MSY Breakpoint Mapper       Home | Breakpoint Mapper | User Guide | Publications | Page Laboratory | Contact

User Guide

Data input

To test your genomic DNA sample for a Y chromosome deletion by assaying for the presence or absence of STSs, we recommend starting with landmark STSs. On the Breakpoint Mapper page, see figure for locations of landmark STSs and click on Table of landmark STSs under Reference Tools for information on their use.

The Reference Tools also contain links to figures displaying deletion maps of common interstitial deletions or of isodicentric Y chromosomes and Y isochromosomes. Having tested your sample with landmark STSs, you can compare your results with these STS maps.

Two modes of querying the database are available:

  • Generate a catalog of STSs between two loci by selecting two landmark STSs from pull-down menus; by selecting any two STSs in the database from pull-down menus; or by entering any two Y chromosome sequence coordinates. See example.

  • Generate a catalog of STSs in the vicinity of a particular STS or Y chromosome sequence coordinate by selecting the STS from a pull-down menu or entering the sequence coordinate, and selecting a surrounding size interval from a pull-down menu. See example.

Data output

The resulting catalog of STSs is displayed as a table and in a custom,Y chromosome browser. Within the browser, you can click on STSs and genes for further information on their sequence.

STS sequence coordinates and Y chromosome browser positions are based on NCBI Build 38.

Due to the abundance of large repeats with >99.9% sequence identity in the MSY, numerous STSs amplify multiple loci. In the output table, such multi-copy STSs are indicated with an asterisk in the second column, and sequence coordinates of co-amplified loci are shown in the final column.

Notes of caution

  • Absence of a single STS should be interpreted with caution as nucleotide polymorphism may account for such a result.

  • Structural polymorphism in the MSY can alter the order and locations of STSs.

  • In the NCBI Build 38 assembly of the Y chromosome, portions of a ~22-kb sequence on Yq appear duplicated in a nearby region that was a gap in the previous assembly. Because this duplicated sequence is based on short reads and not on reliable, high quality sequence, we are not confident in this specific aspect of the new assembly. Nevertheless, we advise caution in the interpretation of the ten STSs found within the original ~22-kb segment: sY1109, sY1213, sY1214, sY3227, sY3222, sY3226, sY3223, sY3228, sY3225, and sY3017.

Browser compatibility

For ease of use, we recommend Mozilla Firefox or Internet Explorer.