Approximately 10,000 BAC clones have been mapped by Fluorescent In-situ Hybridization (FISH) at 300 kb resolution to provide an integration of cytogenetic, radiation hybrid and BAC contig maps with the draft sequence of the Human Genome. Beyond the purpose of map and sequence integration, this set of clones, was also designed to provide a set of diagnostic reagents for studying cancer and other diseases with respect to genomic rearrangements. Most of the clones in the set are derived from Human RPCI-11 constructed in our laboratory (Osoegawa et al.) and a smaller number of clones is derived from the “CalTech” Human BAC Libraries (CIT-A, CIT-B, CIT-C and CIT-D). The clone set is also known as the “Human BAC Resource Consortium_1 Set (HBRC_1 Set)”.

This Project to map these BAC clones by a variety of techniques has been carried out by many groups, partly under the auspices of the NCI CGAP initiative and other funding sources. The collaborative work leading to this clone set has been published ( Nature 409, 953-958, 2001 ) on a manuscript coordinated by Barbara J. Trask at the Fred Hutchinson Cancer Research Center (www.fhcrc.org), Seattle.

These “FISH-confirmed” BAC clones are also listed on a web accessible database by the National Center for Biotechnology Information (NCBI).� The map locations can be viewed on the Human Map Views presented by the NCBI (http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch). The University of California at Santa Cruz also hosts an easy to use browser for the first time user as well as for advanced bioinformatics datamining.

A complete and updated listing of these clones can be found on the NCBI website (http://www.ncbi.nlm.nih.gov/genome/cyto/hbrc.shtml). Different distinct subsets of the 10k FISH confirmed clone set are available from three distributors as indicated at the NCBI web site: BACPAC Resources at Children’s Hospital Oakland Research Institute (CHORI), Research Genetics (InVitrogen), and the Sanger Center (UK).� About one third of the clone collection is distributed by BACPAC Resources and this subset has been mapped mostly through NCI grants to Pieter J. de Jong (then at Roswell Park Cancer Institute; co-PI and later P.I.: Norma Nowak) and to Barbara Trask (FHCRC).

Example 1: If one would like to find clones for regions on chromosome 1.� Start at the NCBI web page (http://www.ncbi.nlm.nih.gov/genome/cyto/hbrc.shtml). Find Table 1: “A cytogenetic resources of FISH mapped, sequence tagged clones (HBRC_1 Set)”. Then select Chromosome 1 by clicking on the hot-linked number at the intersection of the “Chromosome 1” row and the “FISH-mapped” column.� Currently this number indicates that there are 1275 FISH confirmed clones on chromosome 1 (as of 07/01/02). A new web page will open, revealing the mapped clones in approximate map order starting from 1p36.32 down to 1q44 Select clone in the region of interest and realize that the clones may not all be available from the same distributor. The Distributor Information will show you the original clone library and which distributor is responsible for the particular FISH mapped clone from the HBRC_1 Set.� Please realize that CHORI can provide most clones, either from the confirmed clone set or from the address in the original arrayed library (only if the clone is in a library with a name starting with “RP”). All RPCI (RP) libraries are originally constructed in our laboratory. If the clone is from a different distributor than CHORI (“C”) but has a clone name starting with “RP”, CHORI (BACPAC Resources) can still provide the clone.� However, in this case, the bacterial stock may not be clonally-pure and will require re-confirmation in your laboratory after streaking to single colonies. These stocks will likely be over 96-98% pure as compared to a near 100% identity for the “FISH-confirmed” clone set. Once confirmed in your own laboratory, these clones should be identical to the FISH-confirmed clones from HBRC_1 Set available from the other distributors.

Example 2: Select a “FISH-confirmed” clone for a region of interest in chromosome 1 from a graphical representation of chromosome 1. Go to the NCBI web page for Human Genome data resources: http://www.ncbi.nlm.nih.gov/genome/guide/human/.� Click on the graphical image indicating chromosome 1 and the hot-link will bring you to a Map-View for chromosome 1.� You will subsequently need to set the Map View Options to ensure that the FISH-mapped clones are displayed along with the other mapping information (if properly configured, a column “CLONES’ is displayed).� Most likely only a subset of the HBRC_1 Set will be visible. Configure the map view further by setting the “zoom” level.� Everything else should be self-explanatory.� Click on the name of "FISH-confirmed" clone in the desired region. This will open up a page with the specifics on this clone including all the distributor information.

Example 3: Interested only in clones for the particular chromosomal region and all accessible from one distributor. Download an Excel spreadsheet to obtain the complete listing of all mapped human BAC clones in the CHORI part of the HBRC_1 set. ( FISH Mapped Clones V1.3 Download )

The CHORI subset of HBRC_1 clone collection has been arrayed into chromosome specific subsets, approximately according to chromosomal order. The clones are available in two formats: glycerol stocks either in deep-well (96-well) dishes or in individual LB Stab tubes. The entire collection consists of almost 3,400 clones and is contained in 46 dishes or boxes, respectively. Some dishes/boxes are not completely filled to avoid having multiple chromosome represented per box or dish.

Due to the regular updates of the complete listing in NCBI and the possibility of future addition of more clones into our current collection, a version number was assigned in each release. Currently, our collection is on Version 1.3.

Our collection FISH Mapped Clones V1.3 is subject to an ongoing, extensive quality control efforts in our facility, including T1 phage assay, PCR confirmation & DNA fingerprinting confirmation. High fidelity of clone identity is assured. While we don’t assume financial liabilities for this, we are confident that we have an essentially pure and phage-free collection.

Funding for this Project was provided by the National Cancer Institute.

Any publications resulting from the use of these resources, should properly quote this publication and refer to the Distributor of the Resources.