da8db0ef4336e7e3d39b1901d2259e50465f6d8c donnak Thu Mar 6 16:03:38 2014 -0800 Modified info about Karen Miga's work, per input from Karen + Jim. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 5c3e4af..829a605 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -56,34 +56,36 @@
  • Alternate sequences - 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 alternate loci scaffolds (or alt loci). 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 sequences page for a complete list of the reference chromosomes and alternate sequences in GRCh38.)
  • Centromere representation - 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the large megabase-sized gaps that were previously used to represent centromeric regions in human assemblies have been replaced by sequences from centromere models created by Karen Miga et al. of UCSC's - Kent lab, under the - guidance and mentorship of the Willard lab at Duke University. The models, which provide the + target="_blank">Karen Miga et al., using centromere databases developed during her + work in the Willard lab at + Duke University and analysis software developed while working in the + Kent lab at UCSC. + The models, which provide the approximate repeat number and order for each centromere, will be useful for read mapping and variation studies.
  • Mitochondrial genome - The mitochondrial reference sequence included in the GRCh38 assembly and hg38 Genome Browser (termed "chrM" in the browser) is the Revised Cambridge Reference Sequence (rCRS) from MITOMAP with GenBank accession number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM sequence (RefSeq accession number NC_001907) used by the previous hg19 Genome Browser, which was not updated when the GRCh37 assembly later transitioned to the new version.
  • Sequence updates - Several erroneous bases and misassembled regions in GRCh37 have been corrected in the GRCh38 assembly, and more than 100 gaps have been filled or reduced. Much of the data used to improve the reference sequence was obtained from other genome