Characterization of sarcomas by means of gene expression

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Sarcomas represent a heterogeneous group of diseases of a variety of recognized histologic types. Among these subtypes is malignant fibrous histiocytoma (MFH), a diagnosis no longer recognized as a specific diagnosis at some institutions. In this study, gene expression in 38 histologically well-defined sarcoma samples, 17 MFH samples, 12 samples of sarcomas classified simply as high-grade sarcoma (NOS, standing for "not otherwise specified"), and 26 other mesenchymal tumors was determined at Gene Logic Inc (Gaithersburg, MD), with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 known genes and expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic Gene Express® Software System. Differences in gene expression were quantified as the fold change in gene expression between the various sets of well-defined sarcomas. A set of genes was then identified that could be used to distinguish the well-defined sets of 11 liposarcomas, 9 leiomyosarcomas, 4 synovial sarcomas, 8 schwannomas, and 12 cases of aggressive fibromatosis through the use of Eisen clustering. Eisen clustering was then repeated with the same set of gene fragments with the sample set of 38 histologically well-defined sarcomas, the 17 sarcomas classified as MFH, 12 sarcomas classified as high-grade sarcoma (NOS), and 26 other mesenchymal tumors. Under these conditions, each of the samples of well-defined sarcoma formed distinct clusters that contained some of the MFH and NOS samples. In addition, distinct clusters were observed that contained only MFH and NOS samples. We conclude that gene-expression patterns may be useful in helping further classify subtypes of sarcomas.

Original languageEnglish (US)
Pages (from-to)78-91
Number of pages14
JournalJournal of Laboratory and Clinical Medicine
Volume144
Issue number2
DOIs
StatePublished - Aug 1 2004

Fingerprint

Gene expression
Sarcoma
Genes
Gene Expression
Malignant Fibrous Histiocytoma
Tumors
Expressed Sequence Tags
Cluster Analysis
Aggressive Fibromatosis
Synovial Sarcoma
Liposarcoma
Leiomyosarcoma
Neurilemmoma
Neoplasms
Software

Keywords

  • cDNA
  • complementary DNA
  • complementary RNA
  • cRNA
  • dermatofibrosarcoma protuberans
  • DFSP
  • EST
  • expressed sequence tag
  • gastrointestinal stromal tumor
  • GIST
  • malignant fibrous histiocytoma
  • messenger RNA
  • MFH
  • mRNA
  • natural killer
  • NK
  • NOS

Cite this

Characterization of sarcomas by means of gene expression. / Skubitz, Keith M; Skubitz, Amy P.

In: Journal of Laboratory and Clinical Medicine, Vol. 144, No. 2, 01.08.2004, p. 78-91.

Research output: Contribution to journalArticle

@article{55cc666aefca4fa8907195a2f3cd32f2,
title = "Characterization of sarcomas by means of gene expression",
abstract = "Sarcomas represent a heterogeneous group of diseases of a variety of recognized histologic types. Among these subtypes is malignant fibrous histiocytoma (MFH), a diagnosis no longer recognized as a specific diagnosis at some institutions. In this study, gene expression in 38 histologically well-defined sarcoma samples, 17 MFH samples, 12 samples of sarcomas classified simply as high-grade sarcoma (NOS, standing for {"}not otherwise specified{"}), and 26 other mesenchymal tumors was determined at Gene Logic Inc (Gaithersburg, MD), with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 known genes and expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic Gene Express{\circledR} Software System. Differences in gene expression were quantified as the fold change in gene expression between the various sets of well-defined sarcomas. A set of genes was then identified that could be used to distinguish the well-defined sets of 11 liposarcomas, 9 leiomyosarcomas, 4 synovial sarcomas, 8 schwannomas, and 12 cases of aggressive fibromatosis through the use of Eisen clustering. Eisen clustering was then repeated with the same set of gene fragments with the sample set of 38 histologically well-defined sarcomas, the 17 sarcomas classified as MFH, 12 sarcomas classified as high-grade sarcoma (NOS), and 26 other mesenchymal tumors. Under these conditions, each of the samples of well-defined sarcoma formed distinct clusters that contained some of the MFH and NOS samples. In addition, distinct clusters were observed that contained only MFH and NOS samples. We conclude that gene-expression patterns may be useful in helping further classify subtypes of sarcomas.",
keywords = "cDNA, complementary DNA, complementary RNA, cRNA, dermatofibrosarcoma protuberans, DFSP, EST, expressed sequence tag, gastrointestinal stromal tumor, GIST, malignant fibrous histiocytoma, messenger RNA, MFH, mRNA, natural killer, NK, NOS",
author = "Skubitz, {Keith M} and Skubitz, {Amy P}",
year = "2004",
month = "8",
day = "1",
doi = "10.1016/j.lab.2004.04.005",
language = "English (US)",
volume = "144",
pages = "78--91",
journal = "Translational research : the journal of laboratory and clinical medicine",
issn = "1931-5244",
publisher = "Mosby Inc.",
number = "2",

}

TY - JOUR

T1 - Characterization of sarcomas by means of gene expression

AU - Skubitz, Keith M

AU - Skubitz, Amy P

PY - 2004/8/1

Y1 - 2004/8/1

N2 - Sarcomas represent a heterogeneous group of diseases of a variety of recognized histologic types. Among these subtypes is malignant fibrous histiocytoma (MFH), a diagnosis no longer recognized as a specific diagnosis at some institutions. In this study, gene expression in 38 histologically well-defined sarcoma samples, 17 MFH samples, 12 samples of sarcomas classified simply as high-grade sarcoma (NOS, standing for "not otherwise specified"), and 26 other mesenchymal tumors was determined at Gene Logic Inc (Gaithersburg, MD), with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 known genes and expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic Gene Express® Software System. Differences in gene expression were quantified as the fold change in gene expression between the various sets of well-defined sarcomas. A set of genes was then identified that could be used to distinguish the well-defined sets of 11 liposarcomas, 9 leiomyosarcomas, 4 synovial sarcomas, 8 schwannomas, and 12 cases of aggressive fibromatosis through the use of Eisen clustering. Eisen clustering was then repeated with the same set of gene fragments with the sample set of 38 histologically well-defined sarcomas, the 17 sarcomas classified as MFH, 12 sarcomas classified as high-grade sarcoma (NOS), and 26 other mesenchymal tumors. Under these conditions, each of the samples of well-defined sarcoma formed distinct clusters that contained some of the MFH and NOS samples. In addition, distinct clusters were observed that contained only MFH and NOS samples. We conclude that gene-expression patterns may be useful in helping further classify subtypes of sarcomas.

AB - Sarcomas represent a heterogeneous group of diseases of a variety of recognized histologic types. Among these subtypes is malignant fibrous histiocytoma (MFH), a diagnosis no longer recognized as a specific diagnosis at some institutions. In this study, gene expression in 38 histologically well-defined sarcoma samples, 17 MFH samples, 12 samples of sarcomas classified simply as high-grade sarcoma (NOS, standing for "not otherwise specified"), and 26 other mesenchymal tumors was determined at Gene Logic Inc (Gaithersburg, MD), with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 known genes and expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic Gene Express® Software System. Differences in gene expression were quantified as the fold change in gene expression between the various sets of well-defined sarcomas. A set of genes was then identified that could be used to distinguish the well-defined sets of 11 liposarcomas, 9 leiomyosarcomas, 4 synovial sarcomas, 8 schwannomas, and 12 cases of aggressive fibromatosis through the use of Eisen clustering. Eisen clustering was then repeated with the same set of gene fragments with the sample set of 38 histologically well-defined sarcomas, the 17 sarcomas classified as MFH, 12 sarcomas classified as high-grade sarcoma (NOS), and 26 other mesenchymal tumors. Under these conditions, each of the samples of well-defined sarcoma formed distinct clusters that contained some of the MFH and NOS samples. In addition, distinct clusters were observed that contained only MFH and NOS samples. We conclude that gene-expression patterns may be useful in helping further classify subtypes of sarcomas.

KW - cDNA

KW - complementary DNA

KW - complementary RNA

KW - cRNA

KW - dermatofibrosarcoma protuberans

KW - DFSP

KW - EST

KW - expressed sequence tag

KW - gastrointestinal stromal tumor

KW - GIST

KW - malignant fibrous histiocytoma

KW - messenger RNA

KW - MFH

KW - mRNA

KW - natural killer

KW - NK

KW - NOS

UR - http://www.scopus.com/inward/record.url?scp=4344713343&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=4344713343&partnerID=8YFLogxK

U2 - 10.1016/j.lab.2004.04.005

DO - 10.1016/j.lab.2004.04.005

M3 - Article

VL - 144

SP - 78

EP - 91

JO - Translational research : the journal of laboratory and clinical medicine

JF - Translational research : the journal of laboratory and clinical medicine

SN - 1931-5244

IS - 2

ER -