Breaking News
June 19, 2018 - After addiction, the long road back to good health
June 19, 2018 - High blood pressure could be an early sign of dementia
June 19, 2018 - Innovative drugs and new European treatment guidelines refine, improve MS therapy
June 19, 2018 - BIDMC scientists develop new tool to benefit patients with HCV-associated liver failure
June 19, 2018 - Diabetes diagnosis may come with increased risk of pancreatic cancer for African-Americans, Latinos
June 19, 2018 - Personalized Goals, Cash Motivate Heart Patients to Exercise
June 19, 2018 - Nipah Virus (NiV) | CDC
June 19, 2018 - Genomics offers new treatment options for infants with range of soft tissue tumors
June 18, 2018 - Study shows how moderate consumption of alcohol can protect the heart
June 18, 2018 - Gene editing technology predicts heart disease risk
June 18, 2018 - Who Will and Who Won’t Get the Flu?
June 18, 2018 - Research shows effective responses to online feedback
June 18, 2018 - Scientists to focus on big data and genetics to identify risk factors for dementia
June 18, 2018 - Ultrasound-based technology for assessing overweight adolescents with liver disease
June 18, 2018 - Osteochondral knee defect treated using cell technology
June 18, 2018 - Study demonstrates increased levels of gum disease in people at risk of rheumatoid arthritis
June 18, 2018 - Ebola & Marburg | NIH: National Institute of Allergy and Infectious Diseases
June 18, 2018 - Brains, eyes, testes: off-limits for transplants?
June 18, 2018 - Drug used to treat myelofibrosis can awaken ‘dormant’ lymphomas in the bone marrow
June 18, 2018 - New study focuses on best, cost effective practices to bridge treatment gap for brain disorders
June 18, 2018 - New study highlights predictors that prevent from achieving remission in early RA
June 18, 2018 - Neuroscientists map feeling of cool touch to the brain’s insula in mouse model
June 18, 2018 - Study highlights potential use of blood biomarkers as diagnostic tool for sleep apnea
June 18, 2018 - Eating plant-based diet can reduce risk for heart problems in people with type 2 diabetes
June 18, 2018 - Lenabasum has acceptable safety and tolerability in diffuse cutaneous systemic sclerosis
June 18, 2018 - Study shows link between risky opioid prescriptions and increased odds of death
June 18, 2018 - Bone density scans could help determine likelihood of cardiovascular disease
June 18, 2018 - Mechanical thrombectomy appears to be important therapy for acute stroke in very old patients
June 18, 2018 - Novel compound as effective as FDA-approved antibiotics for treating deadly infections
June 18, 2018 - Ironwood Pharmaceuticals Announces FDA Orphan Drug Designation for Olinciguat for the Treatment of Sickle Cell Disease
June 18, 2018 - Surgical outcomes equivalent whether physician anesthesiologist assisted by nurse anesthetist or AA
June 18, 2018 - Studies provide insight into molecular changes prior to onset of arthritis
June 18, 2018 - Dyaco unveils specialist medical and rehabilitation equipment range in the UK
June 18, 2018 - Engineers develop algorithm to monitor joints of patients with arthritis
June 18, 2018 - Women with higher vitamin D blood levels have lower risk for breast cancer
June 18, 2018 - New studies help elucidate role of sleep in chronic pain
June 18, 2018 - Researchers link red meat sensitivity spread by ticks with heart disease
June 18, 2018 - Research explores role of autopsy in cardiovascular medicine
June 18, 2018 - Motif Bio Submits NDA for Iclaprim
June 18, 2018 - NIH-funded researchers identify target for chikungunya treatment
June 18, 2018 - Negative emotions are murkier, less distinct in adolescence
June 18, 2018 - Gut microbiome may be potential contributor to depression, anxiety in people with obesity
June 18, 2018 - Canakinumab reduces gout rate by more than half in atherosclerosis patients, study shows
June 18, 2018 - What Does the Future Hold?
June 18, 2018 - FDA Approves Keytruda (pembrolizumab) for Treatment of Refractory or Relapsed Primary Mediastinal Large B-Cell Lymphoma (PMBCL)
June 18, 2018 - School cliques don’t always click
June 18, 2018 - Three experts from The Tinnitus Clinic contribute to major review on pulsatile tinnitus
June 18, 2018 - Unwieldy health costs often stand between teachers and fatter paychecks
June 18, 2018 - Link between frailty and mortality remains unchanged despite lower death rates, study finds
June 18, 2018 - Sleep disorders appear to be first sign of serious neurological diseases
June 18, 2018 - Childhood, adult obesity raise risk of developing hip and knee osteoarthritis
June 18, 2018 - Study unravels ‘blood stem cell niche’ puzzle
June 18, 2018 - People with heart problems do not take enough exercise, shows study
June 18, 2018 - Strong Link Identified Between T2DM and Parkinson’s Disease
June 18, 2018 - Early childhood interventions show mixed results on child development
June 18, 2018 - Chronic use of opioids related to increased risk of fracture nonunion
June 18, 2018 - AHA: Family Perseveres After Losing Father to Heart Attack
June 18, 2018 - Oral propranolol seems safe for infantile hemangioma
June 18, 2018 - New study gives explanation for food’s prominence in memory
June 18, 2018 - First photoactive drug to fight Parkinson’s disease
June 18, 2018 - Patient’s self-evaluation of personality disorders not as far off as previously perceived
June 18, 2018 - Upadacitinib Monotherapy Meets All Primary and Ranked Secondary Endpoints Versus Methotrexate in a Phase 3 Study in Rheumatoid Arthritis
June 18, 2018 - Vitamin B3 has a positive effect on damaged nerve cells in Parkinson’s patients
June 17, 2018 - Sunovion Announces FDA Acceptance of New Drug Application for Apomorphine Sublingual Film (APL-130277)
June 17, 2018 - Bid to beat obesity focuses on fat that keeps us warm
June 17, 2018 - Work Stress May Increase Risk of Developing Atrial Fibrillation
June 17, 2018 - New Zealand’s secret recipe for active school travel: The neighborhood built environment
June 17, 2018 - New Medscape report reveals sexual harassment rate of physicians
June 17, 2018 - Surgical Blood Transfusions Tied to Clot Risk
June 17, 2018 - CDC chief makes $375K, far exceeding his predecessors’ pay
June 17, 2018 - Education linked to higher risk of short-sightedness
June 17, 2018 - Patients with Moderate-to-Severe Ulcerative Colitis Achieved Clinical and Endoscopic Remission with Mirikizumab in Phase 2 Trial
June 17, 2018 - UA registers a more customised multifocal lens to correct presbyopia
June 17, 2018 - U.S. FDA and European Medicines Agency Accept Regulatory Submissions for Review of Talazoparib for Metastatic Breast Cancer Patients with an Inherited BRCA Mutation
June 17, 2018 - Vaginal estrogen tablets, moisturizers and placebo gel all can improve vaginal discomfort
June 17, 2018 - Addition of Bezafibrate Beneficial in Primary Biliary Cholangitis
June 17, 2018 - Radiation Therapy for Cancer – National Cancer Institute
June 17, 2018 - Technology could help pregnant women detect health complications
June 17, 2018 - Study finds drop in frequent use of ED after Affordable Care Act
June 17, 2018 - Do Antipsychotic Meds for Kids Raise Diabetes Risk?
Study reveals novel statistical algorithm to identify potential disease genes

Study reveals novel statistical algorithm to identify potential disease genes

image_pdfDownload PDFimage_print

A new study, affiliated with UNIST has recently presented a novel statistical algorithm, capable of identifying potential disease genes in a more accurate and cost-effective way. This algorithm has also been considered as a new promising approach for the identification of candidate disease genes, as it works effectively with less genomic data and takes only a minute or two to get results.

This breakthrough has been conducted by Professor Dougu Nam and his research team in the School of Life Sciences at UNIST. Their findings have been published in Nucleic Acids Research on March 19, 2018.

In the study, the research team presented the novel method and software GSA-SNP2 for pathway enrichment analysis of GWAS P-value data. According to the research team, GSA-SNP2 provides high power, decent type I error control and fast computation by incorporating the random set model and SNP-count adjusted gene score.

“GSA-SNP2 is a powerful and efficient tool for pathway enrichment and network analysis of genome-wide association study (GWAS) summary data,” says Professor Nam. “With this algorithm, we can easily identify new drug targets, thereby deepening our understanding of diseases and unlock new therapies to treat it.”

Each individual’s genome is a unique combination of DNA sequences that play major roles in determining who we are. This accounts for all individual differences, including susceptibility for disease and diverse phenotypes. Such genetic variation among humans are known as single nucleotide polymorphisms (SNPs). SNPs that correlate with specific diseases could serve as predictive biomarkers to aid the development of new drugs. Through the statistical analysis of GWAS summary data, it is possible to identify the disease-associated SNPs.

Despite the astronomical amounts of money and time invested in the statistical analysis of SNP data, the conventional SNP detection technologies have been unable to identify all possible SNPs. This is because most of the conventional methods for detecting SNPs are designed to strictly control false-positives in the results. Therefore, among tens of thousands of genomics data and hundreds of thousands of SNPs analyzed, the number of markers described within a candidate disease gene often reaches severl tens.

“Although controlling false positive SNPs is needed for the correct interpretation of the results, too much filtering may hamper its usefulness in drug development,” says Professor Nam. “Therefore, enhanced statistical power is essential to practical statistical algorithms.”

The team aimed to develop an algorithm that improves the statistical predictability while maintaining accurate control of false positives. To do this, they applied the monotone Cubic Spline trend curve to the gene score via the competitive pathway analysis for gene expression data.

In a comparative study using simulated and real GWAS data, GSA-SNP2 exhibited high power and best prioritized gold standard positive pathways compared with six existing enrichment-based methods and two self-contained methods. Based on these results, the difference between pathway analysis approaches was investigated and the effects of the gene correlation structures on the pathway enrichment analysis were also discussed. In addition, GSA-SNP2 is able to visualize protein interaction networks within and across the significant pathways so that the user can prioritize the core subnetworks for further studies.

According to the research team, GSA-SNP2 provides a greatly improved type I error control by using the SNP-count adjusted gene scores, while nevertheless preserving high statistical power. It also provides both local and global protein interaction networks in the associated pathways, and may facilitate integrated pathway and network analysis of GWAS data.

The research team expects that their GSA-SNP2 is able to visualize protein interaction networks within and across the significant pathways so that the user can prioritize the core subnetworks for further studies.​​

Source:

New Method for Finding Disease-Susceptibility Genes

Tagged with:

About author

Related Articles