Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing

doi:10.1186/1471-2164-7-216

BMC Genomics
Volume 7

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Pinard R
de Winter A
Sarkis GJ
Gerstein MB
Tartaro KR
Plant RN
Egholm M
Rothberg JM
Leamon JH

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Pinard R
de Winter A
Sarkis GJ
Gerstein MB
Tartaro KR
Plant RN
Egholm M
Rothberg JM
Leamon JH
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Research article

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing

Robert Pinard¹ , Alex de Winter¹ , Gary J Sarkis¹ , Mark B Gerstein² , Karrie R Tartaro¹ , Ramona N Plant¹ , Michael Egholm¹ , Jonathan M Rothberg¹ and John H Leamon¹

¹454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA

²MB&B Department, Yale University, 266 Whitney Ave., New Haven CT 06520, USA

author email corresponding author email

BMC Genomics 2006, 7:216doi:10.1186/1471-2164-7-216


Published:	23 August 2006

Additional files

Additional File 1:

Table S1. Read distributions between unamplified Halobacterium samples. Kolmogorov-Smirnov comparison of the distributions of reads per bin from an unamplified sample of Halobacterium species NRC-1 with four replicate unamplified control libraries. Bin Size refers to the number of bases comprising each individual bin into which the genome was broken for analysis; 100,000 reads were used for each analysis. As no significant differences were found between the distributions, ranked bias values (derived from D statistics) were assumed equivalent and not assigned. Table S2. Read distributions between unamplified Campylobacter samples. Kolmogorov-Smirnov comparison of the distributions of reads per bin from an unamplified sample of Campylobacter jejuni with four replicate unamplified control libraries. Bin Size refers to the number of bases comprising each individual bin into which the genome was broken for analysis; 100,000 reads were used for each analysis. As no significant differences were found between the distributions, ranked bias values (derived from D statistics) were assumed equivalent and not assigned.

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