TY - JOUR
T1 - Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q
T2 - Partial sequence and polymorphisms
AU - Potier, M. C.
AU - Dutriaux, A.
AU - Orti, R.
AU - Groet, J.
AU - Gibelin, N.
AU - Karadima, G.
AU - Lutfalla, G.
AU - Lynn, A.
AU - Van Broeckhoven, C.
AU - Chakravarti, A.
AU - Petersen, M.
AU - Nizetic, D.
AU - Delabar, J.
AU - Rossier, J.
N1 - Funding Information:
The authors thank Corinne Cruaud and Delphine Samson from Généthon for their help with sequencing and bioinformatics; Bernd Drescher from the Department of Genome Analysis, Institute of Molecular Biotechnology, in Jena for kindly annotating the sequence; Dr. Zucman-Rossi for her advice with the shotgun library; Isabelle Canès from Amersham-Molecular Dynamics for the use of the Vistra DNA Labstation 625; Dr. D. Patterson and Dr. C. Buys for providing the cell lines; Dr. J. Korenberg for helpful discussions; and Jinghui Zhang from NCBI for her help with PowerBlast. This work was supported by EEC Grants Gene CT 93-0015 and Biomed CT 96-0554 and GREG Grant 99/94.
PY - 1998/8/1
Y1 - 1998/8/1
N2 - Physical mapping across a duplication can be a tour de force if the region is larger than the size of a bacterial clone. This was the ease of the 170- to 275-kb duplication present on the long arm of chromosome 21 in normal human at 21q11.1 (proximal region) and at 21q22.1 (distal region), which we described previously. We have constructed sequence-ready contigs of the two copies of the duplication of which all the clones are genuine representatives of one copy or the other. This required the identification of four duplicon polymorphisms that are copy-specific and nonallelic variations in the sequence of the STSs. Thirteen STSs were mapped inside the duplicated region and 5 outside but close to the boundaries. Among these STSs 10 were end clones from YACs, PACs, or cosmids, and the average interval between two markers in the duplicated region was 16 kb. Eight PACS and cosmids showing minimal overlaps were selected in both copies of the duplication. Comparative sequence analysis along the duplication showed three single-basepair changes between the two copies over 659 bp sequenced (4 STSs), suggesting that the duplication is recent (less than 4 mya). Two CpG islands were located in the duplication, but no genes were identified after a 36-kb cosmid from the proximal copy of the duplication was sequenced. The homology of this chromosome 21 duplicated region with the pericentromeric regions of chromosomes 13, 2, and 18 suggests that the mechanism involved is probably similar to pericentromeric-directed mechanisms described in interchromosomal duplications.
AB - Physical mapping across a duplication can be a tour de force if the region is larger than the size of a bacterial clone. This was the ease of the 170- to 275-kb duplication present on the long arm of chromosome 21 in normal human at 21q11.1 (proximal region) and at 21q22.1 (distal region), which we described previously. We have constructed sequence-ready contigs of the two copies of the duplication of which all the clones are genuine representatives of one copy or the other. This required the identification of four duplicon polymorphisms that are copy-specific and nonallelic variations in the sequence of the STSs. Thirteen STSs were mapped inside the duplicated region and 5 outside but close to the boundaries. Among these STSs 10 were end clones from YACs, PACs, or cosmids, and the average interval between two markers in the duplicated region was 16 kb. Eight PACS and cosmids showing minimal overlaps were selected in both copies of the duplication. Comparative sequence analysis along the duplication showed three single-basepair changes between the two copies over 659 bp sequenced (4 STSs), suggesting that the duplication is recent (less than 4 mya). Two CpG islands were located in the duplication, but no genes were identified after a 36-kb cosmid from the proximal copy of the duplication was sequenced. The homology of this chromosome 21 duplicated region with the pericentromeric regions of chromosomes 13, 2, and 18 suggests that the mechanism involved is probably similar to pericentromeric-directed mechanisms described in interchromosomal duplications.
UR - http://www.scopus.com/inward/record.url?scp=0032143624&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0032143624&partnerID=8YFLogxK
U2 - 10.1006/geno.1998.5389
DO - 10.1006/geno.1998.5389
M3 - Article
C2 - 9721212
AN - SCOPUS:0032143624
SN - 0888-7543
VL - 51
SP - 417
EP - 426
JO - Genomics
JF - Genomics
IS - 3
ER -