Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Cosmid Contig Map of a 900-kb Candidate Region for Finnish Congenital Nephrosis in 19q13.1

Anne Olsen[1], Anca Georgescu[1], Laurie Gordon[1], Matt Burgin[1], Marjo Kestilä[2], Minna Männikkä[2], and Karl Tryggvason[2]
[1]Human Genome Center, L-452, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550. [2]Biocenter and Department of Biochemistry, University of Oulu, Oulu, Finland.

Congenital nephrotic syndrome of the Finnish type (CNF) is an autosomal recessive disease with an incidence of about 1 in 8000 in Finland. It is characterized by massive proteinuria and signs of nephrosis at birth. The basic defect is unknown, and the disease represents a unique biological model for kidney dysfunction. Based on results of linkage analysis in 17 Finnish families, the CNF locus was mapped to chromosome 19 between D19S416 and D19S224 [1].

In order to define the physical location of the candidate disease gene region, the genetic markers used for linkage analysis were integrated into the physical map of chromosome 19. PCR primers for microsatellite markers were hybridized to colony filters of a chromosome 19 specific cosmid library, and positive clones were confirmed by PCR. Cosmids corresponding to genetic markers in this region were analyzed by high resolution fluorescence in situ hybridization (FISH) to pronuclei (see poster by Brandriff et al.) to determine the physical order of, and distance between, these markers. The results indicated that the markers were located in q13.1 in the order: cen - (S213, S248, S416) - S425 - (S208, S191) - S224 - S220 - tel. The distance from S416 to S224 was an estimated 2.2 Mb. When the physical order data was combined with additional linkage results, the disease gene location could be further restricted to an 860-kb region between S208 and S224.

Cosmid contigs previously established by fingerprinting were integrated into the ordered FISH map. The contigs were analyzed by EcoRI mapping to verify contig assembly and to determine the distance spanned. Probes from the ends of contigs were used for cosmid walking to extend and merge the previously established contigs. Most of the region from S208 to S224 is currently covered with four contigs of 85-, 318-, 171- and 272-kb. Genes mapped to these contigs include COX6B, COX7A1, MAG, ATP4A and APLP1, as well as two anonymous cDNAs. Further walking in cosmid, BAC and PAC libraries should close the three small gaps remaining between contigs.

New polymorphic markers are being developed from cosmids in the candidate region. Linkage analysis with two of these markers has further decreased the size of the candidate region to less than 750 kb. One of the new markers shows no recombination with the CNF gene in any of the families and may lie close to the disease locus.

This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract no. W-7405-ENG-48.

[1] Kestila et al. (1994) Congenital nephrotic syndrome of the Finnish type maps to the long arm of chromosome 19. Am. J. Hum. Genet. 54, 757-764.