Immortalization of epithelial cells in oral carcinogenesis as revealed by genome-wide array comparative genomic hybridization: A meta-analysis

Head & Neck ◽  
2015 ◽  
Vol 38 (S1) ◽  
pp. E783-E797
Author(s):  
Vui King Vincent-Chong ◽  
Iman Salahshourifar ◽  
Rozaimi Razali ◽  
Arif Anwar ◽  
Rosnah Binti Zain
Keyword(s):  
Epithelial Cells ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Meta Analysis ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Oral Carcinogenesis ◽  
Genome Wide

scholarly journals Integrated Sequencing & Array Comparative Genomic Hybridization in Familial Parkinson’s Disease

2019 ◽  
Author(s):  
Laurie A. Robak ◽  
Renqian Du ◽  
Bo Yuan ◽  
Shen Gu ◽  
Isabel Alfradique-Dunham ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Comparative Genomic Hybridization ◽  
Genetic Risk ◽  
Array Comparative Genomic Hybridization ◽  
Comparative Genomic ◽  
Single Nucleotide Variants ◽  
Genomic Hybridization ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Breakpoint Sequencing

AbstractBackgroundParkinson’s disease (PD) is a genetically heterogeneous condition; both single nucleotide variants (SNVs) and copy number variants (CNVs) are important genetic risk factors. We examined the utility of combining exome sequencing and genome-wide array-based comparative genomic hybridization (aCGH) for identification of PD genetic risk factors.MethodsWe performed exome sequencing on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated exome sequencing and array comparative genomic hybridization data for pathogenic SNVs and CNVs at Mendelian PD gene loci. SNVs were confirmed via Sanger sequencing. CNVs were confirmed with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing.ResultsUsing exome sequencing, we discovered individuals with known pathogenic single nucleotide variants in GBA (p.E365K, p.T408M, p.N409S, p.L483P) and LRRK2 (p.R1441G and p.G2019S). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.N52fs, p.T240M, p.P437L, p.W453*) and likely disrupting CNVs at the PARK2 locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors.ConclusionsIntegrated exome sequencing and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PARK2 CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.

Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances

Blood ◽  
2009 ◽  
Vol 113 (1) ◽  
pp. 137-148 ◽  
Author(s):  
K.-John J. Cheung ◽  
Sohrab P. Shah ◽  
Christian Steidl ◽  
Nathalie Johnson ◽  
Thomas Relander ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Cox Model ◽  
International Prognostic Index ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Prognostic Features ◽  
Genome Wide

Abstract The secondary genetic events associated with follicular lymphoma (FL) progression are not well defined. We applied genome-wide BAC array comparative genomic hybridization to 106 diagnostic biopsies of FL to characterize regional genomic imbalances. Using an analytical approach that defined regions of copy number change as intersections between visual annotations and a Hidden Markov model–based algorithm, we identified 71 regional alterations that were recurrent in at least 10% of cases. These ranged in size from approximately 200 kb to 44 Mb, affecting chromosomes 1, 5, 6, 7, 8, 10, 12, 17, 18, 19, and 22. We also demonstrated by cluster analysis that 46.2% of the 106 cases could be sub-grouped based on the presence of +1q, +6p/6q−, +7, or +18. Survival analysis showed that 21 of the 71 regions correlated significantly with inferior overall survival (OS). Of these 21 regions, 16 were independent predictors of OS using a multivariate Cox model that included the international prognostic index (IPI) score. Two of these 16 regions (1p36.22-p36.33 and 6q21-q24.3) were also predictors of transformation risk and independent of IPI. These prognostic features may be useful to identify high-risk patients as candidates for risk-adapted therapies.

scholarly journals Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma

BMC Cancer ◽  
2004 ◽  
Vol 4 (1) ◽  
Author(s):  
Tsz-Kwong Man ◽  
Xin-Yan Lu ◽  
Kim Jaeweon ◽  
Laszlo Perlaky ◽  
Charles P Harris ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Hybridization Analysis ◽  
Comparative Genomic ◽  
Comparative Genomic Hybridization Analysis ◽  
Genomic Hybridization ◽  
Genome Wide

scholarly journals Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors

Oncogene ◽  
2006 ◽  
Vol 26 (10) ◽  
pp. 1499-1506 ◽  
Author(s):  
K Jong ◽  
E Marchiori ◽  
A van der Vaart ◽  
S-F Chin ◽  
B Carvalho ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Meta Analysis ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Epithelial Tumors ◽  
Cross Platform

Genome-wide screening of severe male factor infertile patients using BAC-array comparative genomic hybridization (CGH)

Gene ◽  
2012 ◽  
Vol 506 (1) ◽  
pp. 248-252 ◽  
Author(s):  
Seung-Hun Song ◽  
Sung Han Shim ◽  
Jeong Kyoon Bang ◽  
Ji Eun Park ◽  
Se Ra Sung ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Male Factor ◽  
Genome Wide ◽  
Infertile Patients

Recurrent Genomic Alterations With Impact on Survival in Colorectal Cancer Identified by Genome-Wide Array Comparative Genomic Hybridization

2006 ◽  
Vol 131 (6) ◽  
pp. 1913-1924 ◽  
Author(s):  
Mi–Young Kim ◽  
Seon–Hee Yim ◽  
Mi–Seon Kwon ◽  
Tae–Min Kim ◽  
Seung–Hun Shin ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Genomic Alterations ◽  
Genome Wide ◽  
Impact On Survival
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