Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)

PloS One
Fehmida BibiEsam Ibraheem Azhar

Abstract

The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 mon...Continue Reading

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Citations

Sep 11, 2019·Biotechnic & Histochemistry : Official Publication of the Biological Stain Commission·E I Cortés-GutiérrezJ Gosálvez
Apr 16, 2020·International Journal of Molecular Sciences·Amelia CasamassimiCiro Abbondanza
Jun 17, 2020·The Journal of Clinical Investigation·Taotao HanJuan Shi
Jun 26, 2021·Pathology, Research and Practice·Han ZhangZhaohui Huang

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Methods Mentioned

BETA
chromosomal aberrations
genotyping
biopsy

Software Mentioned

Broading
Genome Studio
Minitab
Illumina Genome Viewer ( IGV )
SPSS
QuantiSNP
cnvPartition
Studio GT
Illumina
Chromosome Browser ( ICV )

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