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 and more such collaborations. In 2018, I was given the opportunity to do a lateral transfer to the National Cancer Institute (NCI) and to focus the rest of my career on cancer genomics. The transfer happened on October 28, 2018, so this report accounts formally for the period from July 30, 2018 (date when I wrote my 2018 report) through October 27, 2018. To keep my professional commitments and for the mutual benefit of NLM and NCI, it was agreed that: I would continue to maintain the Anabaptist Genealogy database I would try to finish a specific list of projects that I had started at NCBI/NLM and If papers from those projects were finished, I would list both NCBI/NLM and NCI affiliations There are three papers accepted for publication July 30, 2018 that fall under this project and the transfer agreement and in which the NLM funding during July 30-October 27,2018 should be recognized: Lei Hi, Lyu B, Gertz EM, Schaffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R: Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data (conference version) in Proceedinsg of the 23rd Annual International Conference on Research in Computational Molecular Biology (RECOMB), Lecture Notes in Bioinformatics volume 11467, pp. 174--189, 2019; (journal version) invited and accepted to a special issue of Journal of Computational Biology. Johnston JJ, Williamson K, Chou CM, Sapp J, Ansari M, Chapman HM, Cooper DN, Dabir T, Dudley JN, Holt R, Ragge NK, Schaffer AA, Sen SK, Slavotinek A, FitzPatrick DR, Glaser T, Stewart F, Black GCM, Biesecker LG: NAA10 Polyadenylation Signal Variants Cause Syndromic Microphthalmia. Journal of Medical Genetics 56:444--452, 2019. Jin Y, Schaffer AA, Feolo M, Holmes JB, Kattman BL. GRAF-pop: A Fast Distance-based Method to Infer Subject Ancestry from Multiple Genotype Datasets without Principal Components Analysis. G3: Genes Genomes Genetics 9:2489--2496, 2019.

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National Library of Medicine (NLM)
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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

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