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Items: 1 to 20 of 66

1.

Sample-Index Misassignment Impacts Tumour Exome Sequencing.

Vodák D, Lorenz S, Nakken S, Aasheim LB, Holte H, Bai B, Myklebost O, Meza-Zepeda LA, Hovig E.

Sci Rep. 2018 Mar 28;8(1):5307. doi: 10.1038/s41598-018-23563-4.

2.

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.

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.

BMC Genomics. 2018 May 8;19(1):332. doi: 10.1186/s12864-018-4703-0.

3.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE.

BMC Genomics. 2012 Dec 6;13:683. doi: 10.1186/1471-2164-13-683.

4.

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.

van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K.

Mol Ecol Resour. 2019 Mar 8. doi: 10.1111/1755-0998.13009. [Epub ahead of print]

PMID:
30848092
5.

A cancer cell-line titration series for evaluating somatic classification.

Denroche RE, Mullen L, Timms L, Beck T, Yung CK, Stein L, McPherson JD, Brown AM.

BMC Res Notes. 2015 Dec 26;8:823. doi: 10.1186/s13104-015-1803-7.

6.

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.

Kircher M, Sawyer S, Meyer M.

Nucleic Acids Res. 2012 Jan;40(1):e3. doi: 10.1093/nar/gkr771. Epub 2011 Oct 21.

7.

Variant identification in multi-sample pools by illumina genome analyzer sequencing.

Margraf RL, Durtschi JD, Dames S, Pattison DC, Stephens JE, Voelkerding KV.

J Biomol Tech. 2011 Jul;22(2):74-84.

8.

Quality filtering of Illumina index reads mitigates sample cross-talk.

Wright ES, Vetsigian KH.

BMC Genomics. 2016 Nov 4;17(1):876.

9.

Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples.

Wang T, Pradhan K, Ye K, Wong LJ, Rohan TE.

Front Genet. 2011 Aug 17;2:51. doi: 10.3389/fgene.2011.00051. eCollection 2011.

10.

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification.

Bao R, Hernandez K, Huang L, Kang W, Bartom E, Onel K, Volchenboum S, Andrade J.

PLoS One. 2015 Aug 13;10(8):e0135800. doi: 10.1371/journal.pone.0135800. eCollection 2015.

11.

SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing.

Spinella JF, Mehanna P, Vidal R, Saillour V, Cassart P, Richer C, Ouimet M, Healy J, Sinnett D.

BMC Genomics. 2016 Nov 14;17(1):912.

12.

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers.

Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, Dahlman KB, Pao W, Zhao Z.

Genome Med. 2013 Oct 11;5(10):91. doi: 10.1186/gm495. eCollection 2013.

13.

Imputation-based assessment of next generation rare exome variant arrays.

Martin AR, Tse G, Bustamante CD, Kenny EE.

Pac Symp Biocomput. 2014:241-52.

14.

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders.

Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, di Bernardo D.

BMC Genomics. 2014;15 Suppl 3:S5. doi: 10.1186/1471-2164-15-S3-S5. Epub 2014 May 6.

15.

Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.

Samorodnitsky E, Jewell BM, Hagopian R, Miya J, Wing MR, Lyon E, Damodaran S, Bhatt D, Reeser JW, Datta J, Roychowdhury S.

Hum Mutat. 2015 Sep;36(9):903-14. doi: 10.1002/humu.22825. Epub 2015 Jul 15.

16.

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.

Lindberg J, Klevebring D, Liu W, Neiman M, Xu J, Wiklund P, Wiklund F, Mills IG, Egevad L, Grönberg H.

Eur Urol. 2013 Feb;63(2):347-53. doi: 10.1016/j.eururo.2012.03.050. Epub 2012 Mar 31.

PMID:
22502944
17.

Inferring copy number and genotype in tumour exome data.

Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK.

BMC Genomics. 2014 Aug 28;15:732. doi: 10.1186/1471-2164-15-732.

18.

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

de Muinck EJ, Trosvik P, Gilfillan GD, Hov JR, Sundaram AYM.

Microbiome. 2017 Jul 6;5(1):68. doi: 10.1186/s40168-017-0279-1.

19.

The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology.

Zhu Q, Hu Q, Shepherd L, Wang J, Wei L, Morrison CD, Conroy JM, Glenn ST, Davis W, Kwan ML, Ergas IJ, Roh JM, Kushi LH, Ambrosone CB, Liu S, Yao S.

Cancer Epidemiol Biomarkers Prev. 2015 Aug;24(8):1207-13. doi: 10.1158/1055-9965.EPI-15-0205. Epub 2015 May 19.

20.

Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution.

Stead LF, Sutton KM, Taylor GR, Quirke P, Rabbitts P.

Hum Mutat. 2013 Oct;34(10):1432-8. doi: 10.1002/humu.22365. Epub 2013 Jul 11.

PMID:
23766071

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