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1 September 2023
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Cover Image
Cover Image
The cover image is adapted from Fig. 2 in the article, “Using DEPendency of Association on the Number of Top Hits (DEPTH) as a Complementary Tool to Identify Novel Colorectal Cancer Susceptibility Loci,” by Lai and colleagues. Figure 2 is a diagram of the HLA locus (bordered by the GABBR1 and KIFC1 genes) showing a common DEPTH risk region. DEPTH is an approach to identify candidate susceptibility regions by considering the risk signals from overlapping groups of sequential variants across the genome. The authors conducted a DEPTH analysis using a sliding window of 200 SNPs to colorectal cancer data from the Colon Cancer Family Registry (CCFR; 5,735 cases and 3,688 controls), and Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO; 8,865 cases and 10,285 controls) studies. A DEPTH score >1 was used to identify candidate susceptibility regions common to both studies. DEPTH results were compared against those from conventional GWAS analyses of these two studies as well as against published susceptibility regions. The study shows, using two colorectal cancer GWAS data sets (CCFR and GECCO), that more risk regions can be identified using an alternative approach (DEPTH) without needing to increase sample sizes. In fact, this study reduced the number of participants compared to the original CCFR and GECCO data sets due to an extra layer of QC and data harmonization that was applied to this study. Finally, the authors designed DEPTH as an exploratory tool to identify novel risk loci, with the expectation that other methods can later be used to validate these loci. DEPTH has potential as a powerful complementary tool to conventional GWAS analyses for discovering susceptibility regions within the genome. For more information, see the article beginning on page 1153. - PDF Icon PDF LinkTable of Contents
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ISSN 1055-9965
EISSN 1538-7755
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Commentary
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Research Articles
Elevated EVL Methylation Level in the Normal Colon Mucosa Is a Potential Risk Biomarker for Developing Recurrent Adenomas
Ming Yu; Kelly T. Carter; Kelsey K. Baker; Mary W. Redman; Ting Wang; Kathy Vickers; Christopher I. Li; Stacey A. Cohen; Mukta Krane; Jennifer Ose; Biljana Gigic; Jane C. Figueiredo; Adetunji T. Toriola; Erin M. Siegel; David Shibata; Martin Schneider; Cornelia M. Ulrich; Lynda A. Dzubinski; Robert E. Schoen; William M. Grady
Using DEPendency of Association on the Number of Top Hits (DEPTH) as a Complementary Tool to Identify Novel Colorectal Cancer Susceptibility Loci
John Lai; Chi Kuen Wong; Daniel F. Schmidt; Miroslaw K. Kapuscinski; Karen Alpen; Robert J. MacInnis; Daniel D. Buchanan; Aung K. Win; Jane C. Figueiredo; Andrew T. Chan; Tabitha A. Harrison; Michael Hoffmeister; Emily White; Loic Le Marchand; Rish K. Pai; Ulrike Peters; John L. Hopper; Mark A. Jenkins; Enes Makalic
Association between Sleep Duration and Colorectal Adenomas: Findings from a Case–Control Study in Vietnam
Chi Thi-Du Tran; Pedram Paragomi; Mo Thi Tran; Mai Vu-Tuyet Nguyen; Thuy Thi-Van Tuong; Quang Hong Tran; Linh Cu Le; Huong Thi-Thu Pham; Hien Thi-Thu Ha; Nam Chi Bui; Hien Huy Vu; Phuong Que Ta; Martha J. Shrubsole; Qiuyin Cai; Fei Ye; Song Huu Le; Khien Van Vu; Huong Thi-Thanh Tran; Thuan Van Tran; Paolo Boffetta; Xiao-Ou Shu; Hung N. Luu
Intake of Proton-Pump Inhibitors and Gastric Cancer within the Stomach Cancer Pooling (StoP) Project
Michele Sassano; Marco Mariani; Claudio Pelucchi; Nuno Lunet; Samantha Morais; Vicente Martín; Victor Moreno; Maria Paula Curado; Emmanuel Dias-Neto; Marcis Leja; Evita Gašenko; Carlo La Vecchia; Stefania Boccia; Roberta Pastorino
Variations in Genes Encoding Human Papillomavirus Binding Receptors and Susceptibility to Cervical Precancer
Amrita Mukherjee; Yuanfan Ye; Howard W. Wiener; Mark H. Kuniholm; Howard Minkoff; Kate Michel; Joel Palefsky; Gypsyamber D'Souza; Lisa Rahangdale; Kenneth R. Butler; Mirjam-Colette Kempf; Staci L. Sudenga; Bradley E. Aouizerat; Akinyemi I. Ojesina; Sadeep Shrestha
Predicted Proteome Association Studies of Breast, Prostate, Ovarian, and Endometrial Cancers Implicate Plasma Protein Regulation in Cancer Susceptibility
Isabelle Gregga; Paul D. P. Pharoah; Simon A. Gayther; Ani Manichaikul; Hae Kyung Im; Siddhartha P. Kar; Joellen M. Schildkraut; Heather E. Wheeler
Diabetes and Prostate Cancer Outcomes in Men with Nonmetastatic Castration-Resistant Prostate Cancer: Results from the SEARCH Cohort
Andrei Sergeyev; Lin Gu; Amanda M. De Hoedt; Christopher L. Amling; William J. Aronson; Matthew R. Cooperberg; Christopher J. Kane; Zachary Klaassen; Martha K. Terris; Lourdes Guerrios-Rivera; Stephen J. Freedland; Ilona Csizmadi
Validating Wave 1 (2014) Urinary Cotinine and TNE-2 Cut-points for Differentiating Wave 4 (2017) Cigarette Use from Non-use in the United States Using Data from the PATH Study
Kathryn C. Edwards; Asia Khan; Eva Sharma; Lanqing Wang; June Feng; Benjamin C. Blount; Connie S. Sosnoff; Danielle M. Smith; Maciej L. Goniewicz; Jennifer Pearson; Andrea C. Villanti; Cristine D. Delnevo; Michelle T. Bover-Manderski; Dorothy K. Hatsukami; Raymond Niaura; Colm Everard; Heather L. Kimmel; Kara Duffy; Brian L. Rostron; Arseima Y. Del Valle-Pinero; Dana M. van Bemmel; Cassandra A. Stanton; Andrew Hyland
Relationship between ABO Blood Group Alleles and Pancreatic Cancer Is Modulated by Secretor (FUT2) Genotype, but Not Lewis Antigen (FUT3) Genotype
Jihye Kim; Chen Yuan; Laufey T. Amundadottir; Brian M. Wolpin; for the Pancreatic Cancer Cohort Consortium (PanScan); Alison P. Klein; for the Pancreatic Cancer Case–Control Consortium (PanC4); Harvey A. Risch; Peter Kraft
Null Results in Brief
Genetic Susceptibility to Nonalcoholic Fatty Liver Disease and Risk for Pancreatic Cancer: Mendelian Randomization
Sontoria D. King; Swathi Veliginti; Martijn C.G.J. Brouwers; Zhewen Ren; Wei Zheng; Veronica W. Setiawan; Lynne R. Wilkens; Xiao-Ou Shu; Alan A. Arslan; Laura E. Beane Freeman; Paige M. Bracci; Federico Canzian; Mengmeng Du; Steven J. Gallinger; Graham G. Giles; Phyllis J. Goodman; Christopher A. Haiman; Manolis Kogevinas; Charles Kooperberg; Loic LeMarchand; Rachel E. Neale; Kala Visvanathan; Emily White; Demetrius Albanes; Gabriella Andreotti; Ana Babic; Sonja I. Berndt; Lauren K. Brais; Paul Brennan; Julie E. Buring; Kari G. Rabe; William R. Bamlet; Stephen J. Chanock; Charles S. Fuchs; J. Michael Gaziano; Edward L. Giovannucci; Thilo Hackert; Manal M. Hassan; Verena Katzke; Robert C. Kurtz; I.-Min Lee; Núria Malats; Neil Murphy; Ann L. Oberg; Irene Orlow; Miquel Porta; Francisco X. Real; Nathaniel Rothman; Howard D. Sesso; Debra T. Silverman; Ian M. Thompson, Jr; Jean Wactawski-Wende; Xiaoliang Wang; Nicolas Wentzensen; Herbert Yu; Anne Zeleniuch-Jacquotte; Kai Yu; Brian M. Wolpin; Eric J. Duell; Donghui Li; Rayjean J. Hung; Sandra Perdomo; Marjorie L. McCullough; Neal D. Freedman; Alpa V. Patel; Ulrike Peters; Elio Riboli; Malin Sund; Anne Tjønneland; Jun Zhong; Stephen K. Van Den Eeden; Peter Kraft; Harvey A. Risch; Laufey T. Amundadottir; Alison P. Klein; Rachael Z. Stolzenberg-Solomon; Samuel O. Antwi
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