Next Generation Sequencing ~ Techniques / Technology
~ Genetics of Breast & Ovarian Cancer

Technical aspects of next generation sequencing and panel testing (For applications and clinical result reports, see Mutation Spectrum from Gene Panels, mostly.)

List was last updated on Oct 5, 2019 @ 4:19 pm.


    • Adding RNA-Seq, Ambry Genetics Expects to Reduce VUS Results in Hereditary Cancer Tests.
    • [No author given]
    • GenomeWeb. 2019 Oct 4.
    • News
    • 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]
    • Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context.
    • Ivanov M, Ivanov M, Kasianov A, Rozhavskaya E, Musienko S, Baranova A, Mileyko V.
    • Nucleic Acids Res. 2019 Sep 12. pii: gkz775. doi: 10.1093/nar/gkz775. [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]
    • Detection of BRCA 1/2 large genomic rearrangements in breast and ovarian cancer patients: an overview on the current methods.
    • Concolino P, Capoluongo E.
    • Expert Rev Mol Diagn. 2019 Aug 20. doi: 10.1080/14737159.2019.1657011. [Epub ahead of print]
    • Review
    • A research-based gene panel to investigate breast, ovarian and prostate cancer genetic risk.
    • Bishop MR, Huskey ALW, Hetzel J, Merner ND.
    • PLoS One. 2019 Aug 15;14(8):e0220929. doi: 10.1371/journal.pone.0220929. eCollection 2019.
    • BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.
    • Uzbas F, Opperer F, Sönmezer C, Shaposhnikov D, Sass S, Krendl C, Angerer P, Theis FJ, Mueller NS, Drukker M.
    • Genome Biol. 2019 Aug 6;20(1):155. doi: 10.1186/s13059-019-1748-6.
    • Comprehensive mutation detection of BRCA1/2 genes reveals large genomic rearrangements contribute to hereditary breast and ovarian cancer in Chinese women.
    • Cao WM, Zheng YB, Gao Y, Ding XW, Sun Y, Huang Y, Lou CJ, Pan ZW, Peng G, Wang XJ.
    • BMC Cancer. 2019 Jun 7;19(1):551. doi: 10.1186/s12885-019-5765-3.
    • Significant allelic dropout phenomenon of Oncomine BRCA Research Assay on Ion Torrent S5.
    • Jeong TD, Cho SY, Kim MW, Huh J.
    • Clin Chem Lab Med. 2019 May 27;57(6):e124-e127. doi: 10.1515/cclm-2018-0674.
    • Letter
    • Recommendations for the implementation of BRCA testing in ovarian cancer patients and their relatives.
    • Gori S, Barberis M, Bella MA, Buttitta F, Capoluongo E, Carrera P, Colombo N, Cortesi L, Genuardi M, Gion M, Guarneri V, Incorvaia L, La Verde N, Lorusso D, Marchetti A, Marchetti P, Normanno N, Pasini B, Pensabene M, Pignata S, Radice P, Ricevuto E, Sapino A, Tagliaferri P, Tassone P, Trevisiol C, Truini M, Varesco L, Russo A; AIOM-SIGU-SIBIOC-SIAPEC-IAP Working Group.
    • Crit Rev Oncol Hematol. 2019 May 25;140:67-72. doi: 10.1016/j.critrevonc.2019.05.012. [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.
    • A reference system for BRCA mutation detection based on next-generation sequencing in the Chinese population.
    • Qu S, Chen Q, Yi Y, Shao K, Zhang W, Wang Y, Bai J, Li X, Liu Z, Wang X, Jing R, Guan Y, Yi X, Yan M, Cao B, Chen F, Zhu S, Yang X, Wu Y, Huang J.
    • J Mol Diagn. 2019 Apr 23. pii: S1525-1578(18)30284-8. doi: 10.1016/j.jmoldx.2019.03.003. [Epub ahead of print]
    • Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer.
    • Nicolussi A, Belardinilli F, Mahdavian Y, Colicchia V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Valentini V, Ottini L, Giannini G, Capalbo C, Coppa A.
    • PeerJ. 2019 Apr 22;7:e6661. doi: 10.7717/peerj.6661. eCollection 2019.
    • Ambry and My Gene Counsel Team Up on Tests to Confirm DTC Results, Counseling.
    • [No author given.]
    • Clinical OMICs. 2019 Mar 19.

    Original research:

    False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care.

    • DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes.
    • Richardson ME, Chong H, Mu W, Conner BR, Hsuan V, Willett S, Lam S, Tsai P, Pesaran T, Chamberlin AC, Park MS, Gray P, Karam R, Elliott A.
    • Genet Med. 2019 Mar;21(3):683-693. doi: 10.1038/s41436-018-0092-7. Epub 2018 Jul 28.
    • A multi-gene panel beyond BRCA1/BRCA2 to identify new breast cancer-predisposing mutations by a picodroplet PCR followed by a next-generation sequencing strategy: a pilot study.
    • Nunziato M, Esposito MV, Starnone F, Diroma MA, Calabrese A, Del Monaco V, Buono P, Frasci G, Botti G, D'Aiuto M, Salvatore F, D'Argenio V.
    • Anal Chim Acta. 2019 Jan 10;1046:154-162. doi: 10.1016/j.aca.2018.09.032. Epub 2018 Sep 18.
    • A tandem duplication of BRCA1 exons 1-19 through DHX8 exon 2 in four families with hereditary breast and ovarian cancer syndrome.
    • Du C, Mark D, Wappenschmidt B, Böckmann B, Pabst B, Chan S, Cao H, Morlot S, Scholz C, Auber B, Rhiem K, Schmutzler R, Illig T, Schlegelberger B, Steinemann D.
    • Breast Cancer Res Treat. 2018 Dec;172(3):561-569. doi: 10.1007/s10549-018-4957-x. Epub 2018 Sep 6.
    • Case report
    • 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.
    • Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection.
    • Vendrell JA, Vilquin P, Larrieux M, Van Goethem C, Solassol J.
    • J Mol Diagn. 2018 Nov;20(6):754-764. doi: 10.1016/j.jmoldx.2018.06.003. Epub 2018 Jul 25.
    • Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline.
    • Germani A, Libi F, Maggi S, Stanzani G, Lombardi A, Pellegrini P, Mattei M, De Marchis L, Amanti C, Pizzuti A, Torrisi MR, Piane M.
    • Oncotarget. 2018 Sep 14;9(72):33648-33655. doi: 10.18632/oncotarget.26000. eCollection 2018 Sep 14.
    • 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.
    • 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.
    • Evaluation of some direct-to-consumer genetic testing reveals inaccuracies and misinterpretations.
    • [No author given]
    • FORCE. XRAYS. 2018 Jun 28.

    False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care.

    • The ICR639 CPG NGS validation series: A resource to assess analytical sensitivity of cancer predisposition gene testing.
    • Mahamdallie S, Ruark E, Holt E, Poyastro-Pearson E, Renwick A, Strydom A, Seal S, Rahman N.
    • Wellcome Open Res. 2018 Jun 12;3:68. doi: 10.12688/wellcomeopenres.14594.1. eCollection 2018.
    • 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.
    • A comprehensive BRCA1/2 NGS pipeline for an immediate Copy Number Variation (CNV) detection in breast and ovarian cancer molecular diagnosis.
    • Concolino P, Rizza R, Mignone F, Costella A, Guarino D, Carboni I, Capoluongo E, Santonocito C, Urbani A, Minucci A.
    • Clin Chim Acta. 2018 May;480:173-179. doi: 10.1016/j.cca.2018.02.012. Epub 2018 Feb 16.
    • Main implications related to the switch to BRCA1/2 tumor testing in ovarian cancer patients: a proposal of a consensus.
    • Capoluongo E, Scambia G, Nabholtz JM.
    • Oncotarget. 2018 Apr 13;9(28):19463-19468. doi: 10.18632/oncotarget.24728. eCollection 2018 Apr 13.
    • A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis.
    • Scaglione GL, Concolino P, De Bonis M, De Paolis E, Minucci A, Ferrandina G, Scambia G, Capoluongo E.
    • Int J Mol Sci. 2018 Mar 23;19(4). pii: E961. doi: 10.3390/ijms19040961.
    • False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care.
    • Tandy-Connor S, Guiltinan J, Krempely K, LaDuca H, Reineke P, Gutierrez S, Gray P, Tippin Davis B.
    • Genet Med. 2018 Mar 22. doi: 10.1038/gim.2018.38. [Epub ahead of print]

    Commentary:

    Attention: Direct-To-Consumer patrons: Proceed with caution.

    Research news: Evaluation of some direct-to-consumer genetic testing reveals inaccuracies and misinterpretations (FORCE. XRAYS.)

    Press: Wrangle Over DTC Results—Ambry Study Highlights 40% False Positives, 23andMe Defends Tests, and Experts Weigh In. (Clinical OMICs)

    Press: Ambry and My Gene Counsel Team Up on Tests to Confirm DTC Results, Counseling. (Clinical OMICs)

    • Use of deep whole genome sequencing data to identify structure risk variants in breast cancer susceptibility genes.
    • Guo X, Shi J, Cai Q, Shu XO, He J, Wen W, Allen J, Pharoah P, Dunning A, Hunter DJ, Kraft P, Easton DF, Zheng W, Long J.
    • Hum Mol Genet. 2018 Mar 1;27(5):853-859. doi: 10.1093/hmg/ddy005.
    • Homozygous loss of function BRCA1 variant causing a fanconi-anemia-like phenotype, a clinical report and review of previous patients.
    • Freire BL, Homma TK, Funari MFA, Lerario AM, de Medeiros Leal A, Rodrigues Pereira Velloso ED, Malaquias AC, Jorge AAL.
    • Eur J Med Genet. 2018 Mar;61(3):130-133. doi: 10.1016/j.ejmg.2017.11.003. Epub 2017 Nov 10.
    • Case report, Review
    • Identification of a novel truncating mutation in PALB2 gene by a multigene sequencing panel for mutational screening of breast cancer risk-associated and related genes.
    • Guacci A, Cordella A, Rocco T, Giurato G, Nassa G, Rizzo F, Carlomagno C, Pepe S, Tarallo R, Weisz A.
    • J Clin Lab Anal. 2018 Feb 27. doi: 10.1002/jcla.22418. [Epub ahead of print]
    • Clinical testing of BRCA1 and BRCA2: a worldwide snapshot of technological practices.
    • Toland AE, Forman A, Couch FJ, Culver JO, Eccles DM, Foulkes WD, Hogervorst FBL, Houdayer C, Levy-Lahad E, Monteiro AN, Neuhausen SL, Plon SE, Sharan SK, Spurdle AB, Szabo C, Brody LC; BIC Steering Committee.
    • NPJ Genom Med. 2018 Feb 15;3:7. doi: 10.1038/s41525-018-0046-7. eCollection 2018.
    • Rapid detection of BRCA1/2 recurrent mutations in Chinese breast and ovarian cancer patients with multiplex SNaPshot genotyping panels.
    • Kwong A, Ho JCW, Shin VY, Kurian AW, Tai E, Esserman LJ, Weitzel JN, Lin PH, Field M, Domchek SM, Lo J, Ngan HYS, Ma ESK, Chan TL, Ford JM.
    • Oncotarget. 2017 Dec 20;9(8):7832-7843. doi: 10.18632/oncotarget.23471. eCollection 2018 Jan 30.
    • Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2.
    • Hwang SM, Lee KC, Lee MS, Park KU.
    • Cancer Res Treat. 2018 Jan;50(1):255-264. doi: 10.4143/crt.2017.062. Epub 2017 Apr 7.
    • Simultaneous detection of genetic and copy number alterations in BRCA1/2 genes.
    • Hirotsu Y, Ooka Y, Sakamoto I, Nakagomi H, Omata M.
    • Oncotarget. 2017 Dec 6;8(70):114463-114473. doi: 10.18632/oncotarget.22962. eCollection 2017 Dec 29.
    • Fast Detection of a BRCA2 Large Genomic Duplication by Next Generation Sequencing as a Single Procedure: A Case Report.
    • Nunziato M, Starnone F, Lombardo B, Pensabene M, Condello C, Verdesca F, Carlomagno C, De Placido S, Pastore L, Salvatore F, D'Argenio V.
    • Int J Mol Sci. 2017 Nov 22;18(11). pii: E2487. doi: 10.3390/ijms18112487.
    • Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2: Validation of a One-Step Diagnostic Workflow.
    • Schmidt AY, Hansen TVO, Ahlborn LB, Jønson L, Yde CW, Nielsen FC.
    • J Mol Diagn. 2017 Nov;19(6):809-816. doi: 10.1016/j.jmoldx.2017.07.003. Epub 2017 Aug 17.
    • [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]
    • A comparative study of germline BRCA1 and BRCA2 mutation screening methods in use in 20 European clinical diagnostic laboratories.
    • Ellison G, Wallace A, Kohlmann A, Patton S.
    • Br J Cancer. 2017 Aug 22;117(5):710-716. doi: 10.1038/bjc.2017.223. Epub 2017 Jul 27.
    • Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2.
    • Schenk D, Song G, Ke Y, Wang Z.
    • PLoS One. 2017 Jul 12;12(7):e0181062. doi: 10.1371/journal.pone.0181062. eCollection 2017.
    • The spectrum of BRCA mutations and characteristics of BRCA-associated breast cancers in China: Screening of 2,991 patients and 1,043 controls by next-generation sequencing.
    • Lang GT, Shi JX, Hu X, Zhang CH, Shan L, Song CG, Zhuang ZG, Cao AY, Ling H, Yu KD, Shan L, Sun MH, Zhou XY, Huang W, Shao ZM.
    • Int J Cancer. 2017 Jul 1;141(1):129-142. doi: 10.1002/ijc.30692. Epub 2017 Apr 25.
    • Detection of false positive mutations in BRCA gene by next generation sequencing.
    • Suryavanshi M, Kumar D, Panigrahi MK, Chowdhary M, Mehta A.
    • Fam Cancer. 2017 Jul;16(3):311-317. doi: 10.1007/s10689-016-9955-8.
    • 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.
    • Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology.
    • Buzolin AL, Moreira CM, Sacramento PR, Oku AY, Fornari ARDS, Antonio DSM, Quaio CRDAC, Baratela WR, Mitne-Neto M.
    • Hum Genomics. 2017 Jun 26;11(1):14. doi: 10.1186/s40246-017-0110-x.
    • A knowledge-based framework for the discovery of cancer-predisposing variants using large-scale sequencing breast cancer data.
    • Melloni GEM, Mazzarella L, Bernard L, Bodini M, Russo A, Luzi L, Pelicci PG, Riva L.
    • Breast Cancer Res. 2017 May 31;19(1):63. doi: 10.1186/s13058-017-0854-1.
    • Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing.
    • Shin S, Kim Y, Oh SC, Yu N, Lee ST, Choi JR, Lee KA.
    • Oncotarget. 2017 May 23;8(21):34858-34866. doi: 10.18632/oncotarget.16799.
    • Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing.
    • Cheng DT, Prasad M, Chekaluk Y, Benayed R, Sadowska J, Zehir A, Syed A, Wang YE, Somar J, Li Y, Yelskaya Z, Wong D, Robson ME, Offit K, Berger MF, Nafa K, Ladanyi M, Zhang L.
    • BMC Med Genomics. 2017 May 19;10(1):33. doi: 10.1186/s12920-017-0271-4.
    • BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing.
    • Au CH, Ho DN, Kwong A, Chan TL, Ma ESK.
    • Sci Rep. 2017 May 8;7(1):1567. doi: 10.1038/s41598-017-01703-6.
    • Next-generation sequencing of BRCA1/2 in breast cancer patients: potential effects on clinical decision-making using rapid, high-accuracy genetic results.
    • Park HS, Park SJ, Kim JY, Kim S, Ryu J, Sohn J, Park S, Kim GM, Hwang IS, Choi JR, Kim SI.
    • Ann Surg Treat Res. 2017 May;92(5):331-339. doi: 10.4174/astr.2017.92.5.331. Epub 2017 Apr 27.
    • A novel molecular diagnostics platform for somatic and germline precision oncology.
    • Cabanillas R, Diñeiro M, Castillo D, Pruneda PC, Penas C, Cifuentes GA, de Vicente Á, Durán NS, Álvarez R, Ordóñez GR, Cadiñanos J.
    • Mol Genet Genomic Med. 2017 Apr 23;5(4):336-359. doi: 10.1002/mgg3.291. eCollection 2017 Jul.
    • Evaluation of the Ion Torrent PGM sequencing workflow for the routine rapid detection of BRCA1 and BRCA2 germline mutations.
    • Zanella I, Merola F, Biasiotto G, Archetti S, Spinelli E, Di Lorenzo D.
    • Exp Mol Pathol. 2017 Apr;102(2):314-320. doi: 10.1016/j.yexmp.2017.03.001. Epub 2017 Mar 2.
    • Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2.
    • Ahmadloo S, Nakaoka H, Hayano T, Hosomichi K, You H, Utsuno E, Sangai T, Nishimura M, Matsushita K, Hata A, Nomura F, Inoue I.
    • J Hum Genet. 2017 Apr;62(5):561-567. doi: 10.1038/jhg.2017.5. Epub 2017 Feb 9.
    • Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry.
    • Walker LC, Pearson JF, Wiggins GA, Giles GG, Hopper JL, Southey MC.
    • Breast Cancer Res. 2017 Mar 16;19(1):30. doi: 10.1186/s13058-017-0825-6.
    • Exome Sequencing in a Family with Luminal-Type Breast Cancer Underpinned by Variation in the Methylation Pathway.
    • van der Merwe N, Peeters AV, Pienaar FM, Bezuidenhout J, van Rensburg SJ, Kotze MJ.
    • Int J Mol Sci. 2017 Feb 22;18(2). pii: E467. doi: 10.3390/ijms18020467.
    • Retesting BRCA1/BRCA2 mutation negative male breast cancer patients using next generation sequencing technologies.
    • Rizzolo P, Silvestri V, Ottini L.
    • Breast Cancer Res Treat. 2017 Feb;162(1):199-200. doi: 10.1007/s10549-017-4108-9. Epub 2017 Jan 16.
    • Letter
    • BRCA Testing by Single-Molecule Molecular Inversion Probes.
    • Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SM, Adan IB, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJ, Shendure J, Nelen MR, Hoischen A.
    • Clin Chem. 2017 Feb;63(2):503-512. doi: 10.1373/clinchem.2016.263897. Epub 2016 Dec 14.
    • 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.
    • INDELseek: detection of complex insertions and deletions from next-generation sequencing data.
    • Au CH, Leung AY, Kwong A, Chan TL, Ma ES.
    • BMC Genomics. 2017 Jan 5;18(1):16. doi: 10.1186/s12864-016-3449-9.
    • A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.
    • Castellanos E, Gel B, Rosas I, Tornero E, Santín S, Pluvinet R, Velasco J, Sumoy L, Del Valle J, Perucho M, Blanco I, Navarro M, Brunet J, Pineda M, Feliubadaló L, Capellá G, Lázaro C, Serra E.
    • Sci Rep. 2017 Jan 4;7:39348. doi: 10.1038/srep39348.
    • Next-generation sequencing: advances and applications in cancer diagnosis.
    • Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R, Tommasi S, Pinto R.
    • Onco Targets Ther. 2016 Dec 2;9:7355-7365. eCollection 2016.
    • Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN.
    • Fowler A, Mahamdallie S, Ruark E, Seal S, Ramsay E, Clarke M, Uddin I, Wylie H, Strydom A, Lunter G, Rahman N.
    • Wellcome Open Res. 2016 Nov 25;1:20. doi: 10.12688/wellcomeopenres.10069.1.
    • Ready to clone: CNV detection and breakpoint fine-mapping in breast and ovarian cancer susceptibility genes by high-resolution array CGH.
    • Hackmann K, Kuhlee F, Betcheva-Krajcir E, Kahlert AK, Mackenroth L, Klink B, Di Donato N, Tzschach A, Kast K, Wimberger P, Schrock E, Rump A.
    • Breast Cancer Res Treat. 2016 Oct;159(3):585-90. doi: 10.1007/s10549-016-3956-z. Epub 2016 Aug 31.
    • BRCA1-2 diagnostic workflow from next-generation sequencing technologies to variant identification and final report.
    • Pilato B, Pinto R, De Summa S, Petriella D, Lacalamita R, Danza K, Virgilio Paradiso A, Tommasi S.
    • Genes Chromosomes Cancer. 2016 Oct;55(10):803-13. doi: 10.1002/gcc.22383. Epub 2016 Jul 4.
    • 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.
    • 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.
    • A Review of Whole Exome Sequencing Efforts Toward Hereditary Breast Cancer Susceptibility Gene Discovery.
    • Chandler MR, Bilgili EP, Merner ND.
    • Hum Mutat. 2016 Sep;37(9):835-46. doi: 10.1002/humu.23017. Epub 2016 Jun 27.
    • Review
    • Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis.
    • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JH, Ainsworth P, Waye JS, Sadikovic B.
    • J Mol Diagn. 2016 Sep;18(5):657-67. doi: 10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 2.
    • Evaluation of an amplicon-based next-generation sequencing panel for detection of BRCA1 and BRCA2 genetic variants.
    • Shin S, Hwang IS, Lee ST, Choi JR.
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    • NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial.
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    • A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.
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    • Medical implications of technical accuracy in genome sequencing.
    • Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT, Salit M, Ashley EA.
    • Genome Med. 2016 Mar 2;8(1):24. doi: 10.1186/s13073-016-0269-0.
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    • Expert Rev Mol Diagn. 2015 Oct;15(10):1383-403. doi: 10.1586/14737159.2015.1081059. Epub 2015 Aug 26.
    • Review
    • 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.
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    • The importance of proper bioinformatics analysis and clinical interpretation of tumor genomic profiling: a case study of undifferentiated sarcoma and a constitutional pathogenic BRCA2 mutation and an MLH1 variant of uncertain significance.
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    • Development and Validation of a Next-Generation Sequencing Assay for BRCA1 and BRCA2 Variants for the Clinical Laboratory.
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    • CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.
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    • HBOC multi-gene panel testing: comparison of two sequencing centers.
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    • Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing.
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    • Rapid and cost effective screening of breast and ovarian cancer genes using novel sequence capture method in clinical samples.
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    • A preliminary Quality Control (QC) for next generation sequencing (NGS) library evaluation turns out to be a very useful tool for a rapid detection of BRCA1/2 deleterious mutations.
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    Comments on NSGC Discussion Forum Cancer SIG

    Subject: RAD50 Positive Letter

    • gDNA enrichment by a transposase-based technology for NGS analysis of the whole sequence of BRCA1, BRCA2, and 9 genes involved in DNA damage repair.
    • Chevrier S, Boidot R.
    • J Vis Exp. 2014 Oct 6;(92):e51902. doi: 10.3791/51902.
    • First evidence of a large CHEK2 duplication involved in cancer predisposition in an Italian family with hereditary breast cancer.
    • Tedaldi G, Danesi R, Zampiga V, Tebaldi M, Bedei L, Zoli W, Amadori D, Falcini F, Calistri D.
    • BMC Cancer. 2014 Jul 1;14(1):478. doi: 10.1186/1471-2407-14-478.
    • Pathway Genomics Launches BRCA1/2 Genetic Test with One for One Program.
    • [No author given]
    • Business Wire, 2014 Jun 3.
    • The Validation and Clinical Implementation of BRCAplus: A Comprehensive High-Risk Breast Cancer Diagnostic Assay.
    • Chong HK, Wang T, Lu HM, Seidler S, Lu H, Keiles S, Chao EC, Stuenkel AJ, Li X, Elliott AM.
    • PLoS One. 2014 May 15;9(5):e97408. doi: 10.1371/journal.pone.0097408. eCollection 2014.
    • Next-generation sequencing of BRCA1 and BRCA2 in breast cancer patients and control subjects.
    • Balabanski L, Antov G, Dimova I, Ivanov S, Nacheva M, Gavrilov I, Nesheva D, Rukova B, Hadjidekova S, Malinov M, Toncheva D.
    • Mol Clin Oncol. 2014 May;2(3):435-439. Epub 2014 Feb 4.
    • Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model.
    • Tarabeux J, Zeitouni B, Moncoutier V, Tenreiro H, Abidallah K, Lair S, Legoix-Né P, Leroy Q, Rouleau E, Golmard L, Barillot E, Stern MH, Rio-Frio T, Stoppa-Lyonnet D, Houdayer C.
    • Eur J Hum Genet. 2014 Apr;22(4):535-41. doi: 10.1038/ejhg.2013.181. Epub 2013 Aug 14.
    • 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.
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    • Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.
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    • Biomed Res Int. 2014;2014:542541. doi: 10.1155/2014/542541. Epub 2014 Jun 26.
    • 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.
    • A Clinically Validated Diagnostic Second-Generation Sequencing Assay for Detection of Hereditary BRCA1 and BRCA2 Mutations.
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    • Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes.
    • Feliubadaló L, Lopez-Doriga A, Castellsagué E, Del Valle J, Menéndez M, Tornero E, Montes E, Cuesta R, Gómez C, Campos O, Pineda M, González S, Moreno V, Brunet J, Blanco I, Serra E, Capellá G, Lázaro C.
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    Press: The Future of BRCA1/BRCA2 Testing. (OncLive)

    • Myriad to Replace BRACAnalysis, Other Hereditary Cancer Tests with MyRisk Panel.
    • [No author given]
    • GenomeWeb. 2013 May 9.
    • Systematic Detection of Pathogenic Alu Element Insertions in NGS-Based Diagnostic Screens: The BRCA1/BRCA2 Example.
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    • Hum Mutat. 2013 May;34(5):785-91. doi: 10.1002/humu.22297. Epub 2013 Mar 11.
    • Whole Exome Sequencing Suggests Much of Non-BRCA1/BRCA2 Familial Breast Cancer Is Due to Moderate and Low Penetrance Susceptibility Alleles.
    • Gracia-Aznarez FJ, Fernandez V, Pita G, Peterlongo P, Dominguez O, de la Hoya M, Duran M, Osorio A, Moreno L, Gonzalez-Neira A, Rosa-Rosa JM, Sinilnikova O, Mazoyer S, Hopper J, Lazaro C, Southey M, Odefrey F, Manoukian S, Catucci I, Caldes T, Lynch HT, Hilbers FS, van Asperen CJ, Vasen HF, Goldgar D, Radice P, Devilee P, Benitez J.
    • PLoS One. 2013;8(2):e55681. doi: 10.1371/journal.pone.0055681. Epub 2013 Feb 8.
    • Exome sequencing of germline DNA from non-BRCA1/2 familial breast cancer cases selected on the basis of aCGH tumor profiling.
    • Hilbers FS, Meijers CM, Laros JF, van Galen M, Hoogerbrugge N, Vasen HF, Nederlof PM, Wijnen JT, van Asperen CJ, Devilee P.
    • PLoS One. 2013;8(1):e55734. doi: 10.1371/journal.pone.0055734. Epub 2013 Jan 31.
    • Development of a Next-Generation Sequencing Method for BRCA Mutation Screening: A Comparison between a High-Throughput and a Benchtop Platform.
    • Chan M, Ji SM, Yeo ZX, Gan L, Yap E, Yap YS, Ng R, Tan PH, Ho GH, Ang P, Lee AS.
    • J Mol Diagn. 2012 Nov;14(6):602-12. doi: 10.1016/j.jmoldx.2012.06.003. Epub 2012 Aug 22.
    • Molecular analysis of the breast cancer genes BRCA1 and BRCA2 using amplicon-based massive parallelpyrosequencing.
    • Michils G, Hollants S, Dehaspe L, Van Houdt J, Bidet Y, Uhrhammer N, Bignon YJ, Vermeesch JR, Cuppens H, Matthijs G.
    • J Mol Diagn. 2012 Nov;14(6):623-30. doi: 10.1016/j.jmoldx.2012.05.006. Epub 2012 Sep 30.
    • Long-range PCR and next-generation sequencing of BRCA1 and BRCA2 in breast cancer.
    • Ozcelik H, Shi X, Chang MC, Tram E, Vlasschaert M, Di Nicola N, Kiselova A, Yee D, Goldman A, Dowar M, Sukhu B, Kandel R, Siminovitch K.
    • J Mol Diagn. 2012 Sep;14(5):467-75. doi: 10.1016/j.jmoldx.2012.03.006. Epub 2012 Aug 6.

    Press: New BRCA1 and BRCA2 Test May Be More Accurate, Less Expensive. (Breastcancer.org)

    • Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.
    • Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG.
    • Am J Hum Genet. 2012 Jul 13;91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021. Epub 2012 Jun 14.

    Comments from NSGC Discussion Forum Cancer SIG

    Subject: articles needed