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MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome.

Lange J, Skaletsky H, Bell GW, Page DC - Nucleic Acids Res. (2007)

Bottom Line: Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer.Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes.MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.

View Article: PubMed Central - PubMed

Affiliation: Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA.

ABSTRACT
Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer. Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes. Such deletion mapping is usually conducted using polymerase chain reaction (PCR) assays for the presence or absence of a series of Y-chromosomal DNA markers, or sequence-tagged sites (STSs). In the course of mapping intact and aberrant Y chromosomes during the past two decades, we and our colleagues have developed robust PCR assays for 1287 Y-specific STSs. These PCR assays amplify 1698 loci at an average spacing of <14 kb across the MSY euchromatin. To facilitate mapping of deletions, we have compiled a database of these STSs, MSY Breakpoint Mapper (http://breakpointmapper.wi.mit.edu/). When queried, this online database provides regionally targeted catalogs of STSs and nearby genes. MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.

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Related in: MedlinePlus

An example of query results. (A) Querying the database for STSs in the 50-kb interval surrounding sY14. (B) The queried interval contains 14 STSs. For each STS, the table lists sequence coordinates, PCR product length, primers, PCR conditions (as a link to a pop-up), GenBank accession number (as a link to the NCBI entry), and in the case of a multi-copy STS, sequence coordinates of co-amplified loci. (C) The custom Y chromosome browser indicates the location of the queried interval, and the identities and positions of all STSs and protein-coding genes within the interval.
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Figure 3: An example of query results. (A) Querying the database for STSs in the 50-kb interval surrounding sY14. (B) The queried interval contains 14 STSs. For each STS, the table lists sequence coordinates, PCR product length, primers, PCR conditions (as a link to a pop-up), GenBank accession number (as a link to the NCBI entry), and in the case of a multi-copy STS, sequence coordinates of co-amplified loci. (C) The custom Y chromosome browser indicates the location of the queried interval, and the identities and positions of all STSs and protein-coding genes within the interval.

Mentions: Regardless of the mode of query, the resulting catalog of STSs is displayed in two ways: as a table and in a custom Y chromosome browser (Figure 3). For each STS, the table indicates start and end sequence coordinates, PCR product length, primer sequences, amplification conditions and GenBank accession number. Multi-copy STSs are identified as such, and the sequence coordinates of each additional locus of amplification are tabulated. Below the table, a custom Y chromosome browser displays the region encompassing the cataloged STSs. The position of each STS and of each protein-coding gene within the interval is indicated. The user can also interrogate the Y chromosome browser independent of the initial STS database query.Figure 3.


MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome.

Lange J, Skaletsky H, Bell GW, Page DC - Nucleic Acids Res. (2007)

An example of query results. (A) Querying the database for STSs in the 50-kb interval surrounding sY14. (B) The queried interval contains 14 STSs. For each STS, the table lists sequence coordinates, PCR product length, primers, PCR conditions (as a link to a pop-up), GenBank accession number (as a link to the NCBI entry), and in the case of a multi-copy STS, sequence coordinates of co-amplified loci. (C) The custom Y chromosome browser indicates the location of the queried interval, and the identities and positions of all STSs and protein-coding genes within the interval.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238960&req=5

Figure 3: An example of query results. (A) Querying the database for STSs in the 50-kb interval surrounding sY14. (B) The queried interval contains 14 STSs. For each STS, the table lists sequence coordinates, PCR product length, primers, PCR conditions (as a link to a pop-up), GenBank accession number (as a link to the NCBI entry), and in the case of a multi-copy STS, sequence coordinates of co-amplified loci. (C) The custom Y chromosome browser indicates the location of the queried interval, and the identities and positions of all STSs and protein-coding genes within the interval.
Mentions: Regardless of the mode of query, the resulting catalog of STSs is displayed in two ways: as a table and in a custom Y chromosome browser (Figure 3). For each STS, the table indicates start and end sequence coordinates, PCR product length, primer sequences, amplification conditions and GenBank accession number. Multi-copy STSs are identified as such, and the sequence coordinates of each additional locus of amplification are tabulated. Below the table, a custom Y chromosome browser displays the region encompassing the cataloged STSs. The position of each STS and of each protein-coding gene within the interval is indicated. The user can also interrogate the Y chromosome browser independent of the initial STS database query.Figure 3.

Bottom Line: Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer.Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes.MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.

View Article: PubMed Central - PubMed

Affiliation: Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA.

ABSTRACT
Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer. Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes. Such deletion mapping is usually conducted using polymerase chain reaction (PCR) assays for the presence or absence of a series of Y-chromosomal DNA markers, or sequence-tagged sites (STSs). In the course of mapping intact and aberrant Y chromosomes during the past two decades, we and our colleagues have developed robust PCR assays for 1287 Y-specific STSs. These PCR assays amplify 1698 loci at an average spacing of <14 kb across the MSY euchromatin. To facilitate mapping of deletions, we have compiled a database of these STSs, MSY Breakpoint Mapper (http://breakpointmapper.wi.mit.edu/). When queried, this online database provides regionally targeted catalogs of STSs and nearby genes. MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.

Show MeSH
Related in: MedlinePlus