1
|
Mahesh N, Devishamani CS, Raghu K, Mahalingam M, Bysani P, Chakravarthy AV, Raman R. Advancing healthcare: the role and impact of AI and foundation models. Am J Transl Res 2024; 16:2166-2179. [PMID: 39006256 PMCID: PMC11236664 DOI: 10.62347/wqwv9220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/06/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND The integration of artificial intelligence (AI) into the healthcare domain is a monumental shift with profound implications for diagnostics, medical interventions, and the overall structure of healthcare systems. PURPOSE This study explores the transformative journey of foundation AI models in healthcare, shedding light on the challenges, ethical considerations, and vast potential they hold for improving patient outcome and system efficiency. Notably, in this investigation we observe a relatively slow adoption of AI within the public sector of healthcare. The evolution of AI in healthcare is un-paralleled, especially its prowess in revolutionizing diagnostic processes. RESULTS This research showcases how these foundational models can unravel hidden patterns within complex medical datasets. The impact of AI reverberates through medical interventions, encompassing pathology, imaging, genomics, and personalized healthcare, positioning AI as a cornerstone in the quest for precision medicine. The paper delves into the applications of generative AI models in critical facets of healthcare, including decision support, medical imaging, and the prediction of protein structures. The study meticulously evaluates various AI models, such as transfer learning, RNN, autoencoders, and their roles in the healthcare landscape. A pioneering concept introduced in this exploration is that of General Medical AI (GMAI), advocating for the development of reusable and flexible AI models. CONCLUSION The review article discusses how AI can revolutionize healthcare by stressing the significance of transparency, fairness and accountability, in AI applications regarding patient data privacy and biases. By tackling these issues and suggesting a governance structure the article adds to the conversation about AI integration in healthcare environments.
Collapse
Affiliation(s)
- Nandhini Mahesh
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Medical Research Foundation Chennai, Tamil Nadu, India
| | - Chitralekha S Devishamani
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Medical Research Foundation Chennai, Tamil Nadu, India
| | - Keerthana Raghu
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Medical Research Foundation Chennai, Tamil Nadu, India
| | - Maanasi Mahalingam
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Medical Research Foundation Chennai, Tamil Nadu, India
| | - Pragathi Bysani
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Medical Research Foundation Chennai, Tamil Nadu, India
| | | | - Rajiv Raman
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Medical Research Foundation Chennai, Tamil Nadu, India
| |
Collapse
|
2
|
Barnett EJ, Onete DG, Salekin A, Faraone SV. Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:169-177. [PMID: 38109236 DOI: 10.1109/tcbb.2023.3343808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Many studies have been conducted with the goal of correctly predicting diagnostic status of a disorder using the combination of genomic data and machine learning. It is often hard to judge which components of a study led to better results and whether better reported results represent a true improvement or an uncorrected bias inflating performance. We extracted information about the methods used and other differentiating features in genomic machine learning models. We used these features in linear regressions predicting model performance. We tested for univariate and multivariate associations as well as interactions between features. Of the models reviewed, 46% used feature selection methods that can lead to data leakage. Across our models, the number of hyperparameter optimizations reported, data leakage due to feature selection, model type, and modeling an autoimmune disorder were significantly associated with an increase in reported model performance. We found a significant, negative interaction between data leakage and training size. Our results suggest that methods susceptible to data leakage are prevalent among genomic machine learning research, resulting in inflated reported performance. Best practice guidelines that promote the avoidance and recognition of data leakage may help the field avoid biased results.
Collapse
|
3
|
Alowais SA, Alghamdi SS, Alsuhebany N, Alqahtani T, Alshaya AI, Almohareb SN, Aldairem A, Alrashed M, Bin Saleh K, Badreldin HA, Al Yami MS, Al Harbi S, Albekairy AM. Revolutionizing healthcare: the role of artificial intelligence in clinical practice. BMC MEDICAL EDUCATION 2023; 23:689. [PMID: 37740191 PMCID: PMC10517477 DOI: 10.1186/s12909-023-04698-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
INTRODUCTION Healthcare systems are complex and challenging for all stakeholders, but artificial intelligence (AI) has transformed various fields, including healthcare, with the potential to improve patient care and quality of life. Rapid AI advancements can revolutionize healthcare by integrating it into clinical practice. Reporting AI's role in clinical practice is crucial for successful implementation by equipping healthcare providers with essential knowledge and tools. RESEARCH SIGNIFICANCE This review article provides a comprehensive and up-to-date overview of the current state of AI in clinical practice, including its potential applications in disease diagnosis, treatment recommendations, and patient engagement. It also discusses the associated challenges, covering ethical and legal considerations and the need for human expertise. By doing so, it enhances understanding of AI's significance in healthcare and supports healthcare organizations in effectively adopting AI technologies. MATERIALS AND METHODS The current investigation analyzed the use of AI in the healthcare system with a comprehensive review of relevant indexed literature, such as PubMed/Medline, Scopus, and EMBASE, with no time constraints but limited to articles published in English. The focused question explores the impact of applying AI in healthcare settings and the potential outcomes of this application. RESULTS Integrating AI into healthcare holds excellent potential for improving disease diagnosis, treatment selection, and clinical laboratory testing. AI tools can leverage large datasets and identify patterns to surpass human performance in several healthcare aspects. AI offers increased accuracy, reduced costs, and time savings while minimizing human errors. It can revolutionize personalized medicine, optimize medication dosages, enhance population health management, establish guidelines, provide virtual health assistants, support mental health care, improve patient education, and influence patient-physician trust. CONCLUSION AI can be used to diagnose diseases, develop personalized treatment plans, and assist clinicians with decision-making. Rather than simply automating tasks, AI is about developing technologies that can enhance patient care across healthcare settings. However, challenges related to data privacy, bias, and the need for human expertise must be addressed for the responsible and effective implementation of AI in healthcare.
Collapse
Affiliation(s)
- Shuroug A Alowais
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia.
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia.
| | - Sahar S Alghamdi
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Pharmaceutical Sciences, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Nada Alsuhebany
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Tariq Alqahtani
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Pharmaceutical Sciences, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman I Alshaya
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Sumaya N Almohareb
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Atheer Aldairem
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed Alrashed
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Khalid Bin Saleh
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Hisham A Badreldin
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Majed S Al Yami
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Shmeylan Al Harbi
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulkareem M Albekairy
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Prince Mutib Ibn Abdullah Ibn Abdulaziz Rd, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Pharmaceutical Care Department, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| |
Collapse
|
4
|
Raben TG, Lello L, Widen E, Hsu SDH. Biobank-scale methods and projections for sparse polygenic prediction from machine learning. Sci Rep 2023; 13:11662. [PMID: 37468507 PMCID: PMC10356957 DOI: 10.1038/s41598-023-37580-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023] Open
Abstract
In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of [Formula: see text] and for height a correlation of [Formula: see text] for a Taiwanese population. This is above the measured values of [Formula: see text] and [Formula: see text], respectively, for UK Biobank trained predictors applied to a European population.
Collapse
Affiliation(s)
- Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, Michigan, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| |
Collapse
|
5
|
du Toit C, Tran TQB, Deo N, Aryal S, Lip S, Sykes R, Manandhar I, Sionakidis A, Stevenson L, Pattnaik H, Alsanosi S, Kassi M, Le N, Rostron M, Nichol S, Aman A, Nawaz F, Mehta D, Tummala R, McCallum L, Reddy S, Visweswaran S, Kashyap R, Joe B, Padmanabhan S. Survey and Evaluation of Hypertension Machine Learning Research. J Am Heart Assoc 2023; 12:e027896. [PMID: 37119074 PMCID: PMC10227215 DOI: 10.1161/jaha.122.027896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/27/2023] [Indexed: 04/30/2023]
Abstract
Background Machine learning (ML) is pervasive in all fields of research, from automating tasks to complex decision-making. However, applications in different specialities are variable and generally limited. Like other conditions, the number of studies employing ML in hypertension research is growing rapidly. In this study, we aimed to survey hypertension research using ML, evaluate the reporting quality, and identify barriers to ML's potential to transform hypertension care. Methods and Results The Harmonious Understanding of Machine Learning Analytics Network survey questionnaire was applied to 63 hypertension-related ML research articles published between January 2019 and September 2021. The most common research topics were blood pressure prediction (38%), hypertension (22%), cardiovascular outcomes (6%), blood pressure variability (5%), treatment response (5%), and real-time blood pressure estimation (5%). The reporting quality of the articles was variable. Only 46% of articles described the study population or derivation cohort. Most articles (81%) reported at least 1 performance measure, but only 40% presented any measures of calibration. Compliance with ethics, patient privacy, and data security regulations were mentioned in 30 (48%) of the articles. Only 14% used geographically or temporally distinct validation data sets. Algorithmic bias was not addressed in any of the articles, with only 6 of them acknowledging risk of bias. Conclusions Recent ML research on hypertension is limited to exploratory research and has significant shortcomings in reporting quality, model validation, and algorithmic bias. Our analysis identifies areas for improvement that will help pave the way for the realization of the potential of ML in hypertension and facilitate its adoption.
Collapse
Affiliation(s)
- Clea du Toit
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Tran Quoc Bao Tran
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Neha Deo
- Mayo Clinic Alix School of MedicineRochesterMN
| | - Sachin Aryal
- Center for Hypertension and Precision Medicine, Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOH
| | - Stefanie Lip
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Robert Sykes
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Ishan Manandhar
- Center for Hypertension and Precision Medicine, Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOH
| | | | - Leah Stevenson
- Center for Hypertension and Precision Medicine, Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOH
| | | | - Safaa Alsanosi
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
- Department of Pharmacology and Toxicology, Faculty of MedicineUmm Al Qura UniversityMakkahSaudi Arabia
| | - Maria Kassi
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Ngoc Le
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Maggie Rostron
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Sarah Nichol
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Alisha Aman
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | - Faisal Nawaz
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubaiUAE
| | - Dhruven Mehta
- Department of Internal MedicineTriStar Centennial Medical Center, HCA HealthcareNashvilleTN
| | - Ramakumar Tummala
- Center for Hypertension and Precision Medicine, Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOH
| | - Linsay McCallum
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| | | | - Shyam Visweswaran
- Department of Biomedical InformaticsUniversity of PittsburghPittsburghPA
| | - Rahul Kashyap
- Department of Anesthesiology and Critical Care MedicineMayo ClinicRochesterMN
| | - Bina Joe
- Center for Hypertension and Precision Medicine, Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOH
| | - Sandosh Padmanabhan
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUnited Kingdom
| |
Collapse
|
6
|
Conroy MC, Lacey B, Bešević J, Omiyale W, Feng Q, Effingham M, Sellers J, Sheard S, Pancholi M, Gregory G, Busby J, Collins R, Allen NE. UK Biobank: a globally important resource for cancer research. Br J Cancer 2023; 128:519-527. [PMID: 36402876 PMCID: PMC9938115 DOI: 10.1038/s41416-022-02053-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/21/2022] Open
Abstract
UK Biobank is a large-scale prospective study with deep phenotyping and genomic data. Its open-access policy allows researchers worldwide, from academia or industry, to perform health research in the public interest. Between 2006 and 2010, the study recruited 502,000 adults aged 40-69 years from the general population of the United Kingdom. At enrolment, participants provided information on a wide range of factors, physical measurements were taken, and biological samples (blood, urine and saliva) were collected for long-term storage. Participants have now been followed up for over a decade with more than 52,000 incident cancer cases recorded. The study continues to be enhanced with repeat assessments, web-based questionnaires, multi-modal imaging, and conversion of the stored biological samples to genomic and other '-omic' data. The study has already demonstrated its value in enabling research into the determinants of cancer, and future planned enhancements will make the resource even more valuable to cancer researchers. Over 26,000 researchers worldwide are currently using the data, performing a wide range of cancer research. UK Biobank is uniquely placed to transform our understanding of the causes of cancer development and progression, and drive improvements in cancer treatment and prevention over the coming decades.
Collapse
Affiliation(s)
- Megan C Conroy
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK.
| | - Ben Lacey
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
| | - Jelena Bešević
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
| | - Wemimo Omiyale
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
| | - Qi Feng
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
| | | | | | | | | | | | - John Busby
- UK Biobank, Stockport, Greater Manchester, UK
| | - Rory Collins
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
- UK Biobank, Stockport, Greater Manchester, UK
| | - Naomi E Allen
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
| |
Collapse
|
7
|
Lello L, Hsu M, Widen E, Raben TG. Sibling variation in polygenic traits and DNA recombination mapping with UK Biobank and IVF family data. Sci Rep 2023; 13:376. [PMID: 36611071 PMCID: PMC9825593 DOI: 10.1038/s41598-023-27561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
We use UK Biobank and a unique IVF family dataset (including genotyped embryos) to investigate sibling variation in both phenotype and genotype. We compare phenotype (disease status, height, blood biomarkers) and genotype (polygenic scores, polygenic health index) distributions among siblings to those in the general population. As expected, the between-siblings standard deviation in polygenic scores is [Formula: see text] times smaller than in the general population, but variation is still significant. As previously demonstrated, this allows for substantial benefit from polygenic screening in IVF. Differences in sibling genotypes result from distinct recombination patterns in sexual reproduction. We develop a novel sibling-pair method for detection of recombination breaks via statistical discontinuities. The new method is used to construct a dataset of 1.44 million recombination events which may be useful in further study of meiosis.
Collapse
Affiliation(s)
- Louis Lello
- Genomic Prediction, Inc., North Brunswick, NJ, USA.
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA.
| | - Maximus Hsu
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Genomic Prediction, Inc., North Brunswick, NJ, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA
| | - Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA
| |
Collapse
|
8
|
Widen E, Lello L, Raben TG, Tellier LCAM, Hsu SDH. Polygenic Health Index, General Health, and Pleiotropy: Sibling Analysis and Disease Risk Reduction. Sci Rep 2022; 12:18173. [PMID: 36307513 PMCID: PMC9616929 DOI: 10.1038/s41598-022-22637-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
We construct a polygenic health index as a weighted sum of polygenic risk scores for 20 major disease conditions, including, e.g., coronary artery disease, type 1 and 2 diabetes, schizophrenia, etc. Individual weights are determined by population-level estimates of impact on life expectancy. We validate this index in odds ratios and selection experiments using unrelated individuals and siblings (pairs and trios) from the UK Biobank. Individuals with higher index scores have decreased disease risk across almost all 20 diseases (no significant risk increases), and longer calculated life expectancy. When estimated Disability Adjusted Life Years (DALYs) are used as the performance metric, the gain from selection among ten individuals (highest index score vs average) is found to be roughly 4 DALYs. We find no statistical evidence for antagonistic trade-offs in risk reduction across these diseases. Correlations between genetic disease risks are found to be mostly positive and generally mild. These results have important implications for public health and also for fundamental issues such as pleiotropy and genetic architecture of human disease conditions.
Collapse
Affiliation(s)
- Erik Widen
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA. .,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA. .,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA.
| | - Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA
| | - Laurent C A M Tellier
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| |
Collapse
|