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


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.


BMC Genomics


BMC genomics


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




Has Abstract


2015-11-03 00:00:00










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    abstract:BACKGROUND:Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the b...

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    pub_type: 杂志文章


    authors: Pannebakker BA,Cook N,van den Heuvel J,van de Zande L,Shuker DM

    更新日期:2020-07-20 00:00:00

  • Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm.

    abstract:BACKGROUND:Typhoid fever is an acute systemic infection of humans caused by Salmonella enterica subspecies enterica serovar Typhi (S. Typhi). In chronic carriers, the bacteria survive the harsh environment of the gallbladder by producing biofilm. The phenotype of S. Typhi biofilm cells is significantly different from t...

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    authors: Chin KCJ,Taylor TD,Hebrard M,Anbalagan K,Dashti MG,Phua KK

    更新日期:2017-10-31 00:00:00

  • Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data.

    abstract:BACKGROUND:Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and ...

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    authors: Cui W,Qian Y,Zhou X,Lin Y,Jiang J,Chen J,Zhao Z,Shen B

    更新日期:2015-01-01 00:00:00

  • Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa.

    abstract:BACKGROUND:Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elemen...

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    pub_type: 杂志文章


    authors: Karlsen C,Hjerde E,Klemetsen T,Willassen NP

    更新日期:2017-04-20 00:00:00

  • Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma.

    abstract:BACKGROUND:The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim o...

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    authors: Beatty M,Guduric-Fuchs J,Brown E,Bridgett S,Chakravarthy U,Hogg RE,Simpson DA

    更新日期:2014-10-25 00:00:00

  • Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation.

    abstract:BACKGROUND:Celiac disease (CD) is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes) that mediate the stimulation of HL...

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    pub_type: 杂志文章


    authors: Salentijn EM,Mitea DC,Goryunova SV,van der Meer IM,Padioleau I,Gilissen LJ,Koning F,Smulders MJ

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  • Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane.

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    authors: Su Y,Xu L,Wang Z,Peng Q,Yang Y,Chen Y,Que Y

    更新日期:2016-10-12 00:00:00

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    authors: Schubert M,Ginolhac A,Lindgreen S,Thompson JF,Al-Rasheid KA,Willerslev E,Krogh A,Orlando L

    更新日期:2012-05-10 00:00:00

  • Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers.

    abstract:BACKGROUND:Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species ar...

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    authors: Luo H,Sun C,Sun Y,Wu Q,Li Y,Song J,Niu Y,Cheng X,Xu H,Li C,Liu J,Steinmetz A,Chen S

    更新日期:2011-12-23 00:00:00

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    abstract:BACKGROUND:Crohn's disease (CD) is an inflammatory bowel disease caused by genetic and environmental factors. More than 160 susceptibility loci have been identified for IBD, yet a large part of the genetic variance remains unexplained. Recent studies have demonstrated genetic differences between monozygotic twins, who ...

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    authors: Petersen BS,Spehlmann ME,Raedler A,Stade B,Thomsen I,Rabionet R,Rosenstiel P,Schreiber S,Franke A

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    abstract:BACKGROUND:Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate...

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    authors: Baufeld A,Koczan D,Vanselow J

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    abstract:BACKGROUND:Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that ca...

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    authors: Ellison CK,Shaw KL

    更新日期:2010-07-12 00:00:00

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    abstract:BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...

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    authors: Dang X,Xie Z,Liu W,Sun Y,Liu X,Zhu Y,Staehelin C

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  • The human olfactory transcriptome.

    abstract:BACKGROUND:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...

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    authors: Olender T,Keydar I,Pinto JM,Tatarskyy P,Alkelai A,Chien MS,Fishilevich S,Restrepo D,Matsunami H,Gilad Y,Lancet D

    更新日期:2016-08-11 00:00:00

  • Structure and properties of transcriptional networks driving selenite stress response in yeasts.

    abstract:BACKGROUND:Stress responses provide valuable models for deciphering the transcriptional networks controlling the adaptation of the cell to its environment. We analyzed the transcriptome response of yeast to toxic concentrations of selenite. We used gene network mapping tools to identify functional pathways and transcri...

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    authors: Salin H,Fardeau V,Piccini E,Lelandais G,Tanty V,Lemoine S,Jacq C,Devaux F

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  • QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

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    authors: Saatchi M,Beever JE,Decker JE,Faulkner DB,Freetly HC,Hansen SL,Yampara-Iquise H,Johnson KA,Kachman SD,Kerley MS,Kim J,Loy DD,Marques E,Neibergs HL,Pollak EJ,Schnabel RD,Seabury CM,Shike DW,Snelling WM,Spangler ML,

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  • A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf.

    abstract:BACKGROUND:The establishment of C4 photosynthesis in maize is associated with differential accumulation of gene transcripts and proteins between bundle sheath and mesophyll photosynthetic cell types. We have physically separated photosynthetic cell types in the leaf blade to characterize differences in gene expression ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sawers RJ,Liu P,Anufrikova K,Hwang JT,Brutnell TP

    更新日期:2007-01-09 00:00:00

  • Identification of genomic aberrations in hemangioblastoma by droplet digital PCR and SNP microarray highlights novel candidate genes and pathways for pathogenesis.

    abstract:BACKGROUND:The genetic mechanisms underlying hemangioblastoma development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays and droplet digital PCR analysis to detect copy number variations (CNVs) in total of 45 hemangioblastoma tumors. RESULTS:We identified 94 CNVs with a m...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mehrian-Shai R,Yalon M,Moshe I,Barshack I,Nass D,Jacob J,Dor C,Reichardt JK,Constantini S,Toren A

    更新日期:2016-01-14 00:00:00

  • Multiple genetic loci define Ca++ utilization by bloodstream malaria parasites.

    abstract:BACKGROUND:Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilization by genetically distinct lines of P. falciparum. These differences, if identified, may provide...

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    authors: Apolis L,Olivas J,Srinivasan P,Kushwaha AK,Desai SA

    更新日期:2019-01-16 00:00:00

  • XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.

    abstract:BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Magi A,Pippucci T,Sidore C

    更新日期:2017-09-21 00:00:00

  • Comparative analysis of fungal protein kinases and associated domains.

    abstract:BACKGROUND:Protein phosphorylation is responsible for a large portion of the regulatory functions of eukaryotic cells. Although the list of sequenced genomes of filamentous fungi has grown rapidly, the kinomes of recently sequenced species have not yet been studied in detail. The objective of this study is to apply a c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kosti I,Mandel-Gutfreund Y,Glaser F,Horwitz BA

    更新日期:2010-02-24 00:00:00

  • Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis.

    abstract:BACKGROUND:Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. RESULTS:Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondri...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Deng Y,Zhang X,Xie B,Lin L,Hsiang T,Lin X,Lin Y,Zhang X,Ma Y,Miao W,Ming R

    更新日期:2020-06-24 00:00:00

  • Comparative analysis of expression of histone H2a genes in mouse.

    abstract:BACKGROUND:At least 18 replication-dependent histone H2a genes are distributed in 3 Hist gene clusters on different chromosomes of the mouse genome. In this analysis we designed specific PCR primers for each histone H2a transcript and studied the expression levels and patterns using quantitative RT-PCR (qRT-PCR). In ad...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Nishida H,Suzuki T,Ookawa H,Tomaru Y,Hayashizaki Y

    更新日期:2005-08-13 00:00:00

  • Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus.

    abstract:BACKGROUND:Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li RW,Waldbieser GC

    更新日期:2006-06-01 00:00:00

  • CRISPR/Cas9-mediated precise genome modification by a long ssDNA template in zebrafish.

    abstract:BACKGROUND:Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish. Recently, long single-stranded DNA (lssDNA) molecules have been developed...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bai H,Liu L,An K,Lu X,Harrison M,Zhao Y,Yan R,Lu Z,Li S,Lin S,Liang F,Qin W

    更新日期:2020-01-21 00:00:00

  • Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Luck AN,Anderson KG,McClung CM,VerBerkmoes NC,Foster JM,Michalski ML,Slatko BE

    更新日期:2015-11-11 00:00:00

  • Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Schröder W,Bernhardt J,Marincola G,Klein-Hitpass L,Herbig A,Krupp G,Nieselt K,Wolz C

    更新日期:2014-04-16 00:00:00

  • Does replication groups scoring reduce false positive rate in SNP interaction discovery?

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Toplak M,Curk T,Demsar J,Zupan B

    更新日期:2010-01-22 00:00:00

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Xu Z,Shen J,Hua S,Wan D,Chen Q,Han Y,Ren R,Liu F,Du Z,Guo X,Shi J,Zhi Q

    更新日期:2019-09-18 00:00:00