Frequency Asked Questions (FAQs)

1   Can multiple genomic coordinates be entered?

You can enter as many ranges of genomic coordinates as you wish, separated with spaces, and/or commas, and/or new lines.

Ranges of genomic coordinates can be entered in the following formats:

chromosome:start_position-end_position

For example:

1:100000-400000

Or:

chr1:100,000-400,000

2   Which assembly/build is used for the data?

The GRCh38/hg38 assembly is used for all the data in this system.

You can enter genomic coordinate ranges in NCBI36/hg18, or GRCh37/hg19, and select the appropriate assembly. The system will automatically lift-over your coordinate ranges to GRCh38/hg38.

All results are provided using the GRCh38 / hg38 assembly.

3   Can I search on cytogenetic coordinates?

Cytogenetic coordinate searches are not supported in GeneScout but can be searched in OMIM.org.

4   Can I ascertain the overlapping or unique coordinates between two individuals?

Coordinate ranges of two individuals can be compared in GeneScout. Selecting Intersection restricts results to genes in the overlapping region (intersection) between the two sets of coordinates. Selecting Subtraction restricts the results to genes the non-overlapping region (relative complement) between the two sets.

5   How often are the data updated?

The underlying data are updated daily. See the About page for data sources.

6   How do I restrict my retrieval to genes with recessive phenotypes?

The default retrieval includes all RefSeq genes. This retrieval can then be filtered to include only OMIM disorders genes with recessive inheritance using the buttons above the retrieval table.

7   How can I save my results?

Your results can be download in Excel and tab-delimited formats from the links at the top and bottom of the result table. In addition, your results can be printed or saved as a PDF file.

8   Why don’t all my coordinates lift-over?

Segments of the genome may be removed or added between genome builds. Therefore, there is not a 1:1 correlation between genomic regions between builds. When the UCSC Liftover tool cannot map the coordinate range(s) from earlier builds, NCBI/hg18 or GRCh37/hg19 build, to the current build, GRCh38/hg38, the unmapped coordinate range(s) will be listed under "Coordinates that failed liftover." More information about genome builds can be found at the USCS Genome Brower website and NCBI Assembly Help website.

See also, Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. PMID: 12045153, PMCID: PMC186604, DOI: 10.1101/gr.229102.

9   Why do some phenotypes display that do not include the clinical features I submitted?

Clinical features are searched for within the text of allelic variants of gene entries and all phenotype entries and clinical synopses. The phenotype MIM # is highlighted if anything in the phenotype-gene pair contains the submitted clinical feature(s).

10   When I compare two sets of genomic regions why are some excluded?

If coordinate ranges cannot be lifted-over to GRCh38/hg38, the region(s) cannot be compared and will be listed under "Coordinates that Failed to Liftover." See FAQ 8.

11   How are CoI and CoR calculated?

GeneScout sums the total number of basepairs in the input genomic coordinate range(s). This is displayed as the Summed ROH. The CoI is calculated by dividing the Summed ROH by the total number of basepairs in the genome (~3 billion). [Note: The total number of basepairs in the genome is different for each genomic build.] The CoR is calculated by multiplying the CoI by 2. CoI and CoR calculations result in a decimal that is displayed as the nearest fraction for ease of use.