Exceptional Chromosome Regions II
Robert D. Sutherland, Cliff S. Han and Norman A. Doggett
Los Alamos National Laboratory, Joint Genome Institute, MS M888, Los Alamos, NM 87545
We are coordinating the complete sequencing of human chromosome 16 by continued mapping efforts and improvement of the fully integrated map. This includes both restriction fragment and sequence based data for the BAC map of this chromosome. The data is maintained both in the SIGMA application and in multiple MS Excel spreadsheets. The Excel spreadsheets are divided into seven major regions--three p-arm and four q-arm maps. The three p-arm sections are the telomere to the FMF region (16p13.3), FMF region to the beginning of the TIGR effort (16p13.12), and the inner twenty Mb's initially sequenced by TIGR (upto 16p11.2). The q-arm is divided roughly into four equal parts. The size and distribution of the maps has a great deal with the spreadsheet size limitation in MS Excel. As map size increases, they are further subdivided to worksheets to facilitate data handling.
The chromosome 16 map has been years in the making starting with a flow-sorted cosmid library for which fingerprinted cosmids were assembled into cosmid contigs. STS's from these cosmids became the anchor points for assembly of a whole chromosome low-resolution YAC map and then a high-resolution BAC map. Sequencing commenced on this integrated framework. Five of the seven Excel map sections contain overgo and STS versus BAC-hit data.
There are gaps in the high-resolution BAC map resulting primarily from uneven STS or overgo distribution and to a lesser degree to uneven coverage of BAC libraries. These gaps have been identified and flanking BACs are analyzed with TIGR's BAC-end database search to find the optimum new BAC to extend into the gap. Using this technique, we walk across or meet in the middle of the gap. Another strategy is to find unique sequences that have no representation in the already sequenced BACs and screen for new ones.
This full data set, is included in four Excel files, that are available on the Web at www.jgi.doe.gov. Two different files represent the chromosome: 16parm and 16qarm. Both files have multiple worksheets denoting the different sections of the map. The two additional spreadsheets are for reference purposes. The first file is the chromosome 16 tiling set which contains all available genomic sequenced clones with accession numbers in chromosome order. This file also shows the minimal tiling set and size summaries at the bottom. It also contains entries for clones labeled as chromosome 16 but are either bad or reside on other chromosomes. The last file is the chromosome 16 reference list that will help locate on which map a BAC or STS can be found.
Any questions, input, or corrections to the chromosome 16 map may be directed to Robert Sutherland at firstname.lastname@example.org.
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