|Genome Mapping Section
DOE Human Genome Program Contractor-Grantee Workshop
76. Progress Towards a High Resolution Sequence-Ready Map of Human Chromosome 5
Steve Lowry, Ze Peng, Duncan Scott, Yiwen
Zhu, Mei Wang, Roya Hosseini, Michele Bakis, Joel Martin, Ingrid Plajzer-Frick,
Jeff Shreve, and Jan-Fang Cheng
The high resolution map of chromosome 5 at JGI/LBNL began at the distal portion of the long arm. The region was chosen because it contains a cluster of cytokine growth factors (IL3, IL4, IL5, IL9, IL12, IL13, GM-CSF, FGFA, M-CSF) and receptor genes (GRL, ADRB2, M-CSFR, PDGFR) and was thought likely to yield related genes through full sequence analysis. The expanded region also contains a number of disease genes. These include genes associated with susceptibility for asthma, schizophrenia, corneal dystrophies, low-frequency hearing loss, Treacher-Collins syndrome, various types of myeloid disorders including acute myeloid leukemia, Cockayne syndrome, spinal muscular atrophy, split hand/split foot (DSS1), polyposis coli. The putative colorectal cancer tumor suppressor MCC, Zinc-finger Protein 131 associated with lymphadenogenesis, and the Leukemia Inhibitory Factor Receptor (LIFR) are other disease associated genes in the region.
The isolation of BACs is based on a combination of colony hybridization and PCR approaches using STSs obtained mostly from public databases. Contigs are expanded by end-sequence STS walking. Contigs are oriented using STSs developed from known genes and ordered genetic and RH markers. All clones are sized by pulsed-field gel electrophoresis, and their map locations are confirmed by fluorescent in situ hybridization. The size of overlaps between BACs is determined by comparison of restriction fragments from a single endonuclease digest.
We have so far mapped 2463 clones to 5q. Ninety-four percent of these are BACs. A total of 2341 STSs have been employed in the contig forming process. Over 50% of the STSs were derived from clone ends. We have in excess of 120 contigs from the distal 65 Mb of 5q ranging in size from 200 Kb to 4.2 Mb.
Clones with minimal overlap that form contigs as determined by the STS content and restriction maps are selected for sequencing. To date, 390 clones on the q arm of chromosome 5 have entered the sequencing pipeline, totaling approximately 45 Mb of unique target or 71% of the clone insert total.
Detailed information on STS and restriction maps can be found at our Web site: (http://www-hgc.lbl.gov/human-maps.html)
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