Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches and bioinformatic strategies available for the development of an NGS panel for a reliable analysis of selected biomarkers. Compliance with defined analytical steps is crucial to ensure accurate and reproducible results. In addition, a careful validation procedure has to be performed before the application of NGS targeted assays in routine clinical practice. With more focus on bioinformatics, we emphasize the need for thorough pipeline validation and management in relation to the particular experimental setting as an integral part of the NGS method establishment. A robust and reproducible bioinformatic analysis running on powerful machines is essential for proper detection of genomic variants in clinical settings since distinguishing between experimental noise and real biological variants is fundamental. This review summarizes state-of-the-art bioinformatic solutions for careful detection of the SNV/Indels and CNVs for targeted sequencing resulting in translation of sequencing data into clinically relevant information. Finally, we share our experience with the development of a custom targeted NGS panel for an integrated analysis of biomarkers in lymphoproliferative disorders.

Center of Molecular Medicine Central European Institute of Technology Masaryk University Brno Czech Republic

Department of Hematology University Hospital Schleswig Holstein Kiel Germany

Department of Internal Medicine Hematology and Oncology Faculty of Medicine and University Hospital Brno Masaryk University Brno Czech Republic

Department of Medical Genetics and Genomics Faculty of Medicine and University Hospital Brno Masaryk University Brno Czech Republic

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Afgan E, Baker D, Batut B, Van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research. 2018;46(W1):W537–W544. doi: 10.1093/nar/gky379. PubMed DOI PMC

Ahmed N, Lévy J, Ren S, Mushtaq H, Bertels K, Al-Ars Z. GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data. BMC Bioinformatics. 2019;20(1):520. doi: 10.1186/s12859-019-3086-9. PubMed DOI PMC

Allgäuer M, Budczies J, Christopoulos P, Endris V, Lier A, Rempel E, Volckmar A-L, Kirchner M, Von Winterfeld M, Leichsenring J, Neumann O, Fröhling S, Penzel R, Thomas M, Schirmacher P, Stenzinger A. Implementing tumor mutational burden (TMB) analysis in routine diagnostics—a primer for molecular pathologists and clinicians. Translational Lung Cancer Research. 2018;7(5):703–715. doi: 10.21037/tlcr.2018.08.14. PubMed DOI PMC

Armaou S, Pertesi M, Fostira F, Thodi G, Athanasopoulos PS, Kamakari S, Athanasiou A, Gogas H, Yannoukakos D, Fountzilas G, Konstantopoulou I. Contribution of BRCA1 germ-line mutations to breast cancer in Greece: a hospital-based study of 987 unselected breast cancer cases. British Journal of Cancer. 2009;101(1):32–37. doi: 10.1038/sj.bjc.6605115. PubMed DOI PMC

Ascierto PA, Kirkwood JM, Grob J-J, Simeone E, Grimaldi AM, Maio M, Palmieri G, Testori A, Marincola FM, Mozzillo N. The role of BRAF V600 mutation in melanoma. Journal of Translational Medicine. 2012;10(1):85. doi: 10.1186/1479-5876-10-85. PubMed DOI PMC

Amazon AWS Free Tier. 2020. https://aws.amazon.com/free/ [18 December 2020]. https://aws.amazon.com/free/

Baliakas P, Jeromin S, Iskas M, Puiggros A, Plevova K, Nguyen-Khac F, Davis Z, Rigolin GM, Visentin A, Xochelli A, Delgado J, Baran-Marszak F, Stalika E, Abrisqueta P, Durechova K, Papaioannou G, Eclache V, Dimou M, Iliakis T, Collado R, Doubek M, Calasanz MJ, Ruiz-Xiville N, Moreno C, Jarosova M, Leeksma AC, Panayiotidis P, Podgornik H, Cymbalista F, Anagnostopoulos A, Trentin L, Stavroyianni N, Davi F, Ghia P, Kater AP, Cuneo A, Pospisilova S, Espinet B, Athanasiadou A, Oscier D, Haferlach C, Stamatopoulos K, ERIC, the European Research Initiative on CLL Cytogenetic complexity in chronic lymphocytic leukemia: definitions, associations, and clinical impact. Blood. 2019;133(11):1205–1216. doi: 10.1182/blood-2018-09-873083. PubMed DOI PMC

Benjamin D, Sato T, Cibulskis K, Getz G, Stewart C, Lichtenstein L. Calling somatic SNVs and indels with mutect2. bioRxiv. 2019 doi: 10.1101/861054. DOI

Bewicke-Copley F, Arjun Kumar E, Palladino G, Korfi K, Wang J. Applications and analysis of targeted genomic sequencing in cancer studies. Computational and Structural Biotechnology Journal. 2019;17(1029–1041):1348–1359. doi: 10.1016/j.csbj.2019.10.004. PubMed DOI PMC

Bian X, Zhu B, Wang M, Hu Y, Chen Q, Nguyen C, Hicks B, Meerzaman D. Comparing the performance of selected variant callers using synthetic data and genome segmentation. BMC Bioinformatics. 2018;19(1):429. doi: 10.1186/s12859-018-2440-7. PubMed DOI PMC

Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Rio Frio T, Hupé P, Barillot E, Laes J-F. Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. Bioinformatics. 2014;30(24):3443–3450. doi: 10.1093/bioinformatics/btu436. PubMed DOI PMC

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Cacheiro P, Ordóñez-Ugalde A, Quintáns B, Piñeiro-Hermida S, Amigo J, García-Murias M, Pascual-Pascual SI, Grandas F, Arpa J, Carracedo A, Sobrido MJ. Evaluating the calling performance of a rare disease NGS panel for single nucleotide and copy number variants. Molecular Diagnosis & Therapy. 2017;21(3):303–313. doi: 10.1007/s40291-017-0268-x. PubMed DOI

Callari M, Sammut S-J, De Mattos-Arruda L, Bruna A, Rueda OM, Chin S-F, Caldas C. Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome Medicine. 2017;9(1):35. doi: 10.1186/s13073-017-0425-1. PubMed DOI PMC

Cardoso JMP, Fey D, Hannig F, Pionteck T, Schröder-Preikschat W, Teich J. 29th International Conference, Nuremberg, Germany, April 4-7, 2016, Proceedings. Cham: Springer International Publishing; 2016. Architecture of computing systems—ARCS 2016.

Chapman B, Kirchner R, Pantano L, Smet MD, Beltrame L, Khotiainsteva T, Naumenko S, Saveliev V, Guimera RV, Sytchev I, Kern J, Brueffer C, Carrasco G, Giovacchini M, Tang P, Ahdesmaki M, Kanwal S, Porter JJ, Möller S, Le V, Coman A, Svensson V, Bogdang989 M, Edwards M, Hammerbacher M, Pedersen J, Cock B, Apastore P, Turner S. bcbio/bcbio-nextgen. Zenodo. Version 1.2.3http://doi.org/10.5281/zenodo.3743344 2020

Chen J, Li X, Zhong H, Meng Y, Du H. Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers. Scientific Reports. 2019a;9(1):9345. doi: 10.1038/s41598-019-45835-3. PubMed DOI PMC

Chen K, Meric-Bernstam F, Zhao H, Zhang Q, Ezzeddine N, Tang L, Qi Y, Mao Y, Chen T, Chong Z, Zhou W, Zheng X, Johnson A, Aldape KD, Routbort MJ, Luthra R, Kopetz S, Davies MA, De Groot J, Moulder S, Vinod R, Farhangfar CJ, Shaw KM, Mendelsohn J, Mills GB, Karina Eterovic A. Clinical actionability enhanced through deep targeted sequencing of solid tumors. Clinical Chemistry. 2015;61(3):544–553. doi: 10.1373/clinchem.2014.231100. PubMed DOI PMC

Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890. doi: 10.1093/bioinformatics/bty560. PubMed DOI PMC

Chen S, Zhou Y, Chen Y, Huang T, Liao W, Xu Y, Li Z, Gu J. Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data. BMC Bioinformatics. 2019b;20(S23):606. doi: 10.1186/s12859-019-3280-9. PubMed DOI PMC

Chilamakuri CSR, Lorenz S, Madoui M-A, Vodák D, Sun J, Hovig E, Myklebost O, Meza-Zepeda LA. Performance comparison of four exome capture systems for deep sequencing. BMC Genomics. 2014;15(1):449. doi: 10.1186/1471-2164-15-449. PubMed DOI PMC

Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen H-C, Agarwala R, McLaren WM, Ritchie GRS, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T. Modernizing reference genome assemblies. PLOS Biology. 2011;9(7):e1001091. doi: 10.1371/journal.pbio.1001091. PubMed DOI PMC

Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnology. 2013;31(3):213–219. doi: 10.1038/nbt.2514. PubMed DOI PMC

Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80–92. doi: 10.4161/fly.19695. PubMed DOI PMC

Claustres M, Kožich V, Dequeker E, Fowler B, Hehir-Kwa JY, Miller K, Oosterwijk C, Peterlin B, van Ravenswaaij-Arts C, Zimmermann U, Zuffardi O, Hastings RJ, Barton DE, European Society of Human Genetics Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic) European Journal of Human Genetics. 2014;22:160–170. doi: 10.1038/ejhg.2013.125. PubMed DOI PMC

Concolino P, Rizza R, Mignone F, Costella A, Guarino D, Carboni I, Capoluongo E, Santonocito C, Urbani A, Minucci A. A comprehensive BRCA1/2 NGS pipeline for an immediate Copy Number Variation (CNV) detection in breast and ovarian cancer molecular diagnosis. Clinica Chimica Acta. 2018;480:173–179. doi: 10.1016/j.cca.2018.02.012. PubMed DOI

Cooke DP, Wedge DC, Lunter G. A unified haplotype-based method for accurate and comprehensive variant calling. Bioinformatics. 2018;1:20. doi: 10.1101/456103. PubMed DOI PMC

Costello M, Fleharty M, Abreu J, Farjoun Y, Ferriera S, Holmes L, Granger B, Green L, Howd T, Mason T, Vicente G, Dasilva M, Brodeur W, DeSmet T, Dodge S, Lennon NJ, Gabriel S. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms. BMC Genomics. 2018;19(1):332. doi: 10.1186/s12864-018-4703-0. PubMed DOI PMC

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nature Biotechnology. 2017;35(4):316–319. doi: 10.1038/nbt.3820. PubMed DOI

Dubois S, Viailly P-J, Mareschal S, Bohers E, Bertrand P, Ruminy P, Maingonnat C, Jais J-P, Peyrouze P, Figeac M, Molina TJ, Desmots F, Fest T, Haioun C, Lamy T, Copie-Bergman C, Brière J, Petrella T, Canioni D, Fabiani B, Coiffier B, Delarue R, Peyrade F, Bosly A, André M, Ketterer N, Salles G, Tilly H, Leroy K, Jardin F. Next-generation sequencing in diffuse large B-cell lymphoma highlights molecular divergence and therapeutic opportunities: a LYSA study. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 2016;22(12):2919–2928. doi: 10.1158/1078-0432.CCR-15-2305. PubMed DOI

EGI EGI Advanced Computing Services for Research. 2020. https://www.egi.eu/ [18 December 2020]. https://www.egi.eu/

Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang L-W, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012;486(7403):353–360. doi: 10.1038/nature11143. PubMed DOI PMC

Ensembl BED file format. 2020. https://www.ensembl.org/info/website/upload/bed.html. [18 December 2020]. https://www.ensembl.org/info/website/upload/bed.html

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology. 2020;38(3):276–278. doi: 10.1038/s41587-020-0439-x. PubMed DOI

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P’ng C, Waggott D, Sabelnykova VY, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature Methods. 2015;12(7):623–630. doi: 10.1038/nmeth.3407. PubMed DOI PMC

Fan Y, Xi L, Hughes DST, Zhang J, Zhang J, Futreal PA, Wheeler DA, Wang W. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biology. 2016;17(1):178. doi: 10.1186/s13059-016-1029-6. PubMed DOI PMC

fgbio fgbio: Tools for working with genomic and high throughput sequencing data. 2020. http://fulcrumgenomics.github.io/fgbio/ http://fulcrumgenomics.github.io/fgbio/

Gargis AS, Kalman L, Bick DP, Da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FCL, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong L-JC, Zehnbauer BA, Zook JM, Lubin IM. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nature Biotechnology. 2015;33(7):689–693. doi: 10.1038/nbt.3237. PubMed DOI PMC

Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. http://arxiv.org/abs/1207.3907 ArXiv. 2012

Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N. Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nature Communications. 2012;3(1):811. doi: 10.1038/ncomms1814. PubMed DOI

Girardot C, Scholtalbers J, Sauer S, Su S-Y, Furlong EEM. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics. 2016;17(1):419. doi: 10.1186/s12859-016-1284-2. PubMed DOI PMC

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, Bioconda Team Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods. 2018;15(7):475–476. doi: 10.1038/s41592-018-0046-7. PubMed DOI PMC

Guan P, Sung W-K. Structural variation detection using next-generation sequencing data: a comparative technical review. Methods. 2016;102(21):36–49. doi: 10.1016/j.ymeth.2016.01.020. PubMed DOI

Hamblin A, Wordsworth S, Fermont JM, Page S, Kaur K, Camps C, Kaisaki P, Gupta A, Talbot D, Middleton M, Henderson S, Cutts A, Vavoulis DV, Housby N, Tomlinson I, Taylor JC, Schuh A. Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: retrospective validation and prospective audit in the UK National health service. PLOS Medicine. 2017;14(2):e1002230. doi: 10.1371/journal.pmed.1002230. PubMed DOI PMC

Hardwick SA, Deveson IW, Mercer TR. Reference standards for next-generation sequencing. Nature Reviews Genetics. 2017;18(8):473–484. doi: 10.1038/nrg.2017.44. PubMed DOI

Heydt C, Rehker J, Pappesch R, Buhl T, Ball M, Siebolts U, Haak A, Lohneis P, Büttner R, Hillmer AM, Merkelbach-Bruse S. Analysis of tumor mutational burden: correlation of five large gene panels with whole exome sequencing. Scientific Reports. 2020;10(1):11387. doi: 10.1038/s41598-020-68394-4. PubMed DOI PMC

Hung SS, Meissner B, Chavez EA, Ben-Neriah S, Ennishi D, Jones MR, Shulha HP, Chan FC, Boyle M, Kridel R, Gascoyne RD, Mungall AJ, Marra MA, Scott DW, Connors JM, Steidl C. Assessment of capture and amplicon-based approaches for the development of a targeted next-generation sequencing pipeline to personalize lymphoma management. Journal of Molecular Diagnostics. 2018;20(2):203–214. doi: 10.1016/j.jmoldx.2017.11.010. PubMed DOI

Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proceedings of the National Academy of Sciences of the United States of America. 2011;108:20166–20171. doi: 10.1073/pnas.1110064108. PubMed DOI PMC

Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. Guidelines for validation of next-generation sequencing-based oncology panels: a joint consensus recommendation of the association for molecular pathology and college of american pathologists. Journal of Molecular Diagnostics. 2017;19(3):341–365. doi: 10.1016/j.jmoldx.2017.01.011. PubMed DOI PMC

Jones S, Anagnostou V, Lytle K, Parpart-Li S, Nesselbush M, Riley DR, Shukla M, Chesnick B, Kadan M, Papp E, Galens KG, Murphy D, Zhang T, Kann L, Sausen M, Angiuoli SV, Diaz LA, Velculescu VE. Personalized genomic analyses for cancer mutation discovery and interpretation. Science Translational Medicine. 2015;7(283):283ra53. doi: 10.1126/scitranslmed.aaa7161. PubMed DOI PMC

Jones D, Raine KM, Davies H, Tarpey PS, Butler AP, Teague JW, Nik-Zainal S, Campbell PJ. cgpCaVEManWrapper: simple execution of CaVEMan in order to detect somatic single nucleotide variants in NGS data. Current Protocols in Bioinformatics. 2016;56(1):15.10.1–15.10.18. doi: 10.1002/cpbi.20. PubMed DOI PMC

Kalatskaya I, Trinh QM, Spears M, McPherson JD, Bartlett JMS, Stein L. ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. Genome Medicine. 2017;9(1):59. doi: 10.1186/s13073-017-0446-9. PubMed DOI PMC

Kim B, Lee H, Kim E, Shin S, Lee S-T, Choi JR. Clinical utility of targeted NGS panel with comprehensive bioinformatics analysis for patients with acute lymphoblastic leukemia. Leukemia & Lymphoma. 2019;60(13):1–8. doi: 10.1080/10428194.2019.1627538. PubMed DOI

Kim S, Scheffler K, Halpern AL, Bekritsky MA, Noh E, Källberg M, Chen X, Kim Y, Beyter D, Krusche P, Saunders CT. Strelka2: fast and accurate calling of germline and somatic variants. Nature Methods. 2018;15(8):591–594. doi: 10.1038/s41592-018-0051-x. PubMed DOI

Kluk MJ, Lindsley RC, Aster JC, Lindeman NI, Szeto D, Hall D, Kuo FC. Validation and implementation of a custom next-generation sequencing clinical assay for hematologic malignancies. Journal of Molecular Diagnostics. 2016;18(4):507–515. doi: 10.1016/j.jmoldx.2016.02.003. PubMed DOI PMC

Klus P, Lam S, Lyberg D, Cheung MS, Pullan G, McFarlane I, Yeo GS, Lam BY. BarraCUDA—a fast short read sequence aligner using graphics processing units. BMC Research Notes. 2012;5(1):27. doi: 10.1186/1756-0500-5-27. PubMed DOI PMC

Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell. 2013;155(1):27–38. doi: 10.1016/j.cell.2013.09.006. PubMed DOI PMC

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research. 2012;22(3):568–576. doi: 10.1101/gr.129684.111. PubMed DOI PMC

Köster J, Rahmann S. Snakemake-a scalable bioinformatics workflow engine. Bioinformatics. 2018;34:3600. doi: 10.1093/bioinformatics/bty350. PubMed DOI

Kuo FC, Mar BG, Lindsley RC, Lindeman NI. The relative utilities of genome-wide, gene panel, and individual gene sequencing in clinical practice. Blood. 2017;130(4):433–439. doi: 10.1182/blood-2017-03-734533. PubMed DOI PMC

Kurtzer GM, Sochat V, Bauer MW. Singularity: scientific containers for mobility of compute. PLOS ONE. 2017;12(5):e0177459. doi: 10.1371/journal.pone.0177459. PubMed DOI PMC

Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett JC, Dry JR. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Research. 2016;44(11):e108–e108. doi: 10.1093/nar/gkw227. PubMed DOI PMC

Landau DA, Tausch E, Taylor-Weiner AN, Stewart C, Reiter JG, Bahlo J, Kluth S, Bozic I, Lawrence M, Böttcher S, Carter SL, Cibulskis K, Mertens D, Sougnez CL, Rosenberg M, Hess JM, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander ES, Nowak MA, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu CJ. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526(7574):525–530. doi: 10.1038/nature15395. PubMed DOI PMC

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9(4):357–359. doi: 10.1038/nmeth.1923. PubMed DOI PMC

Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012;28(3):311–317. doi: 10.1093/bioinformatics/btr665. PubMed DOI PMC

Lenis J, Senar MA. On the performance of BWA on NUMA architectures. 2015 IEEE Trustcom/BigDataSE/ISPA; 2015. pp. 236–241.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN. Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the association for molecular pathology, American Society of Clinical Oncology, and College of American Pathologists. Journal of Molecular Diagnostics. 2017;19(1):4–23. doi: 10.1016/j.jmoldx.2016.10.002. PubMed DOI PMC

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760. doi: 10.1093/bioinformatics/btp324. PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC

Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research. 2008;18(11):1851–1858. doi: 10.1101/gr.078212.108. PubMed DOI PMC

Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CKY, Schinkel J, Joy JB, Harrigan PR, Poon AFY. Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Research. 2014;42:e98. doi: 10.1093/nar/gku355. PubMed DOI PMC

Lindsley RC, Mar BG, Mazzola E, Grauman PV, Shareef S, Allen SL, Pigneux A, Wetzler M, Stuart RK, Erba HP, Damon LE, Powell BL, Lindeman N, Steensma DP, Wadleigh M, DeAngelo DJ, Neuberg D, Stone RM, Ebert BL. Acute myeloid leukemia ontogeny is defined by distinct somatic mutations. Blood. 2015;125(9):1367–1376. doi: 10.1182/blood-2014-11-610543. PubMed DOI PMC

Liu X, Han S, Wang Z, Gelernter J, Yang B-Z. Variant callers for next-generation sequencing data: a comparison study. PLOS ONE. 2013;8(9):e75619. doi: 10.1371/journal.pone.0075619. PubMed DOI PMC

Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research. 2011;21(6):936–939. doi: 10.1101/gr.111120.110. PubMed DOI PMC

Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. Environmental and Molecular Mutagenesis. 2015;56(5):419–436. doi: 10.1002/em.21943. PubMed DOI PMC

MacConaill LE, Burns RT, Nag A, Coleman HA, Slevin MK, Giorda K, Light M, Lai K, Jarosz M, McNeill MS, Ducar MD, Meyerson M, Thorner AR. Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing. BMC Genomics. 2018;19(1):30. doi: 10.1186/s12864-017-4428-5. PubMed DOI PMC

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17(1):10. doi: 10.14806/ej.17.1.200. DOI

McConnell L, Houghton O, Stewart P, Gazdova J, Srivastava S, Kim C, Catherwood M, Strobl A, Flanagan AM, Oniscu A, Kroeze LI, Groenen P, Taniere P, Salto-Tellez M, Gonzalez D. A novel next generation sequencing approach to improve sarcoma diagnosis. Modern Pathology. 2020;33(7):1350–1359. doi: 10.1038/s41379-020-0488-1. PubMed DOI

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. 2010;20(9):1297–1303. doi: 10.1101/gr.107524.110. PubMed DOI PMC

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The ensembl variant effect predictor. Genome Biology. 2016;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed DOI PMC

Merkel D. Docker: lightweight linux containers for consistent development and deployment. Linux journal. 2014;(239):2.

Metzker ML. Sequencing technologies—the next generation. Nature Reviews Genetics. 2010;11(1):31–46. doi: 10.1038/nrg2626. PubMed DOI

Nadeu F, Delgado J, Royo C, Baumann T, Stankovic T, Pinyol M, Jares P, Navarro A, Martín-García D, Beà S, Salaverria I, Oldreive C, Aymerich M, Suárez-Cisneros H, Rozman M, Villamor N, Colomer D, López-Guillermo A, González M, Alcoceba M, Terol MJ, Colado E, Puente XS, López-Otín C, Enjuanes A, Campo E. Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM mutations in chronic lymphocytic leukemia. Blood. 2016;127(17):2122–2130. doi: 10.1182/blood-2015-07-659144. PubMed DOI PMC

Nikiforova MN, Mercurio S, Wald AI, Barbi de Moura M, Callenberg K, Santana-Santos L, Gooding WE, Yip L, Ferris RL, Nikiforov YE. Analytical performance of the ThyroSeq v3 genomic classifier for cancer diagnosis in thyroid nodules. Cancer. 2018;124(8):1682–1690. doi: 10.1002/cncr.31245. PubMed DOI PMC

Novocraft NovoAlign. 2020. http://www.novocraft.com/products/novoalign/ [18 December 2020]. http://www.novocraft.com/products/novoalign/

Oliveira C, Wolf T. CNVPanelizer: reliable CNV detection in targeted sequencing applications. R package version 1.18.0https://bioconductor.org/packages/release/bioc/html/CNVPanelizer.html 2019

Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5(4):557–572. doi: 10.1093/biostatistics/kxh008. PubMed DOI

Orabi B, Erhan E, McConeghy B, Volik SV, Le Bihan S, Bell R, Collins CC, Chauve C, Hach F. Alignment-free clustering of UMI tagged DNA molecules. Bioinformatics. 2019;35(11):1829–1836. doi: 10.1093/bioinformatics/bty888. PubMed DOI

OSG Open Science Grid. 2020. http://opensciencegrid.org/about/introduction/ [18 December 2020]. http://opensciencegrid.org/about/introduction/

Paasinen-Sohns A, Koelzer VH, Frank A, Schafroth J, Gisler A, Sachs M, Graber A, Rothschild SI, Wicki A, Cathomas G, Mertz KD. Single-center experience with a targeted next generation sequencing assay for assessment of relevant somatic alterations in solid tumors. Neoplasia. 2017;19(3):196–206. doi: 10.1016/j.neo.2017.01.003. PubMed DOI PMC

Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O’Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Genomic classification and prognosis in acute myeloid leukemia. New England Journal of Medicine. 2016;374(23):2209–2221. doi: 10.1056/NEJMoa1516192. PubMed DOI PMC

Paradiso V, Garofoli A, Tosti N, Lanzafame M, Perrina V, Quagliata L, Matter MS, Wieland S, Heim MH, Piscuoglio S, Ng CKY, Terracciano LM. Diagnostic targeted sequencing panel for hepatocellular carcinoma genomic screening. Journal of Molecular Diagnostics. 2018;20(6):836–848. doi: 10.1016/j.jmoldx.2018.07.003. PubMed DOI

Parry M, Rose-Zerilli MJJ, Ljungstrom V, Gibson J, Wang J, Walewska R, Parker H, Parker A, Davis Z, Gardiner A, McIver-Brown N, Kalpadakis C, Xochelli A, Anagnostopoulos A, Fazi C, Gonzalez de Castro D, Dearden C, Pratt G, Rosenquist R, Ashton-Key M, Forconi F, Collins A, Ghia P, Matutes E, Pangalis G, Stamatopoulos K, Oscier D, Strefford JC. Genetics and prognostication in splenic marginal zone lymphoma: revelations from deep sequencing. Clinical Cancer Research. 2015;21(18):4174–4183. doi: 10.1158/1078-0432.CCR-14-2759. PubMed DOI PMC

Pastore A, Jurinovic V, Kridel R, Hoster E, Staiger AM, Szczepanowski M, Pott C, Kopp N, Murakami M, Horn H, Leich E, Moccia AA, Mottok A, Sunkavalli A, Van Hummelen P, Ducar M, Ennishi D, Shulha HP, Hother C, Connors JM, Sehn LH, Dreyling M, Neuberg D, Möller P, Feller AC, Hansmann ML, Stein H, Rosenwald A, Ott G, Klapper W, Unterhalt M, Hiddemann W, Gascoyne RD, Weinstock DM, Weigert O. Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma: a retrospective analysis of a prospective clinical trial and validation in a population-based registry. Lancet Oncology. 2015;16(9):1111–1122. doi: 10.1016/S1470-2045(15)00169-2. PubMed DOI

Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S, Wood NW, Hambleton S, Burns SO, Thrasher AJ, Kumararatne D, Doffinger R, Nejentsev S. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012;28(21):2747–2754. doi: 10.1093/bioinformatics/bts526. PubMed DOI PMC

Poplin R, Chang P-C, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA. A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology. 2018;36(10):983–987. doi: 10.1038/nbt.4235. PubMed DOI

Povysil G, Tzika A, Vogt J, Haunschmid V, Messiaen L, Zschocke J, Klambauer G, Hochreiter S, Wimmer K. panelcn.MOPS: copy-number detection in targeted NGS panel data for clinical diagnostics. Human Mutation. 2017;38(7):889–897. doi: 10.1002/humu.23237. PubMed DOI PMC

Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 2010;26(1):127–129. doi: 10.1093/bioinformatics/btp615. PubMed DOI PMC

Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842. doi: 10.1093/bioinformatics/btq033. PubMed DOI PMC

Ren S, Ahmed N, Bertels K, Al-Ars Z. GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller. BMC Genomics. 2019;20(S2):184. doi: 10.1186/s12864-019-5468-9. PubMed DOI PMC

Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SRF, Wilkie AOM, McVean G, Lunter G, WGS500 Consortium Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics. 2014;46:912–918. doi: 10.1038/ng.3036. PubMed DOI PMC

Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS, Miller ML, Rekhtman N, Moreira AL, Ibrahim F, Bruggeman C, Gasmi B, Zappasodi R, Maeda Y, Sander C, Garon EB, Merghoub T, Wolchok JD, Schumacher TN, Chan TA. Cancer immunology. mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348(6230):124–128. doi: 10.1126/science.aaa1348. PubMed DOI PMC

Rodríguez-Vicente AE, Díaz MG, Hernández-Rivas JM. Chronic lymphocytic leukemia: a clinical and molecular heterogenous disease. Cancer Genetics. 2013;206(3):49–62. doi: 10.1016/j.cancergen.2013.01.003. PubMed DOI

Rossi D, Diop F, Spaccarotella E, Monti S, Zanni M, Rasi S, Deambrogi C, Spina V, Bruscaggin A, Favini C, Serra R, Ramponi A, Boldorini R, Foà R, Gaidano G. Diffuse large B-cell lymphoma genotyping on the liquid biopsy. Blood. 2017;129(14):1947–1957. doi: 10.1182/blood-2016-05-719641. PubMed DOI

Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB. Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the association for molecular pathology and the college of american pathologists. Journal of Molecular Diagnostics. 2018;20(1):4–27. doi: 10.1016/j.jmoldx.2017.11.003. PubMed DOI

Ruffalo M, LaFramboise T, Koyutürk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011;27(20):2790–2796. doi: 10.1093/bioinformatics/btr477. PubMed DOI

Sadedin SP, Pope B, Oshlack A. Bpipe: a tool for running and managing bioinformatics pipelines. Bioinformatics. 2012;28:1525–1526. doi: 10.1093/bioinformatics/bts167. PubMed DOI

Samorodnitsky E, Jewell BM, Hagopian R, Miya J, Wing MR, Lyon E, Damodaran S, Bhatt D, Reeser JW, Datta J, Roychowdhury S. Evaluation of hybridization capture versus amplicon-based methods for whole-exome sequencing. Human Mutation. 2015;36(9):903–914. doi: 10.1002/humu.22825. PubMed DOI PMC

Sater V, Viailly P-J, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries. Bioinformatics. 2020;36(9):2718–2724. doi: 10.1093/bioinformatics/btaa053. PubMed DOI

Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L. Challenges and standards in integrating surveys of structural variation. Nature Genetics. 2007;39(S7):S7–15. doi: 10.1038/ng2093. PubMed DOI PMC

Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen H-C, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood J, Clarke L, Koren S, Boitano M, Li H, Chin C-S, Phillippy AM, Durbin R, Wilson RK, Flicek P, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genomics. 2016;16:24. doi: 10.1101/072116. PubMed DOI PMC

Sengupta S, Gulukota K, Zhu Y, Ober C, Naughton K, Wentworth-Sheilds W, Ji Y. Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples. Nucleic Acids Research. 2016;44(3):e25–e25. doi: 10.1093/nar/gkv953. PubMed DOI PMC

Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S. An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Research. 2013;41(7):e89–e89. doi: 10.1093/nar/gkt126. PubMed DOI PMC

Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics. 2014;15(2):121–132. doi: 10.1038/nrg3642. PubMed DOI

SMALT: Wellcome Sanger Institute SMALT. 2020. https://www.sanger.ac.uk/tool/smalt-0/ [18 December 2020]. https://www.sanger.ac.uk/tool/smalt-0/

Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Research. 2017;27(3):491–499. doi: 10.1101/gr.209601.116. PubMed DOI PMC

Soukupova J, Zemankova P, Lhotova K, Janatova M, Borecka M, Stolarova L, Lhota F, Foretova L, Machackova E, Stranecky V, Tavandzis S, Kleiblova P, Vocka M, Hartmannova H, Hodanova K, Kmoch S, Kleibl Z. Validation of CZECANCA (CZEch CAncer paNel for clinical application) for targeted NGS-based analysis of hereditary cancer syndromes. PLOS ONE. 2018;13(4):e0195761. doi: 10.1371/journal.pone.0195761. PubMed DOI PMC

Steward DL, Carty SE, Sippel RS, Yang SP, Sosa JA, Sipos JA, Figge JJ, Mandel S, Haugen BR, Burman KD, Baloch ZW, Lloyd RV, Seethala RR, Gooding WE, Chiosea SI, Gomes-Lima C, Ferris RL, Folek JM, Khawaja RA, Kundra P, Loh KS, Marshall CB, Mayson S, McCoy KL, Nga ME, Ngiam KY, Nikiforova MN, Poehls JL, Ringel MD, Yang H, Yip L, Nikiforov YE. Performance of a multigene genomic classifier in thyroid nodules with indeterminate cytology: a prospective blinded multicenter study. JAMA Oncology. 2019;5(2):204. doi: 10.1001/jamaoncol.2018.4616. PubMed DOI PMC

Sulonen A-M, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biology. 2011;12(9):R94. doi: 10.1186/gb-2011-12-9-r94. PubMed DOI PMC

Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLOS Computational Biology. 2016;12(4):e1004873. doi: 10.1371/journal.pcbi.1004873. PubMed DOI PMC

Tamborero D, Rubio-Perez C, Deu-Pons J, Schroeder MP, Vivancos A, Rovira A, Tusquets I, Albanell J, Rodon J, Tabernero J, De Torres C, Dienstmann R, Gonzalez-Perez A, Lopez-Bigas N. Cancer genome interpreter annotates the biological and clinical relevance of tumor alterations. Cancer Biology. 2017;13:806. doi: 10.1101/140475. PubMed DOI PMC

Thankaswamy-Kosalai S, Sen P, Nookaew I. Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics. 2017;109(3–4):186–191. doi: 10.1016/j.ygeno.2017.03.001. PubMed DOI

Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics. 2013;14(2):178–192. doi: 10.1093/bib/bbs017. PubMed DOI PMC

Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S. HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. Bioinformatics. 2014;30(23):3302–3309. doi: 10.1093/bioinformatics/btu537. PubMed DOI PMC

Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. From fastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics. 2013;43(1):11 10 1–11 10 33. doi: 10.1002/0471250953.bi1110s43. PubMed DOI PMC

Wade MJ, Curtis TP, Davenport RJ. Modelling computational resources for next generation sequencing bioinformatics analysis of 16S rRNA samples. http://arxiv.org/abs/1503.02974 ArXiv. 2015

Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research. 2010;38(16):e164. doi: 10.1093/nar/gkq603. PubMed DOI PMC

Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014;512(7513):155–160. doi: 10.1038/nature13600. PubMed DOI PMC

Wildeman M, Van Ophuizen E, Den Dunnen JT, Taschner PEM. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Human Mutation. 2008;29(1):6–13. doi: 10.1002/humu.20654. PubMed DOI

Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Research. 2012;40(22):11189–11201. doi: 10.1093/nar/gks918. PubMed DOI PMC

Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Computational and Structural Biotechnology Journal. 2018;16(1):15–24. doi: 10.1016/j.csbj.2018.01.003. PubMed DOI PMC

Yu D, Liu Z, Su C, Han Y, Duan X, Zhang R, Liu X, Yang Y, Xu S. Copy number variation in plasma as a tool for lung cancer prediction using extreme gradient boosting (XGBoost) classifier. Thoracic Cancer. 2020;11(1):95–102. doi: 10.1111/1759-7714.13204. PubMed DOI PMC

Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics. 2013;14(S11):S1. doi: 10.1186/1471-2105-14-S11-S1. PubMed DOI PMC

Zoi K, Cross NCP. Molecular pathogenesis of atypical CML, CMML and MDS/MPN-unclassifiable. International Journal of Hematology. 2015;101(3):229–242. doi: 10.1007/s12185-014-1670-3. PubMed DOI

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre ABR, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GXY, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Scientific Data. 2016;3(1):160025. doi: 10.1038/sdata.2016.25. PubMed DOI PMC

ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-2024 update