SchizophreniaADNeurologicGeneralEvidence or clinical applicability is unclear21743468
EPX34238288Eosinophil peroxidase deficiencyARGeneralGeneralThe clinical relevance is unclear7809065
ESAM1747490952SchizophreniaADNeurologicGeneralEvidence or clinical applicability is unclear21822266
FUT640172528Fucosyltransferase 6 deficiencyARBiochemicalGeneralClinical relevance is unclear8175676
NRIP180018204SchizophreniaADNeurologicGeneralEvidence or clinical applicability is unclear21743468
ZNF48023305147657SchizophreniaADNeurologicGeneralEvidence or clinical applicability unclear21743468
CCDC13733451339230SchizophreniaADNeurologicGeneralEvidence or clinical applicability unclear21743468