Case Studies In Genetics

Schaffer, Alejandro A.

Abstract

During my career I have worked on several projects creating software (FASTLINK, CASPAR, rh_tsp_map, PedHunter, etc.) and a database (Anabaptist Genealogy database) for genetic studies. My association with this software and a past track record of effective collaboration with wet lab scientists leads to more such collaborations. Three highlights from my publications of the past year are: -- release of a new version of the pedigree simulation software SLINK, and publication of an associated paper in Human Heredity -- release of a new version of the genetic linkage and association software PSEUDOMARKER and publication in Human Heredity of a paper announcing the software -- publication in Neurogenetics of the discovery that a mutation in the canine form of the gene mitofusin 2 (MFN2) causes early-onset neuroaxonal dystrophy The work on SLINK was done in collaboration with Daniel Weeks (Univeristy of Pittsburgh) and Mathieu Lemire (Ontario Institute for Cancer Research). The work on PSEUDOMARKER was done in collaboration with Joseph Terwilliger (Columbia University) The work on canine MFN2 was done in collaboration with John Fyfe (Michigan State University) and Paula Henthorn (University of Pennsylvania).

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Library of Medicine (NLM)
• Type: Investigator-Initiated Intramural Research Projects (ZIA)
• Project #: 1ZIALM000097-10
• Application #: 8344952
• Support Year: 10
• Fiscal Year: 2011
• Total Cost: $589,619

Institution

• Name: National Library of Medicine

Publications

Wangsa, Darawalee; Braun, Rüdiger; Schiefer, Madison et al. (2018) The Evolution of Single Cell-derived Colorectal Cancer Cell Lines is Dominated by the Continued Selection of Tumor Specific Genomic Imbalances, Despite Random Chromosomal Instability. Carcinogenesis :

Oltmann, Johanna; Heselmeyer-Haddad, Kerstin; Hernandez, Leanora S et al. (2018) Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients. Genes Chromosomes Cancer 57:165-175

Rogozin, Igor B; Gertz, E Michael; Baranov, Pasha V et al. (2018) Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism. Genome Biol Evol 10:1902-1919

Schubert, Desirée; Klein, Marie-Christine; Hassdenteufel, Sarah et al. (2018) Plasma cell deficiency in human subjects with heterozygous mutations in Sec61 translocon alpha 1 subunit (SEC61A1). J Allergy Clin Immunol 141:1427-1438

Frey-Jakobs, Stefanie; Hartberger, Julia M; Fliegauf, Manfred et al. (2018) ZNF341 controls STAT3 expression and thereby immunocompetence. Sci Immunol 3:

Hatcher, Eneida L; Zhdanov, Sergey A; Bao, Yiming et al. (2017) Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res 45:D482-D490

Witzel, Maximilian; Petersheim, Daniel; Fan, Yanxin et al. (2017) Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Nat Genet 49:742-752

Schwartz, Russell; Schäffer, Alejandro A (2017) The evolution of tumour phylogenetics: principles and practice. Nat Rev Genet 18:213-229

Joehanes, Roby; Zhang, Xiaoling; Huan, Tianxiao et al. (2017) Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies. Genome Biol 18:16

Jin, Yumi; Schäffer, Alejandro A; Sherry, Stephen T et al. (2017) Quickly identifying identical and closely related subjects in large databases using genotype data. PLoS One 12:e0179106