Genome profiling of chondrosarcoma using oligonucleotide array-based comparative genomic hybridization

Hameed, Meera; Ülger, Celal; Yasar, Duygu; Limaye, Neha P.; Kurvathi, Rohini; Streck, Deanna; Benevenia, Joseph; Patterson, Francis; Dermody, James; Toruner, Gokce

doi:10.1016/j.cancergencyto.2009.03.009

Cited by 16 publications

(10 citation statements)

References 15 publications

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“…9,10,15,16,19,23 However, to the best of our knowledge, the present study offers the first case series of whole-genome analysis of a rare subset of chondrosarcomas arising in the skull base. The median patient age among our cases was slightly older than that in the largest case study (200 cases) of SBCS (50 vs 39 years, respectively).…”

Section: Discussionmentioning

confidence: 88%

“…9,10,15,16,19,23 In addition, 8q24.1-qter and 14q24-qter were correlated with shorter overall survival in patients with extracranial chondrosarcomas; 15 a loss of 6 and gain of 12q12 were associated with higher grade chondrosarcomas; 23 and losses of 5q14.2-q21.3, 6q16-q25.3, 9p24.2-p12, and 9p21.3 were associated with higher grade tumors. 10 In comparison with these data for extracranial cases, our series of SBCSs showed frequent gains of 8q21.1 and 19 in 3 of the 7 cases. Although the association of these CNAs with patients' prognoses was not clear possibly due to the small number of cases, the CNA profile for our SBCS specimens is similar to that for extracranial chondrosarcomas, suggesting the absence of distinct chromosomal alterations specific to the skull base localization of the tumors.…”

Section: Discussionmentioning

confidence: 99%

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Genetic characterization of skull base chondrosarcomas

Kanamori¹,

Kitamura²,

Kimura

et al. 2015

JNS

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A lthough chondrosarcoma is the third most frequent primary malignancy of bone after myeloma and osteosarcoma, 7 skull base chondrosarcomas (SBCSs) are rare, accounting for only approximately 1% of all chondrosarcomas. 6 In France, intracranial chondrosarcomas account for 0.05% of all brain tumors, 21 and together with chordoma, they account for 0.09% of central nervous system tumors in the United States.5 However, among malignant bone tumors in the skull base, SBCS and chordoma are the 2 major histological types. Distinction of these 2 tumors is important, because SBCSs of the skull base are reported to show significantly better prognosis than chordomas. 1,4 Clinicians and pathologists are occasionally confronted by diagnostic problems caused by radiological and histological overlap between SBCSs and chordomas, especially with the "chondroid" subtype of chordomas. Recently, brachyury, a new immunohistochemical marker for chordoma, has been used to help distinguish chordomas from chondrosarcomas in addition to traditional markers, including cytokeratin and epithelial membrane antigen (EMA). 18Little is known about the genetic characteristics of SBCSs, because unlike for chordomas and extracranial chondrosarcomas, there have been no reports of whole-genome analysis of a case series of SBCSs to date. An early cytogenetic study of a single case of SBCS was described, obJect Although chondrosarcomas rarely arise in the skull base, chondrosarcomas and chordomas are the 2 major malignant bone neoplasms occurring at this location. The distinction of these 2 tumors is important, but this distinction is occasionally problematic because of radiological and histological overlap. Unlike chordoma and extracranial chondrosarcoma, no case series presenting a whole-genome analysis of skull base chondrosarcomas (SBCSs) has been reported. The goal of this study is to clarify the genetic characteristics of SBCSs and contrast them with those of chordomas. methods The authors analyzed 7 SBCS specimens for chromosomal copy number alterations (CNAs) using comparative genomic hybridization (CGH). They also examined IDH1 and IDH2 mutations and brachyury expression. results In CGH analyses, the authors detected CNAs in 6 of the 7 cases, including chromosomal gains of 8q21.1, 19, 2q22-q32, 5qcen-q14, 8q21-q22, and 15qcen-q14. Mutation of IDH1 was found with a high frequency (5 of 7 cases, 71.4%), of which R132S was most frequently mutated. No IDH2 mutations were found, and immunohistochemical staining for brachyury was negative in all cases. coNclusioNs To the best of the authors' knowledge, this is the first whole-genome study of an SBSC case series. Their findings suggest that these tumors are molecularly consistent with a subset of conventional central chondrosarcomas and different from skull base chordomas.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Genetic characterization of skull base chondrosarcomas

Kanamori¹,

Kitamura²,

Kimura

et al. 2015

JNS

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“…Likewise, amplification of 6p22.3 has been linked to multiple cancers including bladder and hereditary prostate cancer (Janer et al 2003; Veltman et al 2003). 18p11.22 has been linked to lung cancer and 5q13.2 deletions to chemoresistant ovarian tumors, colorectal cancer, and chondrosarcomas (Ahn et al 2012; Dyrso et al 2011; Hameed et al 2009; Kim et al 2007). However, we were unable to directly determine the specific biological relevance for these SNPs.…”

Section: Discussionmentioning

confidence: 99%

Genetic variants associated with breast cancer risk for Ashkenazi Jewish women with strong family histories but no identifiable BRCA1/2 mutation

et al. 2013

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Background The ability to establish genetic risk models is critical for early identification and optimal treatment of breast cancer. For such a model to gain clinical utility, more variants must be identified beyond those discovered in previous genome wide association studies (GWAS). This is especially true for women at high risk because of family history, but without BRCA1/2 mutations. Methods This study incorporates three datasets in a GWAS analysis of women with Ashkenazi Jewish (AJ) homogeneous ancestry. Two independent discovery cohorts were comprised of 239 and 238 AJ women with invasive breast cancer or preinvasive ductal carcinoma in situ and strong family histories of breast cancer, but lacking the three BRCA1/2 founder mutations, along with 294 and 230 AJ controls, respectively. An independent, third cohort of 203 AJ cases with familial breast cancer history and 263 healthy controls of AJ women was used for validation. Results A total of 19 SNPs were identified as associated with familial breast cancer risk in AJ women. Among these SNPs, 13 were identified from a panel of 109 discovery SNPs, including an FGFR2 haplotype. Additionally, 6 previously identified breast cancer GWAS SNPs were confirmed in this population. Seven of the 19 markers were significant in a multivariate predictive model of familial breast cancer in AJ women, 3 novel SNPs [rs17663555(5q13.2), rs566164(6q21), and rs11075884(16q22.2)], the FGFR2 haplotype, and 3 previously published SNPs [rs13387042(2q35), rs2046210(ESR1), and rs3112612(TOX3)], yielding moderate predictive power with an area under the curve (AUC) of the ROC (receiver-operator characteristic curve) of 0.74. Conclusion Population-specific genetic variants in addition to variants shared with populations of European ancestry may improve breast cancer risk prediction among AJ women from high-risk families without founder BRCA1/2 mutations.

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“…BAC-/PAC-aCGH analyses on 15 frozen chondrosarcoma samples and FISH with a MYC-probe on 116 samples showed polysomy 8 and MYC amplification as common aberration 13 . Oligo-aCGH analyses on 23 frozen samples showed deletions in chromosomes 5q, 6q and 9p 14 .…”

Section: Autosomal Stabilitymentioning

confidence: 98%