Rajiv McCoy

Rajiv McCoy

Assistant Professor

PhD, Stanford University

UTL 383
Group/Lab Website

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.

Our lab uses computational and statistical approaches to investigate the evolution and function of human genomes. Specific research interests relate to understanding the functional and fitness consequences of genetic variation–including large-scale chromosome abnormalities. We are also interested in the evolutionary processes that generate and maintain functional genetic variation in human populations.

Functional Evolutionary Genomics: Genetic variation provides the raw material of evolution. How is this variation filtered by the interacting forces of selection, recombination, and demography to produce phenotypic diversity? Humans offer an appealing system to address this question due to the wealth of whole-genome data, large-scale mapping of regulatory mutations, and recent development of high-throughput functional assays. We are leveraging data from both modern and archaic humans to better understand the evolutionary forces that shape our genomes.

Human Aneuploidy: Human reproduction is both inefficient and individually variable, despite its close link to fitness. Only approximately half of conceptions survive to term, mostly due to aneuploidy—the gain or loss of whole chromosomes. Working with collaborators from both academia and industry, we are investigating the molecular origins, functional consequences, and genetic basis of variation in human aneuploidy.

Starostik, M. R., Sosina, O. A., McCoy, R. C.  (2020). Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism. bioRxiv, https://doi.org/10.1101/2020.01.06.894287.

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. (2019). Isolation of Mycobacterium lepromatosis and Development of Molecular Diagnostic Assays to Distinguish M. leprae and M. lepromatosis. Clinical Infectious Diseases, in press.

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

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.

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

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, in press.

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

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

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

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

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.