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E-GEOD-25307 GSE25307 transcription profiling by array Homo sapiens

The retinoblastoma gene is targeted for rearrangements in BRCA1-deficient basal-like breast cancer

·发布 June 26, 2012 ·更新 May 2, 2014

1154

样本数

577

实验数

芯片平台

相关文献

实验描述

Breast tumors from BRCA1 germ line mutation carriers typically exhibit features of the basal-like molecular subtype. However, the specific genes recurrently mutated as a consequence of BRCA1 dysfunction have not been fully elucidated. In this study, we utilized gene expression profiling to molecularly subtype 577 breast tumors, including 73 breast tumors from BRCA1/2 mutation carriers. Focusing on the RB1 locus, we analyzed 33 BRCA1-mutated, 36 BRCA2-mutated and 48 non-BRCA1/2-mutated breast tumors using a custom-designed high-density oligomicroarray covering the RB1 gene. We found a strong association between the basal-like subtype and BRCA1-mutated breast tumors and the luminal B subtype and BRCA2-mutated breast tumors. RB1 was identified as a major target for genomic disruption in tumors arising in BRCA1 mutation carriers and in sporadic tumors with BRCA1 promoter-methylation, but rarely in other breast cancers. Homozygous deletions, intragenic breaks, or microdeletions were found in 33% of BRCA1-mutant tumors, 36% of BRCA1 promoter-methylated basal-like tumors, 13% of non-BRCA1 deficient basal-like tumors, and 3% of BRCA2-mutated tumors. In addition, RB1 was frequently inactivated by gross gene disruption in BRCA1-related hereditary breast cancer and BRCA1-methylated sporadic basal-like breast cancer, but rarely in BRCA2-hereditary breast cancer and non-BRCA1-deficient sporadic breast cancers. Together, our findings demonstrate the existence of genetic heterogeneity within the basal-like breast cancer subtype that is based upon BRCA1-status. Gene expression profiling of breast tumors. Dual color common reference gene expression study using 55K oligonucleotide microarrays.

参考文献

The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer.

Jonsson G, Staaf J, Vallon-Christersson J, Ringner M, Gruvberger-Saal SK, Saal LH, Holm K, Hegardt C, Arason A, Fagerholm R, Persson C, Grabau D, Johnsson E, Lövgren K, Magnusson L, Heikkilä P, Agnarsson BA, Johannsson OT, Malmstrom P, Ferno M, Olsson H, Loman N, Nevanlinna H, Barkardottir RB, Borg A

PMID: 22706203

芯片平台

A-GEOD-5345

SWEGENE H_v2.1.1 55K（577 例）

样本属性

brca status

brca1, brca2, brcax, other, sporadic

brca1 methylation status

negative, non_available, positive

er_neg, er_pos, NA, non_available

familial status

brca1, brca2, familial, non malignant, sporadic

genomic subtype

17q12, amplifier, Basal-complex, Luminal-complex, Luminal-simple, mixed

grade

1, 2, 3, NA

hu subtype

basal, ERBB2, LumA, LumB, nonClassified, normal

Organism

Homo sapiens

organism part

Breast tumor, non malignant

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osbin

1, NA

pam50 classification

basal, HER2enriched, LumA, LumB, normal, Unclassified

pam50 correlation

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0.702951, 0.704144, 0.704496, 0.704662, 0.705129, 0.705755, 0.706296, 0.707419, 0.708775, 0.709855, 0.710818, 0.711288, 0.712758, 0.714965, 0.716499, 0.717424, 0.719374, 0.719429, 0.72043, 0.721505, 0.72467, 0.724751, 0.729601, 0.730162, 0.73111, 0.731714, 0.732266, 0.73249, 0.733618, 0.734032, 0.734967, 0.735927, 0.736995, 0.737272, 0.737633, 0.738839, 0.739242, 0.739885, 0.740416, 0.740884, 0.740922, 0.742628, 0.743416, 0.744403, 0.745056, 0.745841, 0.747684, 0.748297, 0.748669, 0.748825, 0.753518, 0.755176, 0.755841, 0.762758, 0.769649, 0.770917, 0.777153, 0.777655, 0.779048, 0.787949, 0.792978, 0.794589, 0.79487, 0.796397, 0.800252, 0.800563, 0.804058, 0.804455, 0.808389, 0.812709, 0.816231, 0.818028, 0.847481, 0.861586

pgr

NA, pgr_neg, pgr_pos

primary

reference

Stratagene Universal reference RNA

实验信息

登记号

E-GEOD-25307

GEO 编号

GSE25307

实验类型

transcription profiling by array

物种

Homo sapiens

发布日期

June 26, 2012

更新日期

May 2, 2014

提交者

Cecilia Hegardt、 Håkan Olsson、 Ellinor Johnsson、 Per Malmström、 Heli Nevanlinna、 Oskar T Johannsson、 Kristina Lövgren、 Karolina Holm、 Lao H Saal、 Adalgeir Arason、 Åke Borg、 Johan Vallon-Christersson、 Johan Staaf、 Markus Ringner、 Camilla Persson、 Mårten Fernö、 Rainer Fagerholm、 Paivi Heikkilä、 Bjarni A Agnarsson、 Sofia Gruvberger-Saal、 Ake Borg、 Rosa B Barkardottir、 Dorthe Grabau、 Linda Magnusson、 Göran B Jönsson、 Niklas Loman

外部链接

ArrayExpress 原始页 NCBI GEO：GSE25307

分析服务

The retinoblastoma gene is targeted for rearrangements in BRCA1-deficient basal-like breast cancer

联系地址

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