Dan Levy

Dan Levy

Associate Professor
Cancer Center Member

Ph.D., University of California, Berkeley 2005

levy@cshl.edu | 516-367-5039

Faculty Profile

We have recently come to appreciate that many unrelated diseases, such as autism, congenital heart disease and cancer, are derived from rare and unique mutations, many of which are not inherited but instead occur spontaneously. I am generating algorithms to analyze massive datasets comprising thousands of affected families to identify disease-causing mutations.

There is increasing evidence that rare and unique mutations have a significant role in the etiology of many diseases such as autism, congenital heart disease, and cancer. Dan Levy’s group develops algorithms to identify these mutations from large, high-throughput data sets comprising thousands of nuclear families. After earlier working with high-resolution CGH arrays, Levy’s group now uses targeted sequence data. Levy has developed methods for identifying de novo mutations (i.e., those seen in a child but not in his or her parents) by simultaneously genotyping the entire family; the team is currently focused on building algorithms to detect copy-number variants and multiscale genomic rearrangements. Although their copy-number methods are based on “read” density, there are classes of mutations that require analysis at the level of the read. Thus, they are developing algorithms to identify insertions, deletions, inversions, transpositions, and other complex events. Other projects in the Levy lab include analysis of single-cell RNA, phylogenetic reconstruction from sparse data sets, and disentangling haplotypes from sperm and subgenomic sequence data.

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All Publications

Sharing parental genomes by siblings concordant or discordant for autism

14 Jun 2023 | Cell Genomics | 3(6):100319
Wroten, Mathew, Yoon, Seungtai, Andrews, Peter, Yamrom, Boris, Ronemus, Michael, Buja, Andreas, Krieger, Abba, Levy, Dan, Ye, Kenny, Wigler, Michael, Iossifov, Ivan

Accurate measurement of microsatellite length by disrupting its tandem repeat structure

12 Sep 2022 | Nucleic Acids Research | :gkac723
Wang, Zihua, Moffitt, Andrea, Andrews, Peter, Wigler, Michael, Levy, Dan

Targeted de novo phasing and long-range assembly by template mutagenesis

13 Jul 2022 | Nucleic Acids Research
Li, Siran, Park, Sarah, Ye, Catherine, Danyko, Cassidy, Wroten, Matthew, Andrews, Peter, Wigler, Michael, Levy, Dan

Rates of contributory de novo mutation in high and low-risk autism families.

1 Sep 2021 | Communications Biology | 4(1):1026
Yoon, Seungtai, Munoz, Adriana, Yamrom, Boris, Lee, Yoon-Ha, Andrews, Peter, Marks, Steven, Wang, Zihua, Reeves, Catherine, Winterkorn, Lara, Krieger, Abba, Buja, Andreas, Pradhan, Kith, Ronemus, Michael, Baldwin, Kristin, Levy, Dan, Wigler, Michael, Iossifov, Ivan

Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer

24 Feb 2020 | Developmental Cell | 52(4):413-428
Vasudevan, A, Baruah, P, Smith, J, Wang, Z, Sayles, N, Andrews, P, Kendall, J, Leu, J, Chunduri, N, Levy, D, Wigler, M, Storchova, Z, Sheltzer, J

Multiplex Accurate Sensitive Quantitation (MASQ) With Application to Minimal Residual Disease in Acute Myeloid Leukemia

21 Feb 2020 | Nucleic Acids Research | 48(7):e40
Moffitt, A, Spector, M, Andrews, P, Kendall, J, Alexander, J, Stepansky, A, Ma, B, Kolitz, J, Chiorazzi, N, Allen, S, Krasnitz, A, Wigler, M, Levy, D, Wang, Z

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

14 Nov 2019 | Genome Research | 30(1):49-61
Li, S, Kendall, J, Park, S, Wang, Z, Alexander, J, Moffitt, A, Ranade, N, Danyko, C, Gegenhuber, B, Fischer, S, Robinson, B, Lepor, H, Tollkuhn, J, Gillis, J, Brouzes, E, Krasnitz, A, Levy, D, Wigler, M

Partial bisulfite conversion for unique template sequencing

25 Jan 2018 | Nucleic Acids Research | 46(2):e10
Kumar, V, Rosenbaum, J, Wang, Z, Forcier, T, Ronemus, M, Wigler, M, Levy, D

Utility of single cell genomics in diagnostic evaluation of prostate cancer

15 Jan 2018 | Cancer Research | 78(2):348-358
Alexander, J, Kendall, J, McIndoo, J, Rodgers, L, Aboukhalil, R, Levy, D, Stepansky, A, Sun, G, Chobadjiev, L, Riggs, M, Cox, H, Hakker, I, Nowak, D, Laze, J, Llukani, E, Srivastava, A, Gruschow, S, Yadav, S, Robinson, B, Atwal, G, Trotman, L, Lepor, H, Hicks, J, Wigler, M, Krasnitz, A

Measuring shared variants in cohorts of discordant siblings with applications to autism

3 Jul 2017 | Proceedings of the National Academy of Sciences of USA | 114(27):7073-7076
Ye, K, Iossifov, I, Levy, D, Yamrom, B, Buja, A, Krieger, A, Wigler, M

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