Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST).

Abstract:

BACKGROUND:Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) has significantly impaired this process in the field of solid tumors. To evaluate if data generated from FFPE material can be reliably produced and potentially used in routine clinical settings, we performed whole exome sequencing (WES) from tumor samples of Gastrointestinal stromal tumors (GIST), either extracted FF or FFPE, and from matched normal DNA. METHODS:We performed whole exome enrichment and sequencing at 100bp in paired end on four GIST samples, either from FFPE or fresh-frozen tissue, and from matched normal DNA. RESULTS:The integrity of DNA extracted from FFPE was evaluated by a modified RAPD PCR method, thus identifying high quality (HQ) and low quality (LQ) FFPE. DNA library production and exome capture was feasible for both classes of FFPE, despite the smaller yield and insert size of LQ-FFPE. WES produced data of equal quality from FF and FFPE, while only HQ-FFPE yielded an amount of data comparable to FF samples. Bioinformatic analysis showed that the percentage of variants called both in FF and FFPE samples was very high in HQ-FFPE, reaching 94-96 % of the total number of called variants. Classification of somatic variants by nucleotide substitution type showed that HQ-FFPE and FF had similar mutational profiles, while LQ-FFPE samples carried a much higher number of mutations than the FF counterpart, with a significant enrichment of C > T/G > A substitutions. Focusing on potential disease-related variants allowed the discovery of additional somatic variants in GIST samples, apart from the known oncogenic driver mutation, both from sequencing of FF and FFPE material. False positive and false negative calls were present almost exclusively in the analysis of FFPE of low quality. On the whole this study showed that WES is feasible also on FFPE specimens and that it is possible to easily select FFPE samples of high quality that yield sequencing results comparable to the FF counterpart. CONCLUSIONS:WES on FFPE material may represent an important and innovative source for GIST research and for other solid tumors, amenable of possible application in clinical practice.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Astolfi A,Urbini M,Indio V,Nannini M,Genovese CG,Santini D,Saponara M,Mandrioli A,Ercolani G,Brandi G,Biasco G,Pantaleo MA

doi

10.1186/s12864-015-1982-6

subject

Has Abstract

pub_date

2015-11-03 00:00:00

pages

892

issn

1471-2164

pii

10.1186/s12864-015-1982-6

journal_volume

16

pub_type

杂志文章
  • Metabolite and transcriptome analysis during fasting suggest a role for the p53-Ddit4 axis in major metabolic tissues.

    abstract:BACKGROUND:Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-758

    authors: Schupp M,Chen F,Briggs ER,Rao S,Pelzmann HJ,Pessentheiner AR,Bogner-Strauss JG,Lazar MA,Baldwin D,Prokesch A

    更新日期:2013-11-05 00:00:00

  • What lies beneath? Molecular evolution during the radiation of caecilian amphibians.

    abstract:BACKGROUND:Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecili...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5694-1

    authors: Torres-Sánchez M,Gower DJ,Alvarez-Ponce D,Creevey CJ,Wilkinson M,San Mauro D

    更新日期:2019-05-09 00:00:00

  • Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model.

    abstract:BACKGROUND:Due to the high morbidity and mortality of fulminant hepatitis, early diagnosis followed by early effective treatment is the key for prognosis improvement. So far, little is known about the gene expression changes in the early stage of this serious illness. Identification of the genes related to the very ear...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-240

    authors: Chen F,Zhu HH,Zhou LF,Li J,Zhao LY,Wu SS,Wang J,Liu W,Chen Z

    更新日期:2010-04-15 00:00:00

  • Identification of functional regulatory elements in the human genome using pooled CRISPR screens.

    abstract:BACKGROUND:Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise < 2% of the se...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6497-0

    authors: Borys SM,Younger ST

    更新日期:2020-01-31 00:00:00

  • Gene expression changes during caste-specific neuronal development in the damp-wood termite Hodotermopsis sjostedti.

    abstract:BACKGROUND:One of the key characters of social insects is the division of labor, in which different tasks are allocated to various castes. In termites, one of the representative groups of social insects, morphological differences as well as behavioral differences can be recognized among castes. However, very little is ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-314

    authors: Ishikawa Y,Okada Y,Ishikawa A,Miyakawa H,Koshikawa S,Miura T

    更新日期:2010-05-20 00:00:00

  • Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton.

    abstract:BACKGROUND:Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network of S. mutans biofilms upon carolacton treatment was constructed and analyze...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-362

    authors: Sudhakar P,Reck M,Wang W,He FQ,Wagner-Döbler I,Zeng AP

    更新日期:2014-05-12 00:00:00

  • Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq.

    abstract:BACKGROUND:Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics contex...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6603-3

    authors: Martin Cerezo ML,Kucka M,Zub K,Chan YF,Bryk J

    更新日期:2020-03-18 00:00:00

  • A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data.

    abstract:BACKGROUND:The recent advance of high-throughput sequencing makes it feasible to study entire transcriptomes through the application of de novo sequence assembly algorithms. While a popular strategy is to first construct an intermediate de Bruijn graph structure to represent the transcriptome, an additional step is nee...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-S5-S6

    authors: Sze SH,Tarone AM

    更新日期:2014-01-01 00:00:00

  • Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data.

    abstract:BACKGROUND:High throughput experiments resulted in many genomic datasets and hundreds of candidate disease genes. To discover the real disease genes from a set of candidate genes, computational methods have been proposed and worked on various types of genomic data sources. As a single source of genomic data is prone of...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S7-S27

    authors: Li Y,Li J

    更新日期:2012-01-01 00:00:00

  • Correction to: On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments.

    abstract::An amendment to this paper has been published and can be accessed via the original article. ...

    journal_title:BMC genomics

    pub_type: 杂志文章,已发布勘误

    doi:10.1186/s12864-020-6754-2

    authors: Assefa AT,Vandesompele J,Thas O

    更新日期:2020-06-03 00:00:00

  • Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project.

    abstract:BACKGROUND:Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of sm...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-4-40

    authors: Fernández P,Paniego N,Lew S,Hopp HE,Heinz RA

    更新日期:2003-09-30 00:00:00

  • Cell population-specific expression analysis of human cerebellum.

    abstract:BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-610

    authors: Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

    更新日期:2012-11-12 00:00:00

  • Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine.

    abstract:BACKGROUND:Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). RESULT:Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6111-5

    authors: Wang P,Yang Y,Shi H,Wang Y,Ren F

    更新日期:2019-10-15 00:00:00

  • Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue.

    abstract:BACKGROUND:Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and mi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-36

    authors: Kim TH,Kim NS,Lim D,Lee KT,Oh JH,Park HS,Jang GW,Kim HY,Jeon M,Choi BH,Lee HY,Chung HY,Kim H

    更新日期:2006-02-27 00:00:00

  • Genome-wide transcriptome and functional analysis of two contrasting genotypes reveals key genes for cadmium tolerance in barley.

    abstract:BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-611

    authors: Cao F,Chen F,Sun H,Zhang G,Chen ZH,Wu F

    更新日期:2014-07-19 00:00:00

  • Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong.

    abstract:BACKGROUND:Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patte...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1900-y

    authors: Cheng CK,Cheung MK,Nong W,Law PT,Qin J,Ling JM,Kam KM,Cheung WM,Kwan HS

    更新日期:2015-09-14 00:00:00

  • Identification of candidate genes for human pituitary development by EST analysis.

    abstract:BACKGROUND:The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-109

    authors: Ma Y,Qi X,Du J,Song S,Feng D,Qi J,Zhu Z,Zhang X,Xiao H,Han Z,Hao X

    更新日期:2009-03-15 00:00:00

  • Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation.

    abstract:BACKGROUND:Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6322-9

    authors: van Biljon R,van Wyk R,Painter HJ,Orchard L,Reader J,Niemand J,Llinás M,Birkholtz LM

    更新日期:2019-12-03 00:00:00

  • Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.

    abstract:BACKGROUND:Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1737-4

    authors: Wallace-Salinas V,Brink DP,Ahrén D,Gorwa-Grauslund MF

    更新日期:2015-07-09 00:00:00

  • Estimating the total genome length of a metagenomic sample using k-mers.

    abstract:BACKGROUND:Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5467-x

    authors: Hua K,Zhang X

    更新日期:2019-04-04 00:00:00

  • Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer.

    abstract:BACKGROUND:Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for eac...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3166-4

    authors: Hirotsu Y,Kojima Y,Okimoto K,Amemiya K,Mochizuki H,Omata M

    更新日期:2016-10-26 00:00:00

  • Comparative genomic analysis of eutherian fibroblast growth factor genes.

    abstract:BACKGROUND:The eutherian fibroblast growth factors were implicated as key regulators in developmental processes. However, there were major disagreements in descriptions of comprehensive eutherian fibroblast growth factors gene data sets including either 18 or 22 homologues. The present analysis attempted to revise and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06958-4

    authors: Premzl M

    更新日期:2020-08-05 00:00:00

  • Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data.

    abstract:BACKGROUND:Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a gi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2123-y

    authors: Forni D,Martin D,Abujaber R,Sharp AJ,Sironi M,Hollox EJ

    更新日期:2015-11-02 00:00:00

  • GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

    abstract:BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3731-5

    authors: Yu N,Guo X,Zelikovsky A,Pan Y

    更新日期:2017-05-24 00:00:00

  • Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.

    abstract:BACKGROUND:Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insight...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3465-9

    authors: Brockmöller T,Ling Z,Li D,Gaquerel E,Baldwin IT,Xu S

    更新日期:2017-01-13 00:00:00

  • The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements.

    abstract:BACKGROUND:The substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary rela...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1641-y

    authors: Akpinar BA,Magni F,Yuce M,Lucas SJ,Šimková H,Šafář J,Vautrin S,Bergès H,Cattonaro F,Doležel J,Budak H

    更新日期:2015-06-13 00:00:00

  • Arsenic-induced changes in the gene expression of lung epithelial L2 cells: implications in carcinogenesis.

    abstract:BACKGROUND:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic al...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-115

    authors: Posey T,Weng T,Chen Z,Chintagari NR,Wang P,Jin N,Stricker H,Liu L

    更新日期:2008-03-03 00:00:00

  • Population and sex differences in Drosophila melanogaster brain gene expression.

    abstract:BACKGROUND:Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-654

    authors: Catalán A,Hutter S,Parsch J

    更新日期:2012-11-21 00:00:00

  • A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits.

    abstract:BACKGROUND:Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on com...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-606

    authors: Decker JE,Vasco DA,McKay SD,McClure MC,Rolf MM,Kim J,Northcutt SL,Bauck S,Woodward BW,Schnabel RD,Taylor JF

    更新日期:2012-11-09 00:00:00

  • A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation.

    abstract:BACKGROUND:Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-135

    authors: Dong HT,Zhang L,Zheng KL,Yao HG,Chen J,Yu FC,Yu XX,Mao BZ,Zhao D,Yao J,Li DB

    更新日期:2012-04-13 00:00:00