Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers.

Squamous cell carcinomas (SqCC) of the aerodigestive tract have similar etiological risk factors. Although genetic risk variants for individual cancers have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. To identify novel and pleotropic SqCC risk variants, we performed a meta-analysis of GWAS data on lung SqCC (LuSqCC), oro/pharyngeal SqCC (OSqCC), laryngeal SqCC (LaSqCC) and esophageal SqCC (ESqCC) cancers, totaling 13,887 cases and 61,961 controls of European ancestry. We identified one novel genome-wide significant (Pmeta<5x10-8) aerodigestive SqCC susceptibility loci in the 2q33.1 region (rs56321285, TMEM273). Additionally, three previously unknown loci reached suggestive significance (Pmeta<5x10-7): 1q32.1 (rs12133735, near MDM4), 5q31.2 (rs13181561, TMEM173) and 19p13.11 (rs61494113, ABHD8). Multiple previously identified loci for aerodigestive SqCC also showed evidence of pleiotropy in at least another SqCC site, these include: 4q23 (ADH1B), 6p21.33 (STK19), 6p21.32 (HLA-DQB1), 9p21.33 (CDKN2B-AS1) and 13q13.1(BRCA2). Gene-based association and gene set enrichment identified a set of 48 SqCC-related genes rel to DNA damage and epigenetic regulation pathways. Our study highlights the importance of cross-cancer analyses to identify pleiotropic risk loci of histology-related cancers arising at distinct anatomical sites.

Stakeholder Perspectives of Clinical Artificial Intelligence Implementation: Systematic Review of Qualitative Evidence.

BACKGROUND: The rhetoric surrounding clinical artificial intelligence (AI) often exaggerates its effect on real-world care. Limited understanding of the factors that influence its implementation can perpetuate this. OBJECTIVE: In this qualitative systematic review, we aimed to identify key stakeholders, consolidate their perspectives on clinical AI implementation, and characterize the evidence gaps that future qualitative research should target. METHODS: Ovid-MEDLINE, EBSCO-CINAHL, ACM Digital Library, Science Citation Index-Web of Science, and Scopus were searched for primary qualitative studies on individuals' perspectives on any application of clinical AI worldwide (January 2014-April 2021). The definition of clinical AI includes both rule-based and machine learning-enabled or non-rule-based decision support tools. The language of the reports was not an exclusion criterion. Two independent reviewers performed title, abstract, and full-text screening with a third arbiter of disagreement. Two reviewers assigned the Joanna Briggs Institute 10-point checklist for qualitative research scores for each study. A single reviewer extracted free-text data relevant to clinical AI implementation, noting the stakeholders contributing to each excerpt. The best-fit framework synthesis used the Nonadoption, Abandonment, Scale-up, Spread, and Sustainability (NASSS) framework. To validate the data and improve accessibility, coauthors representing each emergent stakeholder group codeveloped summaries of the factors most relevant to their respective groups. RESULTS: The initial search yielded 4437 deduplicated articles, with 111 (2.5%) eligible for inclusion (median Joanna Briggs Institute 10-point checklist for qualitative research score, 8/10). Five distinct stakeholder groups emerged from the data: health care professionals (HCPs), patients, carers and other members of the public, developers, health care managers and leaders, and regulators or policy makers, contributing 1204 (70%), 196 (11.4%), 133 (7.7%), 129 (7.5%), and 59 (3.4%) of 1721 eligible excerpts, respectively. All stakeholder groups independently identified a breadth of implementation factors, with each producing data that were mapped between 17 and 24 of the 27 adapted Nonadoption, Abandonment, Scale-up, Spread, and Sustainability subdomains. Most of the factors that stakeholders found influential in the implementation of rule-based clinical AI also applied to non-rule-based clinical AI, with the exception of intellectual property, regulation, and sociocultural attitudes. CONCLUSIONS: Clinical AI implementation is influenced by many interdependent factors, which are in turn influenced by at least 5 distinct stakeholder groups. This implies that effective research and practice of clinical AI implementation should consider multiple stakeholder perspectives. The current underrepresentation of perspectives from stakeholders other than HCPs in the literature may limit the anticipation and management of the factors that influence successful clinical AI implementation. Future research should not only widen the representation of tools and contexts in qualitative research but also specifically investigate the perspectives of all stakeholder HCPs and emerging aspects of non-rule-based clinical AI implementation. TRIAL REGISTRATION: PROSPERO (International Prospective Register of Systematic Reviews) CRD42021256005; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=256005. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/33145.

Stakeholder Perspectives on Clinical Decision Support Tools to Inform Clinical Artificial Intelligence Implementation: Protocol for a Framework Synthesis for Qualitative Evidence.

BACKGROUND: Quantitative systematic reviews have identified clinical artificial intelligence (AI)-enabled tools with adequate performance for real-world implementation. To our knowledge, no published report or protocol synthesizes the full breadth of stakeholder perspectives. The absence of such a rigorous foundation perpetuates the "AI chasm," which continues to delay patient benefit. OBJECTIVE: The aim of this research is to synthesize stakeholder perspectives of computerized clinical decision support tools in any health care setting. Synthesized findings will inform future research and the implementation of AI into health care services. METHODS: The search strategy will use MEDLINE (Ovid), Scopus, CINAHL (EBSCO), ACM Digital Library, and Science Citation Index (Web of Science). Following deduplication, title, abstract, and full text screening will be performed by 2 independent reviewers with a third topic expert arbitrating. The quality of included studies will be appraised to support interpretation. Best-fit framework synthesis will be performed, with line-by-line coding completed by 2 independent reviewers. Where appropriate, these findings will be assigned to 1 of 22 a priori themes defined by the Nonadoption, Abandonment, Scale-up, Spread, and Sustainability framework. New domains will be inductively generated for outlying findings. The placement of findings within themes will be reviewed iteratively by a study advisory group including patient and lay representatives. RESULTS: Study registration was obtained from PROSPERO (CRD42021256005) in May 2021. Final searches were executed in April, and screening is ongoing at the time of writing. Full text data analysis is due to be completed in October 2021. We anticipate that the study will be submitted for open-access publication in late 2021. CONCLUSIONS: This paper describes the protocol for a qualitative evidence synthesis aiming to define barriers and facilitators to the implementation of computerized clinical decision support tools from all relevant stakeholders. The results of this study are intended to expedite the delivery of patient benefit from AI-enabled clinical tools. TRIAL REGISTRATION: PROSPERO CRD42021256005; https://tinyurl.com/r4x3thvp. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/33145.

A Candidate Gene Association Study of Bone Mineral Density in an Iranian Population.

The genetic epidemiology of variation in bone mineral density (BMD) and osteoporosis is not well studied in Iranian populations and needs more research. We report a candidate gene association study of BMD variation in a healthy cross-sectional study of 501 males and females sampled from the Iranian Multi-Centre Osteoporosis Study, Shiraz, Iran. We selected to study the association with 21 single nucleotide polymorphisms (SNPs) located in the 7 candidate genes LRP5, RANK, RANKL, OPG, P2RX7, VDR, and ESR1. BMD was measured at the three sites L2-L4, neck of femur, and total hip. Association between BMD and each SNP was assessed using multiple linear regression assuming an allele dose (additive effect) on BMD (adjusted for age and sex). Statistically significant (at the unadjusted 5% level) associations were seen with seven SNPs in five of the candidate genes. Two SNPs showed statistically significant association with more than one BMD site. Significant association was seen between BMD at all the three sites with the VDR SNP rs731246 (L2-L4 p = 0.038; neck of femur p = 0.001; and total hip p < 0.001). The T allele was consistently associated with lower BMD than the C allele. Significant association was also seen for the P2RX7 SNP rs3751143, where the G allele was consistently associated with lower BMD than the T allele (L2-L4 p = 0.069; neck of femur p = 0.024; and total hip p = 0.045).

Comparing methods for mapping cis acting polymorphisms using allelic expression ratios.

Genome wide association studies frequently reveal associations between disease susceptibility and polymorphisms outside coding regions. Such associations cannot always be explained by linkage disequilibrium with changes affecting the transcription products. This has stimulated the interest in characterising sequence variation influencing gene expression levels, in particular in changes acting in cis. Differences in transcription between the two alleles at an autosomal locus can be used to test the association between candidate polymorphisms and the modulation of gene expression in cis. This type of approach requires at least one transcribed polymorphism and one candidate polymorphism. In the past five years, different methods have been proposed to analyse such data. Here we use simulations and real data sets to compare the power of some of these methods. The results show that when it is not possible to determine the phase between the transcribed and potentially cis acting allele there is some advantage in using methods that estimate phased genotype and effect on expression simultaneously. However when the phase can be determined, simple regression models seem preferable because of their simplicity and flexibility. The simulations and the analysis of experimental data suggest that in the majority of situations, methods that assume a lognormal distribution of the allelic expression ratios are both robust to deviations from this assumption and more powerful than alternatives that do not make these assumptions.