Rajiv McCoy is an assistant professor in the Department of Biology whose research is focused on human genetics and evolution. He received his PhD from Stanford University and completed his postdoctoral work at Princeton University and the University of Washington.

The McCoy lab seeks to understand the genomic basis of functional and fitness-altering variation through the development and application of computational methods. Our work combines diverse datasets and concepts from population genetics and statistics to achieve quantitative perspectives on human evolution and reproduction.

Human Evolution

• Evolution of poorly resolved and repetitive regions of the genome, including loci harboring structural variation
• Functional and fitness impacts of gene flow from our archaic hominin relatives, the Neanderthals and Denisovans
•  Statistical methods for improving the mapping of complex traits in samples from diverse and admixed populations

Human Reproduction

•  Molecular origins of human aneuploidy, implications for human development, and genetic factors influencing its occurrence
• Preimplantation and prenatal genetic testing, especially with respect to aneuploidy and structural variation
• Deviations of expected patterns of Mendelian inheritance, for example by meiotic drive, embryonic mortality, or other mechanisms of transmission distortion

Preprints

Taylor, D. J., Chhetri, S. B., Tassia, M. G., Biddanda, A., Battle, A., McCoy, R. C. (2023). Sources of gene expression variation in a globally diverse human cohort. bioRxiv, https://doi.org/10.1101/2023.11.04.565639.

DeGorter, M. K., Goddard, P. C., Karakoc, E., Kundu, S., Yan, S. M., Nachun, D., Abell, N., Aguirre, M., Carstensen, T., Chen, Z., Durrant, M., Dwaracherla, V. R., Feng, K., Gloudemans, M. J., Hunter, N., Moorthy, M. P. S., Pomilla, C., Rodrigues, K. B., Smith, C., Smith, K. S., Ungar, R. A., Balliu, B., Fellay, J., Flicek, P., McLaren, P. J., Henn, B., McCoy, R. C., Sugden, L., Kundaje, A., Sandu, M. S., Gurdasani, D., Montgomery, S. B. (2023). Transcriptomics and chromatin accessibility in multiple African population samples. bioRxiv, https://doi.org/10.1101/2023.11.04.564839.

Xiang, G., He, X., Giardine, B. M., Weaver, K. J., Taylor, D. J., McCoy, R. C., Jansen, C., Keller, C. A., Wixom, A., Cockburn, A., Miller, A., Qi, Q., He, Y., Li, Y., Lichtenberg, J., Heuston, E. F., Anderson, S. M., Luan, J., Vermunt, M. W., Yue, F., Sauria, M. E. G., Schatz., M. C., Taylor, J., Gottgens, B., Hughes, J. R., Higgs, D. R., Weiss, M. J., Cheng, Y., Blobel, G. A., Bodine, D., Zhang, Y., Li, Q., Mahony, S., Hardison, R. C. (2023). Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv, https://doi.org/10.1101/2023.04.02.535219

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., …, Yan, S. M., …, McCoy, R. C., …, Eichler, E. E., Miga, K. H., Phillippy, A. M. (2021). The complete sequence of a human genome. bioRxiv, https://doi.org/10.1101/2021.05.26.445798.

Ariad, D., Yan, S. M., Victor, A. R., Barnes, F. L., Zouves, C. G., Viotti, M., McCoy, R. C. (2021). Haplotype-aware inference of human chromosome abnormalities. bioRxiv, https://doi.org/10.1101/2021.01.26.428314.

Hadyniak, S. E., Eldred, K. C., Brenerman, B., Hussey, K. A., McCoy, R. C., Sauria, M. E. G., Kuchenbeker, J. A., Neitz, M., Neitz, J., Taylor, J., Johnston, R. J. (2021). Temporal regulation of green and red cone specification in human retinas and retinal organoids. bioRxiv, https://doi.org/10.1101/2021.03.30.437763.

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. bioRxiv, https://doi.org/10.1101/2021.01.26.428314.

Research Articles

Hadyniak, S. E., Eldred, K. C., Brenerman, B., Hussey, K. A., McCoy, R. C., Sauria, M. E. G., Kuchenbeker, J. A., Neitz, M., Neitz, J., Taylor, J., Johnston, R. J. (2024). Retinoic acid signaling regulates spatiotemporal specification of human green and red cones. PLoS Biology, 22: e3002464.

Ariad, D., Madjunkova, S., Madjunkov, M., Chen, S., Abramov, R., Librach, C., McCoy, R. C. (2023). Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. Genome Research, 34: 70-84.

Sun, S., Aboelenain, M., Ariad, D., Haywood, M. E., Wageman, C. R., Duke, M., Bag, A., Viotti, M., Katz-Jaffe, M., McCoy, R. C., Schindler, K., Xing, J. (2023). A method of identifying risk genes using ultra-low coverage whole-genome sequencing – insights into embryo aneuploidy. American Journal of Human Genetics: 10: 2092-2102.

McCoy, R. C., Summers, M. C., McCollin, A., Ottolini, C. S., Ahuja, K., Handyside, A. H. (2023). Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Medicine, 15: 77.

*Rhie, A., *Nurk, S., *Cechova, M., *Hoyt, S., *Taylor, D., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., McNulty, B. M., Bzikadze, A. V., Chen, N.-C., Chin, C.-S. Diekhans, M., Formenti, G., Flicek, P., …, McCoy, R. C., …, Eichler, E. E., O’Neill, R., Schatz, M. C., Miga, K. H., Makova, K. D., Phillippy, A. M. (2023). The complete sequence of a human Y chromosome. Nature, 621: 344–354. *co-first author

Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Vollger, M. R., Chen, N.-C., Taylor, D. J., Harvey, W. T., Logsdon, G. A., Meng, D., Shi, J., McCoy, R. C., Schatz, M. C., Li, W., Eichler, E. E., Lu, Q., Mao, Y. (2023). Characterization of large-scale genomic differences in the first complete human genome. Genome Biology, 24: 157.

Giraldo, D., Rankin-Turner, S., Corver, A., Tauxe, G. M., Gao, A. L., Jackson, D. M., Simubali, L., Book, C., Stevenson, J. C., Thuma, P. E., McCoy, R. C., Gordus, A., Mburu, M. M., Simulundu, E., McMeniman, C. J. (2023). Human scent guides mosquito thermotaxis and host selection under naturalistic conditions. Current Biology, 33: 2367-2382.e7.

*DeBoy, E. A., *Tassia, M. G., Schratz, K. E., Yan, S. M., Cosner, Z. L., McNally, E. J., Gable, D. L., Xiang, Z., Lombard, D. B., Antonarakis, E. S., Gocke, C. D., McCoy, R. C., Armanios, M. (2023), Familial clonal hematopoiesis in a long telomere syndrome. New England Journal of Medicine, 388:2422-2433. *co-first author

*Carioscia, S. A., *Weaver, K. J., Bortvin, A. N., Pan, H., Ariad, D., Bell, A. D., McCoy, R. C. (2022). A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm. eLife, 11: e76383. *co-first author

Griffin, D. K., Brezina, P. R., Tobler, K., Silvestri, G., McCoy, R. C., Anchan, R., Benner, A., Cutting, G. R., Kearns, W. G. (2022). The human embryonic genome is karyotypically complex, with chromosomally abnormal cells preferentially located away from the developing fetus. Human Reproduction, 38, 180-188.

*Aganezov, S., *Yan, S. M., *Soto, D. C., *Kirsche, M., *Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., Wagner, J., McDaniel, J., Olson, N. D., Sauria, M. E. G., Vollger, M. R., Meredith, M., Martin, S., Koren, S., Rosenfeld, J. A., Paten, B., Layer, R., Chin, C., Sedlazeck, F. J., Hansen, N. F., Miller, D. E., Phillippy, A., Miga, K., †McCoy, R. C., †Dennis, M. Y., †Zook, J. M., †Schatz, M. C. (2022). A complete reference genome improves analysis of human genetic variation. Science, 375, eabl3533. *co-first author; †co-corresponding author

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., …, Yan, S. M., …, McCoy, R. C., …, Eichler, E. E., Miga, K. H., Phillippy, A. M. (2022). The complete sequence of a human genome. Science, 376, eabj6987.

Ariad, D., Yan, S. M., Victor, A. R., Barnes, F. L., Zouves, C. G., Viotti, M., McCoy, R. C. (2021). Haplotype-aware inference of human chromosome abnormalities. PNAS, 118, e2109307118.

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10, e67615.

Ranallo-Benavidez, T. R., Lemmon, Z. H., Soyk, S., Aganezov, S., Salerno, W. J., McCoy, R. C., Lippman, Z. B., Schatz, M. C., Sedlazeck, F. J. (2021). Optimized sample selection for cost-efficient long-read population sequencing. Genome Research, in press.

Starostik, M. R., Sosina, O. A., McCoy, R. C.  (2020). Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism. Genome Research, 30, 814-825.

Tyc, K. M., McCoy, R. C., Schindler, K., Xing, J. (2020). Mathematical modeling of human oocyte aneuploidy. PNAS, 117, 10455-10464.

Sharma, R., Singh, P., McCoy, R. C., Lenz, S. M., Donovan, K., Ochoa, M. T., Mayra Silva-Miranda, I. E., Jurado-Santa Cruz, F., Balagon, M. F., Stryjewska, B., Scollard, D. M., Pena, M. T., Lahiri, R., Williams, D. L., Truman, R. W.,Adams, L. B. (2020). Isolation of Mycobacterium lepromatosis and Development of Molecular Diagnostic Assays to Distinguish M. leprae and M. lepromatosis. Clinical Infectious Diseases, 71(8), e262-e269.

Gruhn, J. R., Zielinska, A. P., Shukla, V., Blanshard, R., Capalbo, A., Cimadomo, D., Nikiforov, D., Chan, A. C., Newnham, L. J., Vogel, I., Scarica, C., Krapchev, M., Taylor, D., Kristensen, S. G., Cheng, J., Ernst, E., Bjørn, A. B., Colmorn, L. B., Blayney, M., Elder, K., Liss, J., Hartshorne, G., Grøndahl, M. L., Rienzi, L., Ubaldi, F., McCoy, R. C., Lukaszuk, K., Andersen, C. Y., Schuh, M., Hoffmann, E. R. (2019). Chromosome errors in human eggs shape natural fertility over reproductive life span. Science, 365(6460), 1466-1469.

Victor, A. R., Tyndall, J. C., Brake, A. J., Lepkowski, L. T., Murphy, A., Griffin, D. K., McCoy, R. C., Barnes, F. L., Zouves, C. G., Viotti, M. (2019). One hundred mosaic embryos transferred prospectively in a single clinic: exploring when and why they result in healthy pregnancies. Fertility & Sterility, 111(2), 280-293.

Victor, A. R., Griffin, D. K., Brake, A. J., Tyndall, J. C., Murphy, A., Lepkowsky, L. T., Lal, A., Zouves, C. G., Barnes, F. L., McCoy, R. C., Viotti, M. (2019). Assessment of aneuploidy concordance between clinical trophectoderm biopsy and blastocyst. Human Reproduction, 34(1), 181-192.

Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B, Robinson, M., Barbieri, C., Fu, W., Purnomo, G. A., Sudoyo, H., Barbujani, G., Visscher, P. M., Akey, J. M., Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science, 361(6401), 511-516.

Press, M. O., McCoy, R. C., Hall, A. N., Akey, J. M., Queitsch, C. (2018). Short tandem repeats with massive variation and functional consequences across strains of Arabidopsis thaliana. Genome Research, 28, 1169-1178.

*McCoy, R. C., *Newnham, L. J., Ottolini, C. S., Hoffmann, E. R., Chatzimeletiou, K., Cornejo, O. E., Zhan, Q., Zaninovic, N., Rosenwaks, Z., Petrov, D. A., Demko, Z. P., Sigurjonsson, S., Handyside, A. H. (2018). Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos. Human Molecular Genetics, 27(14), 2573–2585. *co-first author

Kort, J. D., McCoy, R. C., Demko, Z. P., Lathi, R. B. (2018). Are blastocyst aneuploidy rates different between fertile and infertile populations? Journal of Assisted Reproduction and Genetics, 35(3), 403–408.

McCoy, R. C., Wakefield, J., Akey, J. M. (2017). Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. Cell, 168(5), 916–927.e12.

Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., Scheinfeldt, L. B., Merriwether, D. A., Koki, G., Friedlaender, J. S., Wakefield, J., Pääbo, S., Akey, J. M. (2016). Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science, 352(6282), 235-239.

Demko, Z. P., Simon, A. L., McCoy, R. C., Petrov, D. A., Rabinowitz, M. (2016). Effects of maternal age on euploidy in a large cohort of embryos analyzed with 24-chromosome single-nucleotide polymorphism-based preimplantation genetic screening. Fertility & Sterility, 105(5), 1307-1313.

McCoy, R. C., Demko, Z., Ryan, A., Banjevic, M., Hill, M., Sigurjonsson, S., Rabinowitz, M., Petrov, D. A. (2015). Evidence of selection against complex mitotic-origin aneuploidy during preimplantation development. PLoS Genetics, 11(10), e1005601.

McCoy, R. C., Demko, Z., Ryan, A., Banjevic, M., Hill, M., Sigurjonsson, S., Rabinowitz, M., Fraser, H. B., Petrov, D. A. (2015). Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science, 348(6231), 235-238.

Ahola, V., Lehtonen, R., Somervou, P., Salmela, L., Koskinen, P., Rastas, P., Välimäki, L. P., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E., Ferguson, L., Luo, S., Cao, Z., de Jong, M., Duplouy, A., Smolander, O., McCoy, R. C., Qian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J., Joshi, A., Salojärvi, J., Wheat, C., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkänen, E., Ylinen, J., Waterhouse, R., Turunen, M., Vähärautio, A., Ojanen, S., Schulman, A., Taipale, M., Lawson, D., Ukkonen, E., Mäkinen, V., Goldsmith, M., Holm, L., Auvinen, P., Frilander, M., Hanski, I. (2014). The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications, 5.

McCoy, R. C., Taylor, R. W., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., Petrov, D. A., Fiston-Lavier, A. S. (2014). Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS ONE, 9(9), e106689.

McCoy, R. C., Garud, N. R., Kelley, J. L., Boggs, C. L., Petrov, D. A. (2014). Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population. Molecular Ecology, 23(1), 136-150.

Review Articles

Muter, J., Lynch, V. J., McCoy, R. C., Brosens, J. J. (2023). Human embryo implantation. Development, 150: dev201507.

Brosens, J. J., Bennett, P. R., Abrahams, V., Ramhorst, R., Coomarasamy, A., Quenby, S., Lucas, E. S., McCoy, R. C. (2022). Maternal selection of human embryos in early gestation: insights from recurrent miscarriage. Seminars in Cell and Developmental Biology, 131, 14-24.

Quenby, S., Gallos, I. D., Dhillon-Smith, R. K., Podesek, M., Stephenson, M. D., Fisher, J., Brosens, J. J., Brewin, J., Ramhorst, R., Lucas, E. S., McCoy, R. C., Anderson, R., Daher, S., Regan, L., Al-Memar, M., Bourne, T., MacIntyre, D. A., Rai, R., Christiansen, O. B., Sugiura-Ogasawara, M., Odendaal, J., Devall, A. J., Bennett, P. R., Petrou, S., Coomarasamy, A. (2021). Miscarriage matters: the epidemiological, physical, psychological, and economic costs of early pregnancy loss. The Lancet, 397, 1658-1667.

Wartosch, L., Schindler, K., Schuh, M., Gruhn, J. R., Hoffmann, E. R., McCoy, R. C., Xing, J.  Origins and mechanisms leading to aneuploidy in human eggs. Prenatal Diagnosis, in press.

Levy, B., Hoffmann, E. R., McCoy, R. C., Grati, F. R. Chromosomal mosaicism: origins and clinical implications in preimplantation and prenatal diagnosis. Prenatal Diagnosis, in press.

Yan, S. M., McCoy, R. C. (2020). Archaic hominin genomics provides a window into gene expression evolution. Current Opinion in Genetics & Development, 62, 44-49.

McCoy, R. C. (2017). Mosaicism in preimplantation human embryos: when chromosomal abnormalities are the norm. Trends in Genetics, 33(7), 448–463.

Commentaries and Editorials

Carioscia, S., McCoy, R. C. (2024), A rare genetic variant biases maternal meiotic recombination toward risk of pregnancy loss. Nature Structural & Molecular Biology: in press.

Viotti, M., McCoy, R. C., Griffin, D. K., Spinella, F., Greco, E., Madjunkov, M., Madjunkova, S., Librach, C. L., Victor, A. R., Barnes, F. L., Zouves, C. G. (2021), Let the data do the talking: The Need To Consider Mosaicism During Embryo Selection. Fertility & Sterility, 116: 1212–1219.

Yan, S. M., McCoy, R. C. (2019). Functional divergence among hominins. Nature Ecology & Evolution, 3, 1507-1508.

McCoy, R. C., Kort, J. D. (2019). Quantifying the transcriptional impacts of aneuploidy in human blastocysts. Fertility & Sterility, 111(5), 888-889.

McCoy, R. C., Akey, J. M. (2017). Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation. Genome Biology, 18, 139.

Adashi, E. Y., McCoy, R. C. (2017). Technology versus biology: the limits of pre-implantation genetic screening. EMBO Reports, e201743941.

McCoy, R. C., Akey, J. M. (2016). Patterns of deleterious variation between human populations reveal an unbalanced load. PNAS, 113 (4), 809-811.