A consolidated catalogue and graphical annotation of dbSNP polymorphisms in the human tissue kallikrein (KLK) locus

Goard, Carolyn A.; Bromberg, Irvin L.; Elliott, Marc B.; Diamandis, Eleftherios P.

doi:10.1016/j.molonc.2007.09.001

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Volume 1, Issue 3 , Pages 303-312, December 2007

A consolidated catalogue and graphical annotation of dbSNP polymorphisms in the human tissue kallikrein (KLK) locus

Carolyn A. Goard
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1L5
Irvin L. Bromberg
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1L5
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
Marc B. Elliott
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1L5
Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1L5
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
- Corresponding author. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5. Tel.: +1 416 586 8443; fax: +1 416 619 5521.

Received 29 August 2007; received in revised form 4 September 2007; accepted 7 September 2007. published online 05 October 2007.

Abstract

The human tissue kallikreins, 15 secreted serine proteases, may play diverse roles in pathophysiology. The National Center for Biotechnology Information's dbSNP was mined for polymorphisms located within the kallikrein (KLK) locus using custom-designed “ParSNPs” and “LocusAnnotator” software tools. Using “ParSNPs”, a filterable catalogue of 1856 KLK polymorphisms (1023 validated) was generated. “LocusAnnotator” was used to annotate the KLK locus sequence with gene and polymorphism features. A second locus was examined to validate the use of both programs on a non-kallikrein locus. This report may assist in the informed selection of KLK polymorphisms for future association and biochemical studies in relation to disease. Furthermore, “ParSNPs” and “LocusAnnotator” are available at no cost from our website (www.acdcLab.org/annotations) to examine other loci.

Keywords: Genetic polymorphism, Single nucleotide polymorphism, Kallikreins