Search Help

1.1   Basic search:

Genomic coordinate ranges are required to run a search. Multiple coordinate ranges should be separated with spaces, commas, or on new lines and have the format:

chromosome:start_position-end_position

For example:

1:100000-400000

Or:

chr1:100,000-400,000

1.2   Selecting a genomic build:

This tool supports input coordinates in three builds, NCBI36/hg18, GRCh37/hg19, or GRCh38/hg38. If your coordinates are not in hg38, select either hg18 or hg19 so that your coordinates can be lifted over to hg38. Not all coordinates can be lifted over between assemblies and coordinates that cannot be lifted over will be displayed above your retrieval. Results are provided in the GRCh38/hg38 assembly.

1.3   Calculating Coefficient of Inbreeding and Coefficient of Relationship (CoI/CoR):

If the coordinates you have entered are 'Runs of Homozygosity’ (ROH), select the button to have the CoI and CoR computed and displayed above your search result.

2.1   Comparing coordinates between 2 family members:

Enter coordinates for the proband in the top box and add the relative’s coordinates in the second box, selecting the appropriate genomic build for each set of coordinates. If you want to search for coordinates that are shared between two individuals (the intersection), click the button labeled Intersection. This is useful for showing the minimal regions shared by 2 affected individuals in family. Alternatively, if you want to search for the unique coordinates in the proband by subtracting the shared regions (relative complement) between the two sets of coordinates, click the button labeled Subtraction.

3.1   Refining your search with gene filters:

All displays the genes within your coordinates that are part of the NCBI reference sequence genes. OMIM filters the retrieval set to genes in OMIM that are within your search coordinates. OMIM disease, restricts the set to genes in OMIM that are associated with a phenotype.

3.2   Refining your search by mode of inheritance of a phenotype:

Dominant and Recessive refine the set of OMIM disease genes by the inheritance of the phenotype(s) associated with the gene. Some genes may have multiple phenotypes, each with a unique inheritance mode.

3.3   Refining your search by clinical feature:

An OMIM disease gene filter can be further refined by searching for clinical feature(s) within an OMIM disease gene set. Type your desired clinical features into the Clinical Features search bar. If the feature is more than 2 words, use quotes, (e.g., diaphragmatic hernia would be searched as “diaphragmatic hernia”). It is recommended that no more than 3 features are used to restrict a given search. These features will be used in a search of OMIM’s clinical entries, clinical synopses, and allelic variants. The MIM numbers for the entries containing your clinical feature term(s) will be highlighted in yellow in the search results.

4.1   Comparing the clinical synopses of phenotypes in a retrieval set:

To compare clinical synopses of phenotypes side-by-side in OMIM, check boxes next to the Phenotype MIM#. Up to 6 phenotypes may be selected.