Andrew Kasarskis

Andrew Kasarskis
Born	November 2, 1972 Madison, Wisconsin
Citizenship	American
Fields	bioinformatics, genomics
Institutions	Icahn School of Medicine at Mount Sinai Icahn Institute for Genomics and Multiscale Biology
Alma mater	University of Kentucky University of California, Berkeley

Andrew Kasarskis (born November 2, 1972, in Madison, Wisconsin) is an American biologist. He is co-director of the Icahn Institute for Genomics and Multiscale Biology and vice chair of the department of genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai.^[1] Kasarskis is known for taking a network-based approach to biology and for directing the first medical school class offering students the opportunity to fully sequence and analyze their own genomes.^[2]

Education

Kasarskis completed bachelor's degrees in chemistry and biology at the University of Kentucky in 1992. In 1998, he completed his PhD in molecular and cell biology at the University of California, Berkeley, under the supervision of Kathryn Anderson.^[1]

Research

Throughout his career in industry and academia, Kasarskis’s research has focused on the use of genetic and genomic data together with high-performance computing and advanced analytical tools to address biomedical needs and improve clinical treatment.

After completing his PhD, Kasarskis worked at Stanford University for two years, contributing to the development of various genome databases. In 2000, he entered industry, working in computational biology at DoubleTwist and later Rosetta Inpharmatics (acquired by Merck Research Laboratories). His work there centered on generating and mining complex biological data sets and using that information to build, predict, and model human disease. Kasarskis also worked for Sage Bionetworks and Pacific Biosciences before returning to academia.^[3]

In 2011, Kasarskis became vice chair of the department of genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai and co-director, along with Eric Schadt, of the Icahn Institute for Genomics and Multiscale Biology, where the goal is to use large-scale data analysis to improve patient treatment.^[4][5] His focus is on improving health outcomes through better data mining, and his research program includes sequencing-based pathogen surveillance; pharmacogenomics; electronic health records; and systems biology of sleep, behavior, and stress.^[1]

Kasarskis is known for directing the first class that allowed medical and PhD students to fully sequence and analyze their own genomes, along with co-instructors Michael Linderman, George Diaz, Ali Bashir, and Randi Zinberg. He has said that courses like this will be critical for training teams of people capable of performing this type of analysis in a medical setting. He chose whole genome sequencing because he expects the more limited exome sequencing will not be a relevant technological approach in the long term.^[2]

Kasarskis has called for improvements to informed consent protocols in patient research based on the concept that studies involving DNA cannot fully be made anonymous. He was quoted in the journal Nature saying, “We need to move beyond an assumption that you cannot be identified from the data that exist about you and really work to make sure that we’re protecting people’s rights in ways that allow us to use the data that are out there for individuals’ and researchers’ benefit.”^[6]

Selected publications

Pharmacogenomics

• Smith CC, Wang Q, Chin CS, Salerno S, Damon LE, Levis MJ, Perl AE, Travers KJ, Wang S, Hunt JP, Zarrinkar PP, Schadt EE, Kasarskis A, Kuriyan J, Shah NP. Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature. 2012 May 10;485(7397):260-3.^[7]
• Kasarskis A, Yang X, Schadt E. Integrative genomics strategies to elucidate the complexity of drug response. Pharmacogenomics. 2011 Dec;12(12):1695-715.^[8]
• Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmuller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol. 2012 Nov;30(11):1033-6.^[9]

Pathogens

• Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol. 2012 Jul;30(7):701-7.^[10]
• Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Moller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med. 2011 Aug 25;365(8):709-17.^[11]
• Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK. The origin of the Haitian cholera outbreak strain. N Engl J Med. 2011 Jan 6;364(1):33-42.^[12]

Sleep

• Brunner JI, Gotter AL, Millstein J, Garson S, Binns J, Fox SV, Savitz AT, Yang HS, Fitzpatrick K, Zhou L, Owens JR, Webber AL, Vitaterna MH, Kasarskis A, Uebele VN, Turek F, Renger JJ, Winrow CJ. Pharmacological validation of candidate causal sleep genes identified in an N2 cross. J Neurogenet. 2011 Dec;25(4):167-81.^[13]
• Millstein J, Winrow CJ, Kasarskis A, Owens JR, Zhou L, Summa KC, Fitzpatrick K, Zhang B, Vitaterna MH, Schadt EE, Renger JJ, Turek FW. Identification of causal genes, networks, and transcriptional regulators of REM sleep and wake. Sleep. 2011 Nov;34(11):1469-77.^[14]
• Winrow CJ, Williams DL, Kasarskis A, Millstein J, Laposky AD, Yang HS, Mrazek K, Zhou L, Owens JR, Radzicki D, Preuss F, Schadt EE, Shimomura K, Vitaterna MH, Zhang C, Koblan KS, Renger JJ, Turek FW. Uncovering the genetic landscape for multiple sleep-wake traits. PLoS One. 2009;4(4):e5161.^[15]

References

1. "Andrew Kasarskis - Icahn School of Medicine at Mount Sinai". Icahn.mssm.edu. Retrieved 2013-06-10.
2. Nicholas Tatonetti. "Q&A: Mount Sinai's Andrew Kasarskis on Teaching Students how to Analyze their Own Genomes | Clinical Sequencing News | Sequencing". GenomeWeb. Retrieved 2013-06-10.
3. "BIOMEDIN 206: Informatics in Industry - Stanford University". Stanford.edu. Retrieved 2013-06-10.
4. Samuelson, Tracey (2012-07-12). "Looking at the Big Picture: How Big Data Gets Personal". WNYC. Retrieved 2013-06-10.
5. Nicholas Tatonetti. "Mount Sinai, RPI to Collaborate on Bioinformatics Apps as Part of Academic Research Pact | BioInform | Informatics". GenomeWeb. Retrieved 2013-06-10.
6. jobs (2012-04-25). "Open-data project aims to ease the way for genomic research : Nature News & Comment". Nature.com. Retrieved 2013-06-10.
7. http://www.nature.com/nature/journal/v485/n7397/full/nature11016.html
8. "Integrative genomics strategies to elucidate the complexity of drug response". Pharmacogenomics. Retrieved 2013-06-17.
9. http://www.nature.com/nbt/journal/v30/n11/full/nbt.2403.html
10. http://www.nature.com/nbt/journal/v30/n7/full/nbt.2288.html
11. "Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany". New England Journal of Medicine. Retrieved 2013-06-17.
12. "The origin of the Haitian cholera outbreak strain". New England Journal of Medicine. Retrieved 2013-06-17.
13. "Pharmacological validation of candidate causal sleep genes identified in an N2 cross". Journal of Neurogenetics. Retrieved 2013-06-17.
14. "Identification of causal genes, networks, and transcriptional regulators of REM sleep and wake". SLEEP. Retrieved 2013-06-17.
15. "Uncovering the Genetic Landscape for Multiple Sleep-Wake Traits". Plos One. Retrieved 2013-06-10.