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

Bibi, Fehmida ; Ali, Isse ; Naseer, Muhammad Imran ; Ali Mohamoud, Hussein Sheikh ; Yasir, Muhammad ; Alvi, Sana Akhtar ; Jiman-Fatani, Asif Ahmed ; Sawan, Ali ; Azhar, Esam Ibraheem Tao, Qian

PloS one, 2018-09, Vol.13 (9), p.e0202576 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)
Autor: Bibi, Fehmida ; Ali, Isse ; Naseer, Muhammad Imran ; Ali Mohamoud, Hussein Sheikh ; Yasir, Muhammad ; Alvi, Sana Akhtar ; Jiman-Fatani, Asif Ahmed ; Sawan, Ali ; Azhar, Esam Ibraheem
Tao, Qian
Assuntos: Adult ; Aged ; Aged, 80 and over ; Biology and Life Sciences ; Cancer ; Cancer patients ; Carcinogenesis ; Carcinogens ; Case-Control Studies ; Chromosome 14 ; Chromosome 4 ; Chromosome Aberrations ; Chromosomes ; Comparative genomic hybridization ; Comparative Genomic Hybridization - methods ; Computer and Information Sciences ; Copy number ; Cytogenetics ; Deoxyribonucleic acid ; DNA ; DNA Copy Number Variations ; Female ; Gastric cancer ; Gene Regulatory Networks ; Genes ; Genetic aspects ; Genetics ; Genomes ; Health aspects ; Helicobacter Infections - genetics ; Humans ; Hybridization ; Infections ; Loss of Heterozygosity ; Male ; Medical research ; Medicine ; Medicine and Health Sciences ; Middle Aged ; Monosomy ; Neoplasm Staging ; Nervous system ; Oncology ; Paraffin ; Paraffins ; Patients ; Polymorphism, Single Nucleotide ; Population (statistical) ; Research and Analysis Methods ; Risk factors ; Saudi Arabia ; Statistical analysis ; Statistical methods ; Stomach cancer ; Stomach Neoplasms - genetics ; Stomach Neoplasms - pathology ; Trisomy ; Young Adult
É parte de: PloS one, 2018-09, Vol.13 (9), p.e0202576
Notas: Competing Interests: The authors declare that they have no competing interests.
Descrição: 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 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages. We found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.
Editor: United States: Public Library of Science
Idioma: Inglês

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

Bibi, Fehmida ; Ali, Isse ; Naseer, Muhammad Imran ; Ali Mohamoud, Hussein Sheikh ; Yasir, Muhammad ; Alvi, Sana Akhtar ; Jiman-Fatani, Asif Ahmed ; Sawan, Ali ; Azhar, Esam Ibraheem Tao, Qian

United States: Public Library of Science

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