Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies
The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA...
Saved in:
| Published in | Genome medicine Vol. 5; no. 8; p. 77 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
30.08.2013
BioMed Central Ltd |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1756-994X 1756-994X |
| DOI | 10.1186/gm481 |
Cover
| Abstract | The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. |
|---|---|
| AbstractList | The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay ('QFI-PCR') that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay ('QFI-PCR') that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing.The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay ('QFI-PCR') that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. |
| ArticleNumber | 77 |
| Audience | Academic |
| Author | Houghton, Jeffrey Chen, Liangjing Zeigler, Robert Marko, Adam C Kemppainen, Jon Sah, Sachin Latham, Gary J |
| AuthorAffiliation | 1 Asuragen, Inc, Austin, TX 78744, USA |
| AuthorAffiliation_xml | – name: 1 Asuragen, Inc, Austin, TX 78744, USA |
| Author_xml | – sequence: 1 givenname: Sachin surname: Sah fullname: Sah, Sachin organization: Asuragen, Inc – sequence: 2 givenname: Liangjing surname: Chen fullname: Chen, Liangjing organization: Asuragen, Inc – sequence: 3 givenname: Jeffrey surname: Houghton fullname: Houghton, Jeffrey organization: Asuragen, Inc – sequence: 4 givenname: Jon surname: Kemppainen fullname: Kemppainen, Jon organization: Asuragen, Inc – sequence: 5 givenname: Adam C surname: Marko fullname: Marko, Adam C organization: Asuragen, Inc – sequence: 6 givenname: Robert surname: Zeigler fullname: Zeigler, Robert organization: Asuragen, Inc – sequence: 7 givenname: Gary J surname: Latham fullname: Latham, Gary J email: glatham@asuragen.com organization: Asuragen, Inc |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24001039$$D View this record in MEDLINE/PubMed |
| BookMark | eNqNkl1rFDEUhgep2A_7FyQgSkGnJvORmbkRlmpVKHqj4F3Ix8lsykyyTTJSf0X_stnOtuwuCjIXmZzznDcnJ-9xdmCdhSw7JfickJa-68eqJU-yI9LUNO-66ufB1v9hdhzCNca0KqrmWXZYVBgTXHZH2d3lZGU0zvIBffi6QDcTt9FoI_k6iPrJKAiISzl5HgFZuI15Dxb8nA9wM4GVxvZonOIcUxDhXhIZi7TzIx-MzbW5BfUWrbjnWqc9jAKUAoXiNDqPhHGrYCA8z55qPgQ43awn2Y_Lj98vPudX3z59uVhc5YJWOOZCUAWkoaKoKylqrluM61YIqAuNVVcSWjeadmXZCUiQkIIAKRQA1hRjqMuT7P2su5rECEqCjZ4PbOXNyP1v5rhhuxlrlqx3v1jZNW3b0CTQzgKp838I7GakG9n9I6XSs83Z3qXxhchGEyQMA7fgpsBIXdCmrHHT_Q9aVbigxfpGL2e05wMwY7VLx8o1zhZ1WTVtWbVNos7_QqVPwWhkspQ2Kb5T8HqrYAl8iMvghmn9wGEXfLE90cdJPHgtAW9mQHoXggfNpJktk1owAyOYrZ38OKRXe_SD4D636S-kvO3Bs2s3-WTnsAf-ARUeA0c |
| CitedBy_id | crossref_primary_10_4132_jptm_2016_10_03 crossref_primary_10_1038_s41598_018_24780_7 crossref_primary_10_1016_j_canlet_2016_04_016 crossref_primary_10_1053_j_seminoncol_2015_07_013 crossref_primary_10_1089_bio_2018_0046 crossref_primary_10_1016_j_bbcan_2015_03_002 crossref_primary_10_1373_clinchem_2014_223040 crossref_primary_10_5858_arpa_2016_0501_RA crossref_primary_10_21769_BioProtoc_4095 crossref_primary_10_1038_ncomms11815 crossref_primary_10_1371_journal_pone_0127146 crossref_primary_10_1038_modpathol_2016_116 crossref_primary_10_1016_j_bdq_2018_12_003 crossref_primary_10_1016_j_clinbiochem_2016_11_016 crossref_primary_10_1186_s40425_016_0178_1 crossref_primary_10_1016_j_fertnstert_2014_07_1209 crossref_primary_10_1186_s12967_019_2124_8 crossref_primary_10_1136_jclinpath_2016_204061 crossref_primary_10_1186_s12920_014_0062_0 crossref_primary_10_1016_j_jmoldx_2018_10_003 crossref_primary_10_1016_j_cancergen_2015_05_001 crossref_primary_10_1016_j_isci_2021_102892 crossref_primary_10_1136_jclinpath_2014_202644 crossref_primary_10_2217_pme_14_52 crossref_primary_10_1177_1010428318760342 crossref_primary_10_1016_j_forsciint_2017_09_020 crossref_primary_10_3389_fonc_2014_00078 crossref_primary_10_1002_humu_22561 crossref_primary_10_1016_j_optcom_2023_130160 crossref_primary_10_3390_genes12101472 crossref_primary_10_1093_gigascience_giab065 crossref_primary_10_1371_journal_pone_0104566 crossref_primary_10_1111_pin_12531 crossref_primary_10_1186_s12885_017_3328_z crossref_primary_10_1016_j_jmoldx_2015_06_001 crossref_primary_10_3390_ijms161226129 crossref_primary_10_1002_cncy_21780 crossref_primary_10_1007_s40139_019_00194_6 crossref_primary_10_3390_medicina57121375 crossref_primary_10_1007_s40265_019_01164_3 crossref_primary_10_1016_j_labinv_2023_100280 crossref_primary_10_1016_j_yexmp_2017_11_011 crossref_primary_10_1371_journal_pone_0143092 crossref_primary_10_1373_jalm_2016_020131 crossref_primary_10_2220_biomedres_44_117 crossref_primary_10_1002_cjp2_38 crossref_primary_10_1007_s00432_017_2399_1 crossref_primary_10_1111_cyt_12255 crossref_primary_10_1634_theoncologist_2014_0357 crossref_primary_10_1136_jclinpath_2019_206368 crossref_primary_10_1016_j_jasc_2015_01_001 crossref_primary_10_3892_ol_2017_7001 crossref_primary_10_1093_bib_bbab221 crossref_primary_10_51523_2708_6011_2023_20_4_19 crossref_primary_10_1016_j_jasc_2015_01_007 crossref_primary_10_1016_j_yamp_2018_07_008 crossref_primary_10_1186_1755_8794_7_23 crossref_primary_10_1016_j_cca_2018_11_002 crossref_primary_10_1016_j_tranon_2019_02_012 crossref_primary_10_1002_cncy_21774 crossref_primary_10_5858_arpa_2017_0269_RA crossref_primary_10_1016_j_mam_2019_10_005 crossref_primary_10_1016_j_jmoldx_2016_09_006 crossref_primary_10_1159_000499109 crossref_primary_10_1039_C9LC00196D |
| Cites_doi | 10.1002/gcc.22047 10.2353/jmoldx.2007.070004 10.1016/S1525-1578(10)60006-2 10.1038/nature09534 10.1177/39.3.1704393 10.18632/oncotarget.503 10.1016/j.ab.2006.01.051 10.1038/sj.bjc.6602889 10.1111/j.1750-3639.2007.00073.x 10.3390/ijms13078933 10.1038/nature11219 10.1016/j.bpj.2010.09.012 10.1016/j.jmoldx.2012.09.003 10.1016/j.jmoldx.2012.11.006 10.1371/journal.pone.0062692 10.1200/JCO.2010.33.3757 10.1016/S0002-9440(10)64472-0 10.1373/clinchem.2012.193409 10.1373/clinchem.2012.202390 10.1158/2159-8290.CD-12-0095 10.1016/j.eururo.2012.08.053 10.1126/scisignal.2004088 10.1158/1078-0432.CCR-10-3137 10.1016/S0002-9440(10)65461-2 10.1186/1480-9222-15-5 10.1136/jcp.2010.081539 10.1038/nbt.2403 10.1177/002215540205000802 |
| ContentType | Journal Article |
| Copyright | Sah et al.; licensee BioMed Central Ltd. 2013 COPYRIGHT 2013 BioMed Central Ltd. Copyright © 2013 Sah et al.; licensee BioMed Central Ltd. 2013 Sah et al.; licensee BioMed Central Ltd. |
| Copyright_xml | – notice: Sah et al.; licensee BioMed Central Ltd. 2013 – notice: COPYRIGHT 2013 BioMed Central Ltd. – notice: Copyright © 2013 Sah et al.; licensee BioMed Central Ltd. 2013 Sah et al.; licensee BioMed Central Ltd. |
| DBID | C6C AAYXX CITATION NPM 7QO 7TM 8FD FR3 P64 RC3 7X8 5PM |
| DOI | 10.1186/gm481 |
| DatabaseName | Springer Nature Open Access Journals CrossRef PubMed Biotechnology Research Abstracts Nucleic Acids Abstracts Technology Research Database Engineering Research Database Biotechnology and BioEngineering Abstracts Genetics Abstracts MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef PubMed Genetics Abstracts Engineering Research Database Biotechnology Research Abstracts Technology Research Database Nucleic Acids Abstracts Biotechnology and BioEngineering Abstracts MEDLINE - Academic |
| DatabaseTitleList | CrossRef MEDLINE - Academic PubMed Genetics Abstracts |
| Database_xml | – sequence: 1 dbid: C6C name: Springer Nature OA Free Journals url: http://www.springeropen.com/ sourceTypes: Publisher – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1756-994X |
| EndPage | 77 |
| ExternalDocumentID | PMC3978876 oai_biomedcentral_com_gm481 A534783487 24001039 10_1186_gm481 |
| Genre | Journal Article |
| GroupedDBID | --- 0R~ 2WC 53G 5VS AAFWJ AAJSJ AASML ABDBF ACGFS ACJQM ACUHS ADUKV AENEX AFPKN AHBYD AHSBF ALMA_UNASSIGNED_HOLDINGS AMKLP AOIAM BMC C6C DIK E3Z EBD EBLON EBS EJD ESX GROUPED_DOAJ GX1 H13 HYE HZ~ IAO IHR IHW INH INR ITC KQ8 MK0 M~E O5R O5S OK1 PGMZT RBZ ROL RPM RSV SBL SOJ TUS AAYXX ALIPV CITATION 7X7 88E 8FE 8FH 8FI 8FJ ABUWG AFKRA AHYZX BBNVY BENPR BHPHI BPHCQ BVXVI CCPQU FYUFA HCIFZ HMCUK LK8 M1P M7P NPM PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO UKHRP 7QO 7TM 8FD FR3 P64 RC3 7X8 -56 -5G -BR ABVAZ ACRMQ ADINQ AFGXO AFNRJ C24 5PM |
| ID | FETCH-LOGICAL-b640t-bb6de176b254cb5af80058bbe52f0d931657f69339be6b2bcb1e12dee0f600e53 |
| IEDL.DBID | C6C |
| ISSN | 1756-994X |
| IngestDate | Thu Aug 21 14:25:32 EDT 2025 Wed May 22 07:13:55 EDT 2024 Thu Sep 04 16:36:44 EDT 2025 Thu Sep 04 20:36:24 EDT 2025 Tue Jun 17 22:07:23 EDT 2025 Tue Jun 10 21:03:10 EDT 2025 Thu May 22 21:23:55 EDT 2025 Mon Jul 21 06:01:19 EDT 2025 Thu Apr 24 23:11:50 EDT 2025 Tue Jul 01 04:01:04 EDT 2025 Sat Sep 06 07:28:01 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 8 |
| Keywords | FFPE Sample Qubit Assay Quality Control Metrics PIK3CA H1047R Haploid Copy |
| Language | English |
| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-b640t-bb6de176b254cb5af80058bbe52f0d931657f69339be6b2bcb1e12dee0f600e53 |
| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 |
| OpenAccessLink | https://doi.org/10.1186/gm481 |
| PMID | 24001039 |
| PQID | 1524402625 |
| PQPubID | 23462 |
| PageCount | 1 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_3978876 biomedcentral_primary_oai_biomedcentral_com_gm481 proquest_miscellaneous_1526735079 proquest_miscellaneous_1524402625 gale_infotracmisc_A534783487 gale_infotracacademiconefile_A534783487 gale_healthsolutions_A534783487 pubmed_primary_24001039 crossref_citationtrail_10_1186_gm481 crossref_primary_10_1186_gm481 springer_journals_10_1186_gm481 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2013-08-30 |
| PublicationDateYYYYMMDD | 2013-08-30 |
| PublicationDate_xml | – month: 08 year: 2013 text: 2013-08-30 day: 30 |
| PublicationDecade | 2010 |
| PublicationPlace | London |
| PublicationPlace_xml | – name: London – name: England |
| PublicationTitle | Genome medicine |
| PublicationTitleAbbrev | Genome Med |
| PublicationTitleAlternate | Genome Med |
| PublicationYear | 2013 |
| Publisher | BioMed Central BioMed Central Ltd |
| Publisher_xml | – name: BioMed Central – name: BioMed Central Ltd |
| References | F Molinari (478_CR29) 2011; 17 F Blum (478_CR1) 1893; 10 F Wang (478_CR8) 2007; 9 H Beltran (478_CR11) 2013; 63 M Srinivasan (478_CR3) 2002; 161 C Beadling (478_CR20) 2013; 15 M Simbolo (478_CR10) 2013; 8 K Tuononen (478_CR13) 2013; 52 AG Hadd (478_CR14) 2013; 15 E Cerami (478_CR18) 2012; 2 SR Shi (478_CR27) 2002; 50 H Do (478_CR25) 2012; 3 R Menon (478_CR12) 2012; 13 GP Consortium (478_CR21) 2010; 467 J Gao (478_CR19) 2013; 6 C Williams (478_CR4) 1999; 155 A Didelot (478_CR6) 2013; 59 478_CR17 T Nolan (478_CR16) 2006; 351 I Ferrer (478_CR5) 2007; 17 J Ben-Ezra (478_CR2) 1991; 39 W Laosinchai-Wolf (478_CR22) 2011; 64 AI Dragan (478_CR24) 2010; 99 H Do (478_CR26) 2013; 59 T Sedlackova (478_CR9) 2013; 15 Q Zhou (478_CR30) 2011; 29 EH van Beers (478_CR7) 2006; 94 M Akbari (478_CR15) 2005; 7 AS Gargis (478_CR23) 2012; 30 LA Diaz Jr (478_CR28) 2012; 486 23274167 - J Mol Diagn. 2013 Mar;15(2):171-6 23762227 - PLoS One. 2013 Jun 06;8(6):e62692 12466110 - Am J Pathol. 2002 Dec;161(6):1961-71 23321017 - J Mol Diagn. 2013 Mar;15(2):234-47 21044599 - Biophys J. 2010 Nov 3;99(9):3010-9 23362162 - Genes Chromosomes Cancer. 2013 May;52(5):503-11 1704393 - J Histochem Cytochem. 1991 Mar;39(3):351-4 23406353 - Biol Proced Online. 2013 Feb 13;15(1):5 21632860 - Clin Cancer Res. 2011 Jul 15;17 (14 ):4901-14 23403697 - Clin Chem. 2013 May;59(5):815-23 22722843 - Nature. 2012 Jun 28;486(7404):537-40 20981092 - Nature. 2010 Oct 28;467(7319):1061-73 23138292 - Nat Biotechnol. 2012 Nov;30(11):1033-6 17690213 - J Mol Diagn. 2007 Sep;9(4):441-51 22588877 - Cancer Discov. 2012 May;2(5):401-4 17465988 - Brain Pathol. 2007 Jul;17(3):297-303 21788562 - J Clin Oncol. 2011 Aug 20;29(24):3316-21 23550210 - Sci Signal. 2013 Apr 02;6(269):pl1 22643842 - Oncotarget. 2012 May;3(5):546-58 15681472 - J Mol Diagn. 2005 Feb;7(1):36-9 21030527 - J Clin Pathol. 2011 Jan;64(1):30-6 16333309 - Br J Cancer. 2006 Jan 30;94(2):333-7 23649127 - Clin Chem. 2013 Sep;59(9):1376-83 22942743 - Int J Mol Sci. 2012;13(7):8933-42 12133903 - J Histochem Cytochem. 2002 Aug;50(8):1005-11 16524557 - Anal Biochem. 2006 Apr 15;351(2):308-10 22981675 - Eur Urol. 2013 May;63(5):920-6 10550302 - Am J Pathol. 1999 Nov;155(5):1467-71 |
| References_xml | – volume: 52 start-page: 503 year: 2013 ident: 478_CR13 publication-title: Genes Chromosomes Cancer doi: 10.1002/gcc.22047 – volume: 9 start-page: 441 year: 2007 ident: 478_CR8 publication-title: J Mol Diagn doi: 10.2353/jmoldx.2007.070004 – ident: 478_CR17 – volume: 7 start-page: 36 year: 2005 ident: 478_CR15 publication-title: J Mol Diagn doi: 10.1016/S1525-1578(10)60006-2 – volume: 467 start-page: 1061 year: 2010 ident: 478_CR21 publication-title: Nature doi: 10.1038/nature09534 – volume: 39 start-page: 351 year: 1991 ident: 478_CR2 publication-title: J Histochem Cytochem doi: 10.1177/39.3.1704393 – volume: 3 start-page: 546 year: 2012 ident: 478_CR25 publication-title: Oncotarget doi: 10.18632/oncotarget.503 – volume: 351 start-page: 308 year: 2006 ident: 478_CR16 publication-title: Anal Biochem doi: 10.1016/j.ab.2006.01.051 – volume: 94 start-page: 333 year: 2006 ident: 478_CR7 publication-title: Br J Cancer doi: 10.1038/sj.bjc.6602889 – volume: 17 start-page: 297 year: 2007 ident: 478_CR5 publication-title: Brain Pathol doi: 10.1111/j.1750-3639.2007.00073.x – volume: 10 start-page: 314 year: 1893 ident: 478_CR1 publication-title: Z wiss Mikr – volume: 13 start-page: 8933 year: 2012 ident: 478_CR12 publication-title: Int J Mol Sci doi: 10.3390/ijms13078933 – volume: 486 start-page: 537 year: 2012 ident: 478_CR28 publication-title: Nature doi: 10.1038/nature11219 – volume: 99 start-page: 3010 year: 2010 ident: 478_CR24 publication-title: Biophys J doi: 10.1016/j.bpj.2010.09.012 – volume: 15 start-page: 171 year: 2013 ident: 478_CR20 publication-title: J Mol Diagn doi: 10.1016/j.jmoldx.2012.09.003 – volume: 15 start-page: 234 year: 2013 ident: 478_CR14 publication-title: J Mol Diagn doi: 10.1016/j.jmoldx.2012.11.006 – volume: 8 start-page: e62692 year: 2013 ident: 478_CR10 publication-title: PLoS One doi: 10.1371/journal.pone.0062692 – volume: 29 start-page: 3316 year: 2011 ident: 478_CR30 publication-title: J Clin Oncol doi: 10.1200/JCO.2010.33.3757 – volume: 161 start-page: 1961 year: 2002 ident: 478_CR3 publication-title: Am J Pathol doi: 10.1016/S0002-9440(10)64472-0 – volume: 59 start-page: 815 year: 2013 ident: 478_CR6 publication-title: Clin Chem doi: 10.1373/clinchem.2012.193409 – volume: 59 start-page: 1376 year: 2013 ident: 478_CR26 publication-title: Clin Chem doi: 10.1373/clinchem.2012.202390 – volume: 2 start-page: 401 year: 2012 ident: 478_CR18 publication-title: Cancer Discov doi: 10.1158/2159-8290.CD-12-0095 – volume: 63 start-page: 920 year: 2013 ident: 478_CR11 publication-title: Eur Urol doi: 10.1016/j.eururo.2012.08.053 – volume: 6 start-page: pl1 year: 2013 ident: 478_CR19 publication-title: Sci Signal doi: 10.1126/scisignal.2004088 – volume: 17 start-page: 4901 year: 2011 ident: 478_CR29 publication-title: Clin Cancer Res doi: 10.1158/1078-0432.CCR-10-3137 – volume: 155 start-page: 1467 year: 1999 ident: 478_CR4 publication-title: Am J Pathol doi: 10.1016/S0002-9440(10)65461-2 – volume: 15 start-page: 5 year: 2013 ident: 478_CR9 publication-title: Biol Proced Online doi: 10.1186/1480-9222-15-5 – volume: 64 start-page: 30 year: 2011 ident: 478_CR22 publication-title: J Clin Pathol doi: 10.1136/jcp.2010.081539 – volume: 30 start-page: 1033 year: 2012 ident: 478_CR23 publication-title: Nat Biotechnol doi: 10.1038/nbt.2403 – volume: 50 start-page: 1005 year: 2002 ident: 478_CR27 publication-title: J Histochem Cytochem doi: 10.1177/002215540205000802 – reference: 10550302 - Am J Pathol. 1999 Nov;155(5):1467-71 – reference: 23550210 - Sci Signal. 2013 Apr 02;6(269):pl1 – reference: 17690213 - J Mol Diagn. 2007 Sep;9(4):441-51 – reference: 16524557 - Anal Biochem. 2006 Apr 15;351(2):308-10 – reference: 17465988 - Brain Pathol. 2007 Jul;17(3):297-303 – reference: 21030527 - J Clin Pathol. 2011 Jan;64(1):30-6 – reference: 23403697 - Clin Chem. 2013 May;59(5):815-23 – reference: 23762227 - PLoS One. 2013 Jun 06;8(6):e62692 – reference: 1704393 - J Histochem Cytochem. 1991 Mar;39(3):351-4 – reference: 23406353 - Biol Proced Online. 2013 Feb 13;15(1):5 – reference: 23274167 - J Mol Diagn. 2013 Mar;15(2):171-6 – reference: 21788562 - J Clin Oncol. 2011 Aug 20;29(24):3316-21 – reference: 23362162 - Genes Chromosomes Cancer. 2013 May;52(5):503-11 – reference: 21632860 - Clin Cancer Res. 2011 Jul 15;17 (14 ):4901-14 – reference: 23649127 - Clin Chem. 2013 Sep;59(9):1376-83 – reference: 22942743 - Int J Mol Sci. 2012;13(7):8933-42 – reference: 23321017 - J Mol Diagn. 2013 Mar;15(2):234-47 – reference: 22981675 - Eur Urol. 2013 May;63(5):920-6 – reference: 21044599 - Biophys J. 2010 Nov 3;99(9):3010-9 – reference: 12466110 - Am J Pathol. 2002 Dec;161(6):1961-71 – reference: 22588877 - Cancer Discov. 2012 May;2(5):401-4 – reference: 22722843 - Nature. 2012 Jun 28;486(7404):537-40 – reference: 22643842 - Oncotarget. 2012 May;3(5):546-58 – reference: 16333309 - Br J Cancer. 2006 Jan 30;94(2):333-7 – reference: 12133903 - J Histochem Cytochem. 2002 Aug;50(8):1005-11 – reference: 23138292 - Nat Biotechnol. 2012 Nov;30(11):1033-6 – reference: 20981092 - Nature. 2010 Oct 28;467(7319):1061-73 – reference: 15681472 - J Mol Diagn. 2005 Feb;7(1):36-9 |
| SSID | ssj0064247 |
| Score | 2.3043025 |
| Snippet | The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared... |
| SourceID | pubmedcentral biomedcentral proquest gale pubmed crossref springer |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 77 |
| SubjectTerms | 4. Proteomics & metabolomics in medicine Bioinformatics Biomedical and Life Sciences Biomedicine Cancer Research DNA Formaldehyde Human Genetics Medicine/Public Health Metabolomics Method Systems Biology Tumors |
| Title | Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies |
| URI | https://link.springer.com/article/10.1186/gm481 https://www.ncbi.nlm.nih.gov/pubmed/24001039 https://www.proquest.com/docview/1524402625 https://www.proquest.com/docview/1526735079 http://dx.doi.org/10.1186/gm481 https://pubmed.ncbi.nlm.nih.gov/PMC3978876 |
| Volume | 5 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV1La9tAEF5CQkshhD5TpYm7hUAvFZW8Tx1NWjcUmlMDvi3ah1xDLKexBOmv6F_O7EoyWR3ai8DsYEkzOzvfaF4InVtRZlSDAnIzJSnYa5oWhlUpsSKzuSwBIvh65x9X_PKafl-wxR46G2phHsfvc8k_L9fUF1YfsJzwEIvlF8NBC8iZiqfoMCId1a3fROZmfOg-sjrjjMhRWDRYm_lzdNTDRDzr5PoC7bn6JXrSDY788wr9nYM56r7i4S9XM_y7Lbukn8BnvGxX1m1xaUzrO0Hg2ru3y9BgOqz3-dNwZ7xuu1g8tq4JWVk1XtU4IFkAoGm1unf2E_YNwqsKfru1dnBUWdy0680dBibcbsHXfo2u519_Xlym_WiFVHOaNanW3LpccA3-odGsrKSfL6i1Y9MqswXJORMVLwgptAMibXTu8ql1LqsAITlG3qD9elO7twiDvac90tCUCQCEopDOSGkAi1EmE5RHElG3XRsN5RtbxyugYypIMUHng9SU6XuV-5EZNyr4LJIPZJMd2fCvI4L3XuSqqyndKbOawTP7CSNSJOhjoPDqDHcwZV-VAO_mG2NFlKcRJaihiZY_DNtK-SWfu1a7TbtVgJAoeOngaP6ThgsC2LxI0HG3FXdv5LN8fcA-QSLapBEj45V69St0CgewCUaEAxuG7az6I2obM-rkvxTv0LNpmAQiU5Kdov3mrnVngMcaPQlaOQlfM-D6bZE_ANDPO9g |
| linkProvider | Springer Nature |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV1Lb9NAEF6hVDwkhHgVDKVdpEpcsGrH69310SpEIbS50Eq9rbwPp5Eap9S2BL-Cv8zs2o66PsAxmlEcz-zMfJOdB0LHmhURkWCAVE2TEOI1CTOVlmGiWaRjXgBEsP3O50s6vySLq_SqH5JUD9Xuw5Wk89TOrDk9WW2IbbHe4wBAyATt5fnix2JwuoCiCXuEnnrMox72Gy_0jB3wvQg0ro4cXZG6yDN7jp71kBHnnY5foAemeokedkskf79Cf2YQmrp_9PCXZY5_tkVXAORkjlftWpsaF0q1dioErmyqu3LDph29r6WGJ-NN293LY20aV6FV4XWFHaoFgYXl-pfRn7EdFl6W8NlspAG3pXHTbrZ3GIRwW0Pe_Rpdzr5enM7Dfs1CKCmJmlBKqk3MqIRcUcm0KLndNSilSadlpLMkpikraZYkmTTAJJWMTTzVxkQloCWTJvtoUm0r8xZhiP2kRx2SpAzAIcu4UZwrwGUk5QGKPY2I226khrBDrn0KqF44LQboeNCaUP3ccrs-40a4_IXTge1wxzZ864jhyKpcdP2lO8MWOfxmu22EswB9chzWtOEJqug7FODd7JAsj_PA4wSTVB7543CshCXZOrbKbNtaAFoikLFD0vlPHsoSwOlZgN50R3H3Rrbi117eB4h5h9QTpE-p1tduajgATwgoFMQwHGfRu6vaF9S7_3Icocfzi_MzcfZt-f09ejJ1G0J4mEQHaNLcteYD4LRGHvY2-hcy9kJQ |
| linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV1ba9swFBajZWUwxu7z2rUaFPYyUzuWJfkxtAvdLexhhb4J6-I00DhZbUP7K_qXeyTZYfLD9hjOIY7PRec70bkgdKxZmRAJDkjVJIshXpO4UHkVZ5olOuUlQATb7_xzTs8vyLfL_LLv426GavfhStL3NNgpTXV7stGVd3FOTxYrYtutd4mNdvaGlp4Oxy_gacL20NOAddTNfh0EofFR_FcsGtdJji5LXQyaPUfPevCIp17bL9AjU79Ej_06ybtX6H4GQcr_t4fP5lP8pyt9KZCTPl50S20aXCrV2fkQuLZJ78KNnXb0vqoanoxXnb-hx9q0rlarxssaO3wLoour5a3Rn7EdG15V8NmspIEDTOO2W61vMAhh00AG_hpdzL78Pj2P-4ULsaQkaWMpqTYpoxKyRiXzsuJ266CUJp9UiS6ylOasokWWFdIAk1QyNelEG5NUgJtMnr1BO_W6Nu8QBhRAevwhSc4AJrKCG8W5AoRGch6hNNCI2PjhGsKOuw4pYATCaTFCx4PWhOonmNtFGtfCZTKcDmyHW7bhW0cMR1blwneabl1cTOE3270jnEXok-OwTg5PUGXfqwDvZsdlBZwHASc4pwrIHwezEpZkK9pqs-4aAbiJQO4O6ec_eSjLALEXEXrrTXH7Rrb2117jR4gFRhoIMqTUyys3PxwgKIQWCmIYzFn0B1cTCur9fzmO0N6vs5n48XX-fR89mbhVITzOkgO009505gMAtlYeOgd9AOlXRSY |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Functional+DNA+quantification+guides+accurate+next-generation+sequencing+mutation+detection+in+formalin-fixed%2C+paraffin-embedded+tumor+biopsies&rft.jtitle=Genome+medicine&rft.au=Sah%2C+Sachin&rft.au=Chen%2C+Liangjing&rft.au=Houghton%2C+Jeffrey&rft.au=Kemppainen%2C+Jon&rft.date=2013-08-30&rft.pub=BioMed+Central&rft.eissn=1756-994X&rft.volume=5&rft.issue=8&rft_id=info:doi/10.1186%2Fgm481&rft.externalDocID=10_1186_gm481 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1756-994X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1756-994X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1756-994X&client=summon |