Joseph Cheng

Joseph Cheng, B.A., MBA
Bioinformatics Staff Scientist

In support of the fluorescence in situ hybridization (FISH) laboratory, Mr. Cheng serves as a senior applications engineer for image acquire and data analysis. He is responsible and management FISH microscopy and image data analysis.  Mr. Cheng was involved in the design of FISH and CGH application with Leica and ASI.

Working with the FISH team on The Cancer Chromosome Aberration Project (CCAP) project, Mr. Cheng graphically depicts images of chromosomes with genetic information.  These images are then digitized for spectral karyotyping or for the comparison of chromosome unique wavelength signatures.

Extensive experience in high-throughput data analysis, especially in the area of DNA copy number alteration detection techniques by using microarray (arrayCGH) and recently next-generation sequencing. He has utilized data analysis and visualization techniques such as copy number alteration detection and common gain/loss regions and their association to gnu expression in cancer samples, and data visualization at chromosomal level. Similarly, utilizing exome-capture followed by sequencing method, similar data analysis methods have been utilized to detect loss-of-heterozygous in addition to copy number alteration. Working at NCI/NIH and directly applying these bioinformatics techniques to translational and basic research, he has accumulated deep understanding
and extensive skill sets for high-throughput data analyses.

Areas of Expertise
1) FISH Probe Design, 2) Microarray Analysis, 3) Next Generation Sequence (NGS) Analysis, 4) Sr. Applications Engineering, 5) Network and System Administration, 6) Database Architecture Design and DBA

Contact Info

Joseph Cheng
Center for Cancer Research
National Cancer Institute
Building 50, Room 1408
Bethesda, MD 20892-8010
Ph: 240-760-6358 Office
202-247-7096 Cell

Developed serveral FISH image acquisition and analysis system with Leica Biosystems and Applied Spectral Imaging (ASI).

ASI Hyperspectral Karyotyping (SKY):

  • SKY Imaging for image acquisition
  • SKY View for spectral karyotyping

Leica CW 4000 Cytogenetics Workstation:

  • CW 4000 FISH imaging acquisition and analysis
  • CW 4000 CGH (comparative genome hybridization) analysis


JOINSOLVERreg; is a web-based software program developed for human immunoglobulin V(D)J recombination analysis created by the National Institutes of Health, National Institute of Arthritis and Musculosketelal and Skin Diseases (NIAMS) and the Center for Information Technology (CIT). JOINSOLVERreg; performs immunoglobulin nucleotide and amino acid alignment as well as extensive mutation and CDR3 analysis.

The criteria for JOINSOLVERreg; analysis were established by analyzing more than 1500 human immunoglobulin gene sequences. V(D)J rearrangements are aligned to germline immunoglobulin heavy and light chain genes within the JOINSOLVERreg; database that includes allelic variants, mapped and unmapped functional genes and pseudogenes. Navigational links on the top of the page provide access to JOINSOLVERreg; features.

Clinical Genetics Diagnosis and Analysis Systems (CGDAS):

  • FISH, PCR, Microarray and Sequence data analysisi report include clinical guideline in precision medicine.


Scientific Focus Areas:
Computational Biology, Genetics and Genomics

Selected Publications

  1. Petrovics G, Li H, Stümpel T, Tan SH, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Dobi A, Srivastava S.
    EBioMedicine. 2/12: Amsterdam: Elsevier B.V. 1957-64, 2015. [ Journal Article ]
  2. Heselmeyer-Haddad K1, Chaudhri N, Stoltzfus P, Cheng JC, Wilber K, Morrison L, Auer G, Ried T.
    Cancer Research. Volume 62, Issue 8: AACR 15, 2002. [ Journal Article ]