• iKarios
  • NPHL

Learn more about the elements of our methodology

  1. Chronic Lymphocytic Leukemia (CLL)
  2. Renal Tumors
  3. Colorectal Carcinoma
  4. Breast Cancer
  5. Brain Tumors

Sample Virtual Karyotypes from Select Tumors

Chronic Lymphocytic Leukemia (CLL)

Detection of genomic complexity, acquired uniparental disomy, and atypical deletions.


Hagenkord JM, et al. Array-based Karyotyping for Prognostic Assessment in Chronic Lymphocytic
Leukemia: Performance Comparison of Affymetrixâ„¢ 10K2.0, 250K Nsp, and SNP6.0 Arrays.
J Mol Diagn, 2010 Mar;12(2):184-96.

CLL1 (peripheral blood)
FISH panel results were normal, cytogenetics showed no growth in culture

Capturing Genomic Complexity in One Assay

This CLL sample di not show any copy number abnormalities using the standard CLL FISH panel, while the SNP array karyotype captures the genomic complexity of this case, including acquired uniparental disomy (UPD) of 1q and 10q.

Chromosomes are plotted along the x-axis. Regions of acquired UPD are indicated with black arrowheads.
A = copy number estimate for each SNP on the array, plotted as the log2ratio of tumor/normal (zero = diploid)
B = green heterozygous call bars, which are placed for every AB genotype cell in the tumor
C = allele-specific copy number analysis, with the greater allele in red and the lesser allele in green
D = copy number: dark blue=0, light blue=1, yellow=2, pink=3, red=4, red-pink=5, bright red>5
E = LOH likelihood: yellow=low LOH likelihood, blue=high LOH likelihood

CLL2 (peripheral blood)
FISH panel results showed only trisomy 12, cytogenetics showed no growth in culture

Whole genome view SNP array karyogram for this sample. Chromosomes are plotted in numeric order from left (chromosome 1) to right (X chromosome). A) Log2ratio, zero = copy number of 2. B) Allele-specific analysis of copy number. C) The copy number Hidden Markov Model (HMM) is color-coded as indicated below.

CLL3 (peripheral blood)

Whole genome view SNP array karyogram for this sample. Chromosomes are plotted in numeric order from left (chromosome 1) to right (X chromosome). A) Log2ratio, zero = copy number of 2. B) Green = heterozygous call in tumor. C) The copy number Hidden Markov Model (HMM) is color-coded as indicated below. D) LOH likelihood HMM (yellow = low, blue = high).

CLL4 (fresh lymph node)

Whole genome view SNP array karyogram for this sample. Chromosomes are plotted in numeric order from left (chromosome 1) to right (X chromosome). A) Log2ratio, zero = copy number of 2. B) Allele-specific analysis of copy number. C) The copy number Hidden Markov Model (HMM) is color-coded as indicated below.

Sample Virtual Karyotypes from Select Tumors

Renal Tumors

Renal tumors have characteristic genetic lesions that are useful for the diagnosis
of morphologically challenging tumors.

Adapted from: Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Mod Pathol. 2008 May;21(5):599-608. Epub 2008 Feb 8. PMID: 18246049

Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Mod Pathol. 2008 May;21(5):599-608. Epub 2008 Feb 8. PMID: 18246049

See also these manuscripts for use of virtual karyotypes for renal tumors:

Hagenkord JM, Parwani AV, Lyons-Weiler MA, Alvarez K, Amato R, Gatalica Z, Gonzalez-Berjon JM, Peterson L, Dhir R, Monzon FA. Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors. Diagn Pathol. 2008 Nov 6;3:44. PMID: 18990225

Kim HJ, Shen SS, Ayala AG, Ro JY, Truong LD, Alvarez K, Bridge JA, Gatalica Z, Hagenkord JM, Gonzalez-Berjon JM, Monzon FA. Virtual-Karyotyping with SNP microarrays in morphologically challenging renal cell neoplasms: a practical and useful diagnostic modality. Am J Surg Pathol. 2009 Sep;33(9):1276-86. PMID: 19461508

Monzon FA, Alvarez K, Gatalica Z, Bridge JA, Nelson M, Kim HJ, Hagenkord JM. Detection of chromosomal aberrations in renal tumors: a comparative study of conventional cytogenetics and virtual karyotyping with SNP microarrays. Arch Pathol Lab Med. 2009 Dec;133(12):1917-22. PMID: 19961245

Prognosis in Renal Tumors

Deletion of 9p or 14q in renal clear cells carcinomas are associated with adverse prognosis. Duplication of 1q is a marker of fatal progression.

Brunelli M, Eccher A, Gobbo S, Ficarra V, Novara G, Cossu-Rocca P, Bonetti F, Menestrina F, Cheng L, Eble JN, Martignoni G. Loss of chromosome 9p is an independent prognostic factor in patients with clear cell renal cell carcinoma. Mod Pathol. 2008 Jan;21(1):1-6. Epub 2007 Sep 28. PMID: 17906617

Klatte T, Rao PN, de Martino M, LaRochelle J, Shuch B, Zomorodian N, Said J, Kabbinavar FF, Belldegrun AS, Pantuck AJ. Cytogenetic profile predicts prognosis of patients with clear cell renal cell carcinoma. J Clin Oncol. 2009 Feb 10;27(5):746-53. Epub 2009 Jan 5. PMID: 19124809

Szponar A, Zubakov D, Pawlak J, Jauch A, Kovacs G. Three genetic developmental stages of papillary renal cell tumors: duplication of chromosome 1q marks fatal progression. Int J Cancer. 2009 May 1;124(9):2071-6. PMID: 19123481

Sample Virtual Karyotypes from Select Tumors

Colorectal carcinoma, whole genome view

SNP array Virtual Karyotype of colorectal carcinoma

Sample Virtual Karyotypes from Select Tumors

Breast Cancer

Her2Neu amplification on chromosome 17

Breast Cancer (below): Three whole genome views

Sample Virtual Karyotypes from Select Tumors

Brain Tumors

Adult Glial Tumors

The genomic signature of oligodendroglioma is a 1p/19q co-deletion.

Concurrent monosomy 10 and trisomy 7 are essentially pathognomonic of primary glioblastoma.

Gain of chromosome 7 most common genetic abnormality in astrocytomas. Loss of chromosome 10 is rare low grade astrocytomas and common in glioblastoma. EGFR amplification, loss of PTEN (on 10q), and loss of p16 (on 9p) occur almost exclusively in glioblastoma and can provide means to distinguish anaplastic astrocytoma from glioblastoma.

Tumors of the Central Nervous System. Vol 7. Washington DC: American Registry of Pathology; 2007. Magnani I. Nervous System: Glioma: an overview 2008. Atlas Genet Cytogenet Oncol Haematol.
http://AtlasGeneticsOncology.org/Genes/GliomaOverviewID5763.html. WHO Classification of Tumours of the Central Nervous System. 4th ed. Lyon: IARC; 2007.

Glial1: Oligodendroglioma with a 1p/19q co-deletion

Glial2: Oligodendroglioma by morphology

Glial3: Low grade astrocytoma by morphology

Pediatric Glial Tumors

Top plots shows SNP array virtual karyotype from 10K2.0 array using FFPE tissue showing acquired UPD of 1q and 9p. ArrayCGH of sample sample does not detect any genetic abnormalities. (Data courtesy of Robert Sobel, PhD, University of Pittsburgh)

Neuroblastomas

Janoueix-Lerosey I, et al. Overall Genomic Pattern is a Predictor of Outcome in Neuroblastoma. J Clin Oncol 2009 Mar(27)7;1026-33.