Journal Article

DKFZ-2023-01285

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Using DEPendency of association on the number of Top Hits (DEPTH) as a complementary tool to identify novel colorectal cancer susceptibility loci.

Lai, J. ; Wong, C. K. ; Schmidt, D. F. ; Kapuscinski, M. K. ; Alpen, K. ; Maclnnis, R. J. ; Buchanan, D. D. ; Win, A. K. ; Figueiredo, J. C. ; Chan, A. T. ; Harrison, T. A. ; Hoffmeister, M.DKFZ* ; White, E. ; Le Marchand, L. ; Pai, R. K. ; Peters, U. ; Hopper, J. L. ; Jenkins, M. A. ; Makalic, E.

2023
AACR Philadelphia, Pa.

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Please use a persistent id in citations: doi:10.1158/1055-9965.EPI-22-1209

Abstract: DEPendency of association on the number of Top Hits (DEPTH) is an approach to identify candidate susceptibility regions by considering the risk signals from overlapping groups of sequential variants across the genome.We conducted a DEPTH analysis using a sliding window of 200 SNPs to colorectal cancer (CRC) data from the Colon Cancer Family Registry (CCFR) (5,735 cases and 3,688 controls), and GECCO (8,865 cases and 10,285 controls) studies. A DEPTH score >1 was used to identify candidate susceptibility regions common to both studies. We compared DEPTH results against those from conventional GWAS analyses of these two studies as well as against 132 published susceptibility regions.Initial DEPTH analysis revealed 2,622 (CCFR) and 3,686 (GECCO) candidate susceptibility regions, of which 569 were common to both studies. Bootstrapping revealed 40 and 49 candidate susceptibility regions in the CCFR and GECCO data sets, respectively. Notably, DEPTH identified at least 82 regions that would not be detected using conventional GWAS methods, nor had they been identified by previous CRC GWASs. We found four reproducible candidate susceptibility regions (2q22.2, 2q33.1, 6p21.32, 13q14.3). The highest DEPTH scores were in the HLA locus at 6p21 where the strongest associated SNPs were rs762216297, rs149490268, rs114741460, and rs199707618 for the CCFR data, and rs9270761 for the GECCO data.DEPTH can identify candidate susceptibility regions for CRC not identified using conventional analyses of larger datasets.DEPTH has potential as a powerful complementary tool to conventional GWAS analyses for discovering susceptibility regions within the genome.

Note: 2023 Sep 1;32(9):1153-1159

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Contributing Institute(s):

1. C070 Klinische Epidemiologie und Alternf. (C070)

Research Program(s):

1. 313 - Krebsrisikofaktoren und Prävention (POF4-313) (POF4-313)

Appears in the scientific report 2023

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Clinical Medicine ; Current Contents - Life Sciences ; Essential Science Indicators ; IF < 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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