ERRATUM Open AccessErratum to: Modeling precision treatment ofbreast cancerAnneleen Daemen 1,2,13* , Obi L Griffith 1,3,6* , Laura M Heiser 1,4 , Nicholas J Wang 1,4 , Oana M Enache 1 ,Zachary Sanborn 5 , Francois Pepin 1,14 , Steffen Durinck 1 , James E Korkola 1,4 , Malachi Griffith 6 , Joe S Hur 7 , Nam Huh 8 ,Jongsuk Chung 8 , Leslie Cope 9 , Mary Jo Fackler 9 , Christopher Umbricht 9 , Saraswati Sukumar 9 , Pankaj Seth 10 ,Vikas P Sukhatme 10 , Lakshmi R Jakkula 1 , Yiling Lu 11 , Gordon B Mills 11 , Raymond J Cho 12 , Eric A Collisson 1,2 ,Laura J van’t Veer 2 , Paul T Spellman 1,3 and Joe W Gray 1,4*AbstractDuring the type-setting of the final version of the article [1] some of the additional files were swapped. The correctfiles are republished in this Erratum.ErratumDuring the type-setting of the final version of the article [1]some of the additional files were swapped (with the legendsremaining correct):Additional File 1 was published under Additional File 3hyperlink;Additional File 2 was published under Additional File 1hyperlink;Additional File 3 was published under Additional File 2hyperlink.Additional Files 4–9 are all correct. The editorsapologize for the clerical mistake that led to themismatch of the additional files.Additionally, the authors, based on the input from thereaders, wish to expand some of the descriptions of theexperimental procedures in the Additional File 1. In thesection describing the mutation status analysis theauthors added the following:“For the alignment, pairs of Fastq files (i.e. R1 & R2)sequenced from the same sample were aligned separatelyusing bwa aln & bwa sampe (default parameters) to thehg19 (GRCh37) reference. Each pair of Fastq files gener-ates a single BAM file. Individual BAM files from thesame sample were merged to generate a single BAM filerepresenting all reads from the sequencing run. Usingthe GATK routine CountCovariates, the merged BAMfile was subsequently analyzed to generate the covariatesnecessary to perform base quality recalibration. Briefly,it searches for mismatching bases in reads that do notoverlap known heterozygous sites (1,000 genomes +dbSNP) and collects information on the mismatchingbase’s quality and a series of other covariates (e.g. basequality, read group, neighboring bases, sequencingcycle). Using the GATK routine TableRecalibration, therecalibration metrics obtained from CountCovariateswere used to recalibrate all base qualities from the BAMfile. This step is necessary as the base qualities generatedby the sequencer often inaccurately reflect the truefrequency of mismatching bases. The BAM files withbase quality recalibration are the files used in all post-processing steps.For mutation calling, allele counts and their associatedbase qualities were collected for each individual cell line.Only alleles fulfilling the following criteria were used insubsequent steps: base quality (BQ) >= 10; neighbor-hood base quality (NBQ)>= 10; mapping quality of as-sociated read (MQ)>= 20; and its associated read is nota duplicate. Any base quality exceeding the read’s mappingquality is reduced to the read’s mapping quality. Positionswith less than 2 reads supporting any non-reference allelewere deemed homozygous reference and excluded fromfurther analyses. The likelihoods of all possible genotypes(AA, AT, AC, etc.) given the allelic data collected for the* Correspondence: daemena@gene.com; ogriffit@genome.wustl.edu; grayjo@ohsu.edu1 Department of Cancer & DNA Damage Responses, Life Sciences Division,Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAFull list of author information is available at the end of the article© 2015 Daemen et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly credited. The Creative Commons Public DomainDedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,unless otherwise stated.Daemen et al. Genome Biology (2015) 16:95 DOI 10.1186/s13059-015-0658-5
