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Human genome high-resolution BAC re-arrayed clone set (the “32k set”)

Human BAC libraries have played a critical role for the construction of physical maps and have also been used as intermediate substrates for genome sequencing. The mapped and sequenced BACs have subsequently become invaluable resources for functional analysis of genes and for diagnostic assessment of chromosomal rearrangements by fluorescent in situ hybridization (FISH). A BAC clone set representing the mapped human genome has been generated in collaboration between CHORI scientists and scientists at Marco Marra’s Genome Sciences Centre, Vancouver, BC Canada.

To provide an integration of BAC contig maps with the draft sequence of the Human Genome, 32,000 BAC clones have been selected from the fingerprint map to provide maximum representation of every clone in the map. Additional clones were added to the set to cover regions which were thought to lack coverage, resulting in a final resolution of 46 kb, defined by overlapping BAC segments. The set provides coverage for >99% of both the fingerprint map and the current sequence assembly. Currently (May 2003), the human sequence assembly contains 729 gaps with an estimated combined gap size of 28 Mbp. with 45% of the gaps being smaller than 10 kb. Clones representing these gaps are absent in the 32k BAC clone set. Beyond the purpose of map and sequence integration, this defined set of clones was designed to provide diagnostic reagents to study cancer and other diseases with respect to genomic rearrangements. Most of the clones in the set (30,388 BACs) are derived from the Human RPCI-11 and -13 libraries (Osoegawa et al., 2001) while a smaller number of clones is derived from the “CalTech” Human BAC Libraries (CIT-D, 2,062 BACs).

The Human 32K clone set has been arrayed into chromosome specific subsets. The clones are available in 384-well plates and will be distributed as a complete clone collection or as distinct chromosomal-specific sets. The entire set has been organized through chromosome-specific microtiter plates as follows.

• The entire 32,861 BAC collection is contained in 119 “384-well” microtiter plates.
• Some of the plates contain empty wells, because we elected not to have BACs derived from different chromosomes sharing plates.
• The RP and Caltech BAC clones are kept in separate plates.
  

BAC DNA compatible with DOP-PCR has been prepared from 1 ml cultures of the clones grown in “96-deepwell” blocks. The DNA was extracted using an Autogen 960 robot. The compatibility with the DOP-PCR protocol was determined in collaboration with Eric Schoenmakers, Ph.D. at the Micro-array facility of the University Medical Centre Nijmegen, Dept. of Human Genetics.

Approximately 20 ng DNA per clone was isolated by using our on-site robotic equipment and stored in 96-well PCR plates. The DNA preparations for the entire set of clones have been prepared and are currently available in 96-well PCR plates by either entire set or chromosome specific set. Some dishes or plates are not completely filled to avoid having multiple chromosomes represented per dish.

Some clones have no chromosome assignment because they belong to small map contigs which have no BES clones and no STS markers. We were not able to associate them with a chromosome. The clones have been selected to provide coverage of the map, kept in separate 384-well dishes, and assigned as chromosome 0.

Our Human genome high-resolution BAC re-array clone set V1.1 is subject to an ongoing, extensive quality control efforts ensuring the quality and reliability of our collection in collaboration with Genome Sciences Centre, Vancouver, BC Canada, including T1 phage assay and DNA fingerprint confirmation for all clones. Please contact our BACPAC manager for more information about details related to the quality assessment. Due to the regular updates of the complete listing and the possibility of future addition of more clones into our current collection, a version number was assigned in each release. The currently available collection is the “32k set version 1.1”. High fidelity of clone identity is assured. While we don’t assume financial liability for this, we are confident that we have an essentially pure and phage-free collection.

To find clones of interest, please download an Excel spreadsheet (Human genome high-resolution BAC re-array clone set V1.1 Download, Human genome high-resolution BAC re-array clone set V2.2 Download) to obtain the complete listing of all mapped human BAC clones which are distributed through BACPAC Resources at Children’s Hospital and Research Center at Oakland (CHRCO). Please note that the BACs are listed in the Excel book using an abbreviated format, with "M", "N" and "F" as abbreviations for CTD, RP11 & RP13, respectively. Mapping data for the 32k human rearray is also available in an interactive web format from the genomic rearrays page.

As of April 2006 all the clones sorted by chromosomes in the 32k set were re-fingerprinted and compared to the original fingerprints of the clones by the group of the Genome Sciences Centre, Vancouver, BC Canada. Inconsistent fingerprints were observed from a total of 49 clones sorted into chromosome 3 plate 2. These inconsistencies are due to plate swap during the re-arraying process. To find clones which were re-arrayed erroneously, please download an Excel spreadsheet (Human 32k set incorrect clones). The table contains "intended original clone name", well positions in the re-arrayed set, actual clone name and identical clones in the 32k set. Updated on July 13, 2006.

The clones or derived DNA samples shall not be transferred to other laboratories or used within commercial applications. Materials Transfer Agreements will need to be executed for commercial use with the owners of the library clones used in this collection (Roswell Park Cancer Institute in case of RPCI-11 or -13 BAC clones).

There is no warranty of suitability of the DNA preparation for the user's application, although we have confirmed the compatibility with DOP-PCR. While we don't assume financial liabilities, we recommend that users test the compatibility with their proprietary protocols by ordering a specific subset of clones and/or DNA samples which comprise a test set, prior to ordering the whole set. The costs of the DNA test set is $60/plate of 96 samples. The test set contains 48 clones from chromosome 21 and 48 clones from the X chromosome.

For more details please view the complete Distribution Policy .

Pricing includes labor, reagents, reasonable part of the equipment usage, maintenance costs and institutional overhead charges. In order to recoup the time and effort invested in organizing, the prices for the chromosome specific set and the entire set established in the table below are higher than the typical duplication costs we typically charge for libraries. We will lower the prices for the clone set once the initial costs have been recovered.

Note: Plates can be ordered by subsets of chromosome(s) or the entire chromosome set.

For ordering and shipping details, please view ordering & pricing information page.

Please direct questions concerning this clone set to either Pieter J. de Jong

Krzywinski, M., Bosdet, I., Smailus, D., Chiu, R., Mathewson, C., Wye, N., Barber, S., Brown-John, M., Chan, S., Chand, S., Cloutier, A., Girn, N., Lee, D., Masson, A., Mayo, M., Olson, T., Pandoh, P., Prabhu, A.L., Schoenmakers, E., Tsai, M., Albertson, D., Lam, W., Choy, C.O., Osoegawa, K., Zhao, S., de Jong, P.J., Schein, J., Jones, S., Marra, M.A. 2004. A set of BAC clones spanning the human genome. Nucleic Acids Res . 32: 3651-3660.

Reference for the RPCI-11 library
Osoegawa, K., Mammoser, A. G., Wu, C., Frengen, E., Zeng, C., Catanese, J. J., de Jong, P. J. (2001) A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome, Genome Research, Vol. 11, Issue 3, 483-496, March 2001

Related Links
http://mkweb.bcgsc.ca/bacarray/
It is possible to download a poster related to this work at:
http://www.bcgsc.ca/downloads/posters/agbt2003/agbt-2003-martink2-poster.pdf

Table
HGP Chromosome Specific Set Final Clones & Plates Count
Dynamic web interface to the 32k Clone Set