F1000Research 2019, 8:960 Last updated: 03 AUG 2021 RESEARCH ARTICLE A genome-wide scan of cleft lip triads identifies parent- of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption [version 2; peer review: 2 approved] Øystein Ariansen Haaland 1, Julia Romanowska1,2, Miriam Gjerdevik1,3, Rolv Terje Lie1,4, Håkon Kristian Gjessing 1,4, Astanand Jugessur1,3,4 1Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway 2Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway 3Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway 4Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway v2 First published: 24 Jun 2019, 8:960 Open Peer Review https://doi.org/10.12688/f1000research.19571.1 Latest published: 19 Jul 2019, 8:960 https://doi.org/10.12688/f1000research.19571.2 Reviewer Status Invited Reviewers Abstract Background: Although both genetic and environmental factors have 1 2 been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely version 2 unaccounted for. We recently developed new methods to identify (revision) report parent-of-origin (PoO) interactions with environmental exposures 19 Jul 2019 (PoOxE) and now apply them to data from a genome-wide association study (GWAS) of families with children born with isolated CL/P. version 1 Methods: Genotypes from 1594 complete triads and 314 dyads (1908 24 Jun 2019 report report nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained 1. Evie Stergiakouli , University of Bristol, from the original 569,244. The exposures were maternal cigarette Bristol, UK smoking, use of alcohol, and use of vitamin supplements in the MRC Integrative Epidemiology at the periconceptional period. Our new methodology detects if PoO effects are different across environmental strata and is implemented in the R- University of Bristol, Bristol, UK package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke 2. Yongchu Pan , Nanjing Medical University effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; (NMU), Nanjing, China rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, Any reports and responses or comments on the p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). article can be found at the end of the article. Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental Page 1 of 28 F1000Research 2019, 8:960 Last updated: 03 AUG 2021 exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects. Keywords Orofacial cleft, cleft lip with or without cleft palate, case-parent triads, gene-environment interaction, parent-of-origin, PoOxE, Haplin Corresponding author: Øystein Ariansen Haaland ([email protected]) Author roles: Haaland ØA: Conceptualization, Data Curation, Formal Analysis, Methodology, Software, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Romanowska J: Conceptualization, Formal Analysis, Methodology, Software, Visualization, Writing – Review & Editing; Gjerdevik M: Conceptualization, Formal Analysis, Methodology, Software, Visualization, Writing – Review & Editing; Lie RT: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Software, Supervision, Writing – Review & Editing; Gjessing HK: Conceptualization, Formal Analysis, Funding Acquisition, Methodology, Project Administration, Software, Writing – Review & Editing; Jugessur A: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Methodology, Project Administration, Software, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing Competing interests: No competing interests were disclosed. Grant information: This research was supported by the Bergen Medical Research Foundation [807191], by the Research Council of Norway (RCN) through its Centres of Excellence funding scheme [grant 262700], and by the Biobank Norway II from the RCN [245464]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2019 Haaland ØA et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite this article: Haaland ØA, Romanowska J, Gjerdevik M et al. A genome-wide scan of cleft lip triads identifies parent-of- origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption [version 2; peer review: 2 approved] F1000Research 2019, 8:960 https://doi.org/10.12688/f1000research.19571.2 First published: 24 Jun 2019, 8:960 https://doi.org/10.12688/f1000research.19571.1 Page 2 of 28 F1000Research 2019, 8:960 Last updated: 03 AUG 2021 may also provide an opportunity to intervene on environmen- REVISE D Amendments from Version 1 tal risk factors alone, particularly in subgroups of the popula- In this version we have considered the remarks of Dr. Evie tion that are genetically more susceptible to these environmental Stergiakouli. We have addressed some limitations that were effects. pointed out and generally edited the manuscript for clarity. Abstract: Recently, we went one step further and developed new meth- Removed reference to previously published work and added ods for a genome-wide screening for PoO interactions information about the methodology. with environmental exposures (i.e., PoOxE) in the case-parent Introduction: triad setting22. We applied the new methodology, implemented Rephrased sentence that overemphasized how intriguing the in the R-package Haplin26, to isolated cleft palate only (CPO)27, problem of missing heritability is in clefting. using genotypes and exposure data from the largest pub- Methods: lished GWAS dataset on case-parent triads of orofacial clefts11. Clarified that 59 individuals of other ethnicities than Asian or European were included in the pooled sample and added a Epidemiological and embryological findings have previously sentence about the American Statistical Association’s negative shown that CL/P and CPO may have distinct etiologies. There- attitudes towards using a fixed p-value as a threshold for fore, we used the same GWAS dataset and methodology to per- statistical significance. form a genome-wide scan for PoOxE effects in the larger sample Results: of isolated CL/P. Revised titles of Table 3, Table 4 and Table 7 to include information about which analyses were conducted. Methods Discussion: Study participants Added a paragraph about genomic imprinting as a possible mechanism for PoO effects, clarified that our findings should The study participants were mainly of Asian or European be treated with caution until they have been replicated, and origin and were recruited as part of an international cleft addressed the limitation that we have not imputed genotypes. collaboration11. Information was available on genotypes as In general: well as maternal vitamin use, cigarette smoking and alcohol Corrected minor errors and slightly altered text to improve flow consumption in the periconceptional period (three months and precision. before and three months after pregnancy). The information on See referee reports environmental exposures was based on interviews and question- naires. More detailed characteristics of the study participants can be found in our recent work28. Introduction Cleft lip with or without cleft palate (CL/P) appears in Table 1 shows the distribution of the CL/P families approximately 3.4 to 22.9 per 10,000 live births1. Based on according to ethnicity, triad completeness and maternal exposure. the severity of the cleft, patients undergo varying degrees of There were 1908 families in the pooled sample (5424 individuals medical, dental, speech and psychosocial interventions over the in total), which included all the participants. Of these, 825 fami- first two decades of their lives, a long-term multidisciplinary lies were in the European sample, 1024 families were in the Asian treatment that not only imposes a heavy burden on patients and sample, and 59 families were in the sample consisting of other their families2,3, but also accounts for a substantial outlay in ethnicities (Table 1). We performed three main sets of analyses national healthcare budgets4,5. on the following samples: All participants (denoted as “pooled analysis”), only Asians (“Asian analysis”), and only Europe- Multiple genetic and environmental factors have been reported ans (“European analysis”). The 59 families with other ethnicities to influence the risk of CL/P, individually and through were not analyzed as a group due to the small sample size, but complex interactions in relevant biological pathways6–10. Major they were included in the pooled analysis. In the pooled and