Sequencing from Tissues ~ Techniques / Technology
~ Genetics of Breast & Ovarian Cancer

Sequencing DNA from other than standard (i.e., blood, cheek swab) sources: tumor, FFPE (formalin-fixed paraffin-embedded tumor tissue), pap smear, etc.

List was last updated on Jul 15, 2020 @ 1:25 am.


    • Feasibility of tumor testing for BRCA status in high-grade serous ovarian cancer using fresh-frozen tissue based approach.
    • Marchetti C, Minucci A, D'Indinosante M, Ergasti R, Arcieri M, Capoluongo ED, Pietragalla A, Caricato C, Scambia G, Fagotti A.
    • Gynecol Oncol. 2020 Jun 15:S0090-8258(20)32294-0. doi: 10.1016/j.ygyno.2020.06.479. Epub ahead of print.
    • High resolution melting profiles (HRMPs) obtained by magnetic induction cycler (MIC) have been used to monitor the BRCA2 status highlighted by next generation tumor sequencing (NGTS): a combined approach in a diagnostic environment.
    • Mazzuccato G, De Bonis M, Carboni V, Marchetti C, Urbani A, Scambia G, Capoluongo E, Fagotti A, Minucci A.
    • Mol Biol Rep. 2020 May 28. doi: 10.1007/s11033-020-05504-5. Epub ahead of print.
    • Q&A: ACMG Work Group Hoping to Spark Discussion on Reporting Germline Findings From Tumor Testing.
    • Ray T.
    • Precision Oncology News. 2020 May 21.
    • News

    Related:

    Guidelines:

    Points to consider for reporting of germline variation in patients undergoing tumor testing: a statement of the American College of Medical Genetics and Genomics (ACMG).

    • Points to consider for reporting of germline variation in patients undergoing tumor testing: a statement of the American College of Medical Genetics and Genomics (ACMG).
    • Li MM, Chao E, Esplin ED, Miller DT, Nathanson KL, Plon SE, Scheuner MT, Stewart DR; ACMG Professional Practice and Guidelines Committee.
    • Genet Med. 2020 Apr 23. doi: 10.1038/s41436-020-0783-8. Epub ahead of print.

    Related:

    News, Interview: Q&A: ACMG Work Group Hoping to Spark Discussion on Reporting Germline Findings From Tumor Testing. (Precision Oncology News)

    • Routine plasma-based genotyping to comprehensively detect germline, somatic, and reversion BRCA mutations among patients with advanced solid tumors.
    • Vidula N, Rich TA, Sartor O, Yen J, Hardin A, Nance T, Lilly MB, Nezami MA, Patel SP, Carneiro BA, Fan A, Brufksy AM, Parker BA, Bridges BB, Agarwal N, Maughan BL, Raymond VM, Fairclough SR, Lanman RB, Bardia A, Cristofanilli M.
    • Clin Cancer Res. 2020 Feb 7. pii: clincanres.2933.2019. doi: 10.1158/1078-0432.CCR-19-2933. [Epub ahead of print]
    • Spliceogenic analysis of BRCA1 c.439T>C (rs794727800) variant by High Resolution Melting Analysis.
    • Minucci A, Mazzuccato G, D'Indinosante M, Di Nardo L, Concolino P, De Bonis M, Urbani A, Scambia G, Fagotti A, Capoluongo E.
    • Mol Biol Rep. 2019 Dec 12. doi: 10.1007/s11033-019-05199-3. [Epub ahead of print]
    • Tumor BRCA Test for Patients with Epithelial Ovarian Cancer: The Role of Molecular Pathology in the Era of PARP Inhibitor Therapy.
    • Fumagalli C, Tomao F, Betella I, Rappa A, Calvello M, Bonanni B, Bernard L, Peccatori F, Colombo N, Viale G, Barberis M, Guerini-Rocco E.
    • Cancers (Basel). 2019 Oct 24;11(11). pii: E1641. doi: 10.3390/cancers11111641.
    • Next-generation sequencing-based BRCA testing on cytological specimens from ovarian cancer ascites reveals high concordance with tumour tissue analysis.
    • Fumagalli C, Rappa A, Casadio C, Betella I, Colombo N, Barberis M, Guerini-Rocco E.
    • J Clin Pathol. 2019 Sep 19. pii: jclinpath-2019-206127. doi: 10.1136/jclinpath-2019-206127. [Epub ahead of print]
    • Using next-generation sequencing (NGS) platform to diagnose pathogenic germline BRCA1/2 mutations from archival tumor specimens.
    • Ong PY, Poon SL, Tan KT, Putti TC, Ow SGW, Chen SJ, Chen CH, Lee SC.
    • Gynecol Oncol. 2019 Aug 31. pii: S0090-8258(19)31479-9. doi: 10.1016/j.ygyno.2019.08.027. [Epub ahead of print]
    • BRCA1/2 somatic mutation detection in formalin-fixed paraffin embedded tissue by next-generation sequencing in Korean ovarian cancer patients.
    • Lee A, Kang J, Lee H, Lee YS, Choi YJ, Lee KH, Nistala GJ, Scafe CR, Choi J, Yoo J, Han M D E, Kim Y, Kim M.
    • Pathol Res Pract. 2019 Aug 16:152595. doi: 10.1016/j.prp.2019.152595. [Epub ahead of print]
    • An optimized BRCA1/2 next-generation sequencing for different clinical sample types.
    • Kim Y, Cho CH, Ha JS, Kim DH, Kwon SY, Oh SC, Lee KA.
    • J Gynecol Oncol. 2019 Aug 6. doi: 10.3802/jgo.2020.31.e9. [Epub ahead of print]
    • Targeted capture-based NGS is superior to multiplex PCR-based NGS for hereditary BRCA1 and BRCA2 gene analysis in FFPE tumor samples.
    • Zakrzewski F, Gieldon L, Rump A, Seifert M, Grützmann K, Krüger A, Loos S, Zeugner S, Hackmann K, Porrmann J, Wagner J, Kast K, Wimberger P, Baretton G, Schröck E, Aust D, Klink B.
    • BMC Cancer. 2019 Apr 27;19(1):396. doi: 10.1186/s12885-019-5584-6.
    • Cytology material is equivalent to tumor tissue in determining mutations of BRCA 1/2 genes in patients with tubo-ovarian high grade serous carcinoma.
    • Gornjec A, Novakovic S, Stegel V, Hocevar M, Pohar Marinsek Z, Gazic B, Krajc M, Skof E.
    • BMC Cancer. 2019 Apr 2;19(1):296. doi: 10.1186/s12885-019-5535-2.
    • Peritoneal washing is an adequate source for somatic BRCA1/2 mutation testing in ovarian malignancies.
    • Barquín M, Maximiano C, Pérez-Barrios C, Sanchez-Herrero E, Soriano M, Colmena M, García-Espantaleón M, Tejerina González E, Gutierrez L, Sánchez Ruiz AC, Torrente M, Provencio M, Romero A.
    • Pathol Res Pract. 2019 Feb;215(2):392-394. doi: 10.1016/j.prp.2018.10.028. Epub 2018 Oct 28.
    • BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes.
    • Kechin A, Khrapov E, Boyarskikh U, Kel A, Filipenko M.
    • Comput Biol Chem. 2018 Dec;77:297-306. doi: 10.1016/j.compbiolchem.2018.10.012. Epub 2018 Oct 23.
    • Evaluating Clinical Genome Sequence Analysis by Watson for Genomics.
    • Itahashi K, Kondo S, Kubo T, Fujiwara Y, Kato M, Ichikawa H, Koyama T, Tokumasu R, Xu J, Huettner CS, Michelini VV, Parida L, Kohno T, Yamamoto N.
    • Front Med (Lausanne). 2018 Nov 9;5:305. doi: 10.3389/fmed.2018.00305. eCollection 2018.
    • Validation and Implementation of BRCA1/2 Variant Screening in Ovarian Tumor Tissue.
    • de Jonge MM, Ruano D, van Eijk R, van der Stoep N, Nielsen M, Wijnen JT, Ter Haar NT, Baalbergen A, Bos MEMM, Kagie MJ, Vreeswijk MPG, Gaarenstroom KN, Kroep JR, Smit VTHBM, Bosse T, van Wezel T, van Asperen CJ.
    • J Mol Diagn. 2018 Sep;20(5):600-611. doi: 10.1016/j.jmoldx.2018.05.005. Epub 2018 Jun 21.
    • FFPE breast tumour blocks provide reliable sources of both germline and malignant DNA for investigation of genetic determinants of individual tumour responses to treatment.
    • Wilkins A, Chauhan R, Rust A, Pearson A, Daley F, Manodoro F, Fenwick K, Bliss J, Yarnold J, Somaiah N.
    • Breast Cancer Res Treat. 2018 Aug;170(3):573-581. doi: 10.1007/s10549-018-4798-7. Epub 2018 Feb 22.
    • Sputum Detection of Predisposing Genetic Mutations in Women with Pulmonary Nontuberculous Mycobacterial Disease.
    • Philley JV, Hertweck KL, Kannan A, Brown-Elliott BA, Wallace RJ Jr, Kurdowska A, Ndetan H, Singh KP, Miller EJ, Griffith DE, Dasgupta S.
    • Sci Rep. 2018 Jul 27;8(1):11336. doi: 10.1038/s41598-018-29471-x.
    • High-resolution melting analysis coupled with next-generation sequencing as a simple tool for the identification of a novel somatic BRCA2 variant: a case report.
    • Costella A, De Leo R, Guarino D, D'Indinosante M, Concolino P, Mazzuccato G, Urbani A, Scambia G, Capoluongo E, Fagotti A, Minucci A.
    • Hum Genome Var. 2018 Jun 8;5:10. doi: 10.1038/s41439-018-0006-x. eCollection 2018.
    • Somatic BRCA1 mutations in clinically sporadic breast cancer with medullary histological features.
    • Rechsteiner M, Dedes K, Fink D, Pestalozzi B, Sobottka B, Moch H, Wild P, Varga Z.
    • J Cancer Res Clin Oncol. 2018 May;144(5):865-874. doi: 10.1007/s00432-018-2609-5. Epub 2018 Feb 17.
    • An evaluation of the challenges to developing tumour BRCA1 and BRCA2 testing methodologies for clinical practice.
    • Ellison G, Ahdesmäki M, Luke S, Waring PM, Wallace A, Wright R, Röthlisberger B, Ludin K, Merkelbach-Bruse S, Heydt C, Ligtenberg MJL, Mensenkamp AR, Castro DG, Jones T, Vivancos A, Kondrashova O, Pauwels P, Weyn C, Hahnen E, Hauke J, Soong R, Lai Z, Dougherty B, Carr TH, Johnson J, Mills J, Barrett JC.
    • Hum Mutat. 2018 Mar;39(3):394-405. doi: 10.1002/humu.23375. Epub 2017 Dec 28.
    • Inference of Germline Mutational Status and Evaluation of Loss of Heterozygosity in High-Depth, Tumor-Only Sequencing Data.
    • Khiabanian H, Hirshfield KM, Goldfinger M, Bird S, Stein M, Aisner J, Toppmeyer D, Wong S, Chan N, Dhar K, Gheeya J, Vig H, Hadigol M, Pavlick D, Ansari S, Ali S, Xia B, Rodriguez-Rodriguez L, Ganesan S.
    • JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00148. Epub 2018 Jan 19.
    • Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas.
    • Madubata CJ, Roshan-Ghias A, Chu T, Resnick S, Zhao J, Arnes L, Wang J, Rabadan R.
    • NPJ Genom Med. 2017 Oct 3;2:29. doi: 10.1038/s41525-017-0032-5. eCollection 2017.
    • [A bioinformatic pipeline for NGS data analysis and mutation calling in human solid tumors].
    • Tsukanov KY, Krasnenko AY, Plakhina DA, Korostin DO, Churov AV, Druzhilovskaya OS, Rebrikov DV, Ilinsky VV.
    • Biomed Khim. 2017 Oct;63(5):413-417. doi: 10.18097/PBMC20176305413.
    • [Article in Russian]
    • Breast Cancer Genetic Testing Among African Patients With Breast Cancer: Deoxyribonucleic Acid Extraction From Tumor Tissue and International Multidisciplinary Partnerships.
    • Amankwaa-Frempong E, Yeboah FA, Nguah SB, Newman LA.
    • JAMA Surg. 2017 Aug 1;152(8):800-801. doi: 10.1001/jamasurg.2017.1090.
    • Next-Generation Sequencing-based genomic profiling of brain metastases of primary ovarian cancer identifies high number of BRCA-mutations.
    • Balendran S, Liebmann-Reindl S, Berghoff AS, Reischer T, Popitsch N, Geier CB, Kenner L, Birner P, Streubel B, Preusser M.
    • J Neurooncol. 2017 Jul;133(3):469-476. doi: 10.1007/s11060-017-2459-z. Epub 2017 May 11.
    • Genetic testing and counseling of a recipient after bone marrow transplant from a sibling harboring a germline BRCA1 pathogenic mutation.
    • Škerl P, Krajc M, Blatnik A, Novaković S.
    • Oncol Rep. 2017 Jul;38(1):279-282. doi: 10.3892/or.2017.5703. Epub 2017 Jun 6.
    • Case report
    • Guidance Statement On BRCA1/2 Tumor Testing in Ovarian Cancer Patients.
    • Capoluongo E, Ellison G, López-Guerrero JA, Penault-Llorca F, Ligtenberg MJL, Banerjee S, Singer C, Friedman E, Markiefka B, Schirmacher P, Büttner R, van Asperen CJ, Ray-Coquard I, Endris V, Kamel-Reid S, Percival N, Bryce J, Röthlisberger B, Soong R, de Castro DG.
    • Semin Oncol. 2017 Jun;44(3):187-197. doi: 10.1053/j.seminoncol.2017.08.004. Epub 2017 Sep 15.
    • High Resolution Melting Analysis is Very Useful to Identify Breast Cancer Type 1 Susceptibility Protein (BRCA1) c.4964_4982del19 (rs80359876) Founder Calabrian Pathogenic Variant on Peripheral Blood and Buccal Swab DNA.
    • Minucci A, De Bonis M, De Paolis E, Gentile L, Santonocito C, Concolino P, Mignone F, Capoluongo E.
    • Mol Diagn Ther. 2017 Apr;21(2):217-223. doi: 10.1007/s40291-017-0262-3.
    • Revertant mosaicism for family mutations is not observed in BRCA1/2 phenocopies.
    • Azzollini J, Pesenti C, Ferrari L, Fontana L, Calvello M, Peissel B, Portera G, Tabano S, Carcangiu ML, Riva P, Miozzo M, Manoukian S.
    • PLoS One. 2017 Feb 15;12(2):e0171663. doi: 10.1371/journal.pone.0171663. eCollection 2017.
    • Novel BRCA1 and BRCA2 Tumour Test as Basis for Treatment Decisions and Referral for Genetic Counselling of Patients with Ovarian Carcinomas.
    • Weren RD, Mensenkamp AR, Simons M, Eijkelenboom A, Sie AS, Ouchene H, van Asseldonk M, Gomez-Garcia EB, Blok MJ, de Hullu JA, Nelen MR, Hoischen A, Bulten J, Tops BB, Hoogerbrugge N, Ligtenberg EM.
    • Hum Mutat. 2017 Feb;38(2):226-235. doi: 10.1002/humu.23137. Epub 2016 Nov 9.
    • Molecular analysis of BRCA1 and BRCA2 genes by next generation sequencing and ultrastructural aspects of breast tumor tissue.
    • Mihalcea CE, Moroşanu AM, Murăraşu D, Puiu L, Cinca SA, Voinea SC, Mirancea N.
    • Rom J Morphol Embryol. 2017;58(2):445-455.
    • Performance of multiplicom's BRCA MASTR Dx kit on the detection of BRCA1 and BRCA2 mutations in fresh frozen ovarian and breast tumor samples.
    • Badoer C, Garrec C, Goossens D, Ellison G, Mills J, Dzial M, El Housni H, Berwouts S, Concolino P, Guibert-Le Guevellou V, Delnatte C, Del Favero J, Capoluongo E, Bézieau S.
    • Oncotarget. 2016 Dec 6;7(49):81357-81366. doi: 10.18632/oncotarget.12877
    • Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples.
    • Enyedi MZ, Jaksa G, Pintér L, Sükösd F, Gyuris Z, Hajdu A, Határvölgyi E, Priskin K, Haracska L.
    • Oncotarget. 2016 Sep 20;7(38):61845-61859. doi: 10.18632/oncotarget.11259.
    • [Testing of mutations in BRCA1 and BRCA2 genes in tumor tissues - possibilities and limitations].
    • Vošmiková H, Ryška A, Sieglová K, Laco J.
    • Cesk Patol. 2016 Fall;52(4):210-214.
    • New challenges for BRCA testing: a view from the diagnostic laboratory.
    • Wallace AJ.
    • Eur J Hum Genet. 2016 Sep;24 Suppl 1:S10-8. doi: 10.1038/ejhg.2016.94.
    • Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling.
    • Petersen AH, Aagaard MM, Nielsen HR, Steffensen KD, Waldstrøm M, Bojesen A.
    • Eur J Hum Genet. 2016 Aug;24(8):1104-11. doi: 10.1038/ejhg.2015.268. Epub 2016 Jan 6.
    • In situ hybridization chain reaction mediated ultrasensitive enzyme-free and conjugation-free electrochemcial genosensor for BRCA-1 gene in complex matrices.
    • Yang H, Gao Y, Wang S, Qin Y, Xu L, Jin D, Yang F, Zhang GJ.
    • Biosens Bioelectron. 2016 Jun 15;80:450-5. doi: 10.1016/j.bios.2016.02.011. Epub 2016 Feb 6.
    • NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial.
    • Endris V, Stenzinger A, Pfarr N, Penzel R, Möbs M, Lenze D, Darb-Esfahani S, Hummel M, Sabine-Merkelbach-Bruse, Jung A, Lehmann U, Kreipe H, Kirchner T, Büttner R, Jochum W, Höfler G, Dietel M, Weichert W, Schirmacher P.
    • Virchows Arch. 2016 Jun;468(6):697-705. doi: 10.1007/s00428-016-1919-8. Epub 2016 Mar 22.
    • Sanger Sequencing for BRCA1 c.68_69del, BRCA1 c.5266dup and BRCA2 c.5946del Mutation Screen on Pap Smear Cytology Samples.
    • Lee SH, Zhou S, Zhou T, Hong G.
    • Int J Mol Sci. 2016 Feb 8;17(2). pii: E229. doi: 10.3390/ijms17020229.
    • BRCA somatic and germline mutation detection in paraffin embedded ovarian cancers by next-generation sequencing.
    • Mafficini A, Simbolo M, Parisi A, Rusev B, Luchini C, Cataldo I, Piazzola E, Sperandio N, Turri G, Franchi M, Tortora G, Bovo C, Lawlor RT, Scarpa A.
    • Oncotarget. 2016 Jan 12;7(2):1076-83. doi: 10.18632/oncotarget.6834.
    • Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.
    • Halabi NM, Martinez A, Al-Farsi H, Mery E, Puydenus L, Pujol P, Khalak HG, McLurcan C, Ferron G, Querleu D, Al-Azwani I, Al-Dous E, Mohamoud YA, Malek JA, Rafii A.
    • PLoS Genet. 2016 Jan 6;12(1):e1005755. doi: 10.1371/journal.pgen.1005755. eCollection 2016.
    • Performance Characterization and Validation of Saliva as an Alternative Specimen Source for Detecting Hereditary Breast Cancer Mutations by Next Generation Sequencing.
    • Meghnani V, Mohammed N, Giauque C, Nahire R, David T.
    • Int J Genomics. 2016;2016:2059041. Epub 2016 Oct 13.
    • Development of a Comprehensive NGS Workflow for the Analysis of Tumor BRCA1 and BRCA2 Mutations and Large Rearrangements.
    • Dong Z, Dong H, Zhong X, Peng Z, Zhu X, Sun Y, Chen Y, Liu C, Yin X, Zhu G, Zheng H, Gu Y.
    • J Genet Genome Res 2(2):019. 2015 Sep 28.
    • A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencing.
    • Ellison G, Huang S, Carr H, Wallace A, Ahdesmaki M, Bhaskar S, Mills J.
    • BMC Clin Pathol. 2015 Mar 24;15:5. doi: 10.1186/s12907-015-0004-6. eCollection 2015.
    • One Case of a BRCA1 Germ Line Mutation Ovarian Carcinoma Patient Based on Abnormal Immunohistochemistry Finding.
    • Kim HJ, Park JM, Lee HW, Lee EH, Kim MK.
    • Korean J Pathol. 2014 Oct;48(5):379-81. doi: 10.4132/KoreanJPathol.2014.48.5.379. Epub 2014 Oct 27.
    • Establishing the origin of metastatic deposits in the setting of multiple primary malignancies: the role of massively parallel sequencing.
    • De Mattos-Arruda L, Bidard FC, Won HH, Cortes J, Ng CK, Peg V, Nuciforo P, Jungbluth AA, Weigelt B, Berger MF, Seoane J, Reis-Filho JS.
    • Mol Oncol. 2014 Feb;8(1):150-8. doi: 10.1016/j.molonc.2013.10.006. Epub 2013 Oct 31.
    • Evaluation of ultra-deep targeted sequencing for personalized breast cancer care.
    • Harismendy O, Schwab RB, Alakus H, Yost SE, Matsui H, Hasteh F, Wallace AM, Park HL, Madlensky L, Parker B, Carpenter PM, Jepsen K, Anton-Culver H, Frazer KA.
    • Breast Cancer Res. 2013 Dec 10;15(6):R115. doi: 10.1186/bcr3584.
    • Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2.
    • Nguyen-Dumont T, Teo ZL, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Sabbaghian N, Tischkowitz M, Foulkes WD; Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer (kConFab), Giles GG, Hopper JL; Australian Breast Cancer Family Registry, Southey MC, Park DJ.
    • BMC Med Genomics. 2013 Nov 8;6:48. doi: 10.1186/1755-8794-6-48.