Mapped Clones Collection
How to find Clones Mapping to Regions of Interest
Technical Specifications of Available
Project Funding & Publication
Ordering & Pricing information
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
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
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).
| How to find
clones mapping to regions of interest
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
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 )
| Technical Specifications
of Available Clones
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.
| Project Funding
For pricing information please view our mapped
clones product page.