developer of the Genomoscope™ Visualization

A Whole Genome Analysis and Visualization Software Company

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WholeGenome LLC deploys BIMA and SVAtools to assist researchers interpret their NGS data. WholeGenome's business model is to receive the data from the client, analyze the data in-house using BIMA and SVAtools and produce an executable that contains reports, images, plots and a visualization portal that will empower the client to analyze and interpret their data.


Next Generation Sequencing (NGS) is a powerful tool for inspecting the genome. WholeGenome specializes in detecting structural variants in the cancer genome from genome wide mate-pair sequencing (MPseq). 


Mapping and structural variant calling by our custom algorithms: BIMA and SVAtools. Variant calling includes: prediction of gene fusions, gene expression, disruptions and characterization of complex genomic rearrangements and mutations. 


WholeGenome provides the Genomoscope™ Visualization;
An integrated and interactive genome wide view of all the variants detected in the sample. 


Static reports provide sequencing quality and statistics, and in-depth details for reported structural variants. A summary of all reports is provided in a single pdf format for quick review and sharing among colleagues. 


Platforms: pair-end sequencing, mate-pair sequencing (MPseq), RNAseq, and WES. 

Multiple sets of data can be layered on the Genomoscope™ Visualization in order to affirm gene status, including expression, amplifications, deletions, double hits, fusions, mutations, etc. 


George Vasmatzis, founder of WholeGenome.
@ TEDxMinneapolis:
"How Genomics will change the way we treat Cancer patients"


George Vasmatzis Ph.D 

President and CEO
Genomics Specialist

Sarah H. Johnson M.S.

Bioinformatics Interpretation

Jamie Smadbeck Ph.D.

Bioinformatics Interpretation

Travis Drucker M.S.

High Performance
Computing Developer

Athanasios (Saki) Gaitatzes Ph.D.

Computer Graphics & Visualization Developer

Genomoscope™ Visualization

Features of the Genomoscope™ visualization: 

The Genomoscope™ Visualization is a genome wide, integrated and interactive visualization. 

To maximize space, the autosomal chromosomes are arranged in a U-shape pattern, with X and Y across the bottom.

Visualization of multivariate genomic data may be toggled on and off via multiple layering options. Cytobands, structural rearrangements, copy number variations and genes are just a few of the layering options.  

Structural rearrangements are represented as lines connecting the two breakpoints of a junction. Lines may be arced by the user to differentiate between overlapping junctions.

Copy number variations are color coded blue and red to represent gains and losses respectively, in accordance with standard cytogenetics nomenclature. 


    • Constitutional genetics testing
    • Hematologic Oncology (AML, CLL, etc)
    • Genome-wide, Mate-Pair Sequencing for solid tumors: lung, sarcoma, prostate, ovarian, etc .
    • Detection of junctions/rearrangements, fusion genes, CNVs, cnLOH
    • Identification of targetable genomic changes in cancer
    • Monitoring for cancer recurrence
    • Genomic relationship of independent primary cancers compared to primary-metastasis
    • Lineage relationships in cancer progression
    • Genomic changes indicative of indolent and aggressive cancer
    • Mutational screening on cytological biopsy specimens
    • Genomic characterization of Mouse Avatars
    • Location of viral integration


Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G. BIMA V3: an aligner customized for mate pair library sequencing, Bioinformatics, 2014 June 1, Volume 30, Issue 11, 1627–1629. 

Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes AG, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, and Vasmatzis G. SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq). Cancer Genetics, 2018; 221, 1–18.

Gaitatzes AG, Johnson SH, Smadbeck JB and Vasmatzis G. Genome U-Plot: a whole genome visualization. Bioinformatics 2017 Dec 21.

Feldman AL, Dogan A, Smith DI, Law ME, Ansell SM, Johnson SH, Porcher JC, Ozsan N, Wieben ED, Eckloff BW, Vasmatzis G. Discovery of recurrent t(6;7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas by massively parallel genomic sequencing.  Blood. 2011 Jan 20; 117(3):915-9. 

Vasmatzis G, Johnson SH, Knudson RA, Ketterling RP, Braggio E, Fonseca R, Viswanatha DS, Law ME, Kip NS, Ozsan N, Grebe SK, Frederick LA, Eckloff BW, Thompson EA, Kadin ME, Milosevic D, Porcher JC, Asmann YW, Smith DI, Kovtun IV, Ansell SM, Dogan A, Feldman AL. Genome-wide analysis reveals recurrent structural abnormalities of TP63 and other p53-related genes in peripheral T-cell lymphomas.  Blood. 2012 Sep 13; 120(11):2280-9. 

Murphy SJ, Cheville JC, Zarei S, Johnson SH, Sikkink RA, Kosari F, Feldman AL, Eckloff BW, Karnes RJ, Vasmatzis G. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer.  DNA Res. 2012 Oct; 19(5):395-406. 

Kovtun IV, Cheville JC, Murphy SJ, Johnson SH, Zarei S, Kosari F, Sukov WR, Karnes RJ, Vasmatzis G. Lineage relationship of Gleason patterns in Gleason score 7 prostate cancer. Cancer Research 2013 Jun 1;73(11):3275-84. 

Lasho T, Johnson SH, Smith DI, Crispino JD, Pardanani A, [Vasmatzis G, Tefferi A. co-senior authors]. Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing. Am J Hematol. 2013 Sep;88(9):741-6.

Feldman AL, Vasmatzis G, Asmann YW, Davila J, Middha S, Eckloff BW, Johnson SH, Porcher JC, Ansell SM, Caride A. Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma. Genes Chromosomes Cancer. 2013 Nov;52(11):1097-102. 

Gao G, Johnson SH, Kasperbauer JL, Eckloff BW, Tombers NM, Vasmatzis G, Smith DI. Mate pair sequencing of oropharyngeal squamous cell carcinomas reveals that HPV integration occurs much less frequently than in cervical cancer. J Clin Virol. 2014 Mar;59(3):195-200. 

Cradic KW, Murphy SJ, Drucker TM, Sikkink RA, Eberhardt NL, Neuhauser C, Vasmatzis G, Grebe SK. A simple method for gene phasing using mate pair sequencing. BMC Med Genet. 2014 Feb 6;15(1):19. 


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