108a8292fcf88caf44d11cc9b3dc3b9d1b3b8b29 donnak Mon Apr 14 09:38:32 2014 -0700 Updated Miga et al., Raney et al., and a few other references to reflect latest publication status. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 670e115..32f4f4b 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -84,31 +84,31 @@ <ul> <li> <b>Alternate sequences</b> - Several human chromosomal regions exhibit sufficient variability to prevent adequate representation by a single sequence. To address this, the GRCh38 assembly provides alternate sequence for selected variant regions through the inclusion of <em>alternate loci scaffolds</em> (or <em>alt loci</em>). Alt loci are separate accessioned sequences that are aligned to reference chromosomes. This assembly contains 261 alt loci, many of which are associated with the LRC/KIR area of chr19 and the MHC region on chr6. (See the <a href="../cgi-bin/hgTracks?chromInfoPage=">sequences</a> page for a complete list of the reference chromosomes and alternate sequences in GRCh38.) <li> <b>Centromere representation</b> - Debuting in this release, the large megabase-sized gaps that were previously used to represent centromeric regions in human assemblies have been replaced by sequences from centromere models created by - <a href="http://genome.cshlp.org/content/early/2014/02/05/gr.159624.113.abstract" + <a href="http://genome.cshlp.org/content/24/4/697.abstract" target="_blank">Karen Miga et al.</a>, using centromere databases developed during her work in the <a href="http://www.genome.duke.edu/labs/WillardLab/" target="_blank">Willard lab</a> at Duke University and analysis software developed while working in the <a href="http://cbse.soe.ucsc.edu/people/kent" target="_blank">Kent lab</a> at UCSC. The models, which provide the approximate repeat number and order for each centromere, will be useful for read mapping and variation studies. <li> <b>Mitochondrial genome</b> - The mitochondrial reference sequence included in the GRCh38 assembly and hg38 Genome Browser (termed "chrM" in the browser) is the <a href="http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq" target="_blank">Revised Cambridge Reference Sequence</a> (rCRS) from <a href="http://mitomap.org/MITOMAP" target="_blank">MITOMAP</a> with GenBank accession number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM