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By using genetic variants as instrumental variables, it can mitigate bias due to confounding and reverse causation in observational studies. Current MR analyses have predominantly used common genetic variants as instruments, which represent only part of the genetic architecture of complex traits. Rare variants, which can have larger effect sizes and provide unique biological insights, have been understudied due to statistical and methodological challenges. We introduce MR-common and annotation-informed rare variants (MR-CARV), a novel framework integrating common and rare genetic variants in two-sample MR. This method leverages comprehensive genetic data made available by high-throughput sequencing technologies and large-scale consortia. Rare variants are aggregated into functional categories, such as gene-coding, gene-noncoding, and nongene regions, by leveraging variant annotations and biological impact as weights. The effects of rare variant sets are then estimated with STAARpipeline and combined with the estimated effects of common variants by the existing MR methods. Simulation studies demonstrate that MR-CARV maintains robust type I error and achieves higher statistical power, with up to a 66.3% relative increase compared with existing methods only based on common variants. Consistent with these findings, application to real data on high-density lipoprotein cholesterol (HDL-C) and preeclampsia showed that MR-CARV [inverse variance weighted (IVW)] yielded a more precise and statistically significant effect estimate (\u20130.020, SE = 0.0102, $P$ =.0470) than IVW using only common variants (\u20130.023, SE = 0.0123, $P$ =.0659).<\/jats:p>","DOI":"10.1093\/bib\/bbaf649","type":"journal-article","created":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T16:36:32Z","timestamp":1767803792000},"source":"Crossref","is-referenced-by-count":1,"title":["A novel two-sample Mendelian randomization framework integrating common and rare variants: application to assess the effect of HDL-C on preeclampsia risk"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-2457-2876","authenticated-orcid":false,"given":"Yu","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics , Indiana University School of Public Health-Bloomington, 1025 E. 7th Street, Bloomington, IN 47405,","place":["United States"]}]},{"given":"Ming","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics , Indiana University School of Public Health-Bloomington, 1025 E. 7th Street, Bloomington, IN 47405,","place":["United States"]}]},{"given":"David M","family":"Haas","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , Indiana University School of Medicine, 1130 W. Michigan St., Indianapolis, IN 46202,","place":["United States"]}]},{"given":"C Noel","family":"Bairey Merz","sequence":"additional","affiliation":[{"name":"Barbra Streisand Women\u2019s Heart Center , Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048,","place":["United States"]}]},{"given":"Tsegaselassie","family":"Workalemahu","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , University of Utah Health, 30 N. Mario Capecchi Dr. Level 5, South (HELIX), Salt Lake City, UT 84112,","place":["United States"]}]},{"given":"Kelli","family":"Ryckman","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics , Indiana University School of Public Health-Bloomington, 1025 E. 7th Street, Bloomington, IN 47405,","place":["United States"]}]},{"given":"Janet M","family":"Catov","sequence":"additional","affiliation":[{"name":"Department of Obstetrics , Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA 15213,","place":["United States"]},{"name":"Department of Epidemiology , University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15213,","place":["United States"]}]},{"given":"Lisa D","family":"Levine","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , The University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9745-7768","authenticated-orcid":false,"given":"Alexa","family":"Freedman","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine , Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7925-5302","authenticated-orcid":false,"given":"George R","family":"Saade","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , Eastern Virginia Medical School, 621 W. 21st Street, Norfolk, VA 23507,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6317-7730","authenticated-orcid":false,"given":"Jiaqi","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Chronic Disease Epidemiology , Yale School of Public Health, 60 College Street, New Haven, CT 06510,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1195-9607","authenticated-orcid":false,"given":"Hongyu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Biostatistics ,School of Public Health, Yale University, 60 College Street, New Haven, CT 06520,","place":["United States"]}]},{"given":"Xihao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics , University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599,","place":["United States"]},{"name":"Department of Genetics , University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2565-8154","authenticated-orcid":false,"given":"Nianjun","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics , Indiana University School of Public Health-Bloomington, 1025 E. 7th Street, Bloomington, IN 47405,","place":["United States"]}]},{"given":"Qi","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , Columbia University, 622 West 168th Street, New York, NY 10032,","place":["United 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