Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer.

Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1.BCAC is funded by Cancer Research UK (C1287/A10118, C1287/A12014) and by the European Community's Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS). Meetings of the BCAC have been funded by the European Union COST programme (BM0606). Genotyping on the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175), Cancer Research UK (C1287/A10710, C8197/A16565), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer program and the Ministry of Economic Development, Innovation and Export Trade of Quebec, grant PSR-SIIRI-701. Combination of the GWAS data was supported in part by the US National Institutes of Health (NIH) Cancer Post-Cancer GWAS initiative, grant 1 U19 CA148065-01 (DRIVE, part of the GAME-ON initiative). For a full description of funding and acknowledgments, see the Supplementary Note.This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/ng.324

Evaluating the Efficacy of Automated Smoking Treatment for People With HIV: Protocol for a Randomized Controlled Trial

BackgroundSmoking prevalence rates among people with HIV are nearly 3 times higher than those in the general population. Nevertheless, few smoking cessation trials targeting smokers with HIV have been reported in the literature. Efforts to develop and evaluate sustainable, low-cost, and evidence-based cessation interventions for people with HIV are needed. Given the widespread proliferation of mobile phones, the potential of using mobile health apps to improve the reach and efficacy of cessation interventions is promising, but evidence of efficacy is lacking, particularly among people with HIV. ObjectiveThis study will consist of a 2-group randomized controlled trial to evaluate a fully automated smartphone intervention for people with HIV seeking cessation treatment. MethodsParticipants (N=500) will be randomized to receive either standard treatment (ST; 250/500, 50%) or automated treatment (AT; 250/500, 50%). ST participants will be connected to the Florida Quitline and will receive nicotine replacement therapy in the form of transdermal patches and lozenges. This approach, referred to as Ask Advise Connect, was developed by our team and has been implemented in numerous health systems. ST will be compared with AT, a fully automated behavioral treatment approach. AT participants will receive nicotine replacement therapy and an interactive smartphone-based intervention that comprises individually tailored audiovisual and text content. The major goal is to determine whether AT performs better in terms of facilitating long-term smoking abstinence than the more resource-intensive ST approach. Our primary aim is to evaluate the efficacy of AT in facilitating smoking cessation among people with HIV. As a secondary aim, we will explore potential mediators and moderators and conduct economic evaluations to assess the cost and cost-effectiveness of AT compared with ST. ResultsThe intervention content has been developed and finalized. Recruitment and enrollment will begin in the fall of 2021. ConclusionsThere is a critical need for efficacious, cost-effective, and sustainable cessation treatments for people with HIV who smoke. The AT intervention was designed to help fill this need. If efficacy is established, the AT approach will be readily adoptable by HIV clinics and community-based organizations, and it will offer an efficient way to allocate limited public health resources to tobacco control interventions. Trial RegistrationClinicalTrials.gov NCT05014282; https://clinicaltrials.gov/ct2/show/NCT05014282 International Registered Report Identifier (IRRID)PRR1-10.2196/3318

Mechanisms of virus uncoating

In a virus particle, the genome is highly condensed and protected by proteins and membrane bilayers. Before it can be replicated in a new host cell, uncoating must take place. Recent studies on enveloped and nonenveloped animal viruses indicate that uncoating occurs through complex, multistep processes triggered by virus-host-cell interactions

Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

Genome wide association studies (GWAS) and large scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ~14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS comprising of 15,748 breast cancer cases and 18,084 controls, and 46,785 cases and 42,892 controls from 41 studies genotyped on a 200K custom array (iCOGS). Analyses were restricted to women of European ancestry. Genotypes for more than 11M SNPs were generated by imputation using the 1000 Genomes Project reference panel. We identified 15 novel loci associated with breast cancer at P<5×10−8. Combining association analysis with ChIP-Seq data in mammary cell lines and ChIA-PET chromatin interaction data in ENCODE, we identified likely target genes in two regions: SETBP1 on 18q12.3 and RNF115 and PDZK1 on 1q21.1. One association appears to be driven by an amino-acid substitution in EXO1

Genome-wide association studies identify four ER negative-specific breast cancer risk loci

<p>Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a metaanalysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P= 2.1 x 10(-12) and LGR6, P = 1.4 x 10(-8)), 2p24.1 (P = 4.6 x 10(-8)) and 16q12.2 (FTO, P = 4.0 x 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P> 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.</p>

Association analysis identifies 65 new breast cancer risk loci

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