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| Status |
Public on Dec 27, 2016 |
| Title |
Catalogue of genomic alterations in uterine cervical carcinoma of Indian patients. |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
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| Summary |
To identify genomic alterations in uterine cervical carcinoma of Indian patients. Cancer of the uterine cervix (CACX) is the fourth most frequent carcinoma among women worldwide. In India, it accounts for approximately 132,000 new cases and 74,000 deaths annually contributing to nearly 1/3rd of the global cervical cancer deaths. Although, several etiological factors such as use of oral contraceptives, precocious marriage, multiparity, smoking etc. are seen to modify the risk of CACX, but infection by high risk human papillomavirus (hrHPV) is thought to be the major cause. Interestingly, long latency period for malignant outcome in only a subset of HPV-infected women indicates involvement of additional chromosomal alterations.Since the first report of changes in chromosomal content of CACX, several genome-wide studies reported frequent chromosomal gain of 3q (3q24–29), 1q (1q22–q23, 1q25.3–q32.1) and 5p (5p12–p13) and loss of 3p (3p12–23), 11q (11q22.3–25) and 4p (4p16.3–p16.1). But no study was done to catalogue the precise genomic alterations in CACX of Indian patients. To the best of our knowledge, for the first time the present study revealed precise chromosomal aberrations with differential frequency in Indian CACX patients (n=11). Among these alterations, frequent (>50%) amplifications of distinct chromosomal loci were as follows: 1p36.11-1p31.1, 1q21.1-1q44, 3q13.13-3q29, 5p15.33-5p12, 8q24.3, 16q22.2, 19q13.13-19q13.2, Xp22.33-Xp11.21 and Xq11.2-Xq12. While recurrent (>35%) loss at chromosomal loci, 2q34-2q37.3, 4p16.3-4p12, 4q21.3, 8p23.3, 8p23.2, 8p11.22, 11q14.1-11q25, 13q13.3-13q14.3, and 19p13.3 were also observed. All CACX patients showed precise amplification of chromosome 3 at coordinates 3q25.2-3q26.1 (chr3:154427429-162796745), 3q26.1-3q26.31 (chr3:162901354-175146595) and 3q26.32-3q29 (chr3:175208719-198094926). Highest (72%) loss of chromosomal loci 11q24.3-11q25 (chr11:128926744-135034169) was seen.
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| Overall design |
Agilent two-color CGH+SNP experiment,Organism: Human ,Agilent Human CGH+SNP 2X400K Array (AMADID: 028081)
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| Web link |
http://www.sciencedirect.com/science/article/pii/S0304416516303506
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| Contributor(s) |
Roychowdhury A, Samadder S, Roychoudhury S, Panda CK |
| Citation(s) |
27641506 |
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| Submission date |
Jan 15, 2016 |
| Last update date |
Feb 23, 2017 |
| Contact name |
Susanta Roychoudhury |
| E-mail(s) |
anirbanr91@gmail.com
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| Organization name |
Saroj Gupta Cancer Centre & Research Institute
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| Street address |
Mahatma Gandhi Road, Thakurpukur
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| City |
Kolkata |
| State/province |
West Bengal |
| ZIP/Postal code |
700063 |
| Country |
India |
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| Platforms (1) |
| GPL11363 |
Agilent-028081 Human Genome CGH + SNP Microarray (Probe Name version) |
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| Samples (12)
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| GSM2040579 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#1960 |
| GSM2040580 |
matched normal blood_#854 vs. normal Coriell Sample (Coriell_NA12878)-European_Female |
| GSM2040581 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#4253 |
| GSM2040582 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#1856 |
| GSM2040583 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#1711 |
| GSM2040584 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#6109 |
| GSM2040585 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#854 |
| GSM2040586 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#6341 |
| GSM2040587 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#3341 |
| GSM2040588 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#1763 |
| GSM2040589 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#2702 |
| GSM2040590 |
Primary Tumor vs matched normal blood_Cervical cancer patient_#3389 |
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| Relations |
| BioProject |
PRJNA308930 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76911_RAW.tar |
1.3 Gb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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