title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens.
abstract: A single tumor biopsy specimen is typically used in cancer genome studies. However, it may represent incompletely the underlying mutational and transcriptional profiles of tumor biology. Multi-regional biopsies have the advantage of increased sensitivity for genomic profiling, but they are not cost-effective. The concept of an alternative method such as the pooling of multiple biopsies is a challenge. In order to determine if the pooling of distinct regions is representative at the genomic and transcriptome level, we performed sequencing of four regional samples and pooled samples for four cancer types including colon, stomach, kidney and liver cancer. Subsequently, a comparative analysis was conducted to explore differences in mutations and gene expression profiles between multiple regional biopsies and pooled biopsy for each tumor. Our analysis revealed a marginal level of regional difference in detected variants, but in those with low allele frequency, considerable discrepancies were observed. In conclusion, sequencing pooled samples has the benefit of detecting many variants with moderate allele frequency that occur in partial regions, but it is not applicable for detecting low-frequency mutations that require deep sequencing.
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
authors.forename: Je-Gun
authors.initials: JG
authors.lastname: Joung
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
authors.forename: Joon Seol
authors.initials: JS
authors.lastname: Bae
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
authors.forename: Sang Cheol
authors.initials: SC
authors.lastname: Kim
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
authors.forename: HyunChul
authors.initials: H
authors.lastname: Jung
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.|Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
authors.forename: Woong-Yang
authors.initials: WY
authors.lastname: Park
authors.affiliation: Department of Pathology, Samsung Medical Center, Seoul, Republic of Korea.|Departments of Pathology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
authors.forename: Sang-Yong
authors.initials: SY
authors.lastname: Song
mesh_terms: D001706:Biopsy; D059472:Exome; D020869:Gene Expression Profiling; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000473:pathology*; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome